=> Building biology/protomol Started : Thursday, 30 AUG 2018 at 13:01:10 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-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 protomol-2.0.3_13: EXAMPLES=on: Build and/or install examples GLUT=on: OpenGL Utility Toolkit support ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/protomol XDG_CONFIG_HOME=/construction/biology/protomol HOME=/construction/biology/protomol TMPDIR="/tmp" PATH=/construction/biology/protomol/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --without-irix_mipspro_mpi --with-glut=yes --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/protomol XDG_CONFIG_HOME=/construction/biology/protomol HOME=/construction/biology/protomol TMPDIR="/tmp" PATH=/construction/biology/protomol/.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=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="-I/usr/local/include" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98" 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/biology/protomol/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/protomol" EXAMPLESDIR="share/examples/protomol" DATADIR="share/protomol" WWWDIR="www/protomol" ETCDIR="etc/protomol" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/protomol DOCSDIR=/usr/local/share/doc/protomol EXAMPLESDIR=/usr/local/share/examples/protomol WWWDIR=/usr/local/www/protomol ETCDIR=/usr/local/etc/protomol -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem 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=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> NOTICE: The protomol 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 ===> License GPLv2 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> protomol-2.0.3_13 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> protomol-2.0.3_13 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of protomol-2.0.3_13 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> NOTICE: The protomol 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 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by protomol-2.0.3_13 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> NOTICE: The protomol 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 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by protomol-2.0.3_13 for building => SHA256 Checksum OK for protomol-2.0.3-tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> NOTICE: The protomol 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 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by protomol-2.0.3_13 for building ===> Extracting for protomol-2.0.3_13 ===> NOTICE: The protomol 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 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by protomol-2.0.3_13 for building => SHA256 Checksum OK for protomol-2.0.3-tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for protomol-2.0.3_13 ===> Applying ports patches for protomol-2.0.3_13 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - not found ===> Installing existing package /packages/All/libXmu-1.1.2_3,1.txz Installing libXmu-1.1.2_3,1... `-- Installing libX11-1.6.5,1... | `-- Installing kbproto-1.0.7... | `-- Extracting kbproto-1.0.7: .......... done | `-- Installing libXau-1.0.8_3... | | `-- Installing xproto-7.0.31... | | `-- Extracting xproto-7.0.31: .......... done | `-- Extracting libXau-1.0.8_3: .......... done | `-- Installing libXdmcp-1.1.2... | `-- Extracting libXdmcp-1.1.2: ......... done | `-- Installing libxcb-1.13... | | `-- Installing libpthread-stubs-0.4... | | `-- Extracting libpthread-stubs-0.4: .... done | | `-- Installing libxml2-2.9.7... | | `-- Extracting libxml2-2.9.7: .......... done | `-- Extracting libxcb-1.13: .......... done `-- Extracting libX11-1.6.5,1: .......... done `-- Installing libXext-1.3.3_1,1... | `-- Installing xextproto-7.3.0... | `-- Extracting xextproto-7.3.0: .......... done `-- Extracting libXext-1.3.3_1,1: .......... done `-- Installing libXt-1.1.5,1... | `-- Installing libICE-1.0.9_1,1... | `-- Extracting libICE-1.0.9_1,1: .......... done | `-- Installing libSM-1.2.2_3,1... | `-- Extracting libSM-1.2.2_3,1: .......... done `-- Extracting libXt-1.1.5,1: .......... done Extracting libXmu-1.1.2_3,1: .......... done ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> Returning to build of protomol-2.0.3_13 ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/xi.pc - not found ===> Installing existing package /packages/All/libXi-1.7.9,1.txz Installing libXi-1.7.9,1... `-- Installing inputproto-2.3.2... `-- Extracting inputproto-2.3.2: ........ done `-- Installing libXfixes-5.0.3... | `-- Installing fixesproto-5.0... | `-- Extracting fixesproto-5.0: ....... done `-- Extracting libXfixes-5.0.3: .......... done Extracting libXi-1.7.9,1: .......... done ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/xi.pc - found ===> Returning to build of protomol-2.0.3_13 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> protomol-2.0.3_13 depends on shared library: libpng.so - not found ===> Installing existing package /packages/All/png-1.6.34.txz Installing png-1.6.34... Extracting png-1.6.34: .......... done ===> protomol-2.0.3_13 depends on shared library: libpng.so - found (/usr/local/lib/libpng.so) ===> Returning to build of protomol-2.0.3_13 ===> protomol-2.0.3_13 depends on shared library: libtiff.so - not found ===> Installing existing package /packages/All/tiff-4.0.9_1.txz Installing tiff-4.0.9_1... `-- Installing jbigkit-2.1_1... `-- Extracting jbigkit-2.1_1: .......... done `-- Installing jpeg-turbo-1.5.3... `-- Extracting jpeg-turbo-1.5.3: .......... done Extracting tiff-4.0.9_1: .......... done ===> protomol-2.0.3_13 depends on shared library: libtiff.so - found (/usr/local/lib/libtiff.so) ===> Returning to build of protomol-2.0.3_13 ===> protomol-2.0.3_13 depends on shared library: libjpeg.so - found (/usr/local/lib/libjpeg.so) ===> protomol-2.0.3_13 depends on shared library: libglut.so - not found ===> Installing existing package /packages/All/freeglut-3.0.0_1.txz Installing freeglut-3.0.0_1... `-- Installing libGLU-9.0.0_3... | `-- Installing mesa-libs-18.1.2... | | `-- Installing expat-2.2.5... | | `-- Extracting expat-2.2.5: .......... done | | `-- Installing libXdamage-1.1.4_3... | | `-- Installing damageproto-1.2.1... | | `-- Extracting damageproto-1.2.1: ....... done | | `-- Extracting libXdamage-1.1.4_3: ......... done | | `-- Installing libXxf86vm-1.1.4_1... | | `-- Installing xf86vidmodeproto-2.3.1... | | `-- Extracting xf86vidmodeproto-2.3.1: ....... done | | `-- Extracting libXxf86vm-1.1.4_1: .......... done | | `-- Installing libdrm-2.4.92,1... | | `-- Installing libpciaccess-0.13.5... | | | `-- Installing pciids-20180428... | | | `-- Extracting pciids-20180428: ..... done | | `-- Extracting libpciaccess-0.13.5: ......... done | | `-- Extracting libdrm-2.4.92,1: .......... done | | `-- Installing libelf-0.8.13_3... | | `-- Installing gettext-runtime-0.19.8.1_1... | | | `-- Installing indexinfo-0.3.1... | | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | | `-- Extracting libelf-0.8.13_3: .......... done | | `-- Installing libxshmfence-1.2_2... | | `-- Extracting libxshmfence-1.2_2: ......... done | `-- Extracting mesa-libs-18.1.2: .......... done `-- Extracting libGLU-9.0.0_3: ...... done `-- Installing libXrandr-1.5.1... | `-- Installing libXrender-0.9.10... | | `-- Installing renderproto-0.11.1... | | `-- Extracting renderproto-0.11.1: ....... done | `-- Extracting libXrender-0.9.10: .......... done | `-- Installing randrproto-1.5.0... | `-- Extracting randrproto-1.5.0: ....... done `-- Extracting libXrandr-1.5.1: .......... done Extracting freeglut-3.0.0_1: .......... done Message from freeglut-3.0.0_1: Joystick support is untested and it is unknown if it works. Do not hesitate to contact x11@FreeBSD.org if this causes issues. ===> protomol-2.0.3_13 depends on shared library: libglut.so - found (/usr/local/lib/libglut.so) ===> Returning to build of protomol-2.0.3_13 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for protomol-2.0.3_13 configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking major version... 2 checking minor version... 0 checking patchlevel... 3 checking for C++ compiler default output... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of c++... none checking preset g++ for SUN with optimization flags ... no checking preset CC fro IRIX with MPI and optimization flags ... no checking preset CC for IRIX with MPI and debugging flags ... no checking preset CC for IRIX with optimization flags ... no checking preset CC for IRIX with debugging flags ... no checking preset icc for generic with optimization flags ... no checking preset icc for generic with debugging flags ... no checking preset icc for generic with MPICH flags ... no checking preset icc for generic with MPICH and optimization flags ... no checking preset icc for generic with MPICH and debugging flags ... no checking preset g++ for generic with MPICH flags ... no checking preset g++ for generic with MPICH XEON flags ... no checking preset g++ for generic with MPICH debug flags ... no checking preset g++ for generic with optimization flags ... no checking preset g++ for generic with debugging flags ... no checking preset g++ for generic with debugging and gdb flags ... no checking preset xlC for PPC with optimization flags ... no checking preset xlC for PPC with debugging flags ... no checking preset xlC for AIX with optimization flags ... no checking preset xlC for AIX with debugging flags ... no checking preset xlC for AIX with MPI and optimization flags ... no checking preset xlC for AIX with MPI and debugging flags ... no checking preset aCC for HPUX with optimization flags ... no checking preset aCC for HPUX with debugging flags ... no checking preset aCC for HPUX with MPI and optimization flags ... no checking preset aCC for HPUX with MPI and debugging flags ... no CC : cc CFLAGS : -pipe -O2 -fno-strict-aliasing CXXFLAGS : -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 CXX : c++ CXXCPP : LIBS : CPP : cpp CPPFLAGS : -I/usr/local/include checking whether we are using the GNU C++ compiler... (cached) yes checking whether c++ accepts -g... (cached) yes checking dependency style of c++... (cached) none checking how to run the C++ preprocessor... c++ -E checking for gcc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ANSI C... none needed checking dependency style of cc... none checking for a BSD-compatible install... /usr/bin/install -c checking for ranlib... ranlib checking using MPI... no checking for X... libraries /usr/local/lib, headers /usr/local/include checking for gethostbyname... (cached) yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for limits ... yes checking for sstream ... yes checking for partial template specialization... yes checking for socket in -lsocket... no checking for egrep... grep -E checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/socket.h... (cached) yes checking for socketlen type... socklen_t checking for char... (cached) yes checking size of char... 1 checking for short... (cached) yes checking size of short... 2 checking for int... (cached) yes checking size of int... 4 checking for long... (cached) yes checking size of long... 8 checking for size_t... (cached) yes checking size of size_t... 8 checking for void*... yes checking size of void*... 8 checking for 32-bit int... int checking for inline... inline checking whether time.h and sys/time.h may both be included... yes checking for sys/time.h... (cached) yes checking c_asm.h usability... no checking c_asm.h presence... no checking for c_asm.h... no checking intrinsics.h usability... no checking intrinsics.h presence... no checking for intrinsics.h... no checking for hrtime_t... no checking for gethrtime... no checking for clock_gettime... (cached) yes checking for read_real_time... no checking for time_base_to_time... no checking for _rtc intrinsic... no checking for zfftm1di in -lcomplib.sgimath... no checking for zfftm1d in -lcomplib.sgimath... no checking for zfft2di in -lcomplib.sgimath... no checking for zfft2d in -lcomplib.sgimath... no checking for zfft3di in -lcomplib.sgimath... no checking for zfft3d in -lcomplib.sgimath... no checking fft.h usability... no checking fft.h presence... no checking for fft.h... no checking for dcft in -lessl... no checking essl.h usability... no checking essl.h presence... no checking for essl.h... no checking for fftw3d_mpi_create_plan in -lfftw_mpi... no checking for fftw3d_create_plan in -lfftw... no checking fftw_mpi.h usability... no checking fftw_mpi.h presence... no checking for fftw_mpi.h... no checking fftw.h usability... no checking fftw.h presence... no checking for fftw.h... no checking for fftw_plan_dft_3d in -lfftw3... no checking fftw3.h usability... no checking fftw3.h presence... no checking for fftw3.h... no checking for fftw3d_create_plan in -lfftw... no checking fftw.h usability... no checking fftw.h presence... no checking for fftw.h... no checking FFT SGI complib.sgimath... no checking FFT ESSL... no checking FFT FFTW3... no checking FFT FFTW2... no checking FFT FFTW2 MPI... no using FFT ZFFT checking for compress in -lz... yes checking png.h usability... yes checking png.h presence... yes checking for png.h... yes checking for png_create_write_struct in -lpng... yes using PNG... yes checking for pthread_cancel in -lpthread... yes checking for dlopen in -ldl... yes checking for XmuAllStandardColormaps in -lXmu... yes checking for XtAppInitialize in -lXt... yes checking for SmcOpenConnection in -lSM... yes checking for IceAcceptConnection in -lICE... yes checking for XextCreateExtension in -lXext... yes checking for XOpenDisplay in -lX11... yes checking for XOpenDevice in -lXi... yes checking for pthread_cancel in -lpthread... (cached) yes checking for dlopen in -ldl... (cached) yes checking for glClear in -lGL... yes checking for gluLookAt in -lGLU... yes checking for glutMainLoop in -lglut... yes checking GL/glut.h usability... yes checking GL/glut.h presence... yes checking for GL/glut.h... yes checking for jpeg_CreateDecompress in -ljpeg... yes checking for TIFFSetErrorHandler in -ltiff... yes checking found GLUT... yes using GLUT... yes ./configure: perl: not found configure: creating ./config.status config.status: creating Makefile config.status: creating framework/Makefile config.status: creating framework/base/Makefile config.status: creating framework/io/Makefile config.status: creating framework/parallel/Makefile config.status: creating framework/topology/Makefile config.status: creating framework/forces/Makefile config.status: creating framework/imd/Makefile config.status: creating framework/integrators/Makefile config.status: creating framework/frontend/Makefile config.status: creating framework/factories/Makefile config.status: creating applications/Makefile config.status: creating applications/protomol-app/Makefile config.status: creating applications/coulomb-app/Makefile config.status: creating applications/dcd2dcd-app/Makefile config.status: creating applications/iSGProtomol-app/Makefile config.status: creating applications/iSGProtomol-app/base/Makefile config.status: creating applications/iSGProtomol-app/io/Makefile config.status: creating applications/iSGProtomol-app/frontend/Makefile config.status: creating applications/iSGProtomol-app/forces/Makefile config.status: creating applications/iSGProtomol-app/factories/Makefile config.status: creating applications/iSGProtomol-app/integrators/Makefile config.status: creating applications/coords2coords-app/Makefile config.status: creating applications/xyzviz-app/Makefile config.status: creating protomol_config.h config.status: executing depfiles commands CC : cc CFLAGS : -pipe -O2 -fno-strict-aliasing CXXFLAGS : -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 CXX : c++ CXXCPP : c++ -E LIBS : CPP : cpp CPPFLAGS : -I/usr/local/include make clean; make -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for protomol-2.0.3_13 --- all --- /usr/bin/make all-recursive --- all-recursive --- Making all in framework --- all-recursive --- Making all in base --- BSpline.o --- --- BSplineType.o --- --- Configuration.o --- --- ConstraintValueType.o --- --- FFTComplex.o --- --- Lagrange.o --- --- Makeable.o --- --- Matrix3by3.o --- --- iSGPAR.o --- --- PAR.o --- --- PDB.o --- --- PPM.o --- --- BSpline.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o BSpline.o `test -f 'BSpline.cpp' || echo './'`BSpline.cpp --- BSplineType.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o BSplineType.o `test -f 'BSplineType.cpp' || echo './'`BSplineType.cpp --- Configuration.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Configuration.o `test -f 'Configuration.cpp' || echo './'`Configuration.cpp --- ConstraintValueType.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ConstraintValueType.o `test -f 'ConstraintValueType.cpp' || echo './'`ConstraintValueType.cpp --- FFTComplex.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o FFTComplex.o `test -f 'FFTComplex.cpp' || echo './'`FFTComplex.cpp --- Lagrange.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Lagrange.o `test -f 'Lagrange.cpp' || echo './'`Lagrange.cpp --- Makeable.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Makeable.o `test -f 'Makeable.cpp' || echo './'`Makeable.cpp --- Matrix3by3.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Matrix3by3.o `test -f 'Matrix3by3.cpp' || echo './'`Matrix3by3.cpp --- iSGPAR.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGPAR.o `test -f 'iSGPAR.cpp' || echo './'`iSGPAR.cpp --- PAR.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PAR.o `test -f 'PAR.cpp' || echo './'`PAR.cpp --- PDB.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PDB.o `test -f 'PDB.cpp' || echo './'`PDB.cpp --- PPM.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PPM.o `test -f 'PPM.cpp' || echo './'`PPM.cpp --- PGM.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PGM.o `test -f 'PGM.cpp' || echo './'`PGM.cpp --- PSF.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PSF.o `test -f 'PSF.cpp' || echo './'`PSF.cpp --- Parameter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Parameter.o `test -f 'Parameter.cpp' || echo './'`Parameter.cpp --- ReducedHessAngle.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ReducedHessAngle.o `test -f 'ReducedHessAngle.cpp' || echo './'`ReducedHessAngle.cpp --- reducedHessBond.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o reducedHessBond.o `test -f 'reducedHessBond.cpp' || echo './'`reducedHessBond.cpp --- Report.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Report.o `test -f 'Report.cpp' || echo './'`Report.cpp --- ScalarStructure.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ScalarStructure.o `test -f 'ScalarStructure.cpp' || echo './'`ScalarStructure.cpp --- Timer.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp --- TimerStatistic.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o TimerStatistic.o `test -f 'TimerStatistic.cpp' || echo './'`TimerStatistic.cpp --- Value.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Value.o `test -f 'Value.cpp' || echo './'`Value.cpp --- ValueType.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ValueType.o `test -f 'ValueType.cpp' || echo './'`ValueType.cpp --- Vector3DBlock.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Vector3DBlock.o `test -f 'Vector3DBlock.cpp' || echo './'`Vector3DBlock.cpp --- XYZ.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZ.o `test -f 'XYZ.cpp' || echo './'`XYZ.cpp --- pmconstants.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o pmconstants.o `test -f 'pmconstants.cpp' || echo './'`pmconstants.cpp --- fft.o --- cc -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -c `test -f 'fft.c' || echo './'`fft.c --- mathutilities.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o mathutilities.o `test -f 'mathutilities.cpp' || echo './'`mathutilities.cpp --- stringutilities.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o stringutilities.o `test -f 'stringutilities.cpp' || echo './'`stringutilities.cpp --- systemutilities.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o systemutilities.o `test -f 'systemutilities.cpp' || echo './'`systemutilities.cpp --- libbase.a --- rm -f libbase.a ar cru libbase.a BSpline.o BSplineType.o Configuration.o ConstraintValueType.o FFTComplex.o Lagrange.o Makeable.o Matrix3by3.o iSGPAR.o PAR.o PDB.o PPM.o PGM.o PSF.o Parameter.o ReducedHessAngle.o reducedHessBond.o Report.o ScalarStructure.o Timer.o TimerStatistic.o Value.o ValueType.o Vector3DBlock.o XYZ.o pmconstants.o fft.o mathutilities.o stringutilities.o systemutilities.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libbase.a Making all in io --- ConfigurationReader.o --- --- DCDTrajectoryReader.o --- --- DCDTrajectoryWriter.o --- --- File.o --- --- PARReader.o --- --- PARWriter.o --- --- PDBReader.o --- --- PDBWriter.o --- --- PNGWriter.o --- --- PPMReader.o --- --- PPMWriter.o --- --- PGMReader.o --- --- ConfigurationReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ConfigurationReader.o `test -f 'ConfigurationReader.cpp' || echo './'`ConfigurationReader.cpp --- DCDTrajectoryReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o DCDTrajectoryReader.o `test -f 'DCDTrajectoryReader.cpp' || echo './'`DCDTrajectoryReader.cpp --- DCDTrajectoryWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o DCDTrajectoryWriter.o `test -f 'DCDTrajectoryWriter.cpp' || echo './'`DCDTrajectoryWriter.cpp --- File.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o File.o `test -f 'File.cpp' || echo './'`File.cpp --- PARReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PARReader.o `test -f 'PARReader.cpp' || echo './'`PARReader.cpp --- PARWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PARWriter.o `test -f 'PARWriter.cpp' || echo './'`PARWriter.cpp --- PDBReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PDBReader.o `test -f 'PDBReader.cpp' || echo './'`PDBReader.cpp --- PDBWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PDBWriter.o `test -f 'PDBWriter.cpp' || echo './'`PDBWriter.cpp --- PNGWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PNGWriter.o `test -f 'PNGWriter.cpp' || echo './'`PNGWriter.cpp --- PPMReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PPMReader.o `test -f 'PPMReader.cpp' || echo './'`PPMReader.cpp --- PPMWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PPMWriter.o `test -f 'PPMWriter.cpp' || echo './'`PPMWriter.cpp --- PGMReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PGMReader.o `test -f 'PGMReader.cpp' || echo './'`PGMReader.cpp --- PNGWriter.o --- PNGWriter.cpp: In member function 'bool ProtoMol::PNGWriter::write(const ProtoMol::PPM&)': PNGWriter.cpp:118:21: warning: deprecated conversion from string constant to 'png_charp {aka char*}' [-Wwrite-strings] text_ptr[0].key = "Description"; ^ PNGWriter.cpp:119:22: warning: deprecated conversion from string constant to 'png_charp {aka char*}' [-Wwrite-strings] text_ptr[0].text = "ProtoMol PNG Writer"; ^ PNGWriter.cpp:125:21: warning: deprecated conversion from string constant to 'png_charp {aka char*}' [-Wwrite-strings] text_ptr[1].key = "Software"; ^ PNGWriter.cpp:126:22: warning: deprecated conversion from string constant to 'png_charp {aka char*}' [-Wwrite-strings] text_ptr[1].text = "ProtoMol"; ^ --- PGMWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PGMWriter.o `test -f 'PGMWriter.cpp' || echo './'`PGMWriter.cpp --- PSFReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PSFReader.o `test -f 'PSFReader.cpp' || echo './'`PSFReader.cpp --- PSFWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PSFWriter.o `test -f 'PSFWriter.cpp' || echo './'`PSFWriter.cpp --- Reader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Reader.o `test -f 'Reader.cpp' || echo './'`Reader.cpp --- Writer.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Writer.o `test -f 'Writer.cpp' || echo './'`Writer.cpp --- XFigWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XFigWriter.o `test -f 'XFigWriter.cpp' || echo './'`XFigWriter.cpp --- XYZBinReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZBinReader.o `test -f 'XYZBinReader.cpp' || echo './'`XYZBinReader.cpp --- XYZBinWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZBinWriter.o `test -f 'XYZBinWriter.cpp' || echo './'`XYZBinWriter.cpp --- XYZReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZReader.o `test -f 'XYZReader.cpp' || echo './'`XYZReader.cpp --- XYZTrajectoryReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZTrajectoryReader.o `test -f 'XYZTrajectoryReader.cpp' || echo './'`XYZTrajectoryReader.cpp --- XYZTrajectoryWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZTrajectoryWriter.o `test -f 'XYZTrajectoryWriter.cpp' || echo './'`XYZTrajectoryWriter.cpp --- XYZWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XYZWriter.o `test -f 'XYZWriter.cpp' || echo './'`XYZWriter.cpp --- libio.a --- rm -f libio.a ar cru libio.a ConfigurationReader.o DCDTrajectoryReader.o DCDTrajectoryWriter.o File.o PARReader.o PARWriter.o PDBReader.o PDBWriter.o PNGWriter.o PPMReader.o PPMWriter.o PGMReader.o PGMWriter.o PSFReader.o PSFWriter.o Reader.o Writer.o XFigWriter.o XYZBinReader.o XYZBinWriter.o XYZReader.o XYZTrajectoryReader.o XYZTrajectoryWriter.o XYZWriter.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libio.a Making all in parallel --- Parallel.o --- --- ParallelType.o --- --- Parallel.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Parallel.o `test -f 'Parallel.cpp' || echo './'`Parallel.cpp --- ParallelType.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ParallelType.o `test -f 'ParallelType.cpp' || echo './'`ParallelType.cpp --- libparallel.a --- rm -f libparallel.a ar cru libparallel.a Parallel.o ParallelType.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libparallel.a Making all in topology --- ArrayCellListStructure.o --- --- C1SwitchingFunctionBase.o --- --- C1SwitchingFunction.o --- --- C2SwitchingFunctionBase.o --- --- C2SwitchingFunction.o --- --- buildCellLists.o --- --- ComplementSwitchingFunctionBase.o --- --- CubicCellManager.o --- --- CutoffSwitchingFunctionBase.o --- --- CutoffSwitchingFunction.o --- --- ExclusionTable.o --- --- ExclusionType.o --- --- ArrayCellListStructure.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ArrayCellListStructure.o `test -f 'ArrayCellListStructure.cpp' || echo './'`ArrayCellListStructure.cpp --- C1SwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o C1SwitchingFunctionBase.o `test -f 'C1SwitchingFunctionBase.cpp' || echo './'`C1SwitchingFunctionBase.cpp --- C2SwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o C2SwitchingFunctionBase.o `test -f 'C2SwitchingFunctionBase.cpp' || echo './'`C2SwitchingFunctionBase.cpp --- C2SwitchingFunction.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o C2SwitchingFunction.o `test -f 'C2SwitchingFunction.cpp' || echo './'`C2SwitchingFunction.cpp --- buildCellLists.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o buildCellLists.o `test -f 'buildCellLists.cpp' || echo './'`buildCellLists.cpp --- ComplementSwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ComplementSwitchingFunctionBase.o `test -f 'ComplementSwitchingFunctionBase.cpp' || echo './'`ComplementSwitchingFunctionBase.cpp --- CubicCellManager.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CubicCellManager.o `test -f 'CubicCellManager.cpp' || echo './'`CubicCellManager.cpp --- CutoffSwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CutoffSwitchingFunctionBase.o `test -f 'CutoffSwitchingFunctionBase.cpp' || echo './'`CutoffSwitchingFunctionBase.cpp --- CutoffSwitchingFunction.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CutoffSwitchingFunction.o `test -f 'CutoffSwitchingFunction.cpp' || echo './'`CutoffSwitchingFunction.cpp --- ExclusionTable.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExclusionTable.o `test -f 'ExclusionTable.cpp' || echo './'`ExclusionTable.cpp --- ExclusionType.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExclusionType.o `test -f 'ExclusionType.cpp' || echo './'`ExclusionType.cpp --- C1SwitchingFunction.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o C1SwitchingFunction.o `test -f 'C1SwitchingFunction.cpp' || echo './'`C1SwitchingFunction.cpp --- GenericTopology.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o GenericTopology.o `test -f 'GenericTopology.cpp' || echo './'`GenericTopology.cpp --- LennardJonesParameterTable.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o LennardJonesParameterTable.o `test -f 'LennardJonesParameterTable.cpp' || echo './'`LennardJonesParameterTable.cpp --- PeriodicBoundaryConditions.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PeriodicBoundaryConditions.o `test -f 'PeriodicBoundaryConditions.cpp' || echo './'`PeriodicBoundaryConditions.cpp --- RangeSwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o RangeSwitchingFunctionBase.o `test -f 'RangeSwitchingFunctionBase.cpp' || echo './'`RangeSwitchingFunctionBase.cpp --- ShiftSwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ShiftSwitchingFunctionBase.o `test -f 'ShiftSwitchingFunctionBase.cpp' || echo './'`ShiftSwitchingFunctionBase.cpp --- ShiftSwitchingFunction.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ShiftSwitchingFunction.o `test -f 'ShiftSwitchingFunction.cpp' || echo './'`ShiftSwitchingFunction.cpp --- topologyutilities.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o topologyutilities.o `test -f 'topologyutilities.cpp' || echo './'`topologyutilities.cpp --- UniversalSwitchingFunctionBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o UniversalSwitchingFunctionBase.o `test -f 'UniversalSwitchingFunctionBase.cpp' || echo './'`UniversalSwitchingFunctionBase.cpp --- VacuumBoundaryConditions.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o VacuumBoundaryConditions.o `test -f 'VacuumBoundaryConditions.cpp' || echo './'`VacuumBoundaryConditions.cpp --- AngleInfo.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o AngleInfo.o `test -f 'AngleInfo.cpp' || echo './'`AngleInfo.cpp --- libtopology.a --- rm -f libtopology.a ar cru libtopology.a ArrayCellListStructure.o C1SwitchingFunctionBase.o C1SwitchingFunction.o C2SwitchingFunctionBase.o C2SwitchingFunction.o buildCellLists.o ComplementSwitchingFunctionBase.o CubicCellManager.o CutoffSwitchingFunctionBase.o CutoffSwitchingFunction.o ExclusionTable.o ExclusionType.o GenericTopology.o LennardJonesParameterTable.o PeriodicBoundaryConditions.o RangeSwitchingFunctionBase.o ShiftSwitchingFunctionBase.o ShiftSwitchingFunction.o topologyutilities.o UniversalSwitchingFunctionBase.o VacuumBoundaryConditions.o AngleInfo.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libtopology.a Making all in forces --- AngleSystemForceBase.o --- --- BondSystemForceBase.o --- --- CompareForce.o --- --- CoulombEwaldRealForce.o --- --- CoulombEwaldRealTableForce.o --- --- CoulombForce.o --- --- CoulombMultiGridDirectForceBase.o --- --- CoulombMultiGridDirectTableForceBase.o --- --- DihedralSystemForceBase.o --- --- HarmDihedralSystemForceBase.o --- --- ElectricFieldSystemForceBase.o --- --- ExternalGravitationSystemForce.o --- --- AngleSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o AngleSystemForceBase.o `test -f 'AngleSystemForceBase.cpp' || echo './'`AngleSystemForceBase.cpp --- BondSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o BondSystemForceBase.o `test -f 'BondSystemForceBase.cpp' || echo './'`BondSystemForceBase.cpp --- CompareForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CompareForce.o `test -f 'CompareForce.cpp' || echo './'`CompareForce.cpp --- CoulombEwaldRealForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CoulombEwaldRealForce.o `test -f 'CoulombEwaldRealForce.cpp' || echo './'`CoulombEwaldRealForce.cpp --- CoulombEwaldRealTableForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CoulombEwaldRealTableForce.o `test -f 'CoulombEwaldRealTableForce.cpp' || echo './'`CoulombEwaldRealTableForce.cpp --- CoulombForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CoulombForce.o `test -f 'CoulombForce.cpp' || echo './'`CoulombForce.cpp --- CoulombMultiGridDirectForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CoulombMultiGridDirectForceBase.o `test -f 'CoulombMultiGridDirectForceBase.cpp' || echo './'`CoulombMultiGridDirectForceBase.cpp --- CoulombMultiGridDirectTableForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o CoulombMultiGridDirectTableForceBase.o `test -f 'CoulombMultiGridDirectTableForceBase.cpp' || echo './'`CoulombMultiGridDirectTableForceBase.cpp --- DihedralSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o DihedralSystemForceBase.o `test -f 'DihedralSystemForceBase.cpp' || echo './'`DihedralSystemForceBase.cpp --- HarmDihedralSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o HarmDihedralSystemForceBase.o `test -f 'HarmDihedralSystemForceBase.cpp' || echo './'`HarmDihedralSystemForceBase.cpp --- ElectricFieldSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ElectricFieldSystemForceBase.o `test -f 'ElectricFieldSystemForceBase.cpp' || echo './'`ElectricFieldSystemForceBase.cpp --- ExternalGravitationSystemForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExternalGravitationSystemForce.o `test -f 'ExternalGravitationSystemForce.cpp' || echo './'`ExternalGravitationSystemForce.cpp --- ExternalMagneticFieldExtendedForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExternalMagneticFieldExtendedForce.o `test -f 'ExternalMagneticFieldExtendedForce.cpp' || echo './'`ExternalMagneticFieldExtendedForce.cpp --- ExtendedCompareForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExtendedCompareForce.o `test -f 'ExtendedCompareForce.cpp' || echo './'`ExtendedCompareForce.cpp --- ExtendedForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExtendedForce.o `test -f 'ExtendedForce.cpp' || echo './'`ExtendedForce.cpp --- ExtendedTimeForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ExtendedTimeForce.o `test -f 'ExtendedTimeForce.cpp' || echo './'`ExtendedTimeForce.cpp --- Force.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Force.o `test -f 'Force.cpp' || echo './'`Force.cpp --- ForceGroup.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ForceGroup.o `test -f 'ForceGroup.cpp' || echo './'`ForceGroup.cpp --- FrictionExtendedForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o FrictionExtendedForce.o `test -f 'FrictionExtendedForce.cpp' || echo './'`FrictionExtendedForce.cpp --- GravitationForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o GravitationForce.o `test -f 'GravitationForce.cpp' || echo './'`GravitationForce.cpp --- Hermite.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Hermite.o `test -f 'Hermite.cpp' || echo './'`Hermite.cpp --- ImproperSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ImproperSystemForceBase.o `test -f 'ImproperSystemForceBase.cpp' || echo './'`ImproperSystemForceBase.cpp --- LennardJonesForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o LennardJonesForce.o `test -f 'LennardJonesForce.cpp' || echo './'`LennardJonesForce.cpp --- LennardJonesTableForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o LennardJonesTableForce.o `test -f 'LennardJonesTableForce.cpp' || echo './'`LennardJonesTableForce.cpp --- MagneticDipoleForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MagneticDipoleForce.o `test -f 'MagneticDipoleForce.cpp' || echo './'`MagneticDipoleForce.cpp --- MagneticDipoleMirrorSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MagneticDipoleMirrorSystemForceBase.o `test -f 'MagneticDipoleMirrorSystemForceBase.cpp' || echo './'`MagneticDipoleMirrorSystemForceBase.cpp --- MetaForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MetaForce.o `test -f 'MetaForce.cpp' || echo './'`MetaForce.cpp --- MollyForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MollyForce.o `test -f 'MollyForce.cpp' || echo './'`MollyForce.cpp --- NonbondedCutoffForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NonbondedCutoffForceBase.o `test -f 'NonbondedCutoffForceBase.cpp' || echo './'`NonbondedCutoffForceBase.cpp --- NonbondedFullEwaldSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NonbondedFullEwaldSystemForceBase.o `test -f 'NonbondedFullEwaldSystemForceBase.cpp' || echo './'`NonbondedFullEwaldSystemForceBase.cpp --- NonbondedFullSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NonbondedFullSystemForceBase.o `test -f 'NonbondedFullSystemForceBase.cpp' || echo './'`NonbondedFullSystemForceBase.cpp --- NonbondedMultiGridSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NonbondedMultiGridSystemForceBase.o `test -f 'NonbondedMultiGridSystemForceBase.cpp' || echo './'`NonbondedMultiGridSystemForceBase.cpp --- NonbondedPMEwaldSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NonbondedPMEwaldSystemForceBase.o `test -f 'NonbondedPMEwaldSystemForceBase.cpp' || echo './'`NonbondedPMEwaldSystemForceBase.cpp --- NonbondedSimpleFullSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NonbondedSimpleFullSystemForceBase.o `test -f 'NonbondedSimpleFullSystemForceBase.cpp' || echo './'`NonbondedSimpleFullSystemForceBase.cpp --- PaulTrapExtendedForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PaulTrapExtendedForceBase.o `test -f 'PaulTrapExtendedForceBase.cpp' || echo './'`PaulTrapExtendedForceBase.cpp --- ReducedHessCoulomb.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ReducedHessCoulomb.o `test -f 'ReducedHessCoulomb.cpp' || echo './'`ReducedHessCoulomb.cpp --- ReducedHessLennardJones.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ReducedHessLennardJones.o `test -f 'ReducedHessLennardJones.cpp' || echo './'`ReducedHessLennardJones.cpp --- SphericalSystemForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o SphericalSystemForce.o `test -f 'SphericalSystemForce.cpp' || echo './'`SphericalSystemForce.cpp --- SystemCompareForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o SystemCompareForce.o `test -f 'SystemCompareForce.cpp' || echo './'`SystemCompareForce.cpp --- SystemForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o SystemForce.o `test -f 'SystemForce.cpp' || echo './'`SystemForce.cpp --- SystemTimeForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o SystemTimeForce.o `test -f 'SystemTimeForce.cpp' || echo './'`SystemTimeForce.cpp --- TimeForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o TimeForce.o `test -f 'TimeForce.cpp' || echo './'`TimeForce.cpp --- WrapperMetaForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o WrapperMetaForce.o `test -f 'WrapperMetaForce.cpp' || echo './'`WrapperMetaForce.cpp --- libforces.a --- rm -f libforces.a ar cru libforces.a AngleSystemForceBase.o BondSystemForceBase.o CompareForce.o CoulombEwaldRealForce.o CoulombEwaldRealTableForce.o CoulombForce.o CoulombMultiGridDirectForceBase.o CoulombMultiGridDirectTableForceBase.o DihedralSystemForceBase.o HarmDihedralSystemForceBase.o ElectricFieldSystemForceBase.o ExternalGravitationSystemForce.o ExternalMagneticFieldExtendedForce.o ExtendedCompareForce.o ExtendedForce.o ExtendedTimeForce.o Force.o ForceGroup.o FrictionExtendedForce.o GravitationForce.o Hermite.o ImproperSystemForceBase.o LennardJonesForce.o LennardJonesTableForce.o MagneticDipoleForce.o MagneticDipoleMirrorSystemForceBase.o MetaForce.o MollyForce.o NonbondedCutoffForceBase.o NonbondedFullEwaldSystemForceBase.o NonbondedFullSystemForceBase.o NonbondedMultiGridSystemForceBase.o NonbondedPMEwaldSystemForceBase.o NonbondedSimpleFullSystemForceBase.o PaulTrapExtendedForceBase.o ReducedHessCoulomb.o ReducedHessLennardJones.o SphericalSystemForce.o SystemCompareForce.o SystemForce.o SystemTimeForce.o TimeForce.o WrapperMetaForce.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libforces.a Making all in imd --- IMDElf.o --- --- imd.o --- --- vmdsock.o --- --- HapticSystemForce.o --- --- IMDElf.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o IMDElf.o `test -f 'IMDElf.cpp' || echo './'`IMDElf.cpp --- imd.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o imd.o `test -f 'imd.cpp' || echo './'`imd.cpp --- vmdsock.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o vmdsock.o `test -f 'vmdsock.cpp' || echo './'`vmdsock.cpp --- HapticSystemForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o HapticSystemForce.o `test -f 'HapticSystemForce.cpp' || echo './'`HapticSystemForce.cpp --- libimd.a --- rm -f libimd.a ar cru libimd.a IMDElf.o imd.o vmdsock.o HapticSystemForce.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libimd.a Making all in integrators --- ModifierMetaShake.o --- --- ModifierMetaRattle.o --- --- ModifierMetaRattleShake.o --- --- NPTVerletIntegrator.o --- --- NVTVerletIntegrator.o --- --- BSplineMOLLYIntegrator.o --- --- EquilibriumMOLLYIntegrator.o --- --- DihedralHMCIntegrator.o --- --- DLMCIntegrator.o --- --- ShadowHMCIntegrator.o --- --- HMCIntegrator.o --- --- MCIntegrator.o --- --- ModifierMetaShake.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierMetaShake.o `test -f 'ModifierMetaShake.cpp' || echo './'`ModifierMetaShake.cpp --- ModifierMetaRattle.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierMetaRattle.o `test -f 'ModifierMetaRattle.cpp' || echo './'`ModifierMetaRattle.cpp --- ModifierMetaRattleShake.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierMetaRattleShake.o `test -f 'ModifierMetaRattleShake.cpp' || echo './'`ModifierMetaRattleShake.cpp --- NPTVerletIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NPTVerletIntegrator.o `test -f 'NPTVerletIntegrator.cpp' || echo './'`NPTVerletIntegrator.cpp --- NVTVerletIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NVTVerletIntegrator.o `test -f 'NVTVerletIntegrator.cpp' || echo './'`NVTVerletIntegrator.cpp --- BSplineMOLLYIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o BSplineMOLLYIntegrator.o `test -f 'BSplineMOLLYIntegrator.cpp' || echo './'`BSplineMOLLYIntegrator.cpp --- EquilibriumMOLLYIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o EquilibriumMOLLYIntegrator.o `test -f 'EquilibriumMOLLYIntegrator.cpp' || echo './'`EquilibriumMOLLYIntegrator.cpp --- DihedralHMCIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o DihedralHMCIntegrator.o `test -f 'DihedralHMCIntegrator.cpp' || echo './'`DihedralHMCIntegrator.cpp --- DLMCIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o DLMCIntegrator.o `test -f 'DLMCIntegrator.cpp' || echo './'`DLMCIntegrator.cpp --- ShadowHMCIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ShadowHMCIntegrator.o `test -f 'ShadowHMCIntegrator.cpp' || echo './'`ShadowHMCIntegrator.cpp --- MCIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MCIntegrator.o `test -f 'MCIntegrator.cpp' || echo './'`MCIntegrator.cpp --- HMCIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o HMCIntegrator.o `test -f 'HMCIntegrator.cpp' || echo './'`HMCIntegrator.cpp --- ImpulseIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ImpulseIntegrator.o `test -f 'ImpulseIntegrator.cpp' || echo './'`ImpulseIntegrator.cpp --- Integrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Integrator.o `test -f 'Integrator.cpp' || echo './'`Integrator.cpp --- IntegratorDefinition.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o IntegratorDefinition.o `test -f 'IntegratorDefinition.cpp' || echo './'`IntegratorDefinition.cpp --- LeapfrogIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o LeapfrogIntegrator.o `test -f 'LeapfrogIntegrator.cpp' || echo './'`LeapfrogIntegrator.cpp --- DMDLeapfrogIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o DMDLeapfrogIntegrator.o `test -f 'DMDLeapfrogIntegrator.cpp' || echo './'`DMDLeapfrogIntegrator.cpp --- BBKIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o BBKIntegrator.o `test -f 'BBKIntegrator.cpp' || echo './'`BBKIntegrator.cpp --- ModifierShake.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierShake.o `test -f 'ModifierShake.cpp' || echo './'`ModifierShake.cpp --- ModifierRattle.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierRattle.o `test -f 'ModifierRattle.cpp' || echo './'`ModifierRattle.cpp --- ModifierNPTShake.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierNPTShake.o `test -f 'ModifierNPTShake.cpp' || echo './'`ModifierNPTShake.cpp --- ModifierNPTRattle.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierNPTRattle.o `test -f 'ModifierNPTRattle.cpp' || echo './'`ModifierNPTRattle.cpp --- ModifierNVTShake.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierNVTShake.o `test -f 'ModifierNVTShake.cpp' || echo './'`ModifierNVTShake.cpp --- ModifierNVTRattle.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierNVTRattle.o `test -f 'ModifierNVTRattle.cpp' || echo './'`ModifierNVTRattle.cpp --- PLeapfrogIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PLeapfrogIntegrator.o `test -f 'PLeapfrogIntegrator.cpp' || echo './'`PLeapfrogIntegrator.cpp --- MOLLYIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MOLLYIntegrator.o `test -f 'MOLLYIntegrator.cpp' || echo './'`MOLLYIntegrator.cpp --- UmbrellaIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o UmbrellaIntegrator.o `test -f 'UmbrellaIntegrator.cpp' || echo './'`UmbrellaIntegrator.cpp --- MTSIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o MTSIntegrator.o `test -f 'MTSIntegrator.cpp' || echo './'`MTSIntegrator.cpp --- NoseNVTLeapfrogIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o NoseNVTLeapfrogIntegrator.o `test -f 'NoseNVTLeapfrogIntegrator.cpp' || echo './'`NoseNVTLeapfrogIntegrator.cpp --- PaulTrapIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o PaulTrapIntegrator.o `test -f 'PaulTrapIntegrator.cpp' || echo './'`PaulTrapIntegrator.cpp --- LangevinImpulseIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o LangevinImpulseIntegrator.o `test -f 'LangevinImpulseIntegrator.cpp' || echo './'`LangevinImpulseIntegrator.cpp --- StandardIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o StandardIntegrator.o `test -f 'StandardIntegrator.cpp' || echo './'`StandardIntegrator.cpp --- STSIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o STSIntegrator.o `test -f 'STSIntegrator.cpp' || echo './'`STSIntegrator.cpp --- libintegrators.a --- rm -f libintegrators.a ar cru libintegrators.a ModifierMetaShake.o ModifierMetaRattle.o ModifierMetaRattleShake.o NPTVerletIntegrator.o NVTVerletIntegrator.o BSplineMOLLYIntegrator.o EquilibriumMOLLYIntegrator.o DihedralHMCIntegrator.o DLMCIntegrator.o ShadowHMCIntegrator.o HMCIntegrator.o MCIntegrator.o ImpulseIntegrator.o Integrator.o IntegratorDefinition.o LeapfrogIntegrator.o DMDLeapfrogIntegrator.o BBKIntegrator.o ModifierShake.o ModifierRattle.o ModifierNPTShake.o ModifierNPTRattle.o ModifierNVTShake.o ModifierNVTRattle.o PLeapfrogIntegrator.o MOLLYIntegrator.o UmbrellaIntegrator.o MTSIntegrator.o NoseNVTLeapfrogIntegrator.o PaulTrapIntegrator.o LangevinImpulseIntegrator.o StandardIntegrator.o STSIntegrator.o NPTVerletIntegrator.o NVTVerletIntegrator.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libintegrators.a Making all in frontend --- HelpTextFactory.o --- --- ForceFactoryDetails.o --- --- InputPosVel.o --- --- InputPosVelType.o --- --- IntegratorFactoryDetails.o --- --- Output.o --- --- OutputCache.o --- --- OutputCollection.o --- --- OutputDCDTrajectory.o --- --- OutputDiffusion.o --- --- OutputDihedrals.o --- --- OutputEnergies.o --- --- HelpTextFactory.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o HelpTextFactory.o `test -f 'HelpTextFactory.cpp' || echo './'`HelpTextFactory.cpp --- ForceFactoryDetails.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ForceFactoryDetails.o `test -f 'ForceFactoryDetails.cpp' || echo './'`ForceFactoryDetails.cpp --- InputPosVel.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o InputPosVel.o `test -f 'InputPosVel.cpp' || echo './'`InputPosVel.cpp --- InputPosVelType.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o InputPosVelType.o `test -f 'InputPosVelType.cpp' || echo './'`InputPosVelType.cpp --- Output.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o Output.o `test -f 'Output.cpp' || echo './'`Output.cpp --- OutputCache.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputCache.o `test -f 'OutputCache.cpp' || echo './'`OutputCache.cpp --- OutputCollection.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputCollection.o `test -f 'OutputCollection.cpp' || echo './'`OutputCollection.cpp --- OutputDCDTrajectory.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputDCDTrajectory.o `test -f 'OutputDCDTrajectory.cpp' || echo './'`OutputDCDTrajectory.cpp --- OutputDiffusion.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputDiffusion.o `test -f 'OutputDiffusion.cpp' || echo './'`OutputDiffusion.cpp --- OutputEnergies.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputEnergies.o `test -f 'OutputEnergies.cpp' || echo './'`OutputEnergies.cpp --- OutputDihedrals.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputDihedrals.o `test -f 'OutputDihedrals.cpp' || echo './'`OutputDihedrals.cpp --- IntegratorFactoryDetails.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o IntegratorFactoryDetails.o `test -f 'IntegratorFactoryDetails.cpp' || echo './'`IntegratorFactoryDetails.cpp --- OutputFactoryDetails.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFactoryDetails.o `test -f 'OutputFactoryDetails.cpp' || echo './'`OutputFactoryDetails.cpp --- OutputFile.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFile.o `test -f 'OutputFile.cpp' || echo './'`OutputFile.cpp --- OutputFinalXYZBinPos.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalXYZBinPos.o `test -f 'OutputFinalXYZBinPos.cpp' || echo './'`OutputFinalXYZBinPos.cpp --- OutputFinalXYZBinVel.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalXYZBinVel.o `test -f 'OutputFinalXYZBinVel.cpp' || echo './'`OutputFinalXYZBinVel.cpp --- OutputFinalXYZPos.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalXYZPos.o `test -f 'OutputFinalXYZPos.cpp' || echo './'`OutputFinalXYZPos.cpp --- OutputFinalPDBPos.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalPDBPos.o `test -f 'OutputFinalPDBPos.cpp' || echo './'`OutputFinalPDBPos.cpp --- OutputFinalXYZVel.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalXYZVel.o `test -f 'OutputFinalXYZVel.cpp' || echo './'`OutputFinalXYZVel.cpp --- OutputMomentum.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputMomentum.o `test -f 'OutputMomentum.cpp' || echo './'`OutputMomentum.cpp --- OutputPaulTrap.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputPaulTrap.o `test -f 'OutputPaulTrap.cpp' || echo './'`OutputPaulTrap.cpp --- OutputPDBFramePos.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputPDBFramePos.o `test -f 'OutputPDBFramePos.cpp' || echo './'`OutputPDBFramePos.cpp --- OutputScreen.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputScreen.o `test -f 'OutputScreen.cpp' || echo './'`OutputScreen.cpp --- OutputTemperatures.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputTemperatures.o `test -f 'OutputTemperatures.cpp' || echo './'`OutputTemperatures.cpp --- OutputXYZTrajectoryForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputXYZTrajectoryForce.o `test -f 'OutputXYZTrajectoryForce.cpp' || echo './'`OutputXYZTrajectoryForce.cpp --- OutputXYZTrajectoryPos.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputXYZTrajectoryPos.o `test -f 'OutputXYZTrajectoryPos.cpp' || echo './'`OutputXYZTrajectoryPos.cpp --- OutputXYZTrajectoryVel.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputXYZTrajectoryVel.o `test -f 'OutputXYZTrajectoryVel.cpp' || echo './'`OutputXYZTrajectoryVel.cpp --- TopologyFactoryDetails.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o TopologyFactoryDetails.o `test -f 'TopologyFactoryDetails.cpp' || echo './'`TopologyFactoryDetails.cpp --- buildTopology.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o buildTopology.o `test -f 'buildTopology.cpp' || echo './'`buildTopology.cpp --- inputValueDefinitions.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o inputValueDefinitions.o `test -f 'inputValueDefinitions.cpp' || echo './'`inputValueDefinitions.cpp --- parseCommandLine.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o parseCommandLine.o `test -f 'parseCommandLine.cpp' || echo './'`parseCommandLine.cpp --- libfrontend.a --- rm -f libfrontend.a ar cru libfrontend.a HelpTextFactory.o ForceFactoryDetails.o InputPosVel.o InputPosVelType.o IntegratorFactoryDetails.o Output.o OutputCache.o OutputCollection.o OutputDCDTrajectory.o OutputDiffusion.o OutputDihedrals.o OutputEnergies.o OutputFactoryDetails.o OutputFile.o OutputFinalXYZBinPos.o OutputFinalXYZBinVel.o OutputFinalXYZPos.o OutputFinalPDBPos.o OutputFinalXYZVel.o OutputMomentum.o OutputPaulTrap.o OutputPDBFramePos.o OutputScreen.o OutputTemperatures.o OutputXYZTrajectoryForce.o OutputXYZTrajectoryPos.o OutputXYZTrajectoryVel.o TopologyFactoryDetails.o buildTopology.o inputValueDefinitions.o parseCommandLine.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfrontend.a Making all in factories --- registerForceExemplars.o --- --- registerForceExemplarsBonded.o --- --- registerForceExemplarsCutoff.o --- --- registerForceExemplarsFastElectrostatic.o --- --- registerForceExemplarsFull.o --- --- registerForceExemplarsOther.o --- --- registerForceExemplarsSimpleFull.o --- --- registerIntegratorExemplars.o --- --- registerOutputExemplars.o --- --- registerTopologyExemplars.o --- --- registerForceExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplars.o `test -f 'registerForceExemplars.cpp' || echo './'`registerForceExemplars.cpp --- registerForceExemplarsBonded.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplarsBonded.o `test -f 'registerForceExemplarsBonded.cpp' || echo './'`registerForceExemplarsBonded.cpp --- registerForceExemplarsCutoff.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplarsCutoff.o `test -f 'registerForceExemplarsCutoff.cpp' || echo './'`registerForceExemplarsCutoff.cpp --- registerForceExemplarsFastElectrostatic.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplarsFastElectrostatic.o `test -f 'registerForceExemplarsFastElectrostatic.cpp' || echo './'`registerForceExemplarsFastElectrostatic.cpp --- registerForceExemplarsFull.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplarsFull.o `test -f 'registerForceExemplarsFull.cpp' || echo './'`registerForceExemplarsFull.cpp --- registerForceExemplarsOther.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplarsOther.o `test -f 'registerForceExemplarsOther.cpp' || echo './'`registerForceExemplarsOther.cpp --- registerForceExemplarsSimpleFull.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplarsSimpleFull.o `test -f 'registerForceExemplarsSimpleFull.cpp' || echo './'`registerForceExemplarsSimpleFull.cpp --- registerIntegratorExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerIntegratorExemplars.o `test -f 'registerIntegratorExemplars.cpp' || echo './'`registerIntegratorExemplars.cpp --- registerOutputExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerOutputExemplars.o `test -f 'registerOutputExemplars.cpp' || echo './'`registerOutputExemplars.cpp --- registerTopologyExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerTopologyExemplars.o `test -f 'registerTopologyExemplars.cpp' || echo './'`registerTopologyExemplars.cpp --- libfactories.a --- rm -f libfactories.a ar cru libfactories.a registerForceExemplars.o registerForceExemplarsBonded.o registerForceExemplarsCutoff.o registerForceExemplarsFastElectrostatic.o registerForceExemplarsFull.o registerForceExemplarsOther.o registerForceExemplarsSimpleFull.o registerIntegratorExemplars.o registerOutputExemplars.o registerTopologyExemplars.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfactories.a Making all in applications --- all-recursive --- Making all in protomol-app --- protomol.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o protomol.o `test -f 'protomol.cpp' || echo './'`protomol.cpp --- protomol --- c++ -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -o protomol protomol.o -L../../framework/base -L../../framework/io -L../../framework/parallel -L../../framework/topology -L../../framework/forces -L../../framework/imd -L../../framework/integrators -L../../framework/frontend -L../../framework/factories -lfactories -lfrontend -lintegrators -limd -lforces -ltopology -lparallel -lio -lbase -lpng Making all in coulomb-app --- ./Makefile.in --- --- coulomb.o --- --- registerForceExemplars.o --- --- registerIntegratorExemplars.o --- --- registerOutputExemplars.o --- --- registerTopologyExemplars.o --- --- ./Makefile.in --- cd ../.. && /bin/sh /construction/biology/protomol/protomol/missing --run automake-1.6 --foreign applications/coulomb-app/Makefile /construction/biology/protomol/protomol/missing: automake-1.6: not found WARNING: `automake-1.6' is missing on your system. You should only need it if you modified `Makefile.am', `acinclude.m4' or `configure.in'. You might want to install the `Automake' and `Perl' packages. Grab them from any GNU archive site. --- coulomb.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o coulomb.o `test -f 'coulomb.cpp' || echo './'`coulomb.cpp --- registerForceExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerForceExemplars.o `test -f 'registerForceExemplars.cpp' || echo './'`registerForceExemplars.cpp --- registerIntegratorExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerIntegratorExemplars.o `test -f 'registerIntegratorExemplars.cpp' || echo './'`registerIntegratorExemplars.cpp --- Makefile --- --- registerOutputExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerOutputExemplars.o `test -f 'registerOutputExemplars.cpp' || echo './'`registerOutputExemplars.cpp --- registerTopologyExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/integrators -I../../framework/frontend -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o registerTopologyExemplars.o `test -f 'registerTopologyExemplars.cpp' || echo './'`registerTopologyExemplars.cpp --- Makefile --- cd ../.. && /bin/sh ./config.status applications/coulomb-app/Makefile config.status: creating applications/coulomb-app/Makefile --- coulomb --- c++ -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -o coulomb coulomb.o registerForceExemplars.o registerIntegratorExemplars.o registerOutputExemplars.o registerTopologyExemplars.o -L../../framework/base -L../../framework/io -L../../framework/parallel -L../../framework/topology -L../../framework/forces -L../../framework/integrators -L../../framework/frontend -lfrontend -lintegrators -lforces -ltopology -lparallel -lio -lbase Making all in dcd2dcd-app --- dcd2dcd.o --- --- Makefile --- --- dcd2dcd.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o dcd2dcd.o `test -f 'dcd2dcd.cpp' || echo './'`dcd2dcd.cpp --- Makefile --- cd ../.. && /bin/sh ./config.status applications/dcd2dcd-app/Makefile config.status: creating applications/dcd2dcd-app/Makefile --- dcd2dcd --- c++ -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -o dcd2dcd dcd2dcd.o -L../../framework/base -L../../framework/io -lio -lbase Making all in coords2coords-app --- coords2coords.o --- --- Makefile --- cd ../.. && /bin/sh ./config.status applications/coords2coords-app/Makefile --- coords2coords.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o coords2coords.o `test -f 'coords2coords.cpp' || echo './'`coords2coords.cpp --- Makefile --- config.status: creating applications/coords2coords-app/Makefile --- coords2coords --- c++ -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -o coords2coords coords2coords.o -L../../framework/base -L../../framework/io -lio -lbase Making all in xyzviz-app --- openglutilities.o --- --- xyzviz.o --- --- Makefile --- --- openglutilities.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -DHAVE_GLUT -I/usr/local/include -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o openglutilities.o `test -f 'openglutilities.cpp' || echo './'`openglutilities.cpp --- xyzviz.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -DHAVE_GLUT -I/usr/local/include -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o xyzviz.o `test -f 'xyzviz.cpp' || echo './'`xyzviz.cpp --- Makefile --- cd ../.. && /bin/sh ./config.status applications/xyzviz-app/Makefile config.status: creating applications/xyzviz-app/Makefile --- xyzviz --- c++ -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -o xyzviz openglutilities.o xyzviz.o -L../../framework/base -L../../framework/io -lz -L/usr/local/lib -lglut -lGLU -lGL -lXmu -lXt -lSM -lICE -lXext -lX11 -lXi -lXext -lX11 -lpthread -ldl -ljpeg -ltiff -lio -lbase Making all in iSGProtomol-app --- all-recursive --- Making all in base --- XSC.o --- --- TRANS.o --- --- Makefile --- --- XSC.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/topology -I../../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XSC.o `test -f 'XSC.cpp' || echo './'`XSC.cpp --- TRANS.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/topology -I../../../framework/base -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o TRANS.o `test -f 'TRANS.cpp' || echo './'`TRANS.cpp --- Makefile --- cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/base/Makefile config.status: creating applications/iSGProtomol-app/base/Makefile --- libISGbase.a --- rm -f libISGbase.a ar cru libISGbase.a XSC.o TRANS.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libISGbase.a Making all in io --- iSGPARReader.o --- --- TRANSReader.o --- --- XSCReader.o --- --- XSCWriter.o --- --- Makefile --- --- iSGPARReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGPARReader.o `test -f 'iSGPARReader.cpp' || echo './'`iSGPARReader.cpp --- TRANSReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o TRANSReader.o `test -f 'TRANSReader.cpp' || echo './'`TRANSReader.cpp --- XSCReader.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XSCReader.o `test -f 'XSCReader.cpp' || echo './'`XSCReader.cpp --- XSCWriter.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o XSCWriter.o `test -f 'XSCWriter.cpp' || echo './'`XSCWriter.cpp --- Makefile --- cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/io/Makefile config.status: creating applications/iSGProtomol-app/io/Makefile --- libISGio.a --- rm -f libISGio.a ar cru libISGio.a iSGPARReader.o TRANSReader.o XSCReader.o XSCWriter.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libISGio.a Making all in forces --- iSGAngleSystemForceBase.o --- --- iSGBondSystemForceBase.o --- --- iSGDihedralSystemForceBase.o --- --- iSGImproperSystemForceBase.o --- --- iSGLennardJonesForce.o --- --- iSGCoulombForce.o --- --- iSGNonbondedFullEwaldSystemForceBase.o --- --- iSGNonbondedPMEwaldSystemForceBase.o --- --- iSGIdealGasCoulombForce.o --- --- iSGIdealGasLennardJonesForce.o --- --- iSGLennardJonesTableForce.o --- --- iSGCoulombEwaldRealForce.o --- --- iSGAngleSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGAngleSystemForceBase.o `test -f 'iSGAngleSystemForceBase.cpp' || echo './'`iSGAngleSystemForceBase.cpp --- iSGBondSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGBondSystemForceBase.o `test -f 'iSGBondSystemForceBase.cpp' || echo './'`iSGBondSystemForceBase.cpp --- iSGDihedralSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGDihedralSystemForceBase.o `test -f 'iSGDihedralSystemForceBase.cpp' || echo './'`iSGDihedralSystemForceBase.cpp --- iSGImproperSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGImproperSystemForceBase.o `test -f 'iSGImproperSystemForceBase.cpp' || echo './'`iSGImproperSystemForceBase.cpp --- iSGLennardJonesForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGLennardJonesForce.o `test -f 'iSGLennardJonesForce.cpp' || echo './'`iSGLennardJonesForce.cpp --- iSGCoulombForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGCoulombForce.o `test -f 'iSGCoulombForce.cpp' || echo './'`iSGCoulombForce.cpp --- iSGNonbondedFullEwaldSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGNonbondedFullEwaldSystemForceBase.o `test -f 'iSGNonbondedFullEwaldSystemForceBase.cpp' || echo './'`iSGNonbondedFullEwaldSystemForceBase.cpp --- iSGNonbondedPMEwaldSystemForceBase.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGNonbondedPMEwaldSystemForceBase.o `test -f 'iSGNonbondedPMEwaldSystemForceBase.cpp' || echo './'`iSGNonbondedPMEwaldSystemForceBase.cpp --- iSGIdealGasCoulombForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGIdealGasCoulombForce.o `test -f 'iSGIdealGasCoulombForce.cpp' || echo './'`iSGIdealGasCoulombForce.cpp --- iSGIdealGasLennardJonesForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGIdealGasLennardJonesForce.o `test -f 'iSGIdealGasLennardJonesForce.cpp' || echo './'`iSGIdealGasLennardJonesForce.cpp --- iSGLennardJonesTableForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGLennardJonesTableForce.o `test -f 'iSGLennardJonesTableForce.cpp' || echo './'`iSGLennardJonesTableForce.cpp --- iSGCoulombEwaldRealForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGCoulombEwaldRealForce.o `test -f 'iSGCoulombEwaldRealForce.cpp' || echo './'`iSGCoulombEwaldRealForce.cpp --- iSGCoulombEwaldRealTableForce.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/forces -I../../../framework/base -I../../../framework/topology -I../../../framework/forces -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../framework/parallel -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGCoulombEwaldRealTableForce.o `test -f 'iSGCoulombEwaldRealTableForce.cpp' || echo './'`iSGCoulombEwaldRealTableForce.cpp --- Makefile --- cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/forces/Makefile config.status: creating applications/iSGProtomol-app/forces/Makefile --- libISGforces.a --- rm -f libISGforces.a ar cru libISGforces.a iSGAngleSystemForceBase.o iSGBondSystemForceBase.o iSGDihedralSystemForceBase.o iSGImproperSystemForceBase.o iSGLennardJonesForce.o iSGCoulombForce.o iSGNonbondedFullEwaldSystemForceBase.o iSGNonbondedPMEwaldSystemForceBase.o iSGIdealGasCoulombForce.o iSGIdealGasLennardJonesForce.o iSGLennardJonesTableForce.o iSGCoulombEwaldRealForce.o iSGCoulombEwaldRealTableForce.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libISGforces.a Making all in frontend --- OutputFinalXSC.o --- --- OutputISGProperties.o --- --- OutputFinalPSF.o --- --- buildISGTopology.o --- --- Makefile --- --- OutputFinalXSC.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/integrators -I../../../framework/base -I../../../framework/io -I../../../framework/frontend -I../../../framework/topology -I../../../framework/integrators -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalXSC.o `test -f 'OutputFinalXSC.cpp' || echo './'`OutputFinalXSC.cpp --- OutputISGProperties.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/integrators -I../../../framework/base -I../../../framework/io -I../../../framework/frontend -I../../../framework/topology -I../../../framework/integrators -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputISGProperties.o `test -f 'OutputISGProperties.cpp' || echo './'`OutputISGProperties.cpp --- OutputFinalPSF.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/integrators -I../../../framework/base -I../../../framework/io -I../../../framework/frontend -I../../../framework/topology -I../../../framework/integrators -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o OutputFinalPSF.o `test -f 'OutputFinalPSF.cpp' || echo './'`OutputFinalPSF.cpp --- buildISGTopology.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/base -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/integrators -I../../../framework/base -I../../../framework/io -I../../../framework/frontend -I../../../framework/topology -I../../../framework/integrators -I../../../framework/forces -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o buildISGTopology.o `test -f 'buildISGTopology.cpp' || echo './'`buildISGTopology.cpp --- Makefile --- cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/frontend/Makefile config.status: creating applications/iSGProtomol-app/frontend/Makefile --- libISGfrontend.a --- rm -f libISGfrontend.a ar cru libISGfrontend.a OutputFinalXSC.o OutputISGProperties.o OutputFinalPSF.o buildISGTopology.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libISGfrontend.a Making all in factories --- iSGregisterOutputExemplars.o --- --- iSGregisterIntegratorExemplars.o --- --- iSGregisterForceExemplars.o --- --- iSGregisterForceExemplarsBonded.o --- --- iSGregisterForceExemplarsCutoff.o --- --- iSGregisterForceExemplarsFull.o --- --- iSGregisterForceExemplarsSimpleFull.o --- --- iSGregisterForceExemplarsFastElectrostatic.o --- --- iSGregisterForceExemplarsIdealGas.o --- --- Makefile --- --- iSGregisterOutputExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterOutputExemplars.o `test -f 'iSGregisterOutputExemplars.cpp' || echo './'`iSGregisterOutputExemplars.cpp --- iSGregisterIntegratorExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterIntegratorExemplars.o `test -f 'iSGregisterIntegratorExemplars.cpp' || echo './'`iSGregisterIntegratorExemplars.cpp --- iSGregisterForceExemplars.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplars.o `test -f 'iSGregisterForceExemplars.cpp' || echo './'`iSGregisterForceExemplars.cpp --- iSGregisterForceExemplarsBonded.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplarsBonded.o `test -f 'iSGregisterForceExemplarsBonded.cpp' || echo './'`iSGregisterForceExemplarsBonded.cpp --- iSGregisterForceExemplarsCutoff.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplarsCutoff.o `test -f 'iSGregisterForceExemplarsCutoff.cpp' || echo './'`iSGregisterForceExemplarsCutoff.cpp --- iSGregisterForceExemplarsFull.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplarsFull.o `test -f 'iSGregisterForceExemplarsFull.cpp' || echo './'`iSGregisterForceExemplarsFull.cpp --- iSGregisterForceExemplarsSimpleFull.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplarsSimpleFull.o `test -f 'iSGregisterForceExemplarsSimpleFull.cpp' || echo './'`iSGregisterForceExemplarsSimpleFull.cpp --- iSGregisterForceExemplarsFastElectrostatic.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplarsFastElectrostatic.o `test -f 'iSGregisterForceExemplarsFastElectrostatic.cpp' || echo './'`iSGregisterForceExemplarsFastElectrostatic.cpp --- iSGregisterForceExemplarsIdealGas.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/io -I../../../applications/iSGProtomol-app/base -I../../../framework/io -I../../../framework/base -I../../../applications/iSGProtomol-app/topology -I../../../applications/iSGProtomol-app/forces -I../../../framework/topology -I../../../applications/iSGProtomol-app/frontend -I../../../framework/frontend -I../../../framework/integrators -I../../../applications/iSGProtomol-app -I../../../applications/iSGProtomol-app/integrators -I../../../applications/iSGProtomol-app/factories -I../../../framework/parallel -I../../../framework/forces -I../../../framework/factories -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGregisterForceExemplarsIdealGas.o `test -f 'iSGregisterForceExemplarsIdealGas.cpp' || echo './'`iSGregisterForceExemplarsIdealGas.cpp --- Makefile --- cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/factories/Makefile config.status: creating applications/iSGProtomol-app/factories/Makefile --- libISGfactories.a --- rm -f libISGfactories.a ar cru libISGfactories.a iSGregisterOutputExemplars.o iSGregisterIntegratorExemplars.o iSGregisterForceExemplars.o iSGregisterForceExemplarsBonded.o iSGregisterForceExemplarsCutoff.o iSGregisterForceExemplarsFull.o iSGregisterForceExemplarsSimpleFull.o iSGregisterForceExemplarsFastElectrostatic.o iSGregisterForceExemplarsIdealGas.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libISGfactories.a Making all in integrators --- iSGIntegrator.o --- --- ModifierISG.o --- --- Makefile --- --- iSGIntegrator.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../framework/base -I../../../framework/frontend -I../../../applications/iSGProtomol-app/base -I../../../framework/topology -I../../../framework/frontend -I../../../framework/integrators -I../../../framework/forces -I../../../framework/parallel -I../../../applications/iSGProtomol-app/io -I../../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGIntegrator.o `test -f 'iSGIntegrator.cpp' || echo './'`iSGIntegrator.cpp --- ModifierISG.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../../.. -I../../../applications/iSGProtomol-app/frontend -I../../../framework/base -I../../../framework/frontend -I../../../applications/iSGProtomol-app/base -I../../../framework/topology -I../../../framework/frontend -I../../../framework/integrators -I../../../framework/forces -I../../../framework/parallel -I../../../applications/iSGProtomol-app/io -I../../../framework/io -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o ModifierISG.o `test -f 'ModifierISG.cpp' || echo './'`ModifierISG.cpp --- Makefile --- cd ../../.. && /bin/sh ./config.status applications/iSGProtomol-app/integrators/Makefile config.status: creating applications/iSGProtomol-app/integrators/Makefile --- libISGintegrators.a --- rm -f libISGintegrators.a ar cru libISGintegrators.a iSGIntegrator.o ModifierISG.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libISGintegrators.a --- iSGProtomol.o --- --- Makefile --- --- iSGProtomol.o --- c++ -DHAVE_CONFIG_H -I. -I. -I../.. -I../../framework/base -I../../framework/io -I../../framework/parallel -I../../framework/topology -I../../framework/forces -I../../framework/imd -I../../framework/integrators -I../../framework/frontend -I../../framework/factories -I../../applications/iSGProtomol-app/base -I../../applications/iSGProtomol-app/io -I../../applications/iSGProtomol-app/forces -I../../applications/iSGProtomol-app/frontend -I../../applications/iSGProtomol-app/factories -I../../applications/iSGProtomol-app/integrators -I/usr/local/include -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -c -o iSGProtomol.o `test -f 'iSGProtomol.cpp' || echo './'`iSGProtomol.cpp --- Makefile --- cd ../.. && /bin/sh ./config.status applications/iSGProtomol-app/Makefile config.status: creating applications/iSGProtomol-app/Makefile --- iSGProtomol --- c++ -pipe -O2 -fno-strict-aliasing -L/usr/local/lib -std=c++98 -o iSGProtomol iSGProtomol.o -L../../framework/base -L../../framework/io -L../../framework/parallel -L../../framework/topology -L../../framework/forces -L../../framework/imd -L../../framework/integrators -L../../framework/frontend -L../../applications/iSGProtomol-app/base -L../../applications/iSGProtomol-app/io -L../../applications/iSGProtomol-app/forces -L../../applications/iSGProtomol-app/frontend -L../../applications/iSGProtomol-app/factories -L../../applications/iSGProtomol-app/integrators -lISGintegrators -lISGfactories -lISGfrontend -lISGforces -lISGio -lISGbase ../../framework/factories/registerTopologyExemplars.o -lfrontend -lintegrators -limd -lforces -ltopology -lparallel -lio -lbase -lpng --- Makefile --- cd .. && /bin/sh ./config.status applications/Makefile config.status: creating applications/Makefile --- Makefile --- cd . && /bin/sh ./config.status Makefile config.status: creating Makefile -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/xmu.pc - found ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/xt.pc - found ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> protomol-2.0.3_13 depends on file: /usr/local/libdata/pkgconfig/xi.pc - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for protomol-2.0.3_13 ===> Generating temporary packing list Making install in framework Making install in base cd ../.. && /bin/sh ./config.status framework/base/Makefile config.status: creating framework/base/Makefile Making install in io cd ../.. && /bin/sh ./config.status framework/io/Makefile config.status: creating framework/io/Makefile Making install in parallel cd ../.. && /bin/sh ./config.status framework/parallel/Makefile config.status: creating framework/parallel/Makefile Making install in topology cd ../.. && /bin/sh ./config.status framework/topology/Makefile config.status: creating framework/topology/Makefile Making install in forces cd ../.. && /bin/sh ./config.status framework/forces/Makefile config.status: creating framework/forces/Makefile Making install in imd cd ../.. && /bin/sh ./config.status framework/imd/Makefile config.status: creating framework/imd/Makefile Making install in integrators cd ../.. && /bin/sh ./config.status framework/integrators/Makefile config.status: creating framework/integrators/Makefile Making install in frontend cd ../.. && /bin/sh ./config.status framework/frontend/Makefile config.status: creating framework/frontend/Makefile Making install in factories cd ../.. && /bin/sh ./config.status framework/factories/Makefile config.status: creating framework/factories/Makefile cd .. && /bin/sh ./config.status framework/Makefile config.status: creating framework/Makefile Making install in applications Making install in protomol-app cd ../.. && /bin/sh ./config.status applications/protomol-app/Makefile config.status: creating applications/protomol-app/Makefile /bin/sh ../../mkinstalldirs /construction/biology/protomol/stage/usr/local/bin install -s -m 555 protomol /construction/biology/protomol/stage/usr/local/bin/protomol Making install in coulomb-app /bin/sh ../../mkinstalldirs /construction/biology/protomol/stage/usr/local/bin install -s -m 555 coulomb /construction/biology/protomol/stage/usr/local/bin/coulomb Making install in dcd2dcd-app /bin/sh ../../mkinstalldirs /construction/biology/protomol/stage/usr/local/bin install -s -m 555 dcd2dcd /construction/biology/protomol/stage/usr/local/bin/dcd2dcd Making install in coords2coords-app /bin/sh ../../mkinstalldirs /construction/biology/protomol/stage/usr/local/bin install -s -m 555 coords2coords /construction/biology/protomol/stage/usr/local/bin/coords2coords Making install in xyzviz-app /bin/sh ../../mkinstalldirs /construction/biology/protomol/stage/usr/local/bin install -s -m 555 xyzviz /construction/biology/protomol/stage/usr/local/bin/xyzviz Making install in iSGProtomol-app Making install in base Making install in io Making install in forces Making install in frontend Making install in factories Making install in integrators /bin/sh ../../mkinstalldirs /construction/biology/protomol/stage/usr/local/bin install -s -m 555 iSGProtomol /construction/biology/protomol/stage/usr/local/bin/iSGProtomol cd /construction/biology/protomol/protomol/examples ; /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /construction/biology/protomol/stage/usr/local/share/examples/protomol "! -name .cvsignore" ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for protomol-2.0.3_13 file sizes/checksums [117]: .. done packing files [117]: .. done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:06:14 UTC Duration: 00:05:03