Date: Tue, 16 Apr 2019 22:26:21 GMT From: pkg-fallout@FreeBSD.org To: yuri@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - head-i386-default][science/gromacs] Failed for gromacs-2019.1_1 in build Message-ID: <201904162226.x3GMQLQB071791@beefy11.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Last committer: jbeich@FreeBSD.org Ident: $FreeBSD: head/science/gromacs/Makefile 498698 2019-04-12 06:36:31Z jbeich $ Log URL: http://beefy11.nyi.freebsd.org/data/head-i386-default/p499067_s346255/logs/gromacs-2019.1_1.log Build URL: http://beefy11.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p499067_s346255 Log: =>> Building science/gromacs build started at Tue Apr 16 22:00:06 UTC 2019 port directory: /usr/ports/science/gromacs package name: gromacs-2019.1_1 building for: FreeBSD head-i386-default-job-05 13.0-CURRENT FreeBSD 13.0-CURRENT 1300018 i386 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/science/gromacs/Makefile 498698 2019-04-12 06:36:31Z jbeich $ Poudriere version: 3.2.8-3-g02cc9753 Host OSVERSION: 1300009 Jail OSVERSION: 1300018 Job Id: 05 !!! Jail is newer than host. (Jail: 1300018, Host: 1300009) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1300018 UNAME_v=FreeBSD 13.0-CURRENT 1300018 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-3-g02cc9753 MASTERMNT=/usr/local/poudriere/data/.m/head-i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-i386-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for gromacs-2019.1_1: ATLAS=off: Use ATLAS for BLAS and LAPACK FLOAT=on: Use single instead of double precision OPENCL=off: Heterogeneous computing via OpenCL OPENMP=on: Parallel processing support via OpenMP SIMD=off: Use CPU-specific optimizations X11=on: X11 (graphics) support ====> Multiprocessing: you have to select exactly one of them NOMP=off: No multiprocessing support MPICH=off: Parallel processing support via MPICH OPENMPI=off: Parallel processing support via Open MPI THREAD_MPI=on: Build a thread-MPI-based multithreaded version of GROMACS ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran8" FC="gfortran8" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc8" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc8" ac_cv_path_PERL=/usr/local/bin/perl 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OPENMPI="@comment " NO_OPENMPI="" SIMD="@comment " NO_SIMD="" THREAD_MPI="" NO_THREAD_MPI="@comment " X11="" NO_X11="@comment " PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gromacs DOCSDIR=/usr/local/share/doc/gromacs EXAMPLESDIR=/usr/local/share/examples/gromacs WWWDIR=/usr/local/www/gromacs ETCDIR=/usr/local/etc/gromacs --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. 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[head-i386-default-job-05] Extracting pkg-1.10.5_5: .......... done ===> gromacs-2019.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gromacs-2019.1_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by gromacs-2019.1_1 for building =========================================================================== =======================<phase: checksum >============================ ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by gromacs-2019.1_1 for building => SHA256 Checksum OK for gromacs-2019.1.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ <snip> cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp [ 88%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/mdlib/wall.cpp [ 88%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/mdlib/wnblist.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/mdlib/wnblist.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/mdlib/wnblist.cpp [ 88%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/applied-forces/electricfield.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/applied-forces/electricfield.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp [ 89%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/bonded.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/listed-forces/bonded.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/listed-forces/bonded.cpp [ 89%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/disre.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/listed-forces/disre.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/listed-forces/disre.cpp [ 89%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/gpubonded-impl.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/listed-forces/gpubonded-impl.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/listed-forces/gpubonded-impl.cpp [ 89%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/listed-forces/listed-forces.cpp [ 89%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/listed-internal.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing 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/wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/calculate-spline-moduli.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/calculate-spline-moduli.cpp [ 89%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include 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/wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/ewald-utils.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/ewald-utils.cpp [ 90%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/long-range-correction.cpp [ 90%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/pme.cpp [ 90%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme-gather.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/pme-gather.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/pme-gather.cpp [ 90%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme-grid.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/pme-grid.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/pme-grid.cpp [ 90%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme-load-balancing.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/pme-load-balancing.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/pme-load-balancing.cpp [ 90%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme-only.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/pme-only.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp [ 90%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/pme-pp.cpp [ 90%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/pme-redistribute.cpp [ 90%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/pme-solve.cpp [ 90%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/pme-spline-work.cpp [ 90%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme-spread.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/ewald/pme-spread.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/ewald/pme-spread.cpp [ 90%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/ewald/pme-gpu-program.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem 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/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/fft/calcgrid.cpp [ 92%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/fft/fft.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/tng_io/include -isystem /wrkdirs/usr/ports/science/gromacs/work/.build/tng/include -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -O2 -pipe -fstack-protector -fno-strict-aliasing -fPIC -fopenmp=libomp -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/gromacs/fft/fft.cpp [ 92%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o cd /wrkdirs/usr/ports/science/gromacs/work/.build/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/wrkdirs/usr/ports/science/gromacs/work/.build/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/lmfit -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2019.1/src/external/thread_mpi/include -isystem /usr/local/include -isystem 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