=> Building science/lm Started : Tuesday, 9 JUL 2019 at 19:22:46 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for lm-uiuc-2.3.0_6: MPI=off: MPI (Message Passing Interface) support PYTHON=on: Python bindings or support VMD=off: Build the VMD plugin ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/construction/science/lm XDG_CONFIG_HOME=/construction/science/lm HOME=/construction/science/lm TMPDIR="/tmp" PATH=/construction/science/lm/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- BUILD_DIR=/construction/science/lm/lm-2.3.0 PROTOBUF_DIR=/usr/local XDG_DATA_HOME=/construction/science/lm XDG_CONFIG_HOME=/construction/science/lm HOME=/construction/science/lm TMPDIR="/tmp" PATH=/construction/science/lm/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/science/lm/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- MPI="@comment " NO_MPI="" PYTHON="" NO_PYTHON="@comment " VMD="@comment " NO_VMD="" PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/lm" EXAMPLESDIR="share/examples/lm" DATADIR="share/lm" WWWDIR="www/lm" ETCDIR="etc/lm" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- MPI="@comment " NO_MPI="" PYTHON="" NO_PYTHON="@comment " VMD="@comment " NO_VMD="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/lm DOCSDIR=/usr/local/share/doc/lm EXAMPLESDIR=/usr/local/share/examples/lm WWWDIR=/usr/local/www/lm ETCDIR=/usr/local/etc/lm -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License UIUC_OPEN_SOURCE_LICENSE accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> lm-uiuc-2.3.0_6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> lm-uiuc-2.3.0_6 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of lm-uiuc-2.3.0_6 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License UIUC_OPEN_SOURCE_LICENSE accepted by the user ===> Fetching all distfiles required by lm-uiuc-2.3.0_6 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License UIUC_OPEN_SOURCE_LICENSE accepted by the user ===> Fetching all distfiles required by lm-uiuc-2.3.0_6 for building => SHA256 Checksum OK for lm-2.3.0-src.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License UIUC_OPEN_SOURCE_LICENSE accepted by the user ===> Fetching all distfiles required by lm-uiuc-2.3.0_6 for building ===> Extracting for lm-uiuc-2.3.0_6 ===> License UIUC_OPEN_SOURCE_LICENSE accepted by the user ===> Fetching all distfiles required by lm-uiuc-2.3.0_6 for building => SHA256 Checksum OK for lm-2.3.0-src.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for lm-uiuc-2.3.0_6 ===> Applying ports patches for lm-uiuc-2.3.0_6 ===> Applying dragonfly patches for lm-uiuc-2.3.0_6 /usr/bin/sed -i.bak -e 's@BUILD_DIR := Build-.*@BUILD_DIR := Build-dragonfly@' /construction/science/lm/lm-2.3.0/local.mk -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> lm-uiuc-2.3.0_6 depends on executable: swig3.0 - not found ===> Installing existing package /packages/All/swig30-3.0.12.txz Installing swig30-3.0.12... `-- Installing lua52-5.2.4... | `-- Installing libedit-3.1.20190324,1... | | `-- Installing ncurses-6.1.20190525... | | `-- Extracting ncurses-6.1.20190525: .......... done | `-- Extracting libedit-3.1.20190324,1: .......... done `-- Extracting lua52-5.2.4: ......... done `-- Installing pcre-8.43_1... `-- Extracting pcre-8.43_1: .......... done Extracting swig30-3.0.12: .......... done ===> lm-uiuc-2.3.0_6 depends on executable: swig3.0 - found ===> Returning to build of lm-uiuc-2.3.0_6 ===> lm-uiuc-2.3.0_6 depends on file: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h - not found ===> Installing existing package /packages/All/py36-numpy-1.16.1_2,1.txz Installing py36-numpy-1.16.1_2,1... `-- Installing gcc8-8.3.0_2... | `-- Installing binutils-2.32_1,1... | | `-- Installing gettext-runtime-0.20.1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.20.1: .......... done | `-- Extracting binutils-2.32_1,1: .......... done | `-- Installing gmp-6.1.2_1... | `-- Extracting gmp-6.1.2_1: .......... done | `-- Installing mpc-1.1.0_2... | | `-- Installing mpfr-4.0.2... | | `-- Extracting mpfr-4.0.2: .......... done | `-- Extracting mpc-1.1.0_2: ......... done `-- Extracting gcc8-8.3.0_2: .......... done `-- Installing openblas-0.2.20_8,1... `-- Extracting openblas-0.2.20_8,1: ......... done `-- Installing py36-setuptools-41.0.0... | `-- Installing python36-3.6.8_2... | | `-- Installing expat-2.2.6_1... | | `-- Extracting expat-2.2.6_1: .......... done | | `-- Installing libffi-3.2.1_3... | | `-- Extracting libffi-3.2.1_3: .......... done | | `-- Installing libressl-2.9.2... | | `-- Extracting libressl-2.9.2: .......... done | | `-- Installing readline-8.0.0... | | `-- Extracting readline-8.0.0: .......... done | `-- Extracting python36-3.6.8_2: .......... done `-- Extracting py36-setuptools-41.0.0: .......... done `-- Installing suitesparse-5.2.0_3... | `-- Installing lapack-3.5.0_7... | | `-- Installing blas-3.5.0_5... | | `-- Extracting blas-3.5.0_5: ....... done | `-- Extracting lapack-3.5.0_7: .......... done | `-- Installing metis-5.1.0_7... | `-- Extracting metis-5.1.0_7: .......... done `-- Extracting suitesparse-5.2.0_3: .......... done Extracting py36-numpy-1.16.1_2,1: .......... done Message from gcc8-8.3.0_2: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from python36-3.6.8_2: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== Message from metis-5.1.0_7: ===> NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> lm-uiuc-2.3.0_6 depends on file: /usr/local/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h - found ===> Returning to build of lm-uiuc-2.3.0_6 ===> lm-uiuc-2.3.0_6 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... Extracting gmake-4.2.1_3: .......... done ===> lm-uiuc-2.3.0_6 depends on executable: gmake - found ===> Returning to build of lm-uiuc-2.3.0_6 ===> lm-uiuc-2.3.0_6 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> lm-uiuc-2.3.0_6 depends on shared library: libhdf5.so - not found ===> Installing existing package /packages/All/hdf5-1.10.5_1.txz Installing hdf5-1.10.5_1... `-- Installing hdf-szip-2.1.1... `-- Extracting hdf-szip-2.1.1: .......... done Extracting hdf5-1.10.5_1: .......... done ===> lm-uiuc-2.3.0_6 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> Returning to build of lm-uiuc-2.3.0_6 ===> lm-uiuc-2.3.0_6 depends on shared library: libprotobuf.so - not found ===> Installing existing package /packages/All/protobuf-3.7.1,1.txz Installing protobuf-3.7.1,1... Extracting protobuf-3.7.1,1: .......... done ===> lm-uiuc-2.3.0_6 depends on shared library: libprotobuf.so - found (/usr/local/lib/libprotobuf.so) ===> Returning to build of lm-uiuc-2.3.0_6 ===> lm-uiuc-2.3.0_6 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so) ===> lm-uiuc-2.3.0_6 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for lm-uiuc-2.3.0_6 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for lm-uiuc-2.3.0_6 gmake[2]: Entering directory '/construction/science/lm/lm-2.3.0' Building file: src/protobuf/lm/io/DiffusionModel.proto Building file: src/protobuf/lm/io/FirstPassageTimes.proto Building file: src/protobuf/lm/io/Lattice.proto Building file: src/protobuf/lm/io/ParameterValues.proto Building file: src/protobuf/lm/io/ReactionModel.proto Invoking: /usr/local/bin/protoc Invoking: /usr/local/bin/protoc mkdir -p ./Build-dragonfly/src/protobuf Invoking: /usr/local/bin/protoc mkdir -p ./Build-dragonfly/src/protobuf Invoking: /usr/local/bin/protoc mkdir -p ./Build-dragonfly/src/protobuf Invoking: /usr/local/bin/protoc /usr/local/bin/protoc --proto_path=./src/protobuf --cpp_out=./Build-dragonfly/src/protobuf src/protobuf/lm/io/FirstPassageTimes.proto /usr/local/bin/protoc --proto_path=./src/protobuf --cpp_out=./Build-dragonfly/src/protobuf src/protobuf/lm/io/DiffusionModel.proto mkdir -p ./Build-dragonfly/src/protobuf mkdir -p ./Build-dragonfly/src/protobuf /usr/local/bin/protoc --proto_path=./src/protobuf --cpp_out=./Build-dragonfly/src/protobuf src/protobuf/lm/io/Lattice.proto /usr/local/bin/protoc --proto_path=./src/protobuf --cpp_out=./Build-dragonfly/src/protobuf src/protobuf/lm/io/ParameterValues.proto [libprotobuf WARNING google/protobuf/compiler/parser.cc:564] No syntax specified for the proto file: lm/io/DiffusionModel.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) [libprotobuf WARNING google/protobuf/compiler/parser.cc:564] No syntax specified for the proto file: lm/io/Lattice.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) [libprotobuf WARNING google/protobuf/compiler/parser.cc:564] No syntax specified for the proto file: lm/io/FirstPassageTimes.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) /usr/local/bin/protoc --proto_path=./src/protobuf --cpp_out=./Build-dragonfly/src/protobuf src/protobuf/lm/io/ReactionModel.proto Finished building: src/protobuf/lm/io/Lattice.proto [libprotobuf WARNING google/protobuf/compiler/parser.cc:564] No syntax specified for the proto file: lm/io/ParameterValues.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) [libprotobuf WARNING google/protobuf/compiler/parser.cc:564] No syntax specified for the proto file: lm/io/ReactionModel.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) Finished building: src/protobuf/lm/io/DiffusionModel.proto Finished building: src/protobuf/lm/io/ReactionModel.proto Finished building: src/protobuf/lm/io/FirstPassageTimes.proto Finished building: src/protobuf/lm/io/ParameterValues.proto Building file: src/protobuf/lm/io/SpatialModel.proto Building file: src/protobuf/lm/io/SpeciesCounts.proto Invoking: /usr/local/bin/protoc Building file: src/c/lm/main/MainSA.cpp Invoking: /usr/local/bin/protoc mkdir -p ./Build-dragonfly/src/protobuf mkdir -p ./Build-dragonfly/src/protobuf /usr/local/bin/protoc --proto_path=./src/protobuf --cpp_out=./Build-dragonfly/src/protobuf src/protobuf/lm/io/SpatialModel.proto Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/main Building file: src/c/lm/main/Main.cpp Building file: src/protobuf/lm/message/SimulationParameters.proto c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/main/MainSA.o" "src/c/lm/main/MainSA.cpp" /usr/local/bin/protoc --proto_path=./src/protobuf --cpp_out=./Build-dragonfly/src/protobuf src/protobuf/lm/io/SpeciesCounts.proto Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/main Invoking: /usr/local/bin/protoc mkdir -p ./Build-dragonfly/src/protobuf /usr/local/bin/protoc --proto_path=./src/protobuf --cpp_out=./Build-dragonfly/src/protobuf src/protobuf/lm/message/SimulationParameters.proto [libprotobuf WARNING google/protobuf/compiler/parser.cc:564] No syntax specified for the proto file: lm/io/SpatialModel.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) [libprotobuf WARNING google/protobuf/compiler/parser.cc:564] No syntax specified for the proto file: lm/io/SpeciesCounts.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) [libprotobuf WARNING google/protobuf/compiler/parser.cc:564] No syntax specified for the proto file: lm/message/SimulationParameters.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) Finished building: src/protobuf/lm/io/SpatialModel.proto Building file: src/c/lm/main/ReplicateRunner.cpp Finished building: src/protobuf/lm/message/SimulationParameters.proto c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/main/Main.o" "src/c/lm/main/Main.cpp" Finished building: src/protobuf/lm/io/SpeciesCounts.proto Building file: src/c/lm/main/SignalHandler.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/main Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/main c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/main/SignalHandler.o" "src/c/lm/main/SignalHandler.cpp" Building file: src/c/lm/Print.cpp c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/main/ReplicateRunner.o" "src/c/lm/main/ReplicateRunner.cpp" Invoking: c++ mkdir -p Build-dragonfly/src/c/lm c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/Print.o" "src/c/lm/Print.cpp" In file included from ./src/c/lm/main/Main.h:47, from src/c/lm/main/Main.cpp:65: ./src/c/lm/me/MESolverFactory.h:62:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void setSolver(string solver) throw(lm::InvalidArgException); ^~~~~ ./src/c/lm/me/MESolverFactory.h:64:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool needsReactionModel() throw(lm::Exception); ^~~~~ ./src/c/lm/me/MESolverFactory.h:66:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool needsDiffusionModel() throw(lm::Exception); ^~~~~ ./src/c/lm/me/MESolverFactory.h:70:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] MESolver * instantiate() throw(lm::Exception); ^~~~~ Finished building: src/c/lm/Print.cpp Building file: src/c/lm/main/CheckpointSignaler.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/main c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/main/CheckpointSignaler.o" "src/c/lm/main/CheckpointSignaler.cpp" In file included from ./src/c/lm/main/LocalDataOutputWorker.h:46, from src/c/lm/main/SignalHandler.cpp:42: ./src/c/lm/io/hdf5/SimulationFile.h:88:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:90:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:92:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:94:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:96:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:98:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:100:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, bool initializeModel, unsigned int numberSpecies=0) throw(lm::IOException,HDF5Exception); ^~~~~ In file included from ./src/c/lm/main/LocalDataOutputWorker.h:46, from src/c/lm/main/SignalHandler.cpp:42: ./src/c/lm/io/hdf5/SimulationFile.h:113:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const string filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:115:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const char* filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:117:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~SimulationFile() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:120:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void close() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:122:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void flush() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:125:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual string checkpoint() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:133:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setParameter(string key, string value) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:141:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:144:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:151:172: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, byte * lattice, size_t latticeMaxSize, byte * latticeSites, size_t latticeSitesMaxSize) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:155:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, lm::rdme::Lattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:158:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:164:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:170:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint32_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:175:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::ByteLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:180:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::IntLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:184:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:187:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:194:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual bool replicateExists(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:197:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:201:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts * speciesCounts) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:207:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice(unsigned int replicate, lm::io::Lattice * lattice, byte * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:208:137: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice_U32LE(unsigned int replicate, lm::io::Lattice * lattice, uint32_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:210:119: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSites(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * siteData, size_t siteDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:214:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendParameterValues(unsigned int replicate, lm::io::ParameterValues * parameterValues) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:218:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes * speciesCounts) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual vector getLatticeTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:227:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice * lattice) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:230:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:232:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeAllReplicates() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:253:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getParticleCounts(unsigned int replicate, unsigned int latticeIndex) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:254:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map > getSpeciesCounts(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:255:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector getSpeciesCountTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:256:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSpeciesNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:257:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSiteTypeNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:277:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void open() throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:278:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openGroups() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:279:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadParameters() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:280:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadModel() throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:281:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * openReplicateHandles(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:282:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * createReplicateHandles(string replicateString) throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:283:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicateHandles(ReplicateHandles * handles) throw(HDF5Exception); ^~~~~ In file included from ./src/c/lm/main/CheckpointSignaler.h:45, from src/c/lm/main/CheckpointSignaler.cpp:47: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/main/CheckpointSignaler.h:46, from src/c/lm/main/CheckpointSignaler.cpp:47: ./src/c/lm/thread/Worker.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:56:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:59:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:61:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ In file included from src/c/lm/main/CheckpointSignaler.cpp:47: ./src/c/lm/main/CheckpointSignaler.h:61:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] CheckpointSignaler() throw(PthreadException); ^~~~~ ./src/c/lm/main/CheckpointSignaler.h:62:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~CheckpointSignaler() throw(PthreadException); ^~~~~ ./src/c/lm/main/CheckpointSignaler.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException); ^~~~~ In file included from src/c/lm/main/CheckpointSignaler.cpp:50: ./src/c/lm/thread/WorkerManager.h:66:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] WorkerManager() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:68:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ~WorkerManager() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:72:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void addWorker(Worker * worker) throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:75:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void removeWorker(Worker * worker) throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:77:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void abortWorkers() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:79:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void checkpointWorkers() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:81:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void stopWorkers() throw(PthreadException); ^~~~~ src/c/lm/main/CheckpointSignaler.cpp:58:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] CheckpointSignaler::CheckpointSignaler() throw(PthreadException) ^~~~~ src/c/lm/main/CheckpointSignaler.cpp:66:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] CheckpointSignaler::~CheckpointSignaler() throw(PthreadException) ^~~~~ src/c/lm/main/CheckpointSignaler.cpp:97:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void CheckpointSignaler::wake() throw(PthreadException) ^~~~~ Finished building: src/c/lm/main/Main.cpp Building file: src/c/lm/main/Globals.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/main c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/main/Globals.o" "src/c/lm/main/Globals.cpp" In file included from src/c/lm/main/Globals.cpp:47: ./src/c/lm/me/MESolverFactory.h:62:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void setSolver(string solver) throw(lm::InvalidArgException); ^~~~~ ./src/c/lm/me/MESolverFactory.h:64:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool needsReactionModel() throw(lm::Exception); ^~~~~ ./src/c/lm/me/MESolverFactory.h:66:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool needsDiffusionModel() throw(lm::Exception); ^~~~~ ./src/c/lm/me/MESolverFactory.h:70:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] MESolver * instantiate() throw(lm::Exception); ^~~~~ Finished building: src/c/lm/main/Globals.cpp Building file: src/c/lm/main/LocalDataOutputWorker.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/main c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/main/LocalDataOutputWorker.o" "src/c/lm/main/LocalDataOutputWorker.cpp" In file included from src/c/lm/main/MainSA.cpp:68: ./src/c/lm/io/hdf5/SimulationFile.h:88:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:90:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:92:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:94:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:96:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:98:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:100:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, bool initializeModel, unsigned int numberSpecies=0) throw(lm::IOException,HDF5Exception); ^~~~~ In file included from src/c/lm/main/MainSA.cpp:68: ./src/c/lm/io/hdf5/SimulationFile.h:113:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const string filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:115:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const char* filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:117:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~SimulationFile() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:120:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void close() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:122:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void flush() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:125:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual string checkpoint() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:133:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setParameter(string key, string value) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:141:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:144:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:151:172: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, byte * lattice, size_t latticeMaxSize, byte * latticeSites, size_t latticeSitesMaxSize) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:155:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, lm::rdme::Lattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:158:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:164:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ Finished building: src/c/lm/main/CheckpointSignaler.cpp ./src/c/lm/io/hdf5/SimulationFile.h:170:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint32_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:175:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::ByteLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:180:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::IntLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:184:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:187:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:194:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual bool replicateExists(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:197:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:201:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts * speciesCounts) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:207:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice(unsigned int replicate, lm::io::Lattice * lattice, byte * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:208:137: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice_U32LE(unsigned int replicate, lm::io::Lattice * lattice, uint32_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:210:119: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSites(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * siteData, size_t siteDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:214:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendParameterValues(unsigned int replicate, lm::io::ParameterValues * parameterValues) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:218:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes * speciesCounts) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual vector getLatticeTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:227:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice * lattice) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:230:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:232:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeAllReplicates() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:253:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getParticleCounts(unsigned int replicate, unsigned int latticeIndex) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:254:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map > getSpeciesCounts(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:255:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector getSpeciesCountTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:256:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSpeciesNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:257:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSiteTypeNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:277:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void open() throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:278:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openGroups() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:279:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadParameters() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:280:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadModel() throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:281:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * openReplicateHandles(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:282:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * createReplicateHandles(string replicateString) throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:283:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicateHandles(ReplicateHandles * handles) throw(HDF5Exception); ^~~~~ Building file: src/c/lm/builder/Capsule.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/builder c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/builder/Capsule.o" "src/c/lm/builder/Capsule.cpp" In file included from ./src/c/lm/main/DataOutputQueue.h:47, from ./src/c/lm/main/LocalDataOutputWorker.h:47, from src/c/lm/main/SignalHandler.cpp:42: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/main/LocalDataOutputWorker.h:47, from src/c/lm/main/SignalHandler.cpp:42: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from ./src/c/lm/main/LocalDataOutputWorker.h:47, from src/c/lm/main/SignalHandler.cpp:42: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/main/LocalDataOutputWorker.h:49, from src/c/lm/main/SignalHandler.cpp:42: ./src/c/lm/thread/Worker.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Worker() throw(PthreadException); ^~~~~ In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/main/ReplicateRunner.cpp:44: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/main/ReplicateRunner.cpp:44: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/main/ReplicateRunner.cpp:44: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/NextReactionSolver.h:49, from ./src/c/lm/cme/SelfRegulatingGeneSwitch.h:47, from src/c/lm/main/ReplicateRunner.cpp:47: ./src/c/lm/reaction/ReactionQueue.h: In destructor 'lm::reaction::ReactionQueue::~ReactionQueue()': ./src/c/lm/reaction/ReactionQueue.h:81:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:81:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:82:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:82:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:83:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:83:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~~~~~~~~~~~~~~~~ In file included from ./src/c/lm/main/Main.h:47, from src/c/lm/main/ReplicateRunner.cpp:55: ./src/c/lm/me/MESolverFactory.h: At global scope: ./src/c/lm/me/MESolverFactory.h:62:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void setSolver(string solver) throw(lm::InvalidArgException); ^~~~~ ./src/c/lm/me/MESolverFactory.h:64:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool needsReactionModel() throw(lm::Exception); ^~~~~ ./src/c/lm/me/MESolverFactory.h:66:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool needsDiffusionModel() throw(lm::Exception); ^~~~~ ./src/c/lm/me/MESolverFactory.h:70:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] MESolver * instantiate() throw(lm::Exception); ^~~~~ In file included from ./src/c/lm/main/ReplicateRunner.h:50, from src/c/lm/main/ReplicateRunner.cpp:56: ./src/c/lm/thread/Worker.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:56:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:59:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:61:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ In file included from src/c/lm/main/ReplicateRunner.cpp:56: ./src/c/lm/main/ReplicateRunner.h:76:315: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ReplicateRunner(int replicate, MESolverFactory solverFactory, map * parameters, lm::io::ReactionModel * reactionModel, lm::io::DiffusionModel * diffusionModel, uint8_t * lattice, size_t latticeSize, uint8_t * latticeSites, size_t latticeSitesSize, ResourceAllocator::ComputeResources resources) throw(PthreadException); ^~~~~ ./src/c/lm/main/ReplicateRunner.h:77:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ReplicateRunner() throw(PthreadException); ^~~~~ ./src/c/lm/main/ReplicateRunner.h:80:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:56:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:59:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:61:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ In file included from src/c/lm/main/SignalHandler.cpp:42: ./src/c/lm/main/LocalDataOutputWorker.h:67:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LocalDataOutputWorker(SimulationFile * file) throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:68:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~LocalDataOutputWorker() throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:72:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:75:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:77:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:79:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ In file included from ./src/c/lm/rdme/RDMESolver.h:45, from src/c/lm/main/ReplicateRunner.cpp:58: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from src/c/lm/main/ReplicateRunner.cpp:58: ./src/c/lm/rdme/RDMESolver.h:59:157: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(DiffusionModel * dm, const uint8_t * lattice, size_t latticeSize, const uint8_t * latticeSites, size_t latticeSitesSize) throw(InvalidArgException); ^~~~~ In file included from src/c/lm/main/ReplicateRunner.cpp:58: ./src/c/lm/rdme/RDMESolver.h:60:335: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void buildDiffusionModel(const uint numberSiteTypesA, const double * DFA, const uint * RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, si_dist_t latticeSpacing, const uint8_t * latticeData, const uint8_t * latticeSitesData, bool rowMajorData=true) throw(InvalidArgException); ^~~~~ src/c/lm/main/ReplicateRunner.cpp:70:328: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ReplicateRunner::ReplicateRunner(int replicate, MESolverFactory solverFactory, map * parameters, lm::io::ReactionModel * reactionModel, lm::io::DiffusionModel * diffusionModel, uint8_t * lattice, size_t latticeSize, uint8_t * latticeSites, size_t latticeSitesSize, ResourceAllocator::ComputeResources resources) throw(PthreadException) ^~~~~ src/c/lm/main/ReplicateRunner.cpp:75:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ReplicateRunner::~ReplicateRunner() throw(PthreadException) ^~~~~ src/c/lm/main/ReplicateRunner.cpp:79:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ReplicateRunner::wake() throw(PthreadException) ^~~~~ src/c/lm/main/ReplicateRunner.cpp: In member function 'virtual int lm::main::ReplicateRunner::run()': src/c/lm/main/ReplicateRunner.cpp:95:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from src/c/lm/main/MainSA.cpp:77: ./src/c/lm/main/ReplicateRunner.h:76:315: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ReplicateRunner(int replicate, MESolverFactory solverFactory, map * parameters, lm::io::ReactionModel * reactionModel, lm::io::DiffusionModel * diffusionModel, uint8_t * lattice, size_t latticeSize, uint8_t * latticeSites, size_t latticeSitesSize, ResourceAllocator::ComputeResources resources) throw(PthreadException); ^~~~~ ./src/c/lm/main/ReplicateRunner.h:77:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ReplicateRunner() throw(PthreadException); ^~~~~ ./src/c/lm/main/ReplicateRunner.h:80:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException); ^~~~~ src/c/lm/main/MainSA.cpp:95:340: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ReplicateRunner * startReplicate(int replicate, MESolverFactory solverFactory, std::map & simulationParameters, lm::io::ReactionModel * reactionModel, lm::io::DiffusionModel * diffusionModel, uint8_t * lattice, size_t latticeSize, uint8_t * latticeSites, size_t latticeSitesSize, ResourceAllocator & resourceAllocator) throw(Exception,PthreadException); ^~~~~ src/c/lm/main/MainSA.cpp: In function 'void executeSimulation()': src/c/lm/main/MainSA.cpp:414:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (lattice != NULL) delete [] lattice; lattice = NULL; ^~ src/c/lm/main/MainSA.cpp:414:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (lattice != NULL) delete [] lattice; lattice = NULL; ^~~~~~~ src/c/lm/main/MainSA.cpp:415:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (latticeSites != NULL) delete [] latticeSites; latticeSites = NULL; ^~ src/c/lm/main/MainSA.cpp:415:55: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (latticeSites != NULL) delete [] latticeSites; latticeSites = NULL; ^~~~~~~~~~~~ src/c/lm/main/MainSA.cpp: At global scope: src/c/lm/main/MainSA.cpp:423:340: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ReplicateRunner * startReplicate(int replicate, MESolverFactory solverFactory, std::map & simulationParameters, lm::io::ReactionModel * reactionModel, lm::io::DiffusionModel * diffusionModel, uint8_t * lattice, size_t latticeSize, uint8_t * latticeSites, size_t latticeSitesSize, ResourceAllocator & resourceAllocator) throw(Exception,PthreadException) ^~~~~ Finished building: src/c/lm/main/SignalHandler.cpp Building file: src/c/lm/builder/Cuboid.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/builder c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/builder/Cuboid.o" "src/c/lm/builder/Cuboid.cpp" In file included from ./src/c/lm/builder/Shape.h:48, from src/c/lm/builder/CapsuleShell.cpp:41: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from ./src/c/lm/main/DataOutputQueue.h:47, from src/c/lm/main/LocalDataOutputWorker.cpp:60: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from src/c/lm/main/LocalDataOutputWorker.cpp:60: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/main/LocalDataOutputWorker.cpp:60: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/main/LocalDataOutputWorker.h:46, from src/c/lm/main/LocalDataOutputWorker.cpp:61: ./src/c/lm/io/hdf5/SimulationFile.h:88:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:90:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:92:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:94:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:96:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:98:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:100:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, bool initializeModel, unsigned int numberSpecies=0) throw(lm::IOException,HDF5Exception); ^~~~~ In file included from ./src/c/lm/main/LocalDataOutputWorker.h:46, from src/c/lm/main/LocalDataOutputWorker.cpp:61: ./src/c/lm/io/hdf5/SimulationFile.h:113:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const string filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:115:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const char* filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:117:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~SimulationFile() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:120:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void close() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:122:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void flush() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:125:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual string checkpoint() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:133:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setParameter(string key, string value) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:141:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:144:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:151:172: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, byte * lattice, size_t latticeMaxSize, byte * latticeSites, size_t latticeSitesMaxSize) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:155:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, lm::rdme::Lattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:158:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:164:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:170:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint32_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:175:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::ByteLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:180:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::IntLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:184:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:187:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:194:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual bool replicateExists(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:197:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:201:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts * speciesCounts) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:207:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice(unsigned int replicate, lm::io::Lattice * lattice, byte * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:208:137: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice_U32LE(unsigned int replicate, lm::io::Lattice * lattice, uint32_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:210:119: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSites(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * siteData, size_t siteDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:214:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendParameterValues(unsigned int replicate, lm::io::ParameterValues * parameterValues) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:218:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes * speciesCounts) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual vector getLatticeTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:227:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice * lattice) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:230:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:232:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeAllReplicates() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:253:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getParticleCounts(unsigned int replicate, unsigned int latticeIndex) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:254:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map > getSpeciesCounts(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:255:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector getSpeciesCountTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:256:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSpeciesNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:257:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSiteTypeNames() throw(HDF5Exception); ^~~~~ In file included from ./src/c/lm/builder/Shape.h:48, from src/c/lm/builder/Cuboid.cpp:40: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:277:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void open() throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:278:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openGroups() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:279:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadParameters() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:280:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadModel() throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:281:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * openReplicateHandles(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:282:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * createReplicateHandles(string replicateString) throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:283:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicateHandles(ReplicateHandles * handles) throw(HDF5Exception); ^~~~~ In file included from ./src/c/lm/main/LocalDataOutputWorker.h:49, from src/c/lm/main/LocalDataOutputWorker.cpp:61: ./src/c/lm/thread/Worker.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:56:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:59:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:61:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ In file included from src/c/lm/main/LocalDataOutputWorker.cpp:61: ./src/c/lm/main/LocalDataOutputWorker.h:67:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LocalDataOutputWorker(SimulationFile * file) throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:68:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~LocalDataOutputWorker() throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:72:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:75:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:77:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:79:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ In file included from ./src/c/lm/main/Main.h:47, from src/c/lm/main/LocalDataOutputWorker.cpp:62: ./src/c/lm/me/MESolverFactory.h:62:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void setSolver(string solver) throw(lm::InvalidArgException); ^~~~~ ./src/c/lm/me/MESolverFactory.h:64:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool needsReactionModel() throw(lm::Exception); ^~~~~ ./src/c/lm/me/MESolverFactory.h:66:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool needsDiffusionModel() throw(lm::Exception); ^~~~~ ./src/c/lm/me/MESolverFactory.h:70:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] MESolver * instantiate() throw(lm::Exception); ^~~~~ Finished building: src/c/lm/builder/CapsuleShell.cpp Building file: src/c/lm/builder/Hemisphere.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/builder c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/builder/Hemisphere.o" "src/c/lm/builder/Hemisphere.cpp" Finished building: src/c/lm/builder/Cuboid.cpp Building file: src/c/lm/builder/LatticeBuilder.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/builder c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/builder/LatticeBuilder.o" "src/c/lm/builder/LatticeBuilder.cpp" In file included from ./src/c/lm/rdme/ByteLattice.h:45, from src/c/lm/main/LocalDataOutputWorker.cpp:71: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from src/c/lm/main/LocalDataOutputWorker.cpp:71: ./src/c/lm/rdme/ByteLattice.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ByteLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:75:125: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ByteLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:76:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ByteLattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:81:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:82:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:83:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t siteType) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:84:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t subvolume, site_t site) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:89:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:90:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:91:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:92:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t subvolume, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:93:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:94:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t subvolume, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:95:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:96:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t subvolume) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:116:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void allocateMemory() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:117:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void deallocateMemory() throw(std::bad_alloc); ^~~~~ In file included from src/c/lm/main/LocalDataOutputWorker.cpp:72: ./src/c/lm/rdme/IntLattice.h:72:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] IntLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/IntLattice.h:73:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] IntLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/IntLattice.h:74:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~IntLattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/IntLattice.h:79:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:80:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:81:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t siteType) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:82:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t subvolume, site_t site) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:85:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:86:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:87:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:88:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t subvolume, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:89:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:90:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t subvolume, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:91:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:92:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t subvolume) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:113:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void allocateMemory() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/IntLattice.h:114:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void deallocateMemory() throw(std::bad_alloc); ^~~~~ src/c/lm/main/LocalDataOutputWorker.cpp:83:69: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LocalDataOutputWorker::LocalDataOutputWorker(SimulationFile * file) throw(PthreadException) ^~~~~ src/c/lm/main/LocalDataOutputWorker.cpp:89:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LocalDataOutputWorker::~LocalDataOutputWorker() throw(PthreadException) ^~~~~ src/c/lm/main/LocalDataOutputWorker.cpp:94:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void LocalDataOutputWorker::pushDataSet(DataSet * dataSet) throw(PthreadException) ^~~~~ src/c/lm/main/LocalDataOutputWorker.cpp:119:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void LocalDataOutputWorker::wake() throw(PthreadException) ^~~~~ src/c/lm/main/LocalDataOutputWorker.cpp:128:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void LocalDataOutputWorker::abort() throw(PthreadException) ^~~~~ src/c/lm/main/LocalDataOutputWorker.cpp:143:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void LocalDataOutputWorker::checkpoint() throw(PthreadException) ^~~~~ src/c/lm/main/LocalDataOutputWorker.cpp: In member function 'virtual int lm::main::LocalDataOutputWorker::run()': src/c/lm/main/LocalDataOutputWorker.cpp:402:40: warning: catching polymorphic type 'class lm::io::hdf5::HDF5Exception' by value [-Wcatch-value=] catch (lm::io::hdf5::HDF5Exception e) ^ src/c/lm/main/LocalDataOutputWorker.cpp:406:41: warning: catching polymorphic type 'class lm::thread::PthreadException' by value [-Wcatch-value=] catch (lm::thread::PthreadException e) ^ src/c/lm/main/LocalDataOutputWorker.cpp:410:26: warning: catching polymorphic type 'class lm::Exception' by value [-Wcatch-value=] catch (lm::Exception e) ^ Finished building: src/c/lm/main/MainSA.cpp Building file: src/c/lm/builder/Shape.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/builder c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/builder/Shape.o" "src/c/lm/builder/Shape.cpp" In file included from ./src/c/lm/builder/Shape.h:48, from src/c/lm/builder/Hemisphere.cpp:40: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from ./src/c/lm/builder/Shape.h:48, from ./src/c/lm/builder/Capsule.h:43, from src/c/lm/builder/LatticeBuilder.cpp:46: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ Finished building: src/c/lm/builder/Hemisphere.cpp Building file: src/c/lm/builder/Sphere.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/builder c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/builder/Sphere.o" "src/c/lm/builder/Sphere.cpp" In file included from ./src/c/lm/builder/Shape.h:48, from src/c/lm/builder/Sphere.cpp:40: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from ./src/c/lm/builder/Shape.h:48, from src/c/lm/builder/Shape.cpp:41: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ Finished building: src/c/lm/builder/Sphere.cpp Building file: src/c/lm/builder/Intersection.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/builder c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/builder/Intersection.o" "src/c/lm/builder/Intersection.cpp" In file included from src/c/lm/builder/LatticeBuilder.cpp:60: ./src/c/lm/io/hdf5/SimulationFile.h:88:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:90:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:92:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:94:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:96:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:98:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:100:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, bool initializeModel, unsigned int numberSpecies=0) throw(lm::IOException,HDF5Exception); ^~~~~ In file included from src/c/lm/builder/LatticeBuilder.cpp:60: ./src/c/lm/io/hdf5/SimulationFile.h:113:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const string filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:115:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const char* filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:117:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~SimulationFile() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:120:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void close() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:122:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void flush() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:125:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual string checkpoint() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:133:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setParameter(string key, string value) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:141:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:144:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:151:172: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, byte * lattice, size_t latticeMaxSize, byte * latticeSites, size_t latticeSitesMaxSize) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:155:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, lm::rdme::Lattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:158:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:164:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:170:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint32_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:175:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::ByteLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:180:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::IntLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:184:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:187:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:194:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual bool replicateExists(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:197:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:201:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts * speciesCounts) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:207:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice(unsigned int replicate, lm::io::Lattice * lattice, byte * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:208:137: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice_U32LE(unsigned int replicate, lm::io::Lattice * lattice, uint32_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:210:119: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSites(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * siteData, size_t siteDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:214:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendParameterValues(unsigned int replicate, lm::io::ParameterValues * parameterValues) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:218:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes * speciesCounts) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual vector getLatticeTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:227:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice * lattice) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:230:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:232:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeAllReplicates() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:253:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getParticleCounts(unsigned int replicate, unsigned int latticeIndex) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:254:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map > getSpeciesCounts(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:255:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector getSpeciesCountTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:256:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSpeciesNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:257:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSiteTypeNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:277:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void open() throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:278:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openGroups() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:279:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadParameters() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:280:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadModel() throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:281:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * openReplicateHandles(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:282:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * createReplicateHandles(string replicateString) throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:283:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicateHandles(ReplicateHandles * handles) throw(HDF5Exception); ^~~~~ src/c/lm/builder/LatticeBuilder.cpp: In destructor 'virtual lm::builder::LatticeBuilder::~LatticeBuilder()': src/c/lm/builder/LatticeBuilder.cpp:119:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (rng != NULL) delete rng; rng = NULL; ^~ src/c/lm/builder/LatticeBuilder.cpp:119:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (rng != NULL) delete rng; rng = NULL; ^~~ src/c/lm/builder/LatticeBuilder.cpp:124:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (collisionGrid[i] != NULL) delete [] collisionGrid[i]; collisionGrid[i] = NULL; ^~ src/c/lm/builder/LatticeBuilder.cpp:124:71: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (collisionGrid[i] != NULL) delete [] collisionGrid[i]; collisionGrid[i] = NULL; ^~~~~~~~~~~~~ src/c/lm/builder/LatticeBuilder.cpp:128:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (collisionGridOccupancy != NULL) delete collisionGridOccupancy; collisionGridOccupancy = NULL; ^~ src/c/lm/builder/LatticeBuilder.cpp:128:72: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (collisionGridOccupancy != NULL) delete collisionGridOccupancy; collisionGridOccupancy = NULL; ^~~~~~~~~~~~~~~~~~~~~~ src/c/lm/builder/LatticeBuilder.cpp:129:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (collisionGridSize != NULL) delete collisionGridSize; collisionGridSize = NULL; ^~ src/c/lm/builder/LatticeBuilder.cpp:129:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (collisionGridSize != NULL) delete collisionGridSize; collisionGridSize = NULL; ^~~~~~~~~~~~~~~~~ Finished building: src/c/lm/main/LocalDataOutputWorker.cpp Finished building: src/c/lm/builder/Shape.cpp Building file: src/c/lm/builder/Union.cpp Building file: src/c/lm/builder/Difference.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/builder Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/builder c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/builder/Union.o" "src/c/lm/builder/Union.cpp" c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/builder/Difference.o" "src/c/lm/builder/Difference.cpp" In file included from ./src/c/lm/builder/Shape.h:48, from src/c/lm/builder/Difference.cpp:40: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from ./src/c/lm/builder/Shape.h:48, from src/c/lm/builder/Union.cpp:40: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from ./src/c/lm/builder/Shape.h:48, from src/c/lm/builder/Intersection.cpp:40: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ Finished building: src/c/lm/builder/Union.cpp Building file: src/c/lm/builder/Torus.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/builder c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/builder/Torus.o" "src/c/lm/builder/Torus.cpp" Finished building: src/c/lm/builder/Intersection.cpp Building file: src/c/lm/builder/Ellipse.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/builder c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/builder/Ellipse.o" "src/c/lm/builder/Ellipse.cpp" In file included from ./src/c/lm/builder/Shape.h:48, from src/c/lm/builder/Ellipse.cpp:40: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from ./src/c/lm/builder/Shape.h:48, from src/c/lm/builder/Torus.cpp:40: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ Finished building: src/c/lm/main/ReplicateRunner.cpp Building file: src/c/lm/builder/Cylinder.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/builder c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/builder/Cylinder.o" "src/c/lm/builder/Cylinder.cpp" Finished building: src/c/lm/builder/Torus.cpp Building file: src/c/lm/cme/CMESolver.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/cme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/cme/CMESolver.o" "src/c/lm/cme/CMESolver.cpp" Finished building: src/c/lm/builder/Ellipse.cpp Building file: src/c/lm/cme/FluctuatingNRSolver.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/cme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/cme/FluctuatingNRSolver.o" "src/c/lm/cme/FluctuatingNRSolver.cpp" In file included from ./src/c/lm/builder/Shape.h:48, from src/c/lm/builder/Cylinder.cpp:40: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ Finished building: src/c/lm/builder/Difference.cpp Building file: src/c/lm/cme/GillespieDSolver.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/cme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/cme/GillespieDSolver.o" "src/c/lm/cme/GillespieDSolver.cpp" Finished building: src/c/lm/builder/Cylinder.cpp Building file: src/c/lm/cme/HillSwitch.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/cme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/cme/HillSwitch.o" "src/c/lm/cme/HillSwitch.cpp" In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/NextReactionSolver.h:46, from ./src/c/lm/cme/FluctuatingNRSolver.h:46, from src/c/lm/cme/FluctuatingNRSolver.cpp:51: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/NextReactionSolver.h:46, from ./src/c/lm/cme/FluctuatingNRSolver.h:46, from src/c/lm/cme/FluctuatingNRSolver.cpp:51: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/NextReactionSolver.h:46, from ./src/c/lm/cme/FluctuatingNRSolver.h:46, from src/c/lm/cme/FluctuatingNRSolver.cpp:51: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/NextReactionSolver.h:49, from ./src/c/lm/cme/FluctuatingNRSolver.h:46, from src/c/lm/cme/FluctuatingNRSolver.cpp:51: ./src/c/lm/reaction/ReactionQueue.h: In destructor 'lm::reaction::ReactionQueue::~ReactionQueue()': ./src/c/lm/reaction/ReactionQueue.h:81:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:81:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:82:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:82:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:83:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:83:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~~~~~~~~~~~~~~~~ src/c/lm/cme/FluctuatingNRSolver.cpp: In member function 'virtual void lm::cme::FluctuatingNRSolver::setReactionModel(lm::io::ReactionModel*)': src/c/lm/cme/FluctuatingNRSolver.cpp:128:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (ntau != NULL) delete [] ntau; ntau = NULL; ^~ src/c/lm/cme/FluctuatingNRSolver.cpp:128:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (ntau != NULL) delete [] ntau; ntau = NULL; ^~~~ src/c/lm/cme/FluctuatingNRSolver.cpp:129:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (nvar != NULL) delete [] nvar; nvar = NULL; ^~ src/c/lm/cme/FluctuatingNRSolver.cpp:129:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (nvar != NULL) delete [] nvar; nvar = NULL; ^~~~ src/c/lm/cme/FluctuatingNRSolver.cpp:130:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (K != NULL) delete [] K; K = NULL; ^~ src/c/lm/cme/FluctuatingNRSolver.cpp:130:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (K != NULL) delete [] K; K = NULL; ^ src/c/lm/cme/FluctuatingNRSolver.cpp:131:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionType != NULL) delete [] reactionType; reactionType = NULL; ^~ src/c/lm/cme/FluctuatingNRSolver.cpp:131:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionType != NULL) delete [] reactionType; reactionType = NULL; ^~~~~~~~~~~~ In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/GillespieDSolver.h:46, from src/c/lm/cme/HillSwitch.cpp:50: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/GillespieDSolver.h:46, from src/c/lm/cme/HillSwitch.cpp:50: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/GillespieDSolver.h:46, from src/c/lm/cme/HillSwitch.cpp:50: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/cme/CMESolver.cpp:51: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/cme/CMESolver.cpp:51: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/cme/CMESolver.cpp:51: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from src/c/lm/cme/CMESolver.cpp:55: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/CMESolver.cpp:55: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/CMESolver.cpp:64: ./src/c/lm/thread/Worker.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:56:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:59:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:61:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ src/c/lm/cme/CMESolver.cpp: In destructor 'virtual lm::cme::CMESolver::~CMESolver()': src/c/lm/cme/CMESolver.cpp:88:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (rng != NULL) delete rng; rng = NULL; ^~ src/c/lm/cme/CMESolver.cpp:88:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (rng != NULL) delete rng; rng = NULL; ^~~ src/c/lm/cme/CMESolver.cpp:89:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (speciesLimits != NULL) delete[] speciesLimits; speciesLimits = NULL; ^~ src/c/lm/cme/CMESolver.cpp:89:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (speciesLimits != NULL) delete[] speciesLimits; speciesLimits = NULL; ^~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:90:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (fptTrackedSpecies != NULL) delete[] fptTrackedSpecies; fptTrackedSpecies = NULL; ^~ src/c/lm/cme/CMESolver.cpp:90:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (fptTrackedSpecies != NULL) delete[] fptTrackedSpecies; fptTrackedSpecies = NULL; ^~~~~~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp: In member function 'virtual void lm::cme::CMESolver::destroyModel()': src/c/lm/cme/CMESolver.cpp:233:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (initialSpeciesCounts != NULL) delete[] initialSpeciesCounts; initialSpeciesCounts = NULL; ^~ src/c/lm/cme/CMESolver.cpp:233:70: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (initialSpeciesCounts != NULL) delete[] initialSpeciesCounts; initialSpeciesCounts = NULL; ^~~~~~~~~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:234:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (speciesCounts != NULL) delete[] speciesCounts; speciesCounts = NULL; ^~ src/c/lm/cme/CMESolver.cpp:234:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (speciesCounts != NULL) delete[] speciesCounts; speciesCounts = NULL; ^~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:235:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionTypes != NULL) delete[] reactionTypes; reactionTypes = NULL; ^~ src/c/lm/cme/CMESolver.cpp:235:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionTypes != NULL) delete[] reactionTypes; reactionTypes = NULL; ^~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:236:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (S != NULL) delete[] S; S = NULL; ^~ src/c/lm/cme/CMESolver.cpp:236:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (S != NULL) delete[] S; S = NULL; ^ src/c/lm/cme/CMESolver.cpp:237:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (D != NULL) delete[] D; D = NULL; ^~ src/c/lm/cme/CMESolver.cpp:237:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (D != NULL) delete[] D; D = NULL; ^ src/c/lm/cme/CMESolver.cpp:238:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (propensityFunctions != NULL) delete[] propensityFunctions; propensityFunctions = NULL; ^~ src/c/lm/cme/CMESolver.cpp:238:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (propensityFunctions != NULL) delete[] propensityFunctions; propensityFunctions = NULL; ^~~~~~~~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:241:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (propensityFunctionArgs != NULL) delete[] propensityFunctionArgs; propensityFunctionArgs = NULL; ^~ src/c/lm/cme/CMESolver.cpp:241:74: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (propensityFunctionArgs != NULL) delete[] propensityFunctionArgs; propensityFunctionArgs = NULL; ^~~~~~~~~~~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:246:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (numberDependentSpecies != NULL) delete[] numberDependentSpecies; numberDependentSpecies = NULL; ^~ src/c/lm/cme/CMESolver.cpp:246:74: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (numberDependentSpecies != NULL) delete[] numberDependentSpecies; numberDependentSpecies = NULL; ^~~~~~~~~~~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:263:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (numberDependentReactions != NULL) delete[] numberDependentReactions; numberDependentReactions = NULL; ^~ src/c/lm/cme/CMESolver.cpp:263:78: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (numberDependentReactions != NULL) delete[] numberDependentReactions; numberDependentReactions = NULL; ^~~~~~~~~~~~~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp: In member function 'virtual void lm::cme::CMESolver::setReactionModel(lm::io::ReactionModel*)': src/c/lm/cme/CMESolver.cpp:303:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionType != NULL) delete [] reactionType; reactionType = NULL; ^~ src/c/lm/cme/CMESolver.cpp:303:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionType != NULL) delete [] reactionType; reactionType = NULL; ^~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:304:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (K != NULL) delete [] K; K = NULL; ^~ src/c/lm/cme/CMESolver.cpp:304:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (K != NULL) delete [] K; K = NULL; ^ src/c/lm/cme/CMESolver.cpp: In member function 'virtual void lm::cme::CMESolver::setFptTrackingList(std::__cxx11::list)': src/c/lm/cme/CMESolver.cpp:941:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (fptTrackedSpecies != NULL) delete[] fptTrackedSpecies; fptTrackedSpecies = NULL; ^~ src/c/lm/cme/CMESolver.cpp:941:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (fptTrackedSpecies != NULL) delete[] fptTrackedSpecies; fptTrackedSpecies = NULL; ^~~~~~~~~~~~~~~~~ In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/cme/GillespieDSolver.cpp:53: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/cme/GillespieDSolver.cpp:53: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/cme/GillespieDSolver.cpp:53: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ Finished building: src/c/lm/cme/FluctuatingNRSolver.cpp Building file: src/c/lm/cme/LacHillSwitch.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/cme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/cme/LacHillSwitch.o" "src/c/lm/cme/LacHillSwitch.cpp" Finished building: src/c/lm/builder/LatticeBuilder.cpp Building file: src/c/lm/cme/NextReactionSolver.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/cme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/cme/NextReactionSolver.o" "src/c/lm/cme/NextReactionSolver.cpp" In file included from src/c/lm/cme/HillSwitch.cpp:54: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/HillSwitch.cpp:54: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/GillespieDSolver.cpp:57: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/GillespieDSolver.cpp:57: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/GillespieDSolver.cpp:65: ./src/c/lm/thread/Worker.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:56:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:59:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:61:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ src/c/lm/cme/GillespieDSolver.cpp: In member function 'virtual void lm::cme::GillespieDSolver::destroyModel()': src/c/lm/cme/GillespieDSolver.cpp:104:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (propensities != NULL) delete[] propensities; propensities = NULL; ^~ src/c/lm/cme/GillespieDSolver.cpp:104:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (propensities != NULL) delete[] propensities; propensities = NULL; ^~~~~~~~~~~~ src/c/lm/cme/GillespieDSolver.cpp: In member function 'virtual void lm::cme::GillespieDSolver::generateTrajectory()': src/c/lm/cme/GillespieDSolver.cpp:172:10: warning: variable 'addedParameterValues' set but not used [-Wunused-but-set-variable] bool addedParameterValues; ^~~~~~~~~~~~~~~~~~~~ Finished building: src/c/lm/cme/GillespieDSolver.cpp Building file: src/c/lm/cme/SelfRegulatingGeneSwitch.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/cme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/cme/SelfRegulatingGeneSwitch.o" "src/c/lm/cme/SelfRegulatingGeneSwitch.cpp" src/c/lm/cme/CMESolver.cpp: In member function 'virtual void lm::cme::CMESolver::buildModel(uint, uint, const uint*, const uint*, const double*, const int*, const uint*, uint)': src/c/lm/cme/CMESolver.cpp:599:45: warning: 'thirdDependency' may be used uninitialized in this function [-Wmaybe-uninitialized] } else if (S[thirdDependency*numberReactions+i] == -1) { ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:590:46: warning: 'secondDependency' may be used uninitialized in this function [-Wmaybe-uninitialized] } else if (S[secondDependency*numberReactions+i] == -1) { ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:581:38: warning: 'firstDependency' may be used uninitialized in this function [-Wmaybe-uninitialized] if (S[firstDependency*numberReactions+i] == -1) { ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:535:85: warning: 'secondDependency' may be used uninitialized in this function [-Wmaybe-uninitialized] if (S[firstDependency*numberReactions+i] == -1 && S[secondDependency*numberReactions+i] == 0) { ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:535:38: warning: 'firstDependency' may be used uninitialized in this function [-Wmaybe-uninitialized] if (S[firstDependency*numberReactions+i] == -1 && S[secondDependency*numberReactions+i] == 0) { ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:473:85: warning: 'secondDependency' may be used uninitialized in this function [-Wmaybe-uninitialized] if (S[firstDependency*numberReactions+i] == -1 && S[secondDependency*numberReactions+i] == 0) { ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ src/c/lm/cme/CMESolver.cpp:473:38: warning: 'firstDependency' may be used uninitialized in this function [-Wmaybe-uninitialized] if (S[firstDependency*numberReactions+i] == -1 && S[secondDependency*numberReactions+i] == 0) { ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from src/c/lm/cme/CMESolver.cpp:51: ./src/c/lm/cme/CMESolver.h:93:87: warning: 'firstDependency' may be used uninitialized in this function [-Wmaybe-uninitialized] SecondOrderPropensityArgs(uint s1i, uint s2i, double k) :s1i(s1i),s2i(s2i),k(k) {} ^ src/c/lm/cme/CMESolver.cpp:385:22: note: 'firstDependency' was declared here uint firstDependency; ^~~~~~~~~~~~~~~ In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/NextReactionSolver.h:46, from ./src/c/lm/cme/FluctuatingNRSolver.h:46, from src/c/lm/cme/LacHillSwitch.cpp:49: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/NextReactionSolver.h:46, from ./src/c/lm/cme/FluctuatingNRSolver.h:46, from src/c/lm/cme/LacHillSwitch.cpp:49: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/NextReactionSolver.h:46, from ./src/c/lm/cme/FluctuatingNRSolver.h:46, from src/c/lm/cme/LacHillSwitch.cpp:49: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/NextReactionSolver.h:49, from ./src/c/lm/cme/FluctuatingNRSolver.h:46, from src/c/lm/cme/LacHillSwitch.cpp:49: ./src/c/lm/reaction/ReactionQueue.h: In destructor 'lm::reaction::ReactionQueue::~ReactionQueue()': ./src/c/lm/reaction/ReactionQueue.h:81:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:81:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:82:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:82:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:83:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:83:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~~~~~~~~~~~~~~~~ In file included from src/c/lm/cme/LacHillSwitch.cpp:53: ./src/c/lm/main/DataOutputQueue.h: At global scope: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/LacHillSwitch.cpp:53: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/cme/NextReactionSolver.cpp:51: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/cme/NextReactionSolver.cpp:51: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/cme/NextReactionSolver.cpp:51: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ Finished building: src/c/lm/cme/CMESolver.cpp Building file: src/c/lm/cme/TwoStateExpression.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/cme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/cme/TwoStateExpression.o" "src/c/lm/cme/TwoStateExpression.cpp" In file included from ./src/c/lm/cme/NextReactionSolver.h:49, from src/c/lm/cme/NextReactionSolver.cpp:52: ./src/c/lm/reaction/ReactionQueue.h: In destructor 'lm::reaction::ReactionQueue::~ReactionQueue()': ./src/c/lm/reaction/ReactionQueue.h:81:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:81:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:82:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:82:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:83:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:83:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~~~~~~~~~~~~~~~~ In file included from src/c/lm/cme/NextReactionSolver.cpp:55: ./src/c/lm/main/DataOutputQueue.h: At global scope: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/NextReactionSolver.cpp:55: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/NextReactionSolver.cpp:64: ./src/c/lm/thread/Worker.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:56:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:59:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:61:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ src/c/lm/cme/NextReactionSolver.cpp: In member function 'virtual void lm::cme::NextReactionSolver::destroyModel()': src/c/lm/cme/NextReactionSolver.cpp:104:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionQueue != NULL) delete reactionQueue; reactionQueue = NULL; ^~ src/c/lm/cme/NextReactionSolver.cpp:104:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionQueue != NULL) delete reactionQueue; reactionQueue = NULL; ^~~~~~~~~~~~~ src/c/lm/cme/NextReactionSolver.cpp: In member function 'virtual void lm::cme::NextReactionSolver::generateTrajectory()': src/c/lm/cme/NextReactionSolver.cpp:168:10: warning: variable 'addedParameterValues' set but not used [-Wunused-but-set-variable] bool addedParameterValues; ^~~~~~~~~~~~~~~~~~~~ In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/GillespieDSolver.h:46, from src/c/lm/cme/SelfRegulatingGeneSwitch.cpp:51: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/GillespieDSolver.h:46, from src/c/lm/cme/SelfRegulatingGeneSwitch.cpp:51: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/GillespieDSolver.h:46, from src/c/lm/cme/SelfRegulatingGeneSwitch.cpp:51: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/NextReactionSolver.h:49, from ./src/c/lm/cme/SelfRegulatingGeneSwitch.h:47, from src/c/lm/cme/SelfRegulatingGeneSwitch.cpp:52: ./src/c/lm/reaction/ReactionQueue.h: In destructor 'lm::reaction::ReactionQueue::~ReactionQueue()': ./src/c/lm/reaction/ReactionQueue.h:81:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:81:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:82:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:82:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:83:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:83:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~~~~~~~~~~~~~~~~ In file included from src/c/lm/cme/SelfRegulatingGeneSwitch.cpp:55: ./src/c/lm/main/DataOutputQueue.h: At global scope: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/SelfRegulatingGeneSwitch.cpp:55: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ src/c/lm/cme/SelfRegulatingGeneSwitch.cpp: In static member function 'static double lm::cme::SelfRegulatingGeneSwitch::ouKHillPropensity(double, uint*, void*)': src/c/lm/cme/SelfRegulatingGeneSwitch.cpp:141:14: warning: variable 'addedPv' set but not used [-Wunused-but-set-variable] bool addedPv=false; ^~~~~~~ In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/NextReactionSolver.h:46, from src/c/lm/cme/TwoStateExpression.cpp:49: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/NextReactionSolver.h:46, from src/c/lm/cme/TwoStateExpression.cpp:49: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/NextReactionSolver.h:46, from src/c/lm/cme/TwoStateExpression.cpp:49: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/NextReactionSolver.h:49, from src/c/lm/cme/TwoStateExpression.cpp:49: ./src/c/lm/reaction/ReactionQueue.h: In destructor 'lm::reaction::ReactionQueue::~ReactionQueue()': ./src/c/lm/reaction/ReactionQueue.h:81:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:81:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:82:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:82:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:83:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:83:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~~~~~~~~~~~~~~~~ In file included from src/c/lm/cme/TwoStateExpression.cpp:53: ./src/c/lm/main/DataOutputQueue.h: At global scope: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/TwoStateExpression.cpp:53: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ Finished building: src/c/lm/cme/NextReactionSolver.cpp Building file: src/c/lm/cme/TwoStateHillLoopSwitch.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/cme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/cme/TwoStateHillLoopSwitch.o" "src/c/lm/cme/TwoStateHillLoopSwitch.cpp" Finished building: src/c/lm/cme/SelfRegulatingGeneSwitch.cpp Building file: src/c/lm/cme/TwoStateHillSwitch.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/cme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/cme/TwoStateHillSwitch.o" "src/c/lm/cme/TwoStateHillSwitch.cpp" Finished building: src/c/lm/cme/TwoStateExpression.cpp Building file: Build-dragonfly/src/protobuf/lm/io/DiffusionModel.pb.cc Invoking: c++ mkdir -p Build-dragonfly/src/protobuf/lm/io c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/protobuf/lm/io/DiffusionModel.pb.o" "Build-dragonfly/src/protobuf/lm/io/DiffusionModel.pb.cc" Finished building: src/c/lm/cme/HillSwitch.cpp Building file: Build-dragonfly/src/protobuf/lm/io/FirstPassageTimes.pb.cc Invoking: c++ mkdir -p Build-dragonfly/src/protobuf/lm/io c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/protobuf/lm/io/FirstPassageTimes.pb.o" "Build-dragonfly/src/protobuf/lm/io/FirstPassageTimes.pb.cc" In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/GillespieDSolver.h:46, from src/c/lm/cme/TwoStateHillLoopSwitch.cpp:50: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/GillespieDSolver.h:46, from src/c/lm/cme/TwoStateHillLoopSwitch.cpp:50: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/GillespieDSolver.h:46, from src/c/lm/cme/TwoStateHillLoopSwitch.cpp:50: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from src/c/lm/cme/TwoStateHillLoopSwitch.cpp:55: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/TwoStateHillLoopSwitch.cpp:55: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/GillespieDSolver.h:46, from src/c/lm/cme/TwoStateHillSwitch.cpp:49: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/GillespieDSolver.h:46, from src/c/lm/cme/TwoStateHillSwitch.cpp:49: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/GillespieDSolver.h:46, from src/c/lm/cme/TwoStateHillSwitch.cpp:49: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from src/c/lm/cme/TwoStateHillSwitch.cpp:53: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/cme/TwoStateHillSwitch.cpp:53: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ Finished building: src/c/lm/cme/LacHillSwitch.cpp Building file: Build-dragonfly/src/protobuf/lm/io/Lattice.pb.cc Invoking: c++ mkdir -p Build-dragonfly/src/protobuf/lm/io c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/protobuf/lm/io/Lattice.pb.o" "Build-dragonfly/src/protobuf/lm/io/Lattice.pb.cc" Finished building: Build-dragonfly/src/protobuf/lm/io/FirstPassageTimes.pb.cc Building file: Build-dragonfly/src/protobuf/lm/io/ParameterValues.pb.cc Invoking: c++ mkdir -p Build-dragonfly/src/protobuf/lm/io c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/protobuf/lm/io/ParameterValues.pb.o" "Build-dragonfly/src/protobuf/lm/io/ParameterValues.pb.cc" Finished building: src/c/lm/cme/TwoStateHillSwitch.cpp Building file: Build-dragonfly/src/protobuf/lm/io/ReactionModel.pb.cc Invoking: c++ mkdir -p Build-dragonfly/src/protobuf/lm/io c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/protobuf/lm/io/ReactionModel.pb.o" "Build-dragonfly/src/protobuf/lm/io/ReactionModel.pb.cc" Finished building: src/c/lm/cme/TwoStateHillLoopSwitch.cpp Building file: Build-dragonfly/src/protobuf/lm/io/SpatialModel.pb.cc Invoking: c++ mkdir -p Build-dragonfly/src/protobuf/lm/io c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/protobuf/lm/io/SpatialModel.pb.o" "Build-dragonfly/src/protobuf/lm/io/SpatialModel.pb.cc" Finished building: Build-dragonfly/src/protobuf/lm/io/DiffusionModel.pb.cc Building file: Build-dragonfly/src/protobuf/lm/io/SpeciesCounts.pb.cc Invoking: c++ mkdir -p Build-dragonfly/src/protobuf/lm/io c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/protobuf/lm/io/SpeciesCounts.pb.o" "Build-dragonfly/src/protobuf/lm/io/SpeciesCounts.pb.cc" Finished building: Build-dragonfly/src/protobuf/lm/io/Lattice.pb.cc Building file: src/c/lm/io/SimulationParameters.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/io c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/io/SimulationParameters.o" "src/c/lm/io/SimulationParameters.cpp" Finished building: src/c/lm/io/SimulationParameters.cpp Building file: src/c/lm/io/hdf5/SimulationFile.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/io/hdf5 c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/io/hdf5/SimulationFile.o" "src/c/lm/io/hdf5/SimulationFile.cpp" Finished building: Build-dragonfly/src/protobuf/lm/io/SpatialModel.pb.cc Building file: src/c/lm/io/hdf5/SimulationFile_create.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/io/hdf5 c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/io/hdf5/SimulationFile_create.o" "src/c/lm/io/hdf5/SimulationFile_create.cpp" In file included from src/c/lm/io/hdf5/SimulationFile_create.cpp:46: ./src/c/lm/io/hdf5/SimulationFile.h:88:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:90:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:92:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:94:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:96:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:98:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:100:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, bool initializeModel, unsigned int numberSpecies=0) throw(lm::IOException,HDF5Exception); ^~~~~ In file included from src/c/lm/io/hdf5/SimulationFile_create.cpp:46: ./src/c/lm/io/hdf5/SimulationFile.h:113:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const string filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:115:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const char* filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:117:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~SimulationFile() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:120:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void close() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:122:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void flush() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:125:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual string checkpoint() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:133:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setParameter(string key, string value) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:141:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:144:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:151:172: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, byte * lattice, size_t latticeMaxSize, byte * latticeSites, size_t latticeSitesMaxSize) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:155:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, lm::rdme::Lattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:158:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:164:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:170:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint32_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:175:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::ByteLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:180:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::IntLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:184:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:187:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:194:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual bool replicateExists(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:197:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:201:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts * speciesCounts) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:207:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice(unsigned int replicate, lm::io::Lattice * lattice, byte * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:208:137: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice_U32LE(unsigned int replicate, lm::io::Lattice * lattice, uint32_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:210:119: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSites(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * siteData, size_t siteDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:214:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendParameterValues(unsigned int replicate, lm::io::ParameterValues * parameterValues) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:218:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes * speciesCounts) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual vector getLatticeTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:227:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice * lattice) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:230:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:232:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeAllReplicates() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:253:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getParticleCounts(unsigned int replicate, unsigned int latticeIndex) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:254:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map > getSpeciesCounts(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:255:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector getSpeciesCountTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:256:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSpeciesNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:257:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSiteTypeNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:277:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void open() throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:278:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openGroups() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:279:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadParameters() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:280:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadModel() throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:281:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * openReplicateHandles(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:282:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * createReplicateHandles(string replicateString) throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:283:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicateHandles(ReplicateHandles * handles) throw(HDF5Exception); ^~~~~ src/c/lm/io/hdf5/SimulationFile_create.cpp:55:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::create(const string filename) throw(lm::IOException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile_create.cpp:60:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::create(const char * filename) throw(lm::IOException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile_create.cpp:65:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::create(const string filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile_create.cpp:70:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::create(const char * filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile_create.cpp:75:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::create(const char * filename, bool initializeModel, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception) ^~~~~ Finished building: Build-dragonfly/src/protobuf/lm/io/ParameterValues.pb.cc Building file: src/c/lm/main/DataOutputQueue.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/main c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/main/DataOutputQueue.o" "src/c/lm/main/DataOutputQueue.cpp" Finished building: Build-dragonfly/src/protobuf/lm/io/ReactionModel.pb.cc Building file: src/c/lm/main/ResourceAllocator.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/main c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/main/ResourceAllocator.o" "src/c/lm/main/ResourceAllocator.cpp" Finished building: src/c/lm/io/hdf5/SimulationFile_create.cpp Building file: src/c/lm/me/MESolver.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/me c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/me/MESolver.o" "src/c/lm/me/MESolver.cpp" In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/me/MESolver.h:44, from src/c/lm/me/MESolver.cpp:40: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/me/MESolver.h:44, from src/c/lm/me/MESolver.cpp:40: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/me/MESolver.h:44, from src/c/lm/me/MESolver.cpp:40: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ Finished building: src/c/lm/me/MESolver.cpp Building file: src/c/lm/me/MESolverFactory.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/me c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/me/MESolverFactory.o" "src/c/lm/me/MESolverFactory.cpp" In file included from ./src/c/lm/main/ResourceAllocator.h:45, from src/c/lm/main/ResourceAllocator.cpp:46: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from src/c/lm/main/ResourceAllocator.cpp:46: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from src/c/lm/main/ResourceAllocator.cpp:46: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ src/c/lm/main/ResourceAllocator.cpp:54:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator::ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException) ^~~~~ src/c/lm/main/ResourceAllocator.cpp:60:161: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator::ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException) ^~~~~ src/c/lm/main/ResourceAllocator.cpp:66:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ResourceAllocator::initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException) ^~~~~ src/c/lm/main/ResourceAllocator.cpp:126:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator::~ResourceAllocator() throw(PthreadException) ^~~~~ src/c/lm/main/ResourceAllocator.cpp:162:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator::ComputeResources ResourceAllocator::assignReplicate(int replicate) throw(Exception,PthreadException) ^~~~~ src/c/lm/main/ResourceAllocator.cpp:210:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] int ResourceAllocator::reserveCpuCore() throw(Exception,PthreadException) ^~~~~ src/c/lm/main/ResourceAllocator.cpp:250:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ResourceAllocator::removeReplicate(int replicate) throw(Exception,PthreadException) ^~~~~ In file included from ./src/c/lm/main/DataOutputQueue.h:47, from src/c/lm/main/DataOutputQueue.cpp:44: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from src/c/lm/main/DataOutputQueue.cpp:44: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/main/DataOutputQueue.cpp:44: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ src/c/lm/main/DataOutputQueue.cpp:61:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue::DataOutputQueue() throw(PthreadException) ^~~~~ src/c/lm/main/DataOutputQueue.cpp:66:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue::~DataOutputQueue() throw(PthreadException) ^~~~~ src/c/lm/main/DataOutputQueue.cpp:71:188: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void DataOutputQueue::pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload, size_t payloadSize, void (*payloadSerializer)(void *, void *, size_t)) throw(PthreadException) ^~~~~ src/c/lm/main/DataOutputQueue.cpp:111:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void DataOutputQueue::pushDataSet(void * data, size_t dataSize) throw(PthreadException) ^~~~~ src/c/lm/main/DataOutputQueue.cpp:116:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void DataOutputQueue::pushDataSet(DataSet * dataSet) throw(PthreadException) ^~~~~ In file included from src/c/lm/io/hdf5/SimulationFile.cpp:60: ./src/c/lm/io/hdf5/SimulationFile.h:88:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:90:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:92:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:94:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:96:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:98:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:100:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, bool initializeModel, unsigned int numberSpecies=0) throw(lm::IOException,HDF5Exception); ^~~~~ In file included from src/c/lm/io/hdf5/SimulationFile.cpp:60: ./src/c/lm/io/hdf5/SimulationFile.h:113:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const string filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:115:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const char* filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:117:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~SimulationFile() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:120:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void close() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:122:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void flush() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:125:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual string checkpoint() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:133:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setParameter(string key, string value) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:141:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:144:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:151:172: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, byte * lattice, size_t latticeMaxSize, byte * latticeSites, size_t latticeSitesMaxSize) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:155:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, lm::rdme::Lattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:158:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:164:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:170:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint32_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:175:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::ByteLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:180:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::IntLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:184:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:187:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:194:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual bool replicateExists(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:197:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:201:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts * speciesCounts) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:207:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice(unsigned int replicate, lm::io::Lattice * lattice, byte * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:208:137: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice_U32LE(unsigned int replicate, lm::io::Lattice * lattice, uint32_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:210:119: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSites(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * siteData, size_t siteDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:214:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendParameterValues(unsigned int replicate, lm::io::ParameterValues * parameterValues) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:218:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes * speciesCounts) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual vector getLatticeTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:227:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice * lattice) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:230:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:232:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeAllReplicates() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:253:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getParticleCounts(unsigned int replicate, unsigned int latticeIndex) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:254:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map > getSpeciesCounts(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:255:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector getSpeciesCountTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:256:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSpeciesNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:257:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSiteTypeNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:277:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void open() throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:278:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openGroups() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:279:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadParameters() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:280:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadModel() throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:281:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * openReplicateHandles(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:282:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * createReplicateHandles(string replicateString) throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:283:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicateHandles(ReplicateHandles * handles) throw(HDF5Exception); ^~~~~ In file included from src/c/lm/io/hdf5/SimulationFile.cpp:61: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from src/c/lm/io/hdf5/SimulationFile.cpp:62: ./src/c/lm/rdme/ByteLattice.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ByteLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:75:125: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ByteLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:76:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ByteLattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:81:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:82:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:83:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t siteType) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:84:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t subvolume, site_t site) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:89:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:90:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:91:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:92:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t subvolume, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:93:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:94:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t subvolume, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:95:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:96:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t subvolume) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:116:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void allocateMemory() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:117:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void deallocateMemory() throw(std::bad_alloc); ^~~~~ In file included from src/c/lm/io/hdf5/SimulationFile.cpp:63: ./src/c/lm/rdme/IntLattice.h:72:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] IntLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/IntLattice.h:73:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] IntLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/IntLattice.h:74:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~IntLattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/IntLattice.h:79:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:80:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:81:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t siteType) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:82:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t subvolume, site_t site) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:85:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:86:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:87:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:88:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t subvolume, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:89:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:90:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t subvolume, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:91:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:92:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t subvolume) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:113:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void allocateMemory() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/IntLattice.h:114:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void deallocateMemory() throw(std::bad_alloc); ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:81:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile::SimulationFile(const string filename) throw(lm::IOException,HDF5Exception,Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:87:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile::SimulationFile(const char* filename) throw(lm::IOException,HDF5Exception,Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:93:29: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::open() throw(lm::IOException,HDF5Exception,Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:135:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::openGroups() throw(HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:142:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile::~SimulationFile() throw(lm::IOException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:148:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::flush() throw(HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:157:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] string SimulationFile::checkpoint() throw(lm::IOException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:188:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::close() throw(lm::IOException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:219:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool SimulationFile::isValidFile(const char * filename) throw(lm::IOException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:224:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool SimulationFile::isValidFile(const string filename) throw(lm::IOException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:253:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::loadParameters() throw(HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:321:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::setParameter(string key, string value) throw(HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:338:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::loadModel() throw(Exception,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:362:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::getReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:471:78: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::setReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:556:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::getDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:618:163: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::getDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, size_t latticeSize, uint8_t * latticeSites, size_t latticeSitesSize) throw(Exception,InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:660:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::getDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::Lattice * lattice) throw(Exception,InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:695:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::setDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:832:118: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::setDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:838:119: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::setDiffusionModelLattice(lm::io::DiffusionModel * m, uint32_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:844:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::ByteLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:859:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::IntLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:874:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::getSpatialModel(lm::io::SpatialModel * spatialModel) throw(Exception,InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:969:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::setSpatialModel(lm::io::SpatialModel * spatialModel) throw(Exception,InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:1076:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool SimulationFile::replicateExists(unsigned int replicate) throw(HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:1084:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::openReplicate(unsigned int replicate) throw(HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:1089:105: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts * speciesCounts) throw(HDF5Exception) ^~~~~ Finished building: src/c/lm/main/ResourceAllocator.cpp src/c/lm/io/hdf5/SimulationFile.cpp:1165:134: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::appendLattice(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception) ^~~~~ Building file: Build-dragonfly/src/protobuf/lm/message/SimulationParameters.pb.cc Invoking: c++ mkdir -p Build-dragonfly/src/protobuf/lm/message c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/protobuf/lm/message/SimulationParameters.pb.o" "Build-dragonfly/src/protobuf/lm/message/SimulationParameters.pb.cc" src/c/lm/io/hdf5/SimulationFile.cpp:1266:141: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::appendLattice_U32LE(unsigned int replicate, lm::io::Lattice * lattice, uint32_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:1346:126: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::appendSites(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * siteData, size_t siteDataSize) throw(InvalidArgException,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:1447:111: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::appendParameterValues(unsigned int replicate, lm::io::ParameterValues * parameterValues) throw(HDF5Exception,InvalidArgException) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:1524:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes * firstPassageTimes) throw(HDF5Exception,InvalidArgException) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:1930:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector SimulationFile::getLatticeTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:1952:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector SimulationFile::getSpeciesCountTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:1974:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map > SimulationFile::getSpeciesCounts(unsigned int replicate) throw(HDF5Exception,InvalidArgException) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:2011:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice * lattice) throw(HDF5Exception,InvalidArgException) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:2054:2: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(HDF5Exception,InvalidArgException) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp: In member function 'std::map lm::io::hdf5::SimulationFile::getParticleCounts(unsigned int, unsigned int)': src/c/lm/io/hdf5/SimulationFile.cpp:2069:15: warning: unused variable 'particlesBuffer' [-Wunused-variable] uint8_t * particlesBuffer = new uint8_t[particlesBufferSize]; ^~~~~~~~~~~~~~~ src/c/lm/io/hdf5/SimulationFile.cpp: At global scope: src/c/lm/io/hdf5/SimulationFile.cpp:2117:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::closeReplicate(unsigned int replicate) throw(HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:2129:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::closeAllReplicates() throw(HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:2141:97: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile::ReplicateHandles * SimulationFile::openReplicateHandles(unsigned int replicate) throw(HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:2187:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile::ReplicateHandles * SimulationFile::createReplicateHandles(string replicateString) throw(Exception,HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:2235:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void SimulationFile::closeReplicateHandles(ReplicateHandles * handles) throw(HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp:2245:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map SimulationFile::getSpeciesNames() throw(HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp: In member function 'std::map > lm::io::hdf5::SimulationFile::getSpeciesNames()': src/c/lm/io/hdf5/SimulationFile.cpp:2254:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] while((nextpos=namelist.find(",", pos)) != string::npos) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ src/c/lm/io/hdf5/SimulationFile.cpp: At global scope: src/c/lm/io/hdf5/SimulationFile.cpp:2267:59: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map SimulationFile::getSiteTypeNames() throw(HDF5Exception) ^~~~~ src/c/lm/io/hdf5/SimulationFile.cpp: In member function 'std::map > lm::io::hdf5::SimulationFile::getSiteTypeNames()': src/c/lm/io/hdf5/SimulationFile.cpp:2276:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] while((nextpos=namelist.find(",", pos)) != string::npos) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ Finished building: src/c/lm/main/DataOutputQueue.cpp Building file: src/c/lm/rdme/ByteLattice.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/rdme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/rdme/ByteLattice.o" "src/c/lm/rdme/ByteLattice.cpp" Finished building: Build-dragonfly/src/protobuf/lm/io/SpeciesCounts.pb.cc Building file: src/c/lm/rdme/IntLattice.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/rdme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/rdme/IntLattice.o" "src/c/lm/rdme/IntLattice.cpp" In file included from src/c/lm/rdme/ByteLattice.cpp:46: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from src/c/lm/rdme/ByteLattice.cpp:47: ./src/c/lm/rdme/ByteLattice.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ByteLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:75:125: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ByteLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:76:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ByteLattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:81:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:82:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:83:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t siteType) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:84:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t subvolume, site_t site) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:89:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:90:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:91:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:92:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t subvolume, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:93:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:94:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t subvolume, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:95:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:96:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t subvolume) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:116:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void allocateMemory() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:117:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void deallocateMemory() throw(std::bad_alloc); ^~~~~ src/c/lm/rdme/ByteLattice.cpp:57:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(std::bad_alloc,InvalidArgException,Exception) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:68:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(std::bad_alloc,InvalidArgException,Exception) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:78:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(std::bad_alloc) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:107:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(std::bad_alloc) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:119:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(std::bad_alloc) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:151:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:162:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:171:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:182:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:190:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] site_size_t ByteLattice::getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:211:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] site_size_t ByteLattice::getOccupancy(lattice_size_t index) const throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:240:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException,InvalidParticleException) ^~~~~ src/c/lm/rdme/ByteLattice.cpp: In member function 'virtual particle_t lm::rdme::ByteLattice::getParticle(lattice_size_t, lattice_size_t, lattice_size_t, site_size_t) const': src/c/lm/rdme/ByteLattice.cpp:243:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (x >= size.x || y >= size.y || z >= size.z) ^~ src/c/lm/rdme/ByteLattice.cpp:245:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (particleIndex >= getMaxOccupancy()) ^~ src/c/lm/rdme/ByteLattice.cpp: At global scope: src/c/lm/rdme/ByteLattice.cpp:259:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException,InvalidParticleException) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:285:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException,InvalidParticleException) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:312:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException,InvalidParticleException) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:338:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/ByteLattice.cpp:354:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException) ^~~~~ In file included from src/c/lm/rdme/IntLattice.cpp:46: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from src/c/lm/rdme/IntLattice.cpp:47: ./src/c/lm/rdme/IntLattice.h:72:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] IntLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/IntLattice.h:73:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] IntLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/IntLattice.h:74:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~IntLattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/IntLattice.h:79:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:80:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:81:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t siteType) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:82:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t subvolume, site_t site) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:85:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:86:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:87:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:88:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t subvolume, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:89:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:90:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t subvolume, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:91:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:92:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t subvolume) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:113:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void allocateMemory() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/IntLattice.h:114:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void deallocateMemory() throw(std::bad_alloc); ^~~~~ src/c/lm/rdme/IntLattice.cpp:57:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(std::bad_alloc,InvalidArgException,Exception) ^~~~~ src/c/lm/rdme/IntLattice.cpp:68:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(std::bad_alloc,InvalidArgException,Exception) ^~~~~ src/c/lm/rdme/IntLattice.cpp:78:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(std::bad_alloc) ^~~~~ src/c/lm/rdme/IntLattice.cpp:107:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(std::bad_alloc) ^~~~~ src/c/lm/rdme/IntLattice.cpp:119:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(std::bad_alloc) ^~~~~ src/c/lm/rdme/IntLattice.cpp:135:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/IntLattice.cpp:146:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/IntLattice.cpp:155:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/IntLattice.cpp:166:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/IntLattice.cpp:174:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] site_size_t IntLattice::getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/IntLattice.cpp:194:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] site_size_t IntLattice::getOccupancy(lattice_size_t index) const throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/IntLattice.cpp:221:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException,InvalidParticleException) ^~~~~ src/c/lm/rdme/IntLattice.cpp: In member function 'virtual particle_t lm::rdme::IntLattice::getParticle(lattice_size_t, lattice_size_t, lattice_size_t, site_size_t) const': src/c/lm/rdme/IntLattice.cpp:224:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (x >= size.x || y >= size.y || z >= size.z) ^~ src/c/lm/rdme/IntLattice.cpp:226:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (particleIndex >= getMaxOccupancy()) ^~ src/c/lm/rdme/IntLattice.cpp: At global scope: src/c/lm/rdme/IntLattice.cpp:235:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException,InvalidParticleException) ^~~~~ src/c/lm/rdme/IntLattice.cpp:256:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException,InvalidParticleException) ^~~~~ src/c/lm/rdme/IntLattice.cpp:278:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException,InvalidParticleException) ^~~~~ src/c/lm/rdme/IntLattice.cpp:299:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException) ^~~~~ src/c/lm/rdme/IntLattice.cpp:315:1: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(InvalidSiteException) ^~~~~ In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/NextReactionSolver.h:46, from ./src/c/lm/cme/FluctuatingNRSolver.h:46, from src/c/lm/me/MESolverFactory.cpp:42: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/NextReactionSolver.h:46, from ./src/c/lm/cme/FluctuatingNRSolver.h:46, from src/c/lm/me/MESolverFactory.cpp:42: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from ./src/c/lm/cme/NextReactionSolver.h:46, from ./src/c/lm/cme/FluctuatingNRSolver.h:46, from src/c/lm/me/MESolverFactory.cpp:42: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/NextReactionSolver.h:49, from ./src/c/lm/cme/FluctuatingNRSolver.h:46, from src/c/lm/me/MESolverFactory.cpp:42: ./src/c/lm/reaction/ReactionQueue.h: In destructor 'lm::reaction::ReactionQueue::~ReactionQueue()': ./src/c/lm/reaction/ReactionQueue.h:81:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:81:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:82:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:82:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:83:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:83:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~~~~~~~~~~~~~~~~ In file included from src/c/lm/me/MESolverFactory.cpp:52: ./src/c/lm/me/MESolverFactory.h: At global scope: ./src/c/lm/me/MESolverFactory.h:62:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void setSolver(string solver) throw(lm::InvalidArgException); ^~~~~ ./src/c/lm/me/MESolverFactory.h:64:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool needsReactionModel() throw(lm::Exception); ^~~~~ ./src/c/lm/me/MESolverFactory.h:66:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool needsDiffusionModel() throw(lm::Exception); ^~~~~ ./src/c/lm/me/MESolverFactory.h:70:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] MESolver * instantiate() throw(lm::Exception); ^~~~~ In file included from ./src/c/lm/rdme/NextSubvolumeSolver.h:43, from src/c/lm/me/MESolverFactory.cpp:61: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from ./src/c/lm/rdme/NextSubvolumeSolver.h:44, from src/c/lm/me/MESolverFactory.cpp:61: ./src/c/lm/rdme/RDMESolver.h:59:157: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(DiffusionModel * dm, const uint8_t * lattice, size_t latticeSize, const uint8_t * latticeSites, size_t latticeSitesSize) throw(InvalidArgException); ^~~~~ In file included from ./src/c/lm/rdme/NextSubvolumeSolver.h:44, from src/c/lm/me/MESolverFactory.cpp:61: ./src/c/lm/rdme/RDMESolver.h:60:335: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void buildDiffusionModel(const uint numberSiteTypesA, const double * DFA, const uint * RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, si_dist_t latticeSpacing, const uint8_t * latticeData, const uint8_t * latticeSitesData, bool rowMajorData=true) throw(InvalidArgException); ^~~~~ In file included from src/c/lm/me/MESolverFactory.cpp:61: ./src/c/lm/rdme/NextSubvolumeSolver.h:69:335: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void buildDiffusionModel(const uint numberSiteTypesA, const double * DFA, const uint * RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, si_dist_t latticeSpacing, const uint8_t * latticeData, const uint8_t * latticeSitesData, bool rowMajorData=true) throw(InvalidArgException); ^~~~~ ./src/c/lm/rdme/NextSubvolumeSolver.h:76:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkSpeciesCountsAgainstLattice() throw(Exception); ^~~~~ src/c/lm/me/MESolverFactory.cpp:73:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void MESolverFactory::setSolver(string solver) throw(lm::InvalidArgException) ^~~~~ src/c/lm/me/MESolverFactory.cpp:96:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool MESolverFactory::needsReactionModel() throw(lm::Exception) ^~~~~ src/c/lm/me/MESolverFactory.cpp:104:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool MESolverFactory::needsDiffusionModel() throw(lm::Exception) ^~~~~ src/c/lm/me/MESolverFactory.cpp:112:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] MESolver * MESolverFactory::instantiate() throw(lm::Exception) ^~~~~ Finished building: src/c/lm/rdme/IntLattice.cpp Building file: src/c/lm/rdme/Lattice.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/rdme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/rdme/Lattice.o" "src/c/lm/rdme/Lattice.cpp" Finished building: src/c/lm/rdme/ByteLattice.cpp Building file: src/c/lm/rdme/NextSubvolumeSolver.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/rdme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/rdme/NextSubvolumeSolver.o" "src/c/lm/rdme/NextSubvolumeSolver.cpp" Finished building: src/c/lm/me/MESolverFactory.cpp Building file: src/c/lm/rdme/RDMESolver.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/rdme c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/rdme/RDMESolver.o" "src/c/lm/rdme/RDMESolver.cpp" Finished building: Build-dragonfly/src/protobuf/lm/message/SimulationParameters.pb.cc Building file: src/c/lm/rng/RandomGenerator.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/rng c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/rng/RandomGenerator.o" "src/c/lm/rng/RandomGenerator.cpp" Finished building: src/c/lm/rng/RandomGenerator.cpp Building file: src/c/lm/rng/XORShift.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/rng c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/rng/XORShift.o" "src/c/lm/rng/XORShift.cpp" Finished building: src/c/lm/rng/XORShift.cpp Building file: src/c/lm/thread/Thread.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/thread c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/thread/Thread.o" "src/c/lm/thread/Thread.cpp" In file included from src/c/lm/thread/Thread.cpp:42: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ src/c/lm/thread/Thread.cpp:48:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread::Thread() throw(PthreadException) ^~~~~ src/c/lm/thread/Thread.cpp:59:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread::~Thread() throw(PthreadException) ^~~~~ src/c/lm/thread/Thread.cpp:64:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void Thread::setAffinity(int cpuNumber) throw(PthreadException) ^~~~~ src/c/lm/thread/Thread.cpp:87:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void Thread::start() throw(PthreadException) ^~~~~ src/c/lm/thread/Thread.cpp: In static member function 'static void* lm::thread::Thread::start_thread(void*)': src/c/lm/thread/Thread.cpp:120:26: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] pthread_exit((void *)ret); ^~~ src/c/lm/thread/Thread.cpp: At global scope: src/c/lm/thread/Thread.cpp:123:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void Thread::stop() throw(PthreadException) ^~~~~ In file included from src/c/lm/rdme/Lattice.cpp:52: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ src/c/lm/rdme/Lattice.cpp:74:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Lattice::~Lattice() throw(std::bad_alloc) {} ^~~~~ Finished building: src/c/lm/thread/Thread.cpp Building file: src/c/lm/thread/Worker.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/thread c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/thread/Worker.o" "src/c/lm/thread/Worker.cpp" In file included from src/c/lm/thread/Worker.cpp:40: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from src/c/lm/thread/Worker.cpp:41: ./src/c/lm/thread/Worker.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:56:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:59:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:61:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ In file included from src/c/lm/thread/Worker.cpp:42: ./src/c/lm/thread/WorkerManager.h:66:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] WorkerManager() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:68:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ~WorkerManager() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:72:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void addWorker(Worker * worker) throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:75:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void removeWorker(Worker * worker) throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:77:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void abortWorkers() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:79:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void checkpointWorkers() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:81:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void stopWorkers() throw(PthreadException); ^~~~~ src/c/lm/thread/Worker.cpp:47:18: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Worker::Worker() throw(PthreadException) ^~~~~ src/c/lm/thread/Worker.cpp:53:19: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Worker::~Worker() throw(PthreadException) ^~~~~ src/c/lm/thread/Worker.cpp:58:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void Worker::abort() throw(PthreadException) ^~~~~ src/c/lm/thread/Worker.cpp:74:27: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void Worker::checkpoint() throw(PthreadException) {} ^~~~~ Finished building: src/c/lm/thread/Worker.cpp Building file: src/c/lm/thread/WorkerManager.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/thread c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/thread/WorkerManager.o" "src/c/lm/thread/WorkerManager.cpp" Finished building: src/c/lm/rdme/Lattice.cpp Building file: src/c/lm/main/runSimulation.cpp Invoking: c++ mkdir -p Build-dragonfly/src/c/lm/main c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/c/lm/main/runSimulation.o" "src/c/lm/main/runSimulation.cpp" In file included from src/c/lm/thread/WorkerManager.cpp:42: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from src/c/lm/thread/WorkerManager.cpp:43: ./src/c/lm/thread/Worker.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:56:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:59:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:61:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ In file included from src/c/lm/thread/WorkerManager.cpp:44: ./src/c/lm/thread/WorkerManager.h:66:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] WorkerManager() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:68:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ~WorkerManager() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:72:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void addWorker(Worker * worker) throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:75:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void removeWorker(Worker * worker) throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:77:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void abortWorkers() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:79:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void checkpointWorkers() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:81:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void stopWorkers() throw(PthreadException); ^~~~~ src/c/lm/thread/WorkerManager.cpp:56:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] WorkerManager::WorkerManager() throw(PthreadException) ^~~~~ src/c/lm/thread/WorkerManager.cpp:62:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] WorkerManager::~WorkerManager() throw(PthreadException) ^~~~~ src/c/lm/thread/WorkerManager.cpp:67:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void WorkerManager::addWorker(Worker * worker) throw(PthreadException) ^~~~~ src/c/lm/thread/WorkerManager.cpp:76:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void WorkerManager::removeWorker(Worker * worker) throw(PthreadException) ^~~~~ src/c/lm/thread/WorkerManager.cpp:85:36: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void WorkerManager::abortWorkers() throw(PthreadException) ^~~~~ src/c/lm/thread/WorkerManager.cpp:106:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void WorkerManager::checkpointWorkers() throw(PthreadException) ^~~~~ src/c/lm/thread/WorkerManager.cpp:121:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void WorkerManager::stopWorkers() throw(PthreadException) ^~~~~ Finished building: src/c/lm/thread/WorkerManager.cpp Building file: utils/c/lm_setp.cpp Invoking: c++ mkdir -p Build-dragonfly/utils/c c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./utils/c -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/utils/c/lm_setp.o" "utils/c/lm_setp.cpp" In file included from utils/c/lm_setp.cpp:49: ./src/c/lm/io/hdf5/SimulationFile.h:88:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:90:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:92:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:94:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:96:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:98:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:100:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, bool initializeModel, unsigned int numberSpecies=0) throw(lm::IOException,HDF5Exception); ^~~~~ In file included from utils/c/lm_setp.cpp:49: ./src/c/lm/io/hdf5/SimulationFile.h:113:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const string filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:115:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const char* filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:117:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~SimulationFile() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:120:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void close() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:122:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void flush() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:125:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual string checkpoint() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:133:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setParameter(string key, string value) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:141:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:144:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:151:172: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, byte * lattice, size_t latticeMaxSize, byte * latticeSites, size_t latticeSitesMaxSize) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:155:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, lm::rdme::Lattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:158:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:164:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:170:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint32_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:175:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::ByteLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:180:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::IntLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:184:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:187:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:194:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual bool replicateExists(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:197:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:201:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts * speciesCounts) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:207:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice(unsigned int replicate, lm::io::Lattice * lattice, byte * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:208:137: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice_U32LE(unsigned int replicate, lm::io::Lattice * lattice, uint32_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:210:119: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSites(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * siteData, size_t siteDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:214:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendParameterValues(unsigned int replicate, lm::io::ParameterValues * parameterValues) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:218:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes * speciesCounts) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual vector getLatticeTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:227:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice * lattice) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:230:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:232:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeAllReplicates() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:253:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getParticleCounts(unsigned int replicate, unsigned int latticeIndex) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:254:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map > getSpeciesCounts(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:255:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector getSpeciesCountTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:256:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSpeciesNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:257:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSiteTypeNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:277:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void open() throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:278:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openGroups() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:279:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadParameters() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:280:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadModel() throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:281:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * openReplicateHandles(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:282:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * createReplicateHandles(string replicateString) throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:283:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicateHandles(ReplicateHandles * handles) throw(HDF5Exception); ^~~~~ In file included from src/c/lm/main/runSimulation.cpp:80: ./src/c/lm/io/hdf5/SimulationFile.h:88:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:90:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:92:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:94:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:96:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:98:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:100:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, bool initializeModel, unsigned int numberSpecies=0) throw(lm::IOException,HDF5Exception); ^~~~~ In file included from src/c/lm/main/runSimulation.cpp:80: ./src/c/lm/io/hdf5/SimulationFile.h:113:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const string filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:115:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const char* filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:117:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~SimulationFile() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:120:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void close() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:122:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void flush() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:125:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual string checkpoint() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:133:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setParameter(string key, string value) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:141:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:144:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:151:172: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, byte * lattice, size_t latticeMaxSize, byte * latticeSites, size_t latticeSitesMaxSize) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:155:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, lm::rdme::Lattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:158:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:164:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:170:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint32_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:175:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::ByteLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:180:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::IntLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:184:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:187:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:194:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual bool replicateExists(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:197:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:201:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts * speciesCounts) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:207:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice(unsigned int replicate, lm::io::Lattice * lattice, byte * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:208:137: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice_U32LE(unsigned int replicate, lm::io::Lattice * lattice, uint32_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:210:119: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSites(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * siteData, size_t siteDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:214:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendParameterValues(unsigned int replicate, lm::io::ParameterValues * parameterValues) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:218:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes * speciesCounts) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual vector getLatticeTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:227:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice * lattice) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:230:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:232:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeAllReplicates() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:253:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getParticleCounts(unsigned int replicate, unsigned int latticeIndex) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:254:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map > getSpeciesCounts(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:255:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector getSpeciesCountTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:256:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSpeciesNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:257:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSiteTypeNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:277:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void open() throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:278:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openGroups() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:279:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadParameters() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:280:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadModel() throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:281:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * openReplicateHandles(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:282:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * createReplicateHandles(string replicateString) throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:283:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicateHandles(ReplicateHandles * handles) throw(HDF5Exception); ^~~~~ utils/c/lm_setp.cpp: In function 'int main(int, char**)': utils/c/lm_setp.cpp:131:45: warning: catching polymorphic type 'class lm::CommandLineArgumentException' by value [-Wcatch-value=] catch (lm::CommandLineArgumentException e) ^ utils/c/lm_setp.cpp:136:26: warning: catching polymorphic type 'class lm::Exception' by value [-Wcatch-value=] catch (lm::Exception e) ^ utils/c/lm_setp.cpp:140:27: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] catch (std::exception e) ^ In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/rdme/NextSubvolumeSolver.cpp:43: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/rdme/NextSubvolumeSolver.cpp:43: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/rdme/NextSubvolumeSolver.cpp:43: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from src/c/lm/rdme/NextSubvolumeSolver.cpp:47: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/rdme/NextSubvolumeSolver.cpp:47: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ In file included from src/c/lm/rdme/NextSubvolumeSolver.cpp:48: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from src/c/lm/rdme/NextSubvolumeSolver.cpp:49: ./src/c/lm/rdme/ByteLattice.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ByteLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:75:125: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ByteLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:76:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ByteLattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:81:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:82:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:83:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t siteType) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:84:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t subvolume, site_t site) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:89:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:90:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:91:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:92:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t subvolume, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:93:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:94:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t subvolume, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:95:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:96:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t subvolume) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:116:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void allocateMemory() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:117:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void deallocateMemory() throw(std::bad_alloc); ^~~~~ In file included from ./src/c/lm/rdme/NextSubvolumeSolver.h:44, from src/c/lm/rdme/NextSubvolumeSolver.cpp:50: ./src/c/lm/rdme/RDMESolver.h:59:157: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(DiffusionModel * dm, const uint8_t * lattice, size_t latticeSize, const uint8_t * latticeSites, size_t latticeSitesSize) throw(InvalidArgException); ^~~~~ In file included from ./src/c/lm/rdme/NextSubvolumeSolver.h:44, from src/c/lm/rdme/NextSubvolumeSolver.cpp:50: ./src/c/lm/rdme/RDMESolver.h:60:335: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void buildDiffusionModel(const uint numberSiteTypesA, const double * DFA, const uint * RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, si_dist_t latticeSpacing, const uint8_t * latticeData, const uint8_t * latticeSitesData, bool rowMajorData=true) throw(InvalidArgException); ^~~~~ In file included from ./src/c/lm/rdme/NextSubvolumeSolver.h:45, from src/c/lm/rdme/NextSubvolumeSolver.cpp:50: ./src/c/lm/reaction/ReactionQueue.h: In destructor 'lm::reaction::ReactionQueue::~ReactionQueue()': ./src/c/lm/reaction/ReactionQueue.h:81:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:81:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:82:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:82:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:83:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:83:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~~~~~~~~~~~~~~~~ In file included from src/c/lm/rdme/NextSubvolumeSolver.cpp:50: ./src/c/lm/rdme/NextSubvolumeSolver.h: At global scope: ./src/c/lm/rdme/NextSubvolumeSolver.h:69:335: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void buildDiffusionModel(const uint numberSiteTypesA, const double * DFA, const uint * RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, si_dist_t latticeSpacing, const uint8_t * latticeData, const uint8_t * latticeSitesData, bool rowMajorData=true) throw(InvalidArgException); ^~~~~ ./src/c/lm/rdme/NextSubvolumeSolver.h:76:53: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkSpeciesCountsAgainstLattice() throw(Exception); ^~~~~ src/c/lm/rdme/NextSubvolumeSolver.cpp: In member function 'virtual void lm::rdme::NextSubvolumeSolver::destroyModel()': src/c/lm/rdme/NextSubvolumeSolver.cpp:85:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (currentSubvolumeSpeciesCounts != NULL) delete[] currentSubvolumeSpeciesCounts; currentSubvolumeSpeciesCounts = NULL; ^~ src/c/lm/rdme/NextSubvolumeSolver.cpp:85:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (currentSubvolumeSpeciesCounts != NULL) delete[] currentSubvolumeSpeciesCounts; currentSubvolumeSpeciesCounts = NULL; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/c/lm/rdme/NextSubvolumeSolver.cpp: At global scope: src/c/lm/rdme/NextSubvolumeSolver.cpp:88:339: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void NextSubvolumeSolver::buildDiffusionModel(const uint numberSiteTypesA, const double * DFA, const uint * RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, si_dist_t latticeSpacing, const uint8_t * latticeData, const uint8_t * latticeSitesData, bool rowMajorData) throw(InvalidArgException) ^~~~~ src/c/lm/rdme/NextSubvolumeSolver.cpp: In member function 'virtual void lm::rdme::NextSubvolumeSolver::destroyDiffusionModel()': src/c/lm/rdme/NextSubvolumeSolver.cpp:118:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionQueue != NULL) delete reactionQueue; reactionQueue = NULL; ^~ src/c/lm/rdme/NextSubvolumeSolver.cpp:118:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionQueue != NULL) delete reactionQueue; reactionQueue = NULL; ^~~~~~~~~~~~~ src/c/lm/rdme/NextSubvolumeSolver.cpp: At global scope: src/c/lm/rdme/NextSubvolumeSolver.cpp:328:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void NextSubvolumeSolver::checkSpeciesCountsAgainstLattice() throw(Exception) ^~~~~ Finished building: utils/c/lm_setp.cpp Building file: utils/c/util.cpp Invoking: c++ mkdir -p Build-dragonfly/utils/c c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./utils/c -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/utils/c/util.o" "utils/c/util.cpp" In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/rdme/RDMESolver.cpp:43: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/main/CheckpointSignaler.h:45, from src/c/lm/main/runSimulation.cpp:84: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/main/CheckpointSignaler.h:46, from src/c/lm/main/runSimulation.cpp:84: ./src/c/lm/thread/Worker.h:54:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:56:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Worker() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:59:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Worker.h:61:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ In file included from src/c/lm/main/runSimulation.cpp:84: ./src/c/lm/main/CheckpointSignaler.h:61:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] CheckpointSignaler() throw(PthreadException); ^~~~~ ./src/c/lm/main/CheckpointSignaler.h:62:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~CheckpointSignaler() throw(PthreadException); ^~~~~ ./src/c/lm/main/CheckpointSignaler.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/rdme/RDMESolver.cpp:43: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/CMESolver.h:50, from src/c/lm/rdme/RDMESolver.cpp:43: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from src/c/lm/main/runSimulation.cpp:85: ./src/c/lm/main/DataOutputQueue.h:101:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] DataOutputQueue() throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:102:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~DataOutputQueue() throw(PthreadException); ^~~~~ In file included from src/c/lm/main/runSimulation.cpp:85: ./src/c/lm/main/DataOutputQueue.h:110:195: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(uint type, uint replicate, ::google::protobuf::Message * message, void * payload=NULL, size_t payloadSize=0, void (*payloadSerializer)(void *, void *, size_t)=NULL) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:114:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(void * data, size_t dataSize) throw(PthreadException); ^~~~~ ./src/c/lm/main/DataOutputQueue.h:117:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ In file included from src/c/lm/main/runSimulation.cpp:86: ./src/c/lm/main/LocalDataOutputWorker.h:67:50: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] LocalDataOutputWorker(SimulationFile * file) throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:68:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~LocalDataOutputWorker() throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:72:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void pushDataSet(DataSet * dataSet) throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:75:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:77:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void abort() throw(PthreadException); ^~~~~ ./src/c/lm/main/LocalDataOutputWorker.h:79:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void checkpoint() throw(PthreadException); ^~~~~ In file included from src/c/lm/rdme/RDMESolver.cpp:45: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from src/c/lm/rdme/RDMESolver.cpp:46: ./src/c/lm/rdme/ByteLattice.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ByteLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:75:125: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ByteLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:76:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ByteLattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:81:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:82:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:83:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t siteType) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:84:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t subvolume, site_t site) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:89:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:90:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:91:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:92:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t subvolume, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:93:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:94:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t subvolume, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:95:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:96:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t subvolume) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:116:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void allocateMemory() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:117:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void deallocateMemory() throw(std::bad_alloc); ^~~~~ In file included from src/c/lm/rdme/RDMESolver.cpp:47: ./src/c/lm/rdme/RDMESolver.h:59:157: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(DiffusionModel * dm, const uint8_t * lattice, size_t latticeSize, const uint8_t * latticeSites, size_t latticeSitesSize) throw(InvalidArgException); ^~~~~ In file included from src/c/lm/rdme/RDMESolver.cpp:47: ./src/c/lm/rdme/RDMESolver.h:60:335: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void buildDiffusionModel(const uint numberSiteTypesA, const double * DFA, const uint * RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, si_dist_t latticeSpacing, const uint8_t * latticeData, const uint8_t * latticeSitesData, bool rowMajorData=true) throw(InvalidArgException); ^~~~~ src/c/lm/rdme/RDMESolver.cpp: In member function 'virtual void lm::rdme::RDMESolver::destroyDiffusionModel()': src/c/lm/rdme/RDMESolver.cpp:88:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (DF != NULL) delete[] DF; DF = NULL; ^~ src/c/lm/rdme/RDMESolver.cpp:88:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (DF != NULL) delete[] DF; DF = NULL; ^~ src/c/lm/rdme/RDMESolver.cpp:89:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (RL != NULL) delete[] RL; RL = NULL; ^~ src/c/lm/rdme/RDMESolver.cpp:89:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (RL != NULL) delete[] RL; RL = NULL; ^~ src/c/lm/rdme/RDMESolver.cpp:90:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (lattice != NULL) delete lattice; lattice = NULL; ^~ src/c/lm/rdme/RDMESolver.cpp:90:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (lattice != NULL) delete lattice; lattice = NULL; ^~~~~~~ In file included from ./src/c/lm/main/SignalHandler.h:47, from src/c/lm/main/runSimulation.cpp:87: ./src/c/lm/thread/WorkerManager.h:66:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] WorkerManager() throw(PthreadException); ^~~~~ src/c/lm/rdme/RDMESolver.cpp: At global scope: src/c/lm/rdme/RDMESolver.cpp:96:157: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void RDMESolver::setDiffusionModel(DiffusionModel * dm, const uint8_t * lattice, size_t latticeSize, const uint8_t * latticeSites, size_t latticeSitesSize) throw(InvalidArgException) ^~~~~ ./src/c/lm/thread/WorkerManager.h:68:22: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ~WorkerManager() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:72:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void addWorker(Worker * worker) throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:75:40: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void removeWorker(Worker * worker) throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:77:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void abortWorkers() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:79:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void checkpointWorkers() throw(PthreadException); ^~~~~ ./src/c/lm/thread/WorkerManager.h:81:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void stopWorkers() throw(PthreadException); ^~~~~ src/c/lm/rdme/RDMESolver.cpp:109:330: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void RDMESolver::buildDiffusionModel(const uint numberSiteTypesA, const double * DFA, const uint * RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, si_dist_t latticeSpacing, const uint8_t * latticeData, const uint8_t * latticeSitesData, bool rowMajorData) throw(InvalidArgException) ^~~~~ In file included from src/c/lm/main/runSimulation.cpp:87: ./src/c/lm/main/SignalHandler.h:65:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SignalHandler() throw(PthreadException); ^~~~~ ./src/c/lm/main/SignalHandler.h:66:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~SignalHandler() throw(PthreadException); ^~~~~ ./src/c/lm/main/SignalHandler.h:69:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException); ^~~~~ In file included from ./src/c/lm/main/ReplicateRunner.h:45, from src/c/lm/main/runSimulation.cpp:88: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/main/ReplicateRunner.h:45, from src/c/lm/main/runSimulation.cpp:88: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/main/ReplicateRunner.h:46, from src/c/lm/main/runSimulation.cpp:88: ./src/c/lm/me/MESolverFactory.h:62:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void setSolver(string solver) throw(lm::InvalidArgException); ^~~~~ ./src/c/lm/me/MESolverFactory.h:64:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool needsReactionModel() throw(lm::Exception); ^~~~~ ./src/c/lm/me/MESolverFactory.h:66:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool needsDiffusionModel() throw(lm::Exception); ^~~~~ ./src/c/lm/me/MESolverFactory.h:70:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] MESolver * instantiate() throw(lm::Exception); ^~~~~ In file included from src/c/lm/main/runSimulation.cpp:88: ./src/c/lm/main/ReplicateRunner.h:76:315: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ReplicateRunner(int replicate, MESolverFactory solverFactory, map * parameters, lm::io::ReactionModel * reactionModel, lm::io::DiffusionModel * diffusionModel, uint8_t * lattice, size_t latticeSize, uint8_t * latticeSites, size_t latticeSitesSize, ResourceAllocator::ComputeResources resources) throw(PthreadException); ^~~~~ ./src/c/lm/main/ReplicateRunner.h:77:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ReplicateRunner() throw(PthreadException); ^~~~~ ./src/c/lm/main/ReplicateRunner.h:80:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException); ^~~~~ In file included from ./src/c/lm/rdme/RDMESolver.h:45, from src/c/lm/main/runSimulation.cpp:97: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ In file included from src/c/lm/main/runSimulation.cpp:97: ./src/c/lm/rdme/RDMESolver.h:59:157: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(DiffusionModel * dm, const uint8_t * lattice, size_t latticeSize, const uint8_t * latticeSites, size_t latticeSitesSize) throw(InvalidArgException); ^~~~~ In file included from src/c/lm/main/runSimulation.cpp:97: ./src/c/lm/rdme/RDMESolver.h:60:335: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void buildDiffusionModel(const uint numberSiteTypesA, const double * DFA, const uint * RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, si_dist_t latticeSpacing, const uint8_t * latticeData, const uint8_t * latticeSitesData, bool rowMajorData=true) throw(InvalidArgException); ^~~~~ src/c/lm/main/runSimulation.cpp: In function 'void runSimulation(char*, int, char*, std::vector, time_t)': src/c/lm/main/runSimulation.cpp:127:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (solver != NULL) delete solver; solver = NULL; ^~ src/c/lm/main/runSimulation.cpp:127:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (solver != NULL) delete solver; solver = NULL; ^~~~~~ src/c/lm/main/runSimulation.cpp: In function 'void runSolver(char*, int, lm::me::MESolver*, std::vector, time_t)': src/c/lm/main/runSimulation.cpp:239:26: warning: catching polymorphic type 'class lm::Exception' by value [-Wcatch-value=] catch (lm::Exception e) ^ src/c/lm/main/runSimulation.cpp:268:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (lattice != NULL) delete [] lattice; lattice = NULL; ^~ src/c/lm/main/runSimulation.cpp:268:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (lattice != NULL) delete [] lattice; lattice = NULL; ^~~~~~~ src/c/lm/main/runSimulation.cpp:269:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (latticeSites != NULL) delete [] latticeSites; latticeSites = NULL; ^~ src/c/lm/main/runSimulation.cpp:269:55: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (latticeSites != NULL) delete [] latticeSites; latticeSites = NULL; ^~~~~~~~~~~~ src/c/lm/main/runSimulation.cpp:137:12: warning: unused variable 'cudaDevicesPerReplicate' [-Wunused-variable] double cudaDevicesPerReplicate = 1.0*cudaDevices.size(); ^~~~~~~~~~~~~~~~~~~~~~~ Finished building: utils/c/util.cpp Building file: utils/c/lm_setdm.cpp Invoking: c++ mkdir -p Build-dragonfly/utils/c c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./utils/c -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/utils/c/lm_setdm.o" "utils/c/lm_setdm.cpp" src/c/lm/main/runSimulation.cpp:266:16: warning: 'checkpointSignaler' may be used uninitialized in this function [-Wmaybe-uninitialized] delete checkpointSignaler; ^~~~~~~~~~~~~~~~~~ Finished building: src/c/lm/main/runSimulation.cpp Building file: utils/c/lm_setrm.cpp Invoking: c++ mkdir -p Build-dragonfly/utils/c c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./utils/c -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/utils/c/lm_setrm.o" "utils/c/lm_setrm.cpp" Finished building: src/c/lm/rdme/NextSubvolumeSolver.cpp Building file: utils/c/lm_python.cpp Invoking: c++ mkdir -p Build-dragonfly/utils/c c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./utils/c -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/utils/c/lm_python.o" "utils/c/lm_python.cpp" Finished building: src/c/lm/rdme/RDMESolver.cpp Building file: src/swig/lm.i Invoking: /usr/local/bin/swig3.0 mkdir -p Build-dragonfly/src/swig mkdir -p ./Build-dragonfly/lib /usr/local/bin/swig3.0 -c++ -python -o "Build-dragonfly/src/swig/lm_wrap.cpp" -outdir ./Build-dragonfly/lib "src/swig/lm.i" utils/c/lm_python.cpp: In function 'int main(int, char**)': utils/c/lm_python.cpp:158:45: warning: catching polymorphic type 'class lm::CommandLineArgumentException' by value [-Wcatch-value=] catch (lm::CommandLineArgumentException e) ^ utils/c/lm_python.cpp:163:26: warning: catching polymorphic type 'class lm::Exception' by value [-Wcatch-value=] catch (lm::Exception e) ^ utils/c/lm_python.cpp:167:27: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] catch (std::exception e) ^ In file included from utils/c/lm_setdm.cpp:54: ./src/c/lm/io/hdf5/SimulationFile.h:88:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:90:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:92:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:94:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:96:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:98:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:100:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, bool initializeModel, unsigned int numberSpecies=0) throw(lm::IOException,HDF5Exception); ^~~~~ In file included from utils/c/lm_setdm.cpp:54: ./src/c/lm/io/hdf5/SimulationFile.h:113:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const string filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:115:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const char* filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:117:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~SimulationFile() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:120:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void close() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:122:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void flush() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:125:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual string checkpoint() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:133:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setParameter(string key, string value) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:141:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:144:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:151:172: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, byte * lattice, size_t latticeMaxSize, byte * latticeSites, size_t latticeSitesMaxSize) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:155:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, lm::rdme::Lattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:158:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:164:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:170:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint32_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:175:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::ByteLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:180:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::IntLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:184:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:187:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:194:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual bool replicateExists(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:197:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:201:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts * speciesCounts) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:207:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice(unsigned int replicate, lm::io::Lattice * lattice, byte * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:208:137: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice_U32LE(unsigned int replicate, lm::io::Lattice * lattice, uint32_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:210:119: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSites(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * siteData, size_t siteDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:214:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendParameterValues(unsigned int replicate, lm::io::ParameterValues * parameterValues) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:218:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes * speciesCounts) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual vector getLatticeTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:227:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice * lattice) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:230:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:232:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeAllReplicates() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:253:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getParticleCounts(unsigned int replicate, unsigned int latticeIndex) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:254:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map > getSpeciesCounts(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:255:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector getSpeciesCountTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:256:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSpeciesNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:257:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSiteTypeNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:277:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void open() throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:278:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openGroups() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:279:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadParameters() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:280:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadModel() throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:281:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * openReplicateHandles(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:282:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * createReplicateHandles(string replicateString) throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:283:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicateHandles(ReplicateHandles * handles) throw(HDF5Exception); ^~~~~ In file included from utils/c/lm_setrm.cpp:53: ./src/c/lm/io/hdf5/SimulationFile.h:88:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:90:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:92:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:94:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:96:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:98:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:100:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, bool initializeModel, unsigned int numberSpecies=0) throw(lm::IOException,HDF5Exception); ^~~~~ In file included from utils/c/lm_setrm.cpp:53: ./src/c/lm/io/hdf5/SimulationFile.h:113:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const string filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:115:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const char* filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:117:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~SimulationFile() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:120:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void close() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:122:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void flush() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:125:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual string checkpoint() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:133:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setParameter(string key, string value) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:141:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:144:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:151:172: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, byte * lattice, size_t latticeMaxSize, byte * latticeSites, size_t latticeSitesMaxSize) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:155:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, lm::rdme::Lattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:158:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:164:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:170:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint32_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:175:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::ByteLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:180:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::IntLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:184:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:187:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:194:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual bool replicateExists(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:197:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:201:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts * speciesCounts) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:207:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice(unsigned int replicate, lm::io::Lattice * lattice, byte * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:208:137: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice_U32LE(unsigned int replicate, lm::io::Lattice * lattice, uint32_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:210:119: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSites(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * siteData, size_t siteDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:214:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendParameterValues(unsigned int replicate, lm::io::ParameterValues * parameterValues) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:218:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes * speciesCounts) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual vector getLatticeTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:227:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice * lattice) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:230:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:232:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeAllReplicates() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:253:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getParticleCounts(unsigned int replicate, unsigned int latticeIndex) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:254:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map > getSpeciesCounts(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:255:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector getSpeciesCountTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ Finished building: utils/c/lm_python.cpp Building file: src/c/lm/Print.cpp Invoking: c++ mkdir -p Build-dragonfly/src/swig c++ -DOPT_PYTHON -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/swig/Print_py.o" "src/c/lm/Print.cpp" ./src/c/lm/io/hdf5/SimulationFile.h:256:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSpeciesNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:257:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSiteTypeNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:277:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void open() throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:278:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openGroups() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:279:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadParameters() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:280:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadModel() throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:281:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * openReplicateHandles(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:282:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * createReplicateHandles(string replicateString) throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:283:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicateHandles(ReplicateHandles * handles) throw(HDF5Exception); ^~~~~ Finished building: src/c/lm/io/hdf5/SimulationFile.cpp Copying examples mkdir -p ./Build-dragonfly/bin/examples cp ./src/python/Examples/*.py ./Build-dragonfly/bin/examples Copying pyLM and pySTDLM mkdir -p ./Build-dragonfly/python/pyLM mkdir -p ./Build-dragonfly/python/pySTDLM cp -r ./src/python/pyLM/*.py Build-dragonfly/python/pyLM cp -r ./src/python/pySTDLM/*.py Build-dragonfly/python/pySTDLM mkdir -p Build-dragonfly Building target: Build-dragonfly/lm Invoking: Linker c++ -pthread -lpthread ./Build-dragonfly/src/c/lm/main/MainSA.o ./Build-dragonfly/src/c/lm/main/Main.o ./Build-dragonfly/src/c/lm/main/ReplicateRunner.o ./Build-dragonfly/src/c/lm/main/SignalHandler.o ./Build-dragonfly/src/c/lm/Print.o ./Build-dragonfly/src/c/lm/main/CheckpointSignaler.o ./Build-dragonfly/src/c/lm/main/Globals.o ./Build-dragonfly/src/c/lm/main/LocalDataOutputWorker.o ./Build-dragonfly/src/c/lm/builder/Capsule.o ./Build-dragonfly/src/c/lm/builder/CapsuleShell.o ./Build-dragonfly/src/c/lm/builder/Cuboid.o ./Build-dragonfly/src/c/lm/builder/Hemisphere.o ./Build-dragonfly/src/c/lm/builder/LatticeBuilder.o ./Build-dragonfly/src/c/lm/builder/Shape.o ./Build-dragonfly/src/c/lm/builder/Sphere.o ./Build-dragonfly/src/c/lm/builder/Intersection.o ./Build-dragonfly/src/c/lm/builder/Union.o ./Build-dragonfly/src/c/lm/builder/Difference.o ./Build-dragonfly/src/c/lm/builder/Torus.o ./Build-dragonfly/src/c/lm/builder/Ellipse.o ./Build-dragonfly/src/c/lm/builder/Cylinder.o ./Build-dragonfly/src/c/lm/cme/CMESolver.o ./Build-dragonfly/src/c/lm/cme/FluctuatingNRSolver.o ./Build-dragonfly/src/c/lm/cme/GillespieDSolver.o ./Build-dragonfly/src/c/lm/cme/HillSwitch.o ./Build-dragonfly/src/c/lm/cme/LacHillSwitch.o ./Build-dragonfly/src/c/lm/cme/NextReactionSolver.o ./Build-dragonfly/src/c/lm/cme/SelfRegulatingGeneSwitch.o ./Build-dragonfly/src/c/lm/cme/TwoStateExpression.o ./Build-dragonfly/src/c/lm/cme/TwoStateHillLoopSwitch.o ./Build-dragonfly/src/c/lm/cme/TwoStateHillSwitch.o ./Build-dragonfly/src/protobuf/lm/io/DiffusionModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/FirstPassageTimes.pb.o ./Build-dragonfly/src/protobuf/lm/io/Lattice.pb.o ./Build-dragonfly/src/protobuf/lm/io/ParameterValues.pb.o ./Build-dragonfly/src/protobuf/lm/io/ReactionModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/SpatialModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/SpeciesCounts.pb.o ./Build-dragonfly/src/c/lm/io/SimulationParameters.o ./Build-dragonfly/src/c/lm/io/hdf5/SimulationFile.o ./Build-dragonfly/src/c/lm/io/hdf5/SimulationFile_create.o ./Build-dragonfly/src/c/lm/main/DataOutputQueue.o ./Build-dragonfly/src/c/lm/main/ResourceAllocator.o ./Build-dragonfly/src/c/lm/me/MESolver.o ./Build-dragonfly/src/c/lm/me/MESolverFactory.o ./Build-dragonfly/src/protobuf/lm/message/SimulationParameters.pb.o ./Build-dragonfly/src/c/lm/rdme/ByteLattice.o ./Build-dragonfly/src/c/lm/rdme/IntLattice.o ./Build-dragonfly/src/c/lm/rdme/Lattice.o ./Build-dragonfly/src/c/lm/rdme/NextSubvolumeSolver.o ./Build-dragonfly/src/c/lm/rdme/RDMESolver.o ./Build-dragonfly/src/c/lm/rng/RandomGenerator.o ./Build-dragonfly/src/c/lm/rng/XORShift.o ./Build-dragonfly/src/c/lm/thread/Thread.o ./Build-dragonfly/src/c/lm/thread/Worker.o ./Build-dragonfly/src/c/lm/thread/WorkerManager.o ./Build-dragonfly/src/c/lm/main/runSimulation.o -L/usr/local/lib -L/usr/local/lib -lz -lsz -lhdf5 -lhdf5_hl -lprotobuf `/usr/local/bin/python3.6-config --libs` -o "Build-dragonfly/lm" mkdir -p ./Build-dragonfly/bin cp "Build-dragonfly/lm" ./Build-dragonfly/bin Finished building target: Build-dragonfly/lm Building target: Build-dragonfly/bin/lm_setp Invoking: Linker mkdir -p Build-dragonfly/bin c++ -pthread -lpthread Build-dragonfly/utils/c/lm_setp.o ./Build-dragonfly/utils/c/util.o ./Build-dragonfly/src/c/lm/Print.o ./Build-dragonfly/src/c/lm/main/CheckpointSignaler.o ./Build-dragonfly/src/c/lm/main/Globals.o ./Build-dragonfly/src/c/lm/main/LocalDataOutputWorker.o ./Build-dragonfly/src/c/lm/builder/Capsule.o ./Build-dragonfly/src/c/lm/builder/CapsuleShell.o ./Build-dragonfly/src/c/lm/builder/Cuboid.o ./Build-dragonfly/src/c/lm/builder/Hemisphere.o ./Build-dragonfly/src/c/lm/builder/LatticeBuilder.o ./Build-dragonfly/src/c/lm/builder/Shape.o ./Build-dragonfly/src/c/lm/builder/Sphere.o ./Build-dragonfly/src/c/lm/builder/Intersection.o ./Build-dragonfly/src/c/lm/builder/Union.o ./Build-dragonfly/src/c/lm/builder/Difference.o ./Build-dragonfly/src/c/lm/builder/Torus.o ./Build-dragonfly/src/c/lm/builder/Ellipse.o ./Build-dragonfly/src/c/lm/builder/Cylinder.o ./Build-dragonfly/src/c/lm/cme/CMESolver.o ./Build-dragonfly/src/c/lm/cme/FluctuatingNRSolver.o ./Build-dragonfly/src/c/lm/cme/GillespieDSolver.o ./Build-dragonfly/src/c/lm/cme/HillSwitch.o ./Build-dragonfly/src/c/lm/cme/LacHillSwitch.o ./Build-dragonfly/src/c/lm/cme/NextReactionSolver.o ./Build-dragonfly/src/c/lm/cme/SelfRegulatingGeneSwitch.o ./Build-dragonfly/src/c/lm/cme/TwoStateExpression.o ./Build-dragonfly/src/c/lm/cme/TwoStateHillLoopSwitch.o ./Build-dragonfly/src/c/lm/cme/TwoStateHillSwitch.o ./Build-dragonfly/src/protobuf/lm/io/DiffusionModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/FirstPassageTimes.pb.o ./Build-dragonfly/src/protobuf/lm/io/Lattice.pb.o ./Build-dragonfly/src/protobuf/lm/io/ParameterValues.pb.o ./Build-dragonfly/src/protobuf/lm/io/ReactionModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/SpatialModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/SpeciesCounts.pb.o ./Build-dragonfly/src/c/lm/io/SimulationParameters.o ./Build-dragonfly/src/c/lm/io/hdf5/SimulationFile.o ./Build-dragonfly/src/c/lm/io/hdf5/SimulationFile_create.o ./Build-dragonfly/src/c/lm/main/DataOutputQueue.o ./Build-dragonfly/src/c/lm/main/ResourceAllocator.o ./Build-dragonfly/src/c/lm/me/MESolver.o ./Build-dragonfly/src/c/lm/me/MESolverFactory.o ./Build-dragonfly/src/protobuf/lm/message/SimulationParameters.pb.o ./Build-dragonfly/src/c/lm/rdme/ByteLattice.o ./Build-dragonfly/src/c/lm/rdme/IntLattice.o ./Build-dragonfly/src/c/lm/rdme/Lattice.o ./Build-dragonfly/src/c/lm/rdme/NextSubvolumeSolver.o ./Build-dragonfly/src/c/lm/rdme/RDMESolver.o ./Build-dragonfly/src/c/lm/rng/RandomGenerator.o ./Build-dragonfly/src/c/lm/rng/XORShift.o ./Build-dragonfly/src/c/lm/thread/Thread.o ./Build-dragonfly/src/c/lm/thread/Worker.o ./Build-dragonfly/src/c/lm/thread/WorkerManager.o ./Build-dragonfly/src/c/lm/main/runSimulation.o -L/usr/local/lib -L/usr/local/lib -lz -lsz -lhdf5 -lhdf5_hl -lprotobuf `/usr/local/bin/python3.6-config --libs` -o "Build-dragonfly/bin/lm_setp" Finished building target: Build-dragonfly/bin/lm_setp Finished building: src/c/lm/Print.cpp Finished building: utils/c/lm_setdm.cpp Building target: Build-dragonfly/bin/lm_setdm Invoking: Linker mkdir -p Build-dragonfly/bin c++ -pthread -lpthread Build-dragonfly/utils/c/lm_setdm.o ./Build-dragonfly/utils/c/util.o ./Build-dragonfly/src/c/lm/Print.o ./Build-dragonfly/src/c/lm/main/CheckpointSignaler.o ./Build-dragonfly/src/c/lm/main/Globals.o ./Build-dragonfly/src/c/lm/main/LocalDataOutputWorker.o ./Build-dragonfly/src/c/lm/builder/Capsule.o ./Build-dragonfly/src/c/lm/builder/CapsuleShell.o ./Build-dragonfly/src/c/lm/builder/Cuboid.o ./Build-dragonfly/src/c/lm/builder/Hemisphere.o ./Build-dragonfly/src/c/lm/builder/LatticeBuilder.o ./Build-dragonfly/src/c/lm/builder/Shape.o ./Build-dragonfly/src/c/lm/builder/Sphere.o ./Build-dragonfly/src/c/lm/builder/Intersection.o ./Build-dragonfly/src/c/lm/builder/Union.o ./Build-dragonfly/src/c/lm/builder/Difference.o ./Build-dragonfly/src/c/lm/builder/Torus.o ./Build-dragonfly/src/c/lm/builder/Ellipse.o ./Build-dragonfly/src/c/lm/builder/Cylinder.o ./Build-dragonfly/src/c/lm/cme/CMESolver.o ./Build-dragonfly/src/c/lm/cme/FluctuatingNRSolver.o ./Build-dragonfly/src/c/lm/cme/GillespieDSolver.o ./Build-dragonfly/src/c/lm/cme/HillSwitch.o ./Build-dragonfly/src/c/lm/cme/LacHillSwitch.o ./Build-dragonfly/src/c/lm/cme/NextReactionSolver.o ./Build-dragonfly/src/c/lm/cme/SelfRegulatingGeneSwitch.o ./Build-dragonfly/src/c/lm/cme/TwoStateExpression.o ./Build-dragonfly/src/c/lm/cme/TwoStateHillLoopSwitch.o ./Build-dragonfly/src/c/lm/cme/TwoStateHillSwitch.o ./Build-dragonfly/src/protobuf/lm/io/DiffusionModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/FirstPassageTimes.pb.o ./Build-dragonfly/src/protobuf/lm/io/Lattice.pb.o ./Build-dragonfly/src/protobuf/lm/io/ParameterValues.pb.o ./Build-dragonfly/src/protobuf/lm/io/ReactionModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/SpatialModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/SpeciesCounts.pb.o ./Build-dragonfly/src/c/lm/io/SimulationParameters.o ./Build-dragonfly/src/c/lm/io/hdf5/SimulationFile.o ./Build-dragonfly/src/c/lm/io/hdf5/SimulationFile_create.o ./Build-dragonfly/src/c/lm/main/DataOutputQueue.o ./Build-dragonfly/src/c/lm/main/ResourceAllocator.o ./Build-dragonfly/src/c/lm/me/MESolver.o ./Build-dragonfly/src/c/lm/me/MESolverFactory.o ./Build-dragonfly/src/protobuf/lm/message/SimulationParameters.pb.o ./Build-dragonfly/src/c/lm/rdme/ByteLattice.o ./Build-dragonfly/src/c/lm/rdme/IntLattice.o ./Build-dragonfly/src/c/lm/rdme/Lattice.o ./Build-dragonfly/src/c/lm/rdme/NextSubvolumeSolver.o ./Build-dragonfly/src/c/lm/rdme/RDMESolver.o ./Build-dragonfly/src/c/lm/rng/RandomGenerator.o ./Build-dragonfly/src/c/lm/rng/XORShift.o ./Build-dragonfly/src/c/lm/thread/Thread.o ./Build-dragonfly/src/c/lm/thread/Worker.o ./Build-dragonfly/src/c/lm/thread/WorkerManager.o ./Build-dragonfly/src/c/lm/main/runSimulation.o -L/usr/local/lib -L/usr/local/lib -lz -lsz -lhdf5 -lhdf5_hl -lprotobuf `/usr/local/bin/python3.6-config --libs` -o "Build-dragonfly/bin/lm_setdm" Finished building target: Build-dragonfly/bin/lm_setdm Finished building: src/swig/lm.i Building file: Build-dragonfly/src/swig/lm_wrap.cpp Invoking: c++ mkdir -p Build-dragonfly/src/swig c++ -pipe -O2 -fno-strict-aliasing -DLINUX -I/usr/local/lib/python3.6/site-packages/numpy/core/include -std=c++11 -fPIC -Wall -c -fmessage-length=0 -pthread -DLINUX -DCUDA_3D_GRID_LAUNCH -DVERBOSITY_LEVEL= -DBUILD_INFO="\"by root on pkgbox64 at 2019-07-09 19:23:45\"" -I./src/c -I/usr/local/include -I/usr/local/include -I./profile -I./Build-dragonfly/src/protobuf `/usr/local/bin/python3.6-config --includes` -MMD -MP -o "Build-dragonfly/src/swig/lm_wrap.o" "Build-dragonfly/src/swig/lm_wrap.cpp" In file included from ./src/c/lm/builder/Shape.h:48, from ./src/c/lm/builder/Capsule.h:43, from Build-dragonfly/src/swig/lm_wrap.cpp:4132: ./src/c/lm/rdme/Lattice.h:160:21: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Lattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/Lattice.h:185:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:187:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:189:94: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:191:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t index, site_t site) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:207:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:209:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t index) const throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:212:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:214:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t index, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:217:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:219:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t index, particle_t particle) throw(InvalidSiteException,InvalidParticleException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:221:86: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException)=0; ^~~~~ ./src/c/lm/rdme/Lattice.h:223:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t index) throw(InvalidSiteException)=0; ^~~~~ Finished building: utils/c/lm_setrm.cpp Building target: Build-dragonfly/bin/lm_setrm Invoking: Linker mkdir -p Build-dragonfly/bin c++ -pthread -lpthread Build-dragonfly/utils/c/lm_setrm.o ./Build-dragonfly/utils/c/util.o ./Build-dragonfly/src/c/lm/Print.o ./Build-dragonfly/src/c/lm/main/CheckpointSignaler.o ./Build-dragonfly/src/c/lm/main/Globals.o ./Build-dragonfly/src/c/lm/main/LocalDataOutputWorker.o ./Build-dragonfly/src/c/lm/builder/Capsule.o ./Build-dragonfly/src/c/lm/builder/CapsuleShell.o ./Build-dragonfly/src/c/lm/builder/Cuboid.o ./Build-dragonfly/src/c/lm/builder/Hemisphere.o ./Build-dragonfly/src/c/lm/builder/LatticeBuilder.o ./Build-dragonfly/src/c/lm/builder/Shape.o ./Build-dragonfly/src/c/lm/builder/Sphere.o ./Build-dragonfly/src/c/lm/builder/Intersection.o ./Build-dragonfly/src/c/lm/builder/Union.o ./Build-dragonfly/src/c/lm/builder/Difference.o ./Build-dragonfly/src/c/lm/builder/Torus.o ./Build-dragonfly/src/c/lm/builder/Ellipse.o ./Build-dragonfly/src/c/lm/builder/Cylinder.o ./Build-dragonfly/src/c/lm/cme/CMESolver.o ./Build-dragonfly/src/c/lm/cme/FluctuatingNRSolver.o ./Build-dragonfly/src/c/lm/cme/GillespieDSolver.o ./Build-dragonfly/src/c/lm/cme/HillSwitch.o ./Build-dragonfly/src/c/lm/cme/LacHillSwitch.o ./Build-dragonfly/src/c/lm/cme/NextReactionSolver.o ./Build-dragonfly/src/c/lm/cme/SelfRegulatingGeneSwitch.o ./Build-dragonfly/src/c/lm/cme/TwoStateExpression.o ./Build-dragonfly/src/c/lm/cme/TwoStateHillLoopSwitch.o ./Build-dragonfly/src/c/lm/cme/TwoStateHillSwitch.o ./Build-dragonfly/src/protobuf/lm/io/DiffusionModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/FirstPassageTimes.pb.o ./Build-dragonfly/src/protobuf/lm/io/Lattice.pb.o ./Build-dragonfly/src/protobuf/lm/io/ParameterValues.pb.o ./Build-dragonfly/src/protobuf/lm/io/ReactionModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/SpatialModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/SpeciesCounts.pb.o ./Build-dragonfly/src/c/lm/io/SimulationParameters.o ./Build-dragonfly/src/c/lm/io/hdf5/SimulationFile.o ./Build-dragonfly/src/c/lm/io/hdf5/SimulationFile_create.o ./Build-dragonfly/src/c/lm/main/DataOutputQueue.o ./Build-dragonfly/src/c/lm/main/ResourceAllocator.o ./Build-dragonfly/src/c/lm/me/MESolver.o ./Build-dragonfly/src/c/lm/me/MESolverFactory.o ./Build-dragonfly/src/protobuf/lm/message/SimulationParameters.pb.o ./Build-dragonfly/src/c/lm/rdme/ByteLattice.o ./Build-dragonfly/src/c/lm/rdme/IntLattice.o ./Build-dragonfly/src/c/lm/rdme/Lattice.o ./Build-dragonfly/src/c/lm/rdme/NextSubvolumeSolver.o ./Build-dragonfly/src/c/lm/rdme/RDMESolver.o ./Build-dragonfly/src/c/lm/rng/RandomGenerator.o ./Build-dragonfly/src/c/lm/rng/XORShift.o ./Build-dragonfly/src/c/lm/thread/Thread.o ./Build-dragonfly/src/c/lm/thread/Worker.o ./Build-dragonfly/src/c/lm/thread/WorkerManager.o ./Build-dragonfly/src/c/lm/main/runSimulation.o -L/usr/local/lib -L/usr/local/lib -lz -lsz -lhdf5 -lhdf5_hl -lprotobuf `/usr/local/bin/python3.6-config --libs` -o "Build-dragonfly/bin/lm_setrm" Finished building target: Build-dragonfly/bin/lm_setrm In file included from Build-dragonfly/src/swig/lm_wrap.cpp:4150: ./src/c/lm/io/hdf5/SimulationFile.h:88:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:90:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static bool isValidFile(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:92:47: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:94:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:96:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const string filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:98:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, unsigned int numberSpecies) throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:100:99: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] static void create(const char * filename, bool initializeModel, unsigned int numberSpecies=0) throw(lm::IOException,HDF5Exception); ^~~~~ In file included from Build-dragonfly/src/swig/lm_wrap.cpp:4150: ./src/c/lm/io/hdf5/SimulationFile.h:113:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const string filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:115:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] SimulationFile(const char* filename) throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:117:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~SimulationFile() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:120:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void close() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:122:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void flush() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:125:33: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual string checkpoint() throw(lm::IOException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:133:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setParameter(string key, string value) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:138:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:141:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setReactionModel(lm::io::ReactionModel * reactionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:144:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:151:172: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, byte * lattice, size_t latticeMaxSize, byte * latticeSites, size_t latticeSitesMaxSize) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:155:113: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getDiffusionModelLattice(lm::io::DiffusionModel * diffusionModel, lm::rdme::Lattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:158:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(lm::io::DiffusionModel * diffusionModel) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:164:114: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint8_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:170:115: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, uint32_t * lattice, uint8_t * latticeSites) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:175:104: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::ByteLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:180:103: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModelLattice(lm::io::DiffusionModel * m, lm::rdme::IntLattice * lattice) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:184:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:187:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getSpatialModel(lm::io::SpatialModel * model) throw(Exception,InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:194:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual bool replicateExists(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:197:56: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:201:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSpeciesCounts(unsigned int replicate, lm::io::SpeciesCounts * speciesCounts) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:207:127: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice(unsigned int replicate, lm::io::Lattice * lattice, byte * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:208:137: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendLattice_U32LE(unsigned int replicate, lm::io::Lattice * lattice, uint32_t * latticeData, size_t latticeDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:210:119: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendSites(unsigned int replicate, lm::io::Lattice * lattice, uint8_t * siteData, size_t siteDataSize) throw(InvalidArgException,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:214:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void appendParameterValues(unsigned int replicate, lm::io::ParameterValues * parameterValues) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:218:106: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setFirstPassageTimes(unsigned int replicate, lm::io::FirstPassageTimes * speciesCounts) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:222:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual vector getLatticeTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:227:109: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void getLattice(unsigned int replicate, unsigned int latticeIndex, lm::rdme::Lattice * lattice) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:230:57: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicate(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:232:39: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeAllReplicates() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:253:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getParticleCounts(unsigned int replicate, unsigned int latticeIndex) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:254:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map > getSpeciesCounts(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:255:62: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] vector getSpeciesCountTimes(unsigned int replicate) throw(HDF5Exception,InvalidArgException); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:256:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSpeciesNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:257:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] std::map getSiteTypeNames() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:277:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void open() throw(lm::IOException,HDF5Exception,Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:278:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void openGroups() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:279:35: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadParameters() throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:280:30: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void loadModel() throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:281:77: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * openReplicateHandles(unsigned int replicate) throw(HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:282:79: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ReplicateHandles * createReplicateHandles(string replicateString) throw(Exception,HDF5Exception); ^~~~~ ./src/c/lm/io/hdf5/SimulationFile.h:283:68: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void closeReplicateHandles(ReplicateHandles * handles) throw(HDF5Exception); ^~~~~ In file included from Build-dragonfly/src/swig/lm_wrap.cpp:4151: ./src/c/lm/rdme/ByteLattice.h:74:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ByteLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:75:125: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ByteLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:76:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ByteLattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:81:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:82:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:83:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t siteType) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:84:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t subvolume, site_t site) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:89:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:90:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:91:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:92:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t subvolume, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:93:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:94:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t subvolume, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:95:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:96:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t subvolume) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:116:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void allocateMemory() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/ByteLattice.h:117:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void deallocateMemory() throw(std::bad_alloc); ^~~~~ In file included from Build-dragonfly/src/swig/lm_wrap.cpp:4152: ./src/c/lm/rdme/IntLattice.h:72:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] IntLattice(lattice_coord_t size, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/IntLattice.h:73:124: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] IntLattice(lattice_size_t xSize, lattice_size_t ySize, lattice_size_t zSize, si_dist_t spacing, uint particlesPerSite) throw(std::bad_alloc,InvalidArgException,Exception); ^~~~~ ./src/c/lm/rdme/IntLattice.h:74:24: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~IntLattice() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/IntLattice.h:79:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:80:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_t getSiteType(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:81:98: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_t siteType) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:82:66: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setSiteType(lattice_size_t subvolume, site_t site) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:85:95: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t x, lattice_size_t y, lattice_size_t z) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:86:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual site_size_t getOccupancy(lattice_size_t subvolume) const throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:87:120: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:88:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual particle_t getParticle(lattice_size_t subvolume, site_size_t particleIndex) const throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:89:102: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t x, lattice_size_t y, lattice_size_t z, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:90:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void addParticle(lattice_size_t subvolume, particle_t particle) throw(InvalidSiteException,InvalidParticleException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:91:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t x,lattice_size_t y,lattice_size_t z) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:92:60: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeParticles(lattice_size_t subvolume) throw(InvalidSiteException); ^~~~~ ./src/c/lm/rdme/IntLattice.h:113:32: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void allocateMemory() throw(std::bad_alloc); ^~~~~ ./src/c/lm/rdme/IntLattice.h:114:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void deallocateMemory() throw(std::bad_alloc); ^~~~~ In file included from ./src/c/lm/main/ResourceAllocator.h:45, from ./src/c/lm/me/MESolver.h:44, from ./src/c/lm/main/runSimulation.h:1, from Build-dragonfly/src/swig/lm_wrap.cpp:4158: ./src/c/lm/thread/Thread.h:63:14: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:65:23: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~Thread() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:68:26: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void start() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:70:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void stop() throw(PthreadException); ^~~~~ ./src/c/lm/thread/Thread.h:72:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void wake() throw(PthreadException)=0; ^~~~~ ./src/c/lm/thread/Thread.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setAffinity(int cpuNumber) throw(PthreadException); ^~~~~ In file included from ./src/c/lm/me/MESolver.h:44, from ./src/c/lm/main/runSimulation.h:1, from Build-dragonfly/src/swig/lm_wrap.cpp:4158: ./src/c/lm/main/ResourceAllocator.h:75:90: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/me/MESolver.h:44, from ./src/c/lm/main/runSimulation.h:1, from Build-dragonfly/src/swig/lm_wrap.cpp:4158: ./src/c/lm/main/ResourceAllocator.h:82:146: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] ResourceAllocator(int processNumber, int numberCpuCores, float cpuCoresPerReplicate, vector cudaDevices, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:83:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ~ResourceAllocator() throw(PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:90:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual ComputeResources assignReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:93:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void removeReplicate(int replicate) throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:96:34: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual int reserveCpuCore() throw(Exception,PthreadException); ^~~~~ ./src/c/lm/main/ResourceAllocator.h:99:80: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void initialize(float cpuCoresPerReplicate, float cudaDevicesPerReplicate) throw(Exception,PthreadException); ^~~~~ In file included from ./src/c/lm/cme/NextReactionSolver.h:49, from Build-dragonfly/src/swig/lm_wrap.cpp:4163: ./src/c/lm/reaction/ReactionQueue.h: In destructor 'lm::reaction::ReactionQueue::~ReactionQueue()': ./src/c/lm/reaction/ReactionQueue.h:81:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:81:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionEvents != NULL) delete[] reactionEvents; reactionEvents = NULL; ^~~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:82:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:82:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionQueue != NULL) delete[] reactionQueue; reactionQueue = NULL; ^~~~~~~~~~~~~ ./src/c/lm/reaction/ReactionQueue.h:83:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~ ./src/c/lm/reaction/ReactionQueue.h:83:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (reactionPositions != NULL) delete[] reactionPositions; reactionPositions = NULL; ^~~~~~~~~~~~~~~~~ In file included from Build-dragonfly/src/swig/lm_wrap.cpp:4164: ./src/c/lm/rdme/RDMESolver.h: At global scope: ./src/c/lm/rdme/RDMESolver.h:59:157: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void setDiffusionModel(DiffusionModel * dm, const uint8_t * lattice, size_t latticeSize, const uint8_t * latticeSites, size_t latticeSitesSize) throw(InvalidArgException); ^~~~~ In file included from Build-dragonfly/src/swig/lm_wrap.cpp:4164: ./src/c/lm/rdme/RDMESolver.h:60:335: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void buildDiffusionModel(const uint numberSiteTypesA, const double * DFA, const uint * RLA, lattice_size_t latticeXSize, lattice_size_t latticeYSize, lattice_size_t latticeZSize, site_size_t particlesPerSite, si_dist_t latticeSpacing, const uint8_t * latticeData, const uint8_t * latticeSitesData, bool rowMajorData=true) throw(InvalidArgException); ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_iterator(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:7146:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:7142:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___nonzero__(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:7196:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:7192:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___bool__(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:7246:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:7242:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___len__(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:7296:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:7292:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___getslice__(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:7373:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:7369:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___setslice____SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:7449:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:7445:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___setslice____SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:7539:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:7535:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___delslice__(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:7683:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:7679:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___delitem____SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:7750:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:7746:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___getitem____SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:7817:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:7813:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___setitem____SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:7897:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:7893:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___setitem____SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:7965:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:7961:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___delitem____SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8031:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8027:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___getitem____SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8145:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8141:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt___setitem____SWIG_2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8269:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8265:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_pop(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8398:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8394:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_append(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8458:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8454:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_stdVectorInt__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8499:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8495:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_stdVectorInt__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8554:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8550:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_empty(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8606:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8602:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_size(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8656:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8652:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_swap(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8717:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8713:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_begin(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8767:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8763:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_end(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8818:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8814:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_rbegin(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8869:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8865:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_rend(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8920:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8916:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_clear(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:8970:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:8966:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_get_allocator(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9020:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9016:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_stdVectorInt__SWIG_2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9070:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9066:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_pop_back(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9119:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9115:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_resize__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9177:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9173:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_erase__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9242:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9238:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_erase__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9323:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9319:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_stdVectorInt__SWIG_3(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9438:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9434:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_push_back(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9559:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9555:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_front(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9609:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9605:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_back(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9659:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9655:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_assign(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9728:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9724:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_resize__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9797:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9793:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_insert__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:9929:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:9925:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_insert__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:10014:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:10010:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_reserve(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:10138:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:10134:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_stdVectorInt_capacity(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:10188:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:10184:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_stdVectorInt(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:10237:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:10233:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_point__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:10319:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:10315:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_point__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:10378:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:10374:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_point__SWIG_2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:10428:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:10424:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_point__SWIG_3(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:10469:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:10465:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_point_distanceSquared(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:10762:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:10758:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_point_distance(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:10824:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:10820:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_point(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:10873:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:10869:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_bounding_box__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:10975:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:10971:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_bounding_box__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:11061:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:11057:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_bounding_box__SWIG_2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:11138:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:11134:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_bounding_box__SWIG_3(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:11206:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:11202:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_bounding_box__SWIG_4(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:11265:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:11261:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_bounding_box__SWIG_5(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:11315:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:11311:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_bounding_box__SWIG_6(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:11356:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:11352:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_bounding_box__SWIG_7(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:11431:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:11427:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_bounding_box_joinWith(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:11795:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:11791:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_bounding_box(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:11844:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:11840:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_vector__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:11919:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:11915:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_vector__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:11978:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:11974:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_vector__SWIG_2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12028:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12024:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_vector__SWIG_3(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12069:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12065:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_vector(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12349:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12345:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Shape_boundingBoxesIntersect(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12415:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12411:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Shape_intersects(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12474:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12470:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Shape_contains(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12533:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12529:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Shape_getBoundingBox(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12583:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12579:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Shape_getType(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12633:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12629:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Shape_getVolume(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12683:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12679:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_Shape(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12732:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12728:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Sphere(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12815:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12811:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_Sphere(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12864:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12860:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Sphere_intersects(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12923:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12919:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Sphere_contains(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:12982:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:12978:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Sphere_setCenter(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13048:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13044:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Sphere_getCenter(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13098:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13094:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Sphere_getRadius(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13148:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13144:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Hemisphere(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13248:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13244:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_Hemisphere(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13297:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13293:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Hemisphere_intersects(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13356:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13352:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Hemisphere_contains(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13415:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13411:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Hemisphere_getCenter(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13465:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13461:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Hemisphere_getRadius(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13515:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13511:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Hemisphere_getOrientation(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13565:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13561:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Capsule(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13665:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13661:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_Capsule(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13714:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13710:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Capsule_intersects(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13773:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13769:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Capsule_contains(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13832:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13828:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Capsule_getP1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13882:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13878:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Capsule_getP2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13932:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13928:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Capsule_getRadius(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:13982:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:13978:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Cylinder(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14082:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14078:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_Cylinder(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14131:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14127:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Cylinder_intersects(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14190:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14186:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Cylinder_contains(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14249:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14245:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Cylinder_getP1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14299:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14295:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Cylinder_getP2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14349:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14345:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Cylinder_getRadius(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14399:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14395:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_CapsuleShell(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14508:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14504:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_CapsuleShell(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14557:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14553:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_CapsuleShell_intersects(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14616:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14612:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_CapsuleShell_contains(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14675:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14671:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_CapsuleShell_getP1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14725:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14721:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_CapsuleShell_getP2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14775:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14771:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_CapsuleShell_getInnerRadius(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14825:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14821:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_CapsuleShell_getOuterRadius(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14875:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14871:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Cuboid__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:14966:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:14962:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Cuboid__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:15094:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:15090:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Cuboid__SWIG_2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:15205:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:15201:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Cuboid__SWIG_3(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:15299:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:15295:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_Cuboid(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:15498:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:15494:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Cuboid_intersects(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:15557:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:15553:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Cuboid_contains(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:15616:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:15612:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Cuboid_getP1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:15666:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:15662:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Cuboid_getP2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:15716:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:15712:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Union(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:15791:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:15787:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_Union(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:15840:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:15836:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Union_intersects(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:15899:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:15895:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Union_contains(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:15958:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:15954:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Difference__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:16042:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:16038:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Difference__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:16110:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:16106:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_Difference(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:16227:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:16223:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Difference_intersects(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:16286:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:16282:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Difference_contains(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:16345:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:16341:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Intersection(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:16420:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:16416:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_Intersection(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:16469:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:16465:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Intersection_intersects(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:16528:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:16524:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Intersection_contains(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:16587:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:16583:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Torus__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:16713:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:16709:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Torus__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:16815:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:16811:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Torus__SWIG_2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:16900:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:16896:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_Torus(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:17062:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:17058:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Torus_intersects(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:17121:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:17117:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Torus_contains(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:17180:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:17176:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Torus_setCenter(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:17246:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:17242:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Torus_getCenter(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:17296:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:17292:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Torus_getRadius1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:17346:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:17342:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Torus_getRadius2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:17396:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:17392:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Ellipse__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:17531:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:17527:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Ellipse__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:17642:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:17638:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_Ellipse__SWIG_2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:17736:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:17732:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_Ellipse(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:17916:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:17912:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Ellipse_intersects(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:17975:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:17971:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Ellipse_contains(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18034:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18030:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Ellipse_setCenter(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18100:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18096:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Ellipse_getCenter(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18150:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18146:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Ellipse_getRadius1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18200:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18196:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Ellipse_getRadius2(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18250:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18246:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Ellipse_getRadius3(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18300:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18296:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_LatticeBuilder(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18402:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18398:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_LatticeBuilder(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18451:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18447:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_LatticeBuilder_addRegion(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18509:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18505:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_LatticeBuilder_placeSphere(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18594:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18590:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_LatticeBuilder_removeSphere(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18678:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18674:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_LatticeBuilder_placeRandomSphere(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18755:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18751:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_LatticeBuilder_placeRandomSpheres(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18840:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18836:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_LatticeBuilder_fillWithRandomSpheres(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18925:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18921:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_LatticeBuilder_getSpatialModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:18983:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:18979:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_LatticeBuilder_addParticles(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19059:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19055:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_LatticeBuilder_discretizeTo(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19135:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19131:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_DiffusionModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19183:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19179:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_number_species(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19233:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19229:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_number_site_types(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19283:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19279:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_lattice_spacing(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19333:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19329:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_lattice_x_size(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19383:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19379:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_lattice_y_size(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19433:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19429:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_lattice_z_size(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19483:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19479:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_particles_per_site(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19533:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19529:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_bytes_per_particle(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19583:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19579:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_set_lattice_spacing(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19641:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19637:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_set_lattice_x_size(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19699:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19695:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_set_lattice_y_size(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19757:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19753:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_set_lattice_z_size(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19815:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19811:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_set_particles_per_site(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19873:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19869:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_set_number_reactions(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19931:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19927:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_set_number_species(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:19989:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:19985:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_set_number_site_types(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20047:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20043:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_set_bytes_per_particle(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20105:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20101:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_diffusion_matrix(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20164:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20160:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_add_diffusion_matrix(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20222:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20218:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_set_diffusion_matrix(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20289:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20285:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_reaction_location_matrix(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20348:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20344:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_add_reaction_location_matrix(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20406:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20402:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_DiffusionModel_set_reaction_location_matrix(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20473:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20469:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_DiffusionModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20522:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20518:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_ReactionModel_Reaction(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20570:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20566:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_Reaction_type(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20620:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20616:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_Reaction_set_type(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20678:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20674:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_Reaction_rate_constant_size(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20728:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20724:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_Reaction_add_rate_constant(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20786:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20782:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_Reaction_set_rate_constant(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20853:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20849:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_ReactionModel_Reaction(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20902:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20898:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_ReactionModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:20950:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20946:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_number_species(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21000:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:20996:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_set_number_species(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21058:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21054:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_number_reactions(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21108:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21104:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_set_number_reactions(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21166:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21162:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_initial_species_count_size(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21216:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21212:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_add_initial_species_count(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21274:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21270:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_set_initial_species_count(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21341:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21337:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_reaction_size(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21391:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21387:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_add_reaction(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21440:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21436:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_reaction(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21499:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21495:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_mutable_reaction(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21558:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21554:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_add_stoichiometric_matrix(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21616:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21612:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ReactionModel_add_dependency_matrix(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21674:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21670:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_ReactionModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21723:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21719:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_SpatialModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21771:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21767:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_SpatialModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21820:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21816:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_isValidFile(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21887:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21883:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_create(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:21948:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21944:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_SimulationFile(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22001:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:21997:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_SimulationFile(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22052:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22048:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_close(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22101:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22097:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_getDiffusionModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22159:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22155:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_setDiffusionModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22229:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22225:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_getReactionModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22287:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22283:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_setReactionModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22357:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22353:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_getDiffusionModelLattice(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22436:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22432:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_setDiffusionModelLattice__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22515:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22511:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_setDiffusionModelLattice__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22594:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22590:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_getSpatialModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22712:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22708:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_setSpatialModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22770:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22766:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_getLatticeTimes(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22838:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22834:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_getLattice(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22930:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22926:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_getParameter(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:22991:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:22987:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_setParameter(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23062:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23058:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_getSpeciesCountTimes(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23130:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23126:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_getSpeciesCounts(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23205:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23201:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_SimulationFile_getSpeciesNames(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23261:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23257:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_CMESolver(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23325:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23321:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_CMESolver_initialize(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23401:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23397:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_CMESolver_getSpeciesCountView(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23458:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23454:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_CMESolver_getReactionRateConstantsView(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23534:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23530:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_GillespieDSolver(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23601:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23597:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_GillespieDSolver(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23650:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23646:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_GillespieDSolver_initialize(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23735:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23731:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_GillespieDSolver_needsReactionModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23797:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23793:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_GillespieDSolver_needsDiffusionModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23859:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23855:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_GillespieDSolver_generateTrajectory(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23920:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23916:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_GillespieDSolver_getSpeciesCountView(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:23989:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:23985:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_GillespieDSolver_getReactionRateConstantsView(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24077:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24073:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_GillespieDSolver_hookSimulation(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24164:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24160:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_NextReactionSolver__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24249:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24245:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_NextReactionSolver__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24316:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24312:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_NextReactionSolver_initialize(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24441:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24437:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_NextReactionSolver(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24493:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24489:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_NextReactionSolver_needsReactionModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24552:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24548:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_NextReactionSolver_needsDiffusionModel(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24614:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24610:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_NextReactionSolver_generateTrajectory(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24675:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24671:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_NextReactionSolver_getSpeciesCountView(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24744:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24740:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_NextReactionSolver_getReactionRateConstantsView(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24832:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24828:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_NextReactionSolver_hookSimulation(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24919:7: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24915:7: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_getCompiledLatticeMaxOccupancy(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:24995:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:24991:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_getMaxOccupancy(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25045:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25041:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_getSize(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25095:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25091:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_getXSize(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25150:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25146:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_getYSize(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25200:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25196:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_getZSize(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25250:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25246:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_getNumberSites(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25300:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25296:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_getSpacing(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25350:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25346:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_getSiteType(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25427:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25423:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_setSiteType(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25512:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25508:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_getOccupancy(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25595:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25591:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_getParticle(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25690:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25686:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_findParticles(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25758:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25754:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_addParticle(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25865:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25861:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_removeParticles(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25947:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25943:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_Lattice_getParticleCounts(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:25997:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:25993:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_Lattice(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:26053:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:26049:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_ByteLattice__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:26139:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:26135:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_ByteLattice__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:26237:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:26233:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_ByteLattice(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:26365:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:26361:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ByteLattice_getSiteType(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:26442:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:26438:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ByteLattice_setSiteType(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:26527:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:26523:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ByteLattice_getOccupancy(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:26610:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:26606:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ByteLattice_getParticle(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:26705:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:26701:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ByteLattice_findParticles(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:26773:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:26769:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ByteLattice_addParticle(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:26880:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:26876:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ByteLattice_removeParticles(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:26962:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:26958:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ByteLattice_getParticleCounts(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:27012:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:27008:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ByteLattice_getSiteLatticeView(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:27082:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:27078:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_ByteLattice_getParticleLatticeView(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:27161:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:27157:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_IntLattice__SWIG_0(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:27257:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:27253:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_new_IntLattice__SWIG_1(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:27355:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:27351:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_delete_IntLattice(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:27483:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:27479:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_IntLattice_getSiteType(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:27560:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:27556:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_IntLattice_setSiteType(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:27645:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:27641:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_IntLattice_getOccupancy(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:27728:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:27724:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_IntLattice_getParticle(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:27823:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:27819:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_IntLattice_findParticles(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:27891:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:27887:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_IntLattice_addParticle(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:27998:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:27994:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_IntLattice_removeParticles(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:28080:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:28076:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_IntLattice_getParticleCounts(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:28130:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:28126:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_IntLattice_getSiteLatticeView(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:28200:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:28196:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_IntLattice_getParticleLatticeView(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:28313:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:28309:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_runSimulation(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:28417:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:28413:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'PyObject* _wrap_runSolver(PyObject*, PyObject*)': Build-dragonfly/src/swig/lm_wrap.cpp:28517:5: warning: exception of type 'lm::rdme::InvalidSiteException' will be caught catch (InvalidSiteException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp:28513:5: warning: by earlier handler for 'lm::InvalidArgException' catch (InvalidArgException& e) { ^~~~~ Build-dragonfly/src/swig/lm_wrap.cpp: In function 'void SWIG_Python_FixMethods(PyMethodDef*, swig_const_info*, swig_type_info**, swig_type_info**)': Build-dragonfly/src/swig/lm_wrap.cpp:29720:22: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying 10 bytes from a string of the same length [-Wstringop-truncation] strncpy(buff, "swig_ptr: ", 10); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ Finished building: Build-dragonfly/src/swig/lm_wrap.cpp c++ -shared -pthread -lpthread ./Build-dragonfly/src/swig/lm_wrap.o ./Build-dragonfly/src/swig/Print_py.o ./Build-dragonfly/src/c/lm/main/CheckpointSignaler.o ./Build-dragonfly/src/c/lm/main/Globals.o ./Build-dragonfly/src/c/lm/main/LocalDataOutputWorker.o ./Build-dragonfly/src/c/lm/builder/Capsule.o ./Build-dragonfly/src/c/lm/builder/CapsuleShell.o ./Build-dragonfly/src/c/lm/builder/Cuboid.o ./Build-dragonfly/src/c/lm/builder/Hemisphere.o ./Build-dragonfly/src/c/lm/builder/LatticeBuilder.o ./Build-dragonfly/src/c/lm/builder/Shape.o ./Build-dragonfly/src/c/lm/builder/Sphere.o ./Build-dragonfly/src/c/lm/builder/Intersection.o ./Build-dragonfly/src/c/lm/builder/Union.o ./Build-dragonfly/src/c/lm/builder/Difference.o ./Build-dragonfly/src/c/lm/builder/Torus.o ./Build-dragonfly/src/c/lm/builder/Ellipse.o ./Build-dragonfly/src/c/lm/builder/Cylinder.o ./Build-dragonfly/src/c/lm/cme/CMESolver.o ./Build-dragonfly/src/c/lm/cme/FluctuatingNRSolver.o ./Build-dragonfly/src/c/lm/cme/GillespieDSolver.o ./Build-dragonfly/src/c/lm/cme/HillSwitch.o ./Build-dragonfly/src/c/lm/cme/LacHillSwitch.o ./Build-dragonfly/src/c/lm/cme/NextReactionSolver.o ./Build-dragonfly/src/c/lm/cme/SelfRegulatingGeneSwitch.o ./Build-dragonfly/src/c/lm/cme/TwoStateExpression.o ./Build-dragonfly/src/c/lm/cme/TwoStateHillLoopSwitch.o ./Build-dragonfly/src/c/lm/cme/TwoStateHillSwitch.o ./Build-dragonfly/src/protobuf/lm/io/DiffusionModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/FirstPassageTimes.pb.o ./Build-dragonfly/src/protobuf/lm/io/Lattice.pb.o ./Build-dragonfly/src/protobuf/lm/io/ParameterValues.pb.o ./Build-dragonfly/src/protobuf/lm/io/ReactionModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/SpatialModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/SpeciesCounts.pb.o ./Build-dragonfly/src/c/lm/io/SimulationParameters.o ./Build-dragonfly/src/c/lm/io/hdf5/SimulationFile.o ./Build-dragonfly/src/c/lm/io/hdf5/SimulationFile_create.o ./Build-dragonfly/src/c/lm/main/DataOutputQueue.o ./Build-dragonfly/src/c/lm/main/ResourceAllocator.o ./Build-dragonfly/src/c/lm/me/MESolver.o ./Build-dragonfly/src/c/lm/me/MESolverFactory.o ./Build-dragonfly/src/protobuf/lm/message/SimulationParameters.pb.o ./Build-dragonfly/src/c/lm/rdme/ByteLattice.o ./Build-dragonfly/src/c/lm/rdme/IntLattice.o ./Build-dragonfly/src/c/lm/rdme/Lattice.o ./Build-dragonfly/src/c/lm/rdme/NextSubvolumeSolver.o ./Build-dragonfly/src/c/lm/rdme/RDMESolver.o ./Build-dragonfly/src/c/lm/rng/RandomGenerator.o ./Build-dragonfly/src/c/lm/rng/XORShift.o ./Build-dragonfly/src/c/lm/thread/Thread.o ./Build-dragonfly/src/c/lm/thread/Worker.o ./Build-dragonfly/src/c/lm/thread/WorkerManager.o ./Build-dragonfly/src/c/lm/main/runSimulation.o -L/usr/local/lib -L/usr/local/lib -lz -lsz -lhdf5 -lhdf5_hl -lprotobuf `/usr/local/bin/python3.6-config --libs` -o Build-dragonfly/lib/_lm.so Building target: Build-dragonfly/bin/lm_python Invoking: Linker mkdir -p Build-dragonfly/bin c++ -pthread -lpthread Build-dragonfly/utils/c/lm_python.o ./Build-dragonfly/utils/c/util.o ./Build-dragonfly/src/c/lm/Print.o ./Build-dragonfly/src/c/lm/main/CheckpointSignaler.o ./Build-dragonfly/src/c/lm/main/Globals.o ./Build-dragonfly/src/c/lm/main/LocalDataOutputWorker.o ./Build-dragonfly/src/c/lm/builder/Capsule.o ./Build-dragonfly/src/c/lm/builder/CapsuleShell.o ./Build-dragonfly/src/c/lm/builder/Cuboid.o ./Build-dragonfly/src/c/lm/builder/Hemisphere.o ./Build-dragonfly/src/c/lm/builder/LatticeBuilder.o ./Build-dragonfly/src/c/lm/builder/Shape.o ./Build-dragonfly/src/c/lm/builder/Sphere.o ./Build-dragonfly/src/c/lm/builder/Intersection.o ./Build-dragonfly/src/c/lm/builder/Union.o ./Build-dragonfly/src/c/lm/builder/Difference.o ./Build-dragonfly/src/c/lm/builder/Torus.o ./Build-dragonfly/src/c/lm/builder/Ellipse.o ./Build-dragonfly/src/c/lm/builder/Cylinder.o ./Build-dragonfly/src/c/lm/cme/CMESolver.o ./Build-dragonfly/src/c/lm/cme/FluctuatingNRSolver.o ./Build-dragonfly/src/c/lm/cme/GillespieDSolver.o ./Build-dragonfly/src/c/lm/cme/HillSwitch.o ./Build-dragonfly/src/c/lm/cme/LacHillSwitch.o ./Build-dragonfly/src/c/lm/cme/NextReactionSolver.o ./Build-dragonfly/src/c/lm/cme/SelfRegulatingGeneSwitch.o ./Build-dragonfly/src/c/lm/cme/TwoStateExpression.o ./Build-dragonfly/src/c/lm/cme/TwoStateHillLoopSwitch.o ./Build-dragonfly/src/c/lm/cme/TwoStateHillSwitch.o ./Build-dragonfly/src/protobuf/lm/io/DiffusionModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/FirstPassageTimes.pb.o ./Build-dragonfly/src/protobuf/lm/io/Lattice.pb.o ./Build-dragonfly/src/protobuf/lm/io/ParameterValues.pb.o ./Build-dragonfly/src/protobuf/lm/io/ReactionModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/SpatialModel.pb.o ./Build-dragonfly/src/protobuf/lm/io/SpeciesCounts.pb.o ./Build-dragonfly/src/c/lm/io/SimulationParameters.o ./Build-dragonfly/src/c/lm/io/hdf5/SimulationFile.o ./Build-dragonfly/src/c/lm/io/hdf5/SimulationFile_create.o ./Build-dragonfly/src/c/lm/main/DataOutputQueue.o ./Build-dragonfly/src/c/lm/main/ResourceAllocator.o ./Build-dragonfly/src/c/lm/me/MESolver.o ./Build-dragonfly/src/c/lm/me/MESolverFactory.o ./Build-dragonfly/src/protobuf/lm/message/SimulationParameters.pb.o ./Build-dragonfly/src/c/lm/rdme/ByteLattice.o ./Build-dragonfly/src/c/lm/rdme/IntLattice.o ./Build-dragonfly/src/c/lm/rdme/Lattice.o ./Build-dragonfly/src/c/lm/rdme/NextSubvolumeSolver.o ./Build-dragonfly/src/c/lm/rdme/RDMESolver.o ./Build-dragonfly/src/c/lm/rng/RandomGenerator.o ./Build-dragonfly/src/c/lm/rng/XORShift.o ./Build-dragonfly/src/c/lm/thread/Thread.o ./Build-dragonfly/src/c/lm/thread/Worker.o ./Build-dragonfly/src/c/lm/thread/WorkerManager.o ./Build-dragonfly/src/c/lm/main/runSimulation.o ./Build-dragonfly/src/swig/lm_wrap.o -L/usr/local/lib -L/usr/local/lib -lz -lsz -lhdf5 -lhdf5_hl -lprotobuf `/usr/local/bin/python3.6-config --libs` `/usr/local/bin/python3.6-config --libs` -o "Build-dragonfly/bin/lm_python" Python interface (lm.py, _lm.so) bulit in ./Build-dragonfly/lib Finished building target: Build-dragonfly/bin/lm_python gmake[2]: Leaving directory '/construction/science/lm/lm-2.3.0' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> lm-uiuc-2.3.0_6 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for lm-uiuc-2.3.0_6 ===> Generating temporary packing list gmake[2]: Entering directory '/construction/science/lm/lm-2.3.0' Installing LM binaries install -d /construction/science/lm/stage/usr/local/bin install -m 0755 ./Build-dragonfly/lm ./Build-dragonfly/bin/lm_setp ./Build-dragonfly/bin/lm_setdm ./Build-dragonfly/bin/lm_setrm ./Build-dragonfly/bin/lm_python /construction/science/lm/stage/usr/local/bin Installing LM libraries install -d /construction/science/lm/stage/usr/local/lib/lm install -m 0644 ./Build-dragonfly/lib/_lm.so ./Build-dragonfly/lib/lm.py /construction/science/lm/stage/usr/local/lib/lm install -d /construction/science/lm/stage/usr/local/lib/python/pySTDLM install -d /construction/science/lm/stage/usr/local/lib/python/pyLM install -m 0644 ./src/python/pyLM/* /construction/science/lm/stage/usr/local/lib/python/pyLM install -m 0644 ./src/python/pySTDLM/* /construction/science/lm/stage/usr/local/lib/python/pySTDLM gmake[2]: Leaving directory '/construction/science/lm/lm-2.3.0' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for lm-uiuc-2.3.0_6 file sizes/checksums [27]: . done packing files [27]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Tuesday, 9 JUL 2019 at 19:25:22 UTC Duration: 00:02:35