=> Building science/pnetcdf Started : Thursday, 19 APR 2018 at 05:44:45 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.81.g32506c-DEVELOPMENT #29: Tue Apr 10 08:49:52 PDT 2018 marino@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.0-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.0-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 pnetcdf-1.8.1_3: DOCS=on: Build and/or install documentation ====> MPI (Message Passing Interface) support: you have to select exactly one of them OPENMPI=on: Parallel processing support via Open MPI 1.x OPENMPI2=off: Parallel processing support via Open MPI 2.x MPICH2=off: Parallel processing support via MPICH2 ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/science/pnetcdf XDG_CONFIG_HOME=/construction/science/pnetcdf HOME=/construction/science/pnetcdf TMPDIR="/tmp" PATH=/construction/science/pnetcdf/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- ac_cv_fc_compiler_nag=no --with-mpi=/usr/local/mpi/openmpi --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/science/pnetcdf XDG_CONFIG_HOME=/construction/science/pnetcdf HOME=/construction/science/pnetcdf TMPDIR="/tmp" PATH=/construction/science/pnetcdf/.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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -fPIC -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin" LIBS="" CXX="c++" CXXFLAGS=" -pipe -fPIC -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/science/pnetcdf/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.26.1 PERL_VER=5.26 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.26 PROFILE="@comment " DOCSDIR="share/doc/pnetcdf" EXAMPLESDIR="share/examples/pnetcdf" DATADIR="share/pnetcdf" WWWDIR="www/pnetcdf" ETCDIR="etc/pnetcdf" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pnetcdf DOCSDIR=/usr/local/share/doc/pnetcdf EXAMPLESDIR=/usr/local/share/examples/pnetcdf WWWDIR=/usr/local/www/pnetcdf ETCDIR=/usr/local/etc/pnetcdf -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.0 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500000 OSVERSION=9999999 OSREL=5.0 _OSRELEASE=5.0-SYNTH -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> pnetcdf-1.8.1_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5.txz Installing pkg-1.10.5... Extracting pkg-1.10.5: .......... done ===> pnetcdf-1.8.1_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pnetcdf-1.8.1_3 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> Fetching all distfiles required by pnetcdf-1.8.1_3 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by pnetcdf-1.8.1_3 for building => SHA256 Checksum OK for parallel-netcdf-1.8.1.tar.bz2. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by pnetcdf-1.8.1_3 for building ===> Extracting for pnetcdf-1.8.1_3 => SHA256 Checksum OK for parallel-netcdf-1.8.1.tar.bz2. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for pnetcdf-1.8.1_3 ===> Applying ports patches for pnetcdf-1.8.1_3 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> pnetcdf-1.8.1_3 depends on executable: gfortran5 - not found ===> Installing existing package /packages/All/gcc5-5.5.0_2.txz Installing gcc5-5.5.0_2... `-- Installing binutils-2.30_2,1... | `-- 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 binutils-2.30_2,1: .......... done `-- Installing gmp-6.1.2... `-- Extracting gmp-6.1.2: .......... done `-- Installing mpc-1.1.0... | `-- Installing mpfr-3.1.6... | `-- Extracting mpfr-3.1.6: .......... done `-- Extracting mpc-1.1.0: ...... done Extracting gcc5-5.5.0_2: .......... done Message from gcc5-5.5.0_2: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unsupported by upstream. Use GCC 6 or newer instead.. ===> pnetcdf-1.8.1_3 depends on executable: gfortran5 - found ===> Returning to build of pnetcdf-1.8.1_3 ===> pnetcdf-1.8.1_3 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz Installing gmake-4.2.1_2... Extracting gmake-4.2.1_2: .......... done ===> pnetcdf-1.8.1_3 depends on executable: gmake - found ===> Returning to build of pnetcdf-1.8.1_3 ===> pnetcdf-1.8.1_3 depends on file: /usr/local/bin/as - found ===> pnetcdf-1.8.1_3 depends on package: perl5>=5.26<5.27 - not found ===> Installing existing package /packages/All/perl5-5.26.1.txz Installing perl5-5.26.1... Extracting perl5-5.26.1: .......... done Message from perl5-5.26.1: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> pnetcdf-1.8.1_3 depends on package: perl5>=5.26<5.27 - found ===> Returning to build of pnetcdf-1.8.1_3 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> pnetcdf-1.8.1_3 depends on shared library: libmpi.so - not found ===> Installing existing package /packages/All/openmpi-1.10.7_2.txz Installing openmpi-1.10.7_2... `-- Installing hwloc-1.11.7_2... | `-- Installing libpciaccess-0.13.5... | | `-- Installing pciids-20180219... | | `-- Extracting pciids-20180219: ..... done | `-- Extracting libpciaccess-0.13.5: ...... done | `-- Installing libxml2-2.9.7... | `-- Extracting libxml2-2.9.7: .......... done `-- Extracting hwloc-1.11.7_2: .......... done `-- Installing libevent-2.1.8_1... | `-- Installing libressl-2.6.4... | `-- Extracting libressl-2.6.4: .......... done `-- Extracting libevent-2.1.8_1: .......... done `-- Installing libltdl-2.4.6... `-- Extracting libltdl-2.4.6: .......... done Extracting openmpi-1.10.7_2: .......... done ===> pnetcdf-1.8.1_3 depends on shared library: libmpi.so - found (/usr/local/mpi/openmpi/lib/libmpi.so) ===> Returning to build of pnetcdf-1.8.1_3 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for pnetcdf-1.8.1_3 configure: loading site script /xports/Templates/config.site checking for mpicc... /usr/local/mpi/openmpi/bin/mpicc checking for gcc... /usr/local/mpi/openmpi/bin/mpicc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /usr/local/mpi/openmpi/bin/mpicc accepts -g... yes checking for /usr/local/mpi/openmpi/bin/mpicc option to accept ISO C89... none needed checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking how to make dependencies... false checking for MPI_Comm_rank... yes checking for MPI_File_open... yes checking for mpicxx... /usr/local/mpi/openmpi/bin/mpicxx checking whether we are using the GNU C++ compiler... yes checking whether /usr/local/mpi/openmpi/bin/mpicxx accepts -g... yes checking for MPI_File_close... yes checking if MPI C++ compiler redefines SEEK_SET ... no checking for mpif77... /usr/local/mpi/openmpi/bin/mpif77 checking for mpif90... /usr/local/mpi/openmpi/bin/mpif90 checking whether we are using the GNU Fortran compiler... yes checking whether /usr/local/mpi/openmpi/bin/mpif90 accepts -g... yes checking build system type... x86_64-portbld-dragonfly5.0 checking host system type... x86_64-portbld-dragonfly5.0 checking how to get verbose linking output from /usr/local/mpi/openmpi/bin/mpif90... -v checking for Fortran libraries of /usr/local/mpi/openmpi/bin/mpif90... -L/usr/local/lib/gcc5 -L/usr/local/mpi/openmpi/lib -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.0/5.5.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.0/5.5.0/../../../../../x86_64-portbld-dragonfly5.0/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.0/5.5.0/../../.. -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lm -lquadmath -lpthread checking whether /usr/local/mpi/openmpi/bin/mpicc links with FCLIBS found by autoconf... yes checking if mpi.mod is available... yes checking if MPIF90 is valid... yes checking whether we are using the GNU Fortran 77 compiler... yes checking whether /usr/local/mpi/openmpi/bin/mpif77 accepts -g... yes checking how to get verbose linking output from /usr/local/mpi/openmpi/bin/mpif77... -v checking for Fortran 77 libraries of /usr/local/mpi/openmpi/bin/mpif77... -L/usr/local/lib/gcc5 -L/usr/local/mpi/openmpi/lib -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.0/5.5.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.0/5.5.0/../../../../../x86_64-portbld-dragonfly5.0/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.0/5.5.0/../../.. -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lm -lquadmath -lpthread checking for Fortran flag needed to accept free-form source... -ffree-form checking if MPIF77 is valid... yes checking for Fortran flag to compile preprocessed .f files... -cpp checking for Fortran flag to compile preprocessed .F files... none checking for Fortran flag to compile preprocessed .f90 files... -cpp checking for Fortran flag to compile preprocessed .F90 files... none checking for Fortran flag to compile preprocessed .F files... (cached) checking how to define symbols for preprocessed Fortran... -D checking for Fortran flag to compile .f files... none checking for Fortran flag to compile .F files... none checking for Fortran flag to compile .f90 files... none checking for Fortran flag to compile .F90 files... none checking for Fortran flag needed to accept fixed-form source... -ffixed-form checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking for C-equivalent to Fortran routine "SUB_A"... sub_a_ checking if Fortran compiler is NAG... (cached) no checking Fortran compiler treating constant modifier... 8 checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking whether gmake sets $(MAKE)... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for m4... m4 checking m4 flags... "none" checking for /usr/local/bin/ar... /usr/local/bin/ar checking ar flags... cru checking for /usr/local/bin/nm... /usr/local/bin/nm checking nm flags... checking for ranlib... /usr/local/bin/ranlib checking how to run the C preprocessor... cpp 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 stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for inline... inline checking for IEEE floating point format... yes checking for strerror... (cached) yes checking for access... yes checking for unlink... (cached) yes checking for MPI_Offset... yes checking size of MPI_Offset... 8 checking size of MPI_Aint... 8 checking for MPI_Info_dup... yes checking for MPI_Info_free... yes checking for MPI_Get_address... yes checking for MPI_Type_create_subarray... yes checking for MPI_Type_create_hvector... yes checking for MPI_Type_create_hindexed... yes checking for MPI_Type_create_struct... yes checking for MPI_Type_create_resized... yes checking for MPI_Type_get_extent... yes checking if MPI constant MPI_COMBINER_DUP is defined ... yes checking if MPI constant MPI_COMBINER_HVECTOR_INTEGER is defined ... yes checking if MPI constant MPI_COMBINER_HINDEXED_INTEGER is defined ... yes checking if MPI constant MPI_COMBINER_SUBARRAY is defined ... yes checking if MPI constant MPI_COMBINER_DARRAY is defined ... yes checking if MPI constant MPI_COMBINER_RESIZED is defined ... yes checking if MPI constant MPI_COMBINER_STRUCT_INTEGER is defined ... yes checking if MPI constant MPI_COMBINER_INDEXED_BLOCK is defined ... yes checking if MPI constant MPI_COMBINER_F90_REAL is defined ... yes checking if MPI constant MPI_COMBINER_F90_INTEGER is defined ... yes checking if MPI constant MPI_COMBINER_F90_COMPLEX is defined ... yes checking if MPI constant MPI_ERR_FILE_EXISTS is defined ... yes checking if MPI constant MPI_ERR_NO_SUCH_FILE is defined ... yes checking if MPI constant MPI_ERR_AMODE is defined ... yes checking if MPI constant MPI_ERR_NOT_SAME is defined ... yes checking if MPI constant MPI_ERR_BAD_FILE is defined ... yes checking if MPI constant MPI_ERR_READ_ONLY is defined ... yes checking if MPI constant MPI_ERR_ACCESS is defined ... yes checking if MPI constant MPI_ERR_NO_SPACE is defined ... yes checking if MPI constant MPI_ERR_QUOTA is defined ... yes checking if MPI datatype MPI_CHAR is defined ... yes checking if MPI datatype MPI_BYTE is defined ... yes checking if MPI datatype MPI_SIGNED_CHAR is defined ... yes checking if MPI datatype MPI_UNSIGNED_CHAR is defined ... yes checking if MPI datatype MPI_SHORT is defined ... yes checking if MPI datatype MPI_UNSIGNED_SHORT is defined ... yes checking if MPI datatype MPI_INT is defined ... yes checking if MPI datatype MPI_UNSIGNED is defined ... yes checking if MPI datatype MPI_LONG is defined ... yes checking if MPI datatype MPI_FLOAT is defined ... yes checking if MPI datatype MPI_DOUBLE is defined ... yes checking if MPI datatype MPI_LONG_LONG_INT is defined ... yes checking if MPI datatype MPI_UNSIGNED_LONG_LONG is defined ... yes checking if MPI datatype MPI_UB is defined ... yes checking if MPI datatype MPI_LB is defined ... yes checking if MPI datatype MPI_OFFSET is defined ... yes checking if MPI datatype MPI_CHARACTER is defined ... yes checking if MPI datatype MPI_REAL is defined ... yes checking if MPI datatype MPI_INTEGER is defined ... yes checking if MPI datatype MPI_DOUBLE_PRECISION is defined ... yes checking if MPI datatype MPI_INTEGER1 is defined ... yes checking if MPI datatype MPI_INTEGER2 is defined ... yes checking if MPI datatype MPI_INTEGER4 is defined ... yes checking if MPI datatype MPI_INTEGER8 is defined ... yes checking if MPI datatype MPI_INTEGER16 is defined ... no checking if MPI datatype MPI_REAL4 is defined ... yes checking if MPI datatype MPI_REAL8 is defined ... yes checking if MPI datatype MPI_REAL16 is defined ... yes checking if MPI datatype MPI_COMPLEX8 is defined ... yes checking if MPI datatype MPI_COMPLEX16 is defined ... yes checking if MPI datatype MPI_COMPLEX32 is defined ... yes checking whether char is unsigned... no checking whether byte ordering is bigendian... no checking for size_t... (cached) yes checking for off_t... (cached) yes checking for ssize_t... (cached) yes checking for ptrdiff_t... (cached) yes checking for uchar... no checking for ushort... yes checking for uint... yes checking for longlong... no checking for ulonglong... no checking for int64... no checking for uint64... no checking size of size_t... 8 checking size of off_t... 8 checking size of signed char... 1 checking size of unsigned char... 1 checking size of short... 2 checking size of unsigned short int... 2 checking size of unsigned short... 2 checking size of int... 4 checking size of unsigned int... 4 checking size of long... 8 checking size of float... 4 checking size of double... 8 checking size of long long... 8 checking size of unsigned long long... 8 checking size of ushort... 2 checking size of uint... 4 checking for C-equivalent to Fortran routine "SUB"... sub_ checking for Fortran "integer*1"... yes checking for Fortran "integer*2"... yes checking for Fortran "integer*8"... yes checking if Fortran "integer*1" is ... "signed char" in C checking if Fortran "integer*2" is ... "short" in C checking if Fortran "integer*8" is ... "int" in C checking if Fortran "integer" is ... "int" in C checking if Fortran "real" is ... "float" in C checking if Fortran "doubleprecision" is ... "double" in C checking for Fortran-equivalent to netCDF "byte"... byte checking for Fortran-equivalent to netCDF "short"... integer*2 checking for Fortran NFMPI_OFFSET "integer*8"... yes checking Fortran 90 module extension... mod checking Fortran 90 module inclusion flag... -I checking Fortran 90 module output flag... -J checking for Fortran 77 GNU intrinsic INT... yes checking for Fortran 77 intrinsic INT1... no checking for Fortran 77 intrinsic INT2... yes checking for Fortran 77 intrinsic INT8... yes checking if Fortran 90 compiler capitalizes .mod filenames... no checking for catman... catman checking for manual-page index command... catman -w -M $(MANDIR) checking if C++ macro __func__ or __FUNCTION__ is defined... yes checking for latex... no checking for dvipdf... no checking for gcc... /usr/bin/gcc configure: creating ./config.status config.status: creating macros.make config.status: creating Makefile config.status: creating pnetcdf_pc config.status: creating src/Makefile config.status: creating src/lib/Makefile config.status: creating src/lib/pnetcdf.h config.status: creating src/utils/Makefile config.status: creating src/utils/ncmpidump/Makefile config.status: creating src/utils/ncmpidiff/Makefile config.status: creating src/utils/ncmpigen/Makefile config.status: creating src/utils/ncmpivalid/Makefile config.status: creating src/utils/pnetcdf_version/Makefile config.status: creating src/utils/ncoffsets/Makefile config.status: creating test/Makefile config.status: creating test/common/Makefile config.status: creating test/nc_test/Makefile config.status: creating test/C/Makefile config.status: creating test/fandc/Makefile config.status: creating test/testcases/Makefile config.status: creating test/nonblocking/Makefile config.status: creating test/header/Makefile config.status: creating test/cdf_format/Makefile config.status: creating test/largefile/Makefile config.status: creating examples/C/Makefile config.status: creating examples/tutorial/Makefile config.status: creating examples/Makefile config.status: creating doc/Makefile config.status: creating man/Makefile config.status: creating scripts/Makefile config.status: creating benchmarks/Makefile config.status: creating benchmarks/C/Makefile config.status: creating test/nf_test/Makefile config.status: creating test/nf_test/tests.inc config.status: creating test/nf90_test/Makefile config.status: creating test/F90/Makefile config.status: creating examples/F77/Makefile config.status: creating examples/F90/Makefile config.status: creating src/libf90/Makefile config.status: creating src/libf90/pnetcdf.f90 config.status: creating src/libf90/api.f90 config.status: creating src/libf90/nfmpi_constants.f90 config.status: creating src/libf/Makefile config.status: creating src/libf/pnetcdf.inc config.status: creating src/libcxx/Makefile config.status: creating examples/CXX/Makefile config.status: creating test/CXX/Makefile config.status: creating benchmarks/FLASH-IO/Makefile config.status: creating test/subfile/Makefile config.status: creating stamp-h config.status: creating pnetcdf-config config.status: creating check_install config.status: creating src/lib/ncconfig.h config.status: creating src/libf/nfconfig_inc ------------------------------------------------------------------------------ parallel-netcdf Version 1.8.1 Features: Support for large files (> 4 GB) - yes Build Fortran APIs - yes Build C++ APIs - yes Build CDF-2 and CDF-5 support - yes Compilers: MPICC = /usr/local/mpi/openmpi/bin/mpicc MPICXX = /usr/local/mpi/openmpi/bin/mpicxx MPIF77 = /usr/local/mpi/openmpi/bin/mpif77 MPIF90 = /usr/local/mpi/openmpi/bin/mpif90 CFLAGS = -pipe -fPIC -O2 -fno-strict-aliasing CXXFLAGS = -pipe -fPIC -O2 -fno-strict-aliasing F77FLAGS = -O -Wl,-rpath=/usr/local/lib/gcc5 F90FLAGS = -Wl,-rpath=/usr/local/lib/gcc5 LDFLAGS = -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin Now type 'make' to build the library and utility tools and then type 'make []' for testing and installation, where the optional is: check - test PnetCDF build for sequential run ptest - test PnetCDF build for parallel run install - install PnetCDF ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for pnetcdf-1.8.1_3 gmake[1]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1' gmake -w -C src gmake[2]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src' gmake -w -C lib objs gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/lib' m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DERANGE_FILL ncx_h.m4 >ncx.h /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c mpinetcdf.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c header.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c mpincio.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c dim.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c error.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c nc.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c string.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c var.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c ncmpidtype.c ncmpidtype.c: In function 'ncmpii_type_filter': ncmpidtype.c:196:5: warning: 'ompi_mpi_lb' is deprecated: MPI_LB is deprecated in MPI-2.0 [-Wdeprecated-declarations] if (type == MPI_LB) { ^ In file included from ncmpidtype.c:16:0: /usr/local/mpi/openmpi/include/mpi.h:914:56: note: declared here OMPI_DECLSPEC extern struct ompi_predefined_datatype_t ompi_mpi_lb __mpi_interface_deprecated__("MPI_LB is deprecated in MPI-2.0"); ^ ncmpidtype.c:205:5: warning: 'ompi_mpi_ub' is deprecated: MPI_UB is deprecated in MPI-2.0 [-Wdeprecated-declarations] if (type == MPI_UB) { ^ In file included from ncmpidtype.c:16:0: /usr/local/mpi/openmpi/include/mpi.h:915:56: note: declared here OMPI_DECLSPEC extern struct ompi_predefined_datatype_t ompi_mpi_ub __mpi_interface_deprecated__("MPI_UB is deprecated in MPI-2.0"); ^ /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c filetype.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c nonblocking.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c malloc.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c utf8proc.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c vard.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c fill.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c util.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c hash_func.c m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DERANGE_FILL getput.m4 >getput.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c getput.c m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DERANGE_FILL i_getput.m4 >i_getput.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c i_getput.c m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DERANGE_FILL bput.m4 >bput.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c bput.c m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DERANGE_FILL ncx.m4 >ncx.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c ncx.c m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DERANGE_FILL m_getput_varx.m4 >m_getput_varx.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c m_getput_varx.c m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DERANGE_FILL varn.m4 >varn.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c varn.c m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DERANGE_FILL i_varn.m4 >i_varn.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c i_varn.c m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DERANGE_FILL attr.m4 >attr.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c attr.c m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DERANGE_FILL convert_swap.m4 >convert_swap.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I. -DHAVE_CONFIG_H -c convert_swap.c gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/lib' gmake -w -C libcxx objs gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libcxx' cp -f ./pnetcdf.in pnetcdf set -e; for i in ncmpi_notyet.h ncmpiCheck.h ncmpiType.h ncmpiAtt.h ncmpiEnumType.h ncmpiGroupAtt.h ncmpiGroup.h ncmpiByte.h ncmpiChar.h ncmpiCompoundType.h ncmpiDouble.h ncmpiFloat.h ncmpiInt.h ncmpiInt64.h ncmpiOpaqueType.h ncmpiShort.h ncmpiUbyte.h ncmpiUint.h ncmpiUint64.h ncmpiUshort.h ncmpiException.h ncmpiDim.h ncmpiFile.h ncmpiVarAtt.h ncmpiVar.h ncmpiVlenType.h; do ( \ sed -e '/#ifndef/d' -e '/#define/d' -e '/#endif/d' -e '/#include/d' ./$i >> pnetcdf; \ ) ; done /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpi_notyet.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiCheck.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiType.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiAtt.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiEnumType.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiGroupAtt.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiGroup.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiByte.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiChar.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiCompoundType.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiDouble.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiFloat.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiInt.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiInt64.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiOpaqueType.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiShort.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiUbyte.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiUint.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiUint64.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiUshort.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiException.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiDim.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiFile.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiVarAtt.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiVar.cpp /usr/local/mpi/openmpi/bin/mpicxx -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -DHAVE_CONFIG_H -c ncmpiVlenType.cpp gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libcxx' gmake -w -C libf objs gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf' rm -f nfconfig.inc sed -e "s%/\*%!%g" -e "s%\*/%%g" nfconfig_inc > nfconfig.inc rm -f mpifnetcdf.h allf.c ./buildiface -infile=../lib/pnetcdf.h -deffile=./defs > allf.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -I. -DHAVE_CONFIG_H -c allf.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -I. -DHAVE_CONFIG_H -c issyserrf.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -I. -DHAVE_CONFIG_H -c xstrerrorf.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -I. -DHAVE_CONFIG_H -c xstrerrnof.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I../lib -I. -DHAVE_CONFIG_H -c xinq_libversf.c /usr/local/mpi/openmpi/bin/mpif77 -I../lib -I. -O -Wl,-rpath=/usr/local/lib/gcc5 -c strerrorf.f /usr/local/mpi/openmpi/bin/mpif77 -I../lib -I. -O -Wl,-rpath=/usr/local/lib/gcc5 -c strerrnof.f /usr/local/mpi/openmpi/bin/mpif77 -I../lib -I. -O -Wl,-rpath=/usr/local/lib/gcc5 -c inq_libversf.f gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf' gmake -w -C libf90 objs gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf90' m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DINTENTV=INOUT getput_text.m4 >getput_text.f90 m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DINTENTV=INOUT getput_var.m4 >getput_var.f90 m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DINTENTV=INOUT getput_varn.m4 >getput_varn.f90 m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DINTENTV=INOUT getput_vard.m4 >getput_vard.f90 /usr/local/mpi/openmpi/bin/mpif90 -I. -I. -Wl,-rpath=/usr/local/lib/gcc5 -J. -c pnetcdf.f90 gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf90' gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/lib' /usr/local/bin/ar cru libpnetcdf.a mpinetcdf.o header.o mpincio.o dim.o error.o nc.o string.o var.o ncmpidtype.o filetype.o nonblocking.o malloc.o utf8proc.o vard.o fill.o util.o hash_func.o getput.o i_getput.o bput.o ncx.o m_getput_varx.o varn.o i_varn.o attr.o convert_swap.o /usr/local/bin/ar: `u' modifier ignored since `D' is the default (see `U') /usr/local/bin/ranlib libpnetcdf.a gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/lib' gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libcxx' /usr/local/bin/ar cru ../lib/libpnetcdf.a ncmpi_notyet.o ncmpiCheck.o ncmpiType.o ncmpiAtt.o ncmpiEnumType.o ncmpiGroupAtt.o ncmpiGroup.o ncmpiByte.o ncmpiChar.o ncmpiCompoundType.o ncmpiDouble.o ncmpiFloat.o ncmpiInt.o ncmpiInt64.o ncmpiOpaqueType.o ncmpiShort.o ncmpiUbyte.o ncmpiUint.o ncmpiUint64.o ncmpiUshort.o ncmpiException.o ncmpiDim.o ncmpiFile.o ncmpiVarAtt.o ncmpiVar.o ncmpiVlenType.o /usr/local/bin/ar: `u' modifier ignored since `D' is the default (see `U') /usr/local/bin/ranlib ../lib/libpnetcdf.a gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libcxx' gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf' /usr/local/bin/ar cru ../lib/libpnetcdf.a allf.o issyserrf.o xstrerrorf.o xstrerrnof.o xinq_libversf.o strerrorf.o strerrnof.o inq_libversf.o /usr/local/bin/ar: `u' modifier ignored since `D' is the default (see `U') /usr/local/bin/ranlib ../lib/libpnetcdf.a gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf' gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf90' /usr/local/bin/ar cru ../lib/libpnetcdf.a pnetcdf.o /usr/local/bin/ar: `u' modifier ignored since `D' is the default (see `U') /usr/local/bin/ranlib ../lib/libpnetcdf.a gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf90' gmake -w -C utils gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils' gmake -w -C ncmpigen gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpigen' /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I../../lib -DHAVE_CONFIG_H -c main.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I../../lib -DHAVE_CONFIG_H -c load.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I../../lib -DHAVE_CONFIG_H -c escapes.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I../../lib -DHAVE_CONFIG_H -c getfill.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I../../lib -DHAVE_CONFIG_H -c init.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I../../lib -DHAVE_CONFIG_H -c genlib.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I. -I../../lib -DHAVE_CONFIG_H -c ncmpigentab.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -o ncmpigen main.o load.o escapes.o getfill.o init.o genlib.o ncmpigentab.o -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L../../lib -lpnetcdf gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpigen' gmake -w -C ncmpidump gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpidump' /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I../../lib -DHAVE_CONFIG_H -c ncmpidump.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I../../lib -DHAVE_CONFIG_H -c vardata.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I../../lib -DHAVE_CONFIG_H -c dumplib.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -o ncmpidump ncmpidump.o vardata.o dumplib.o -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L../../lib -lpnetcdf gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpidump' gmake -w -C ncmpidiff gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpidiff' /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I../../lib -DHAVE_CONFIG_H -c ncmpidiff.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -o ncmpidiff ncmpidiff.o -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L../../lib -lpnetcdf gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpidiff' gmake -w -C ncmpivalid gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpivalid' /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -I../../lib -I./../../lib -DHAVE_CONFIG_H -c ncmpivalid.c /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -o ncmpivalid ncmpivalid.o -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L../../lib -lpnetcdf gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpivalid' gmake -w -C pnetcdf_version gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/pnetcdf_version' /usr/bin/gcc -DMPICC="\"/usr/local/mpi/openmpi/bin/mpicc\"" -DCFLAGS="\"-pipe -fPIC -O2 -fno-strict-aliasing\"" -DCONFIGURE_ARGS_CLEAN="\"ac_cv_fc_compiler_nag=no --with-mpi=/usr/local/mpi/openmpi --prefix=/usr/local --localstatedir=/var --mandir=/usr/local/man --infodir=/usr/local/info/ --build=x86_64-portbld-dragonfly5.0\"" -DPNETCDF_VERSION="\"1.8.1\"" -DPNETCDF_RELEASE_DATE="\"28 Jan 2017\"" -DMPICXX="\"/usr/local/mpi/openmpi/bin/mpicxx\"" -DCXXFLAGS="\"-pipe -fPIC -O2 -fno-strict-aliasing\"" -DMPIF77="\"/usr/local/mpi/openmpi/bin/mpif77\"" -DF77FLAGS="\"-O -Wl,-rpath=/usr/local/lib/gcc5 \"" -DMPIF90="\"/usr/local/mpi/openmpi/bin/mpif90\"" -DF90FLAGS="\"-Wl,-rpath=/usr/local/lib/gcc5 \"" -o pnetcdf_version pnetcdf_version.c gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/pnetcdf_version' gmake -w -C ncoffsets gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncoffsets' /usr/bin/gcc -o ncoffsets ncoffsets.c gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncoffsets' gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils' gmake[2]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src' gmake[1]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> pnetcdf-1.8.1_3 depends on executable: gfortran5 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for pnetcdf-1.8.1_3 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1' gmake -w -C src install gmake[2]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src' gmake -w -C lib objs gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/lib' gmake[3]: Nothing to be done for 'objs'. gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/lib' gmake -w -C libcxx objs gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libcxx' gmake[3]: Nothing to be done for 'objs'. gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libcxx' gmake -w -C libf objs gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf' gmake[3]: Nothing to be done for 'objs'. gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf' gmake -w -C libf90 objs gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf90' gmake[3]: Nothing to be done for 'objs'. gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf90' gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/lib' /usr/local/bin/ar cru libpnetcdf.a mpinetcdf.o header.o mpincio.o dim.o error.o nc.o string.o var.o ncmpidtype.o filetype.o nonblocking.o malloc.o utf8proc.o vard.o fill.o util.o hash_func.o getput.o i_getput.o bput.o ncx.o m_getput_varx.o varn.o i_varn.o attr.o convert_swap.o /usr/local/bin/ar: `u' modifier ignored since `D' is the default (see `U') /usr/local/bin/ranlib libpnetcdf.a gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/lib' gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libcxx' /usr/local/bin/ar cru ../lib/libpnetcdf.a ncmpi_notyet.o ncmpiCheck.o ncmpiType.o ncmpiAtt.o ncmpiEnumType.o ncmpiGroupAtt.o ncmpiGroup.o ncmpiByte.o ncmpiChar.o ncmpiCompoundType.o ncmpiDouble.o ncmpiFloat.o ncmpiInt.o ncmpiInt64.o ncmpiOpaqueType.o ncmpiShort.o ncmpiUbyte.o ncmpiUint.o ncmpiUint64.o ncmpiUshort.o ncmpiException.o ncmpiDim.o ncmpiFile.o ncmpiVarAtt.o ncmpiVar.o ncmpiVlenType.o /usr/local/bin/ar: `u' modifier ignored since `D' is the default (see `U') /usr/local/bin/ranlib ../lib/libpnetcdf.a gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libcxx' gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf' /usr/local/bin/ar cru ../lib/libpnetcdf.a allf.o issyserrf.o xstrerrorf.o xstrerrnof.o xinq_libversf.o strerrorf.o strerrnof.o inq_libversf.o /usr/local/bin/ar: `u' modifier ignored since `D' is the default (see `U') /usr/local/bin/ranlib ../lib/libpnetcdf.a gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf' gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf90' /usr/local/bin/ar cru ../lib/libpnetcdf.a pnetcdf.o /usr/local/bin/ar: `u' modifier ignored since `D' is the default (see `U') /usr/local/bin/ranlib ../lib/libpnetcdf.a gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf90' gmake -w -C utils gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils' gmake -w -C ncmpigen gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpigen' /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -o ncmpigen main.o load.o escapes.o getfill.o init.o genlib.o ncmpigentab.o -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L../../lib -lpnetcdf gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpigen' gmake -w -C ncmpidump gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpidump' /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -o ncmpidump ncmpidump.o vardata.o dumplib.o -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L../../lib -lpnetcdf gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpidump' gmake -w -C ncmpidiff gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpidiff' /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -o ncmpidiff ncmpidiff.o -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L../../lib -lpnetcdf gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpidiff' gmake -w -C ncmpivalid gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpivalid' /usr/local/mpi/openmpi/bin/mpicc -pipe -fPIC -O2 -fno-strict-aliasing -o ncmpivalid ncmpivalid.o -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L../../lib -lpnetcdf gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpivalid' gmake -w -C pnetcdf_version gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/pnetcdf_version' gmake[4]: Nothing to be done for 'all'. gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/pnetcdf_version' gmake -w -C ncoffsets gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncoffsets' gmake[4]: Nothing to be done for 'all'. gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncoffsets' gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils' gmake -w -C lib install gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/lib' /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage//usr/local/lib install -m 0644 libpnetcdf.a /construction/science/pnetcdf/stage//usr/local/lib/libpnetcdf.a /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage//usr/local/include install -m 0644 pnetcdf.h /construction/science/pnetcdf/stage//usr/local/include/pnetcdf.h gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/lib' gmake -w -C libcxx install gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libcxx' /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage//usr/local/include install -m 0644 pnetcdf /construction/science/pnetcdf/stage//usr/local/include gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libcxx' gmake -w -C libf install gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf' /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage//usr/local/include install -m 0644 pnetcdf.inc /construction/science/pnetcdf/stage//usr/local/include gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf' gmake -w -C libf90 install gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf90' /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage//usr/local/include install -m 0644 pnetcdf.mod /construction/science/pnetcdf/stage//usr/local/include gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/libf90' gmake -w -C utils install gmake[3]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils' gmake -w -C ncmpigen install gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpigen' /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage//usr/local/man/man1 install -m 0644 ./ncmpigen.1 /construction/science/pnetcdf/stage//usr/local/man/man1/ncmpigen.1 /usr/bin/install -c -d /construction/science/pnetcdf/stage//usr/local/bin /usr/bin/install -c -m 755 ncmpigen /construction/science/pnetcdf/stage//usr/local/bin/ncmpigen gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpigen' gmake -w -C ncmpidump install gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpidump' /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage//usr/local/man/man1 install -m 0644 ./ncmpidump.1 /construction/science/pnetcdf/stage//usr/local/man/man1/ncmpidump.1 /usr/bin/install -c -d /construction/science/pnetcdf/stage//usr/local/bin /usr/bin/install -c -m 755 ncmpidump /construction/science/pnetcdf/stage//usr/local/bin/ncmpidump gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpidump' gmake -w -C ncmpidiff install gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpidiff' /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage//usr/local/man/man1 install -m 0644 ./ncmpidiff.1 /construction/science/pnetcdf/stage//usr/local/man/man1/ncmpidiff.1 /usr/bin/install -c -d /construction/science/pnetcdf/stage//usr/local/bin /usr/bin/install -c -m 755 ncmpidiff /construction/science/pnetcdf/stage//usr/local/bin/ncmpidiff gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpidiff' gmake -w -C ncmpivalid install gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpivalid' /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage//usr/local/man/man1 install -m 0644 ./ncmpivalid.1 /construction/science/pnetcdf/stage//usr/local/man/man1/ncmpivalid.1 /usr/bin/install -c -d /construction/science/pnetcdf/stage//usr/local/bin /usr/bin/install -c -m 755 ncmpivalid /construction/science/pnetcdf/stage//usr/local/bin/ncmpivalid gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncmpivalid' gmake -w -C pnetcdf_version install gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/pnetcdf_version' /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage//usr/local/man/man1 install -m 0644 ./pnetcdf_version.1 /construction/science/pnetcdf/stage//usr/local/man/man1/pnetcdf_version.1 /usr/bin/install -c -d /construction/science/pnetcdf/stage//usr/local/bin /usr/bin/install -c -m 755 pnetcdf_version /construction/science/pnetcdf/stage//usr/local/bin/pnetcdf_version gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/pnetcdf_version' gmake -w -C ncoffsets install gmake[4]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncoffsets' /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage//usr/local/man/man1 install -m 0644 ./ncoffsets.1 /construction/science/pnetcdf/stage//usr/local/man/man1/ncoffsets.1 /usr/bin/install -c -d /construction/science/pnetcdf/stage//usr/local/bin /usr/bin/install -c -m 755 ncoffsets /construction/science/pnetcdf/stage//usr/local/bin/ncoffsets gmake[4]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils/ncoffsets' gmake[3]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src/utils' gmake[2]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/src' gmake -w -C man install gmake[2]: Entering directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/man' m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DAPI=C -DRELEASE_STR="1.8.1 of 28 Jan 2017" -DRELEASE_DATE="2017-01-28" pnetcdf.m4 > pnetcdf.3 || rm -f pnetcdf.3 m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DAPI=F -DRELEASE_STR="1.8.1 of 28 Jan 2017" -DRELEASE_DATE="2017-01-28" pnetcdf.m4 > pnetcdf_f77.3 || rm -f pnetcdf_f77.3 m4 -I/construction/science/pnetcdf/parallel-netcdf-1.8.1/scripts -DPNETCDF -DRELEASE_STR="1.8.1 of 28 Jan 2017" -DRELEASE_DATE="2017-01-28" pnetcdf_f90.m4 > pnetcdf_f90.3 || rm -f pnetcdf_f90.3 /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage//usr/local/man/man3 gmake[2]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1/man' rm -f pnetcdf.pc sed -e "s%INSTALL_PREFIX%/usr/local%g" pnetcdf_pc > pnetcdf.pc /usr/bin/install -c -d -m 755 /construction/science/pnetcdf/stage/usr/local/libdata/pkgconfig install -m 0644 pnetcdf.pc /construction/science/pnetcdf/stage/usr/local/libdata/pkgconfig/pnetcdf.pc /usr/bin/install -c -d /construction/science/pnetcdf/stage//usr/local/bin /usr/bin/install -c -m 755 pnetcdf-config /construction/science/pnetcdf/stage//usr/local/bin/pnetcdf-config +----------------------------------------------------------------------------+ | | PnetCDF has been successfully installed under /usr/local | | * PnetCDF header files are installed in /usr/local/include | * PnetCDF library file is installed in /usr/local/lib | * PnetCDF utility programs are installed in /usr/local/bin | * PnetCDF man pages are installed in /usr/local/man/man1 and | /usr/local/man/man3 | | To compile your PnetCDF programs, please add the following to the command | line, so the compiler can find the PnetCDF header files: | -I/usr/local/include | | Add the following line to link your program to PnetCDF library: | -L/usr/local/lib -lpnetcdf | | PnetCDF is jointly developed by a team at Northwestern University and | Argonne National Laboratory. | | Visit PnetCDF web sites for more information | http://cucis.ece.northwestern.edu/projects/PnetCDF | http://trac.mcs.anl.gov/projects/parallel-netcdf | +----------------------------------------------------------------------------+ gmake[1]: Leaving directory '/construction/science/pnetcdf/parallel-netcdf-1.8.1' /usr/bin/strip /construction/science/pnetcdf/stage/usr/local/bin/n* /construction/science/pnetcdf/stage/usr/local/bin/pnetcdf_version /bin/mkdir -p /construction/science/pnetcdf/stage/usr/local/share/doc/pnetcdf/ cd /construction/science/pnetcdf/parallel-netcdf-1.8.1/ && install -m 0644 COPYRIGHT INSTALL README /construction/science/pnetcdf/stage/usr/local/share/doc/pnetcdf/ ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for pnetcdf-1.8.1_3 file sizes/checksums [25]: . done packing files [25]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 19 APR 2018 at 05:49:22 UTC Duration: 00:04:37