=>> Building science/gromacs build started at Fri May 2 10:31:21 BST 2025 port directory: /usr/ports/science/gromacs package name: gromacs-2025.0_1 building for: FreeBSD pkg-builder.dan.net.uk 14.2-RELEASE FreeBSD 14.2-RELEASE amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 4434 Feb 16 09:27 /usr/ports/science/gromacs/Makefile Ports top last git commit: 5529c5919b Ports top unclean checkout: yes Port dir last git commit: abc07dd3b2 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1402000 Jail OSVERSION: 1402000 Job Id: 05 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1402000 UNAME_v=FreeBSD 14.2-RELEASE UNAME_r=14.2-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/05/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=14-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/14-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for gromacs-2025.0_1: ATLAS=off: Use ATLAS for BLAS and LAPACK FLOAT=off: Use single instead of double precision HWLOC=on: Build with HWLOC2, portable hardware locality package LEGACY=on: Install legacy API OPENMP=on: Parallel processing support via OpenMP SIMD=off: Use CPU-specific optimizations ====> 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 ====> Heterogeneous computing via OpenCL: you have to select exactly one of them OPENCL_NONE=on: No OpenCL OPENCL_ICD=off: OpenCL via Installable Client Driver OPENCL_SYCL=off: OpenCL via the OpenSYCL implementation of SYCL ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.11" BLA_VENDOR="Generic" XDG_DATA_HOME=/wrkdirs/usr/ports/science/gromacs/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/gromacs/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/gromacs/work/.cache HOME=/wrkdirs/usr/ports/science/gromacs/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/gromacs/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/gromacs/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/science/gromacs/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/gromacs/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/gromacs/work/.cache HOME=/wrkdirs/usr/ports/science/gromacs/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/gromacs/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/gromacs/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/science/gromacs/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -L/usr/local/lib -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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" --End MAKE_ENV-- --PLIST_SUB-- ATLAS="@comment " NO_ATLAS="" FLOAT="@comment " NO_FLOAT="" SUFFIX_D="_d" HWLOC="" NO_HWLOC="@comment " LEGACY="" NO_LEGACY="@comment " MPICH="@comment " NO_MPICH="" NOMP="@comment " NO_NOMP="" OPENCL_ICD="@comment " NO_OPENCL_ICD="" OPENCL_NONE="" NO_OPENCL_NONE="@comment " OPENCL_SYCL="@comment " NO_OPENCL_SYCL="" OPENMP="" NO_OPENMP="@comment " OPENMPI="@comment " NO_OPENMPI="" SIMD="@comment " NO_SIMD="" THREAD_MPI="" NO_THREAD_MPI="@comment " SUFFIX_MPI="" CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 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/5.36 DOCSDIR="share/doc/gromacs" EXAMPLESDIR="share/examples/gromacs" DATADIR="share/gromacs" WWWDIR="www/gromacs" ETCDIR="etc/gromacs" --End PLIST_SUB-- --SUB_LIST-- ATLAS="@comment " NO_ATLAS="" FLOAT="@comment " NO_FLOAT="" HWLOC="" NO_HWLOC="@comment " LEGACY="" NO_LEGACY="@comment " MPICH="@comment " NO_MPICH="" NOMP="@comment " NO_NOMP="" OPENCL_ICD="@comment " NO_OPENCL_ICD="" OPENCL_NONE="" NO_OPENCL_NONE="@comment " OPENCL_SYCL="@comment " NO_OPENCL_SYCL="" OPENMP="" NO_OPENMP="@comment " OPENMPI="@comment " NO_OPENMPI="" SIMD="@comment " NO_SIMD="" THREAD_MPI="" NO_THREAD_MPI="@comment " PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_EXT_SUFFIX=.cpython-311 PYTHON_VER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" 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 FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl apache=2.4 imagemagick=7 java=21 linux=c7 mysql=8.0 php=8.3 samba=4.19 varnish=7 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE ALLOW_UNSUPPORTED_SYSTEM=yes WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gromacs-2025.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.1.2.pkg [pkg-builder.dan.net.uk] Installing pkg-2.1.2... [pkg-builder.dan.net.uk] Extracting pkg-2.1.2: .......... done ===> gromacs-2025.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gromacs-2025.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by gromacs-2025.0_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by gromacs-2025.0_1 for building => SHA256 Checksum OK for gromacs-2025.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by gromacs-2025.0_1 for building ===> Extracting for gromacs-2025.0_1 => SHA256 Checksum OK for gromacs-2025.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for gromacs-2025.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gromacs-2025.0_1 depends on package: boost-libs>=1.44 - not found ===> Installing existing package /packages/All/boost-libs-1.87.0_1.pkg [pkg-builder.dan.net.uk] Installing boost-libs-1.87.0_1... [pkg-builder.dan.net.uk] `-- Installing icu-76.1,1... [pkg-builder.dan.net.uk] `-- Extracting icu-76.1,1: .......... done [pkg-builder.dan.net.uk] Extracting boost-libs-1.87.0_1: .......... done ===== Message from boost-libs-1.87.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> gromacs-2025.0_1 depends on package: boost-libs>=1.44 - found ===> Returning to build of gromacs-2025.0_1 ===> gromacs-2025.0_1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.31.6.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.31.6... [pkg-builder.dan.net.uk] `-- Installing expat-2.7.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.7.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.6_1... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.6_1: .......... done [pkg-builder.dan.net.uk] `-- Installing libidn2-2.3.8... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1_1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1_1: . done [pkg-builder.dan.net.uk] | `-- Installing libunistring-1.3... [pkg-builder.dan.net.uk] | `-- Extracting libunistring-1.3: .......... done [pkg-builder.dan.net.uk] `-- Extracting libidn2-2.3.8: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.51.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.51.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.16,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.16,1: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.23.1... [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.31.6: .......... done ===> gromacs-2025.0_1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of gromacs-2025.0_1 ===> gromacs-2025.0_1 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,4.pkg [pkg-builder.dan.net.uk] Installing ninja-1.11.1,4... [pkg-builder.dan.net.uk] `-- Installing python311-3.11.12... [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.8... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.8: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-4.0.0... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-4.0.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.13_2... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.13_2: .......... done [pkg-builder.dan.net.uk] `-- Extracting python311-3.11.12: .......... done [pkg-builder.dan.net.uk] Extracting ninja-1.11.1,4: ..... done ===== Message from python311-3.11.12: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> gromacs-2025.0_1 depends on executable: ninja - found ===> Returning to build of gromacs-2025.0_1 ===> gromacs-2025.0_1 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.3.0_1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.3.0_1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.3.0_1,1: .......... done ===> gromacs-2025.0_1 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of gromacs-2025.0_1 ===> gromacs-2025.0_1 depends on file: /usr/local/bin/python3.11 - found ===> gromacs-2025.0_1 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_3.pkg [pkg-builder.dan.net.uk] Installing perl5-5.36.3_3... [pkg-builder.dan.net.uk] Extracting perl5-5.36.3_3: .......... done ===> gromacs-2025.0_1 depends on package: perl5>=5.36<5.37 - found ===> Returning to build of gromacs-2025.0_1 ===> gromacs-2025.0_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg-builder.dan.net.uk] Installing ccache-3.7.12_8... [pkg-builder.dan.net.uk] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> gromacs-2025.0_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of gromacs-2025.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gromacs-2025.0_1 depends on shared library: liblmfit.so - not found ===> Installing existing package /packages/All/lmfit-9.0.pkg [pkg-builder.dan.net.uk] Installing lmfit-9.0... [pkg-builder.dan.net.uk] Extracting lmfit-9.0: .......... done ===> gromacs-2025.0_1 depends on shared library: liblmfit.so - found (/usr/local/lib/liblmfit.so) ===> Returning to build of gromacs-2025.0_1 ===> gromacs-2025.0_1 depends on shared library: libmuparser.so - not found ===> Installing existing package /packages/All/muparser-2.3.5.pkg [pkg-builder.dan.net.uk] Installing muparser-2.3.5... [pkg-builder.dan.net.uk] Extracting muparser-2.3.5: .......... done ===> gromacs-2025.0_1 depends on shared library: libmuparser.so - found (/usr/local/lib/libmuparser.so) ===> Returning to build of gromacs-2025.0_1 ===> gromacs-2025.0_1 depends on shared library: libfftw3.so - not found ===> Installing existing package /packages/All/fftw3-3.3.10_5.pkg [pkg-builder.dan.net.uk] Installing fftw3-3.3.10_5... [pkg-builder.dan.net.uk] Extracting fftw3-3.3.10_5: .......... done ===> gromacs-2025.0_1 depends on shared library: libfftw3.so - found (/usr/local/lib/libfftw3.so) ===> Returning to build of gromacs-2025.0_1 ===> gromacs-2025.0_1 depends on shared library: libhwloc.so - not found ===> Installing existing package /packages/All/hwloc2-2.11.2.pkg [pkg-builder.dan.net.uk] Installing hwloc2-2.11.2... [pkg-builder.dan.net.uk] `-- Installing level-zero-1.21.9... [pkg-builder.dan.net.uk] | `-- Installing libfmt-10.2.1... [pkg-builder.dan.net.uk] | `-- Extracting libfmt-10.2.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing spdlog-1.15.2... [pkg-builder.dan.net.uk] | `-- Extracting spdlog-1.15.2: .......... done [pkg-builder.dan.net.uk] `-- Extracting level-zero-1.21.9: .......... done [pkg-builder.dan.net.uk] `-- Installing libpciaccess-0.18.1_1... [pkg-builder.dan.net.uk] | `-- Installing hwdata-0.394,1... [pkg-builder.dan.net.uk] | `-- Extracting hwdata-0.394,1: ...... done [pkg-builder.dan.net.uk] `-- Extracting libpciaccess-0.18.1_1: ..... done [pkg-builder.dan.net.uk] `-- Installing libxml2-2.11.9... [pkg-builder.dan.net.uk] `-- Extracting libxml2-2.11.9: .......... done [pkg-builder.dan.net.uk] Extracting hwloc2-2.11.2: .......... done ===> gromacs-2025.0_1 depends on shared library: libhwloc.so - found (/usr/local/lib/libhwloc.so) ===> Returning to build of gromacs-2025.0_1 ===> gromacs-2025.0_1 depends on shared library: libblas.so - not found ===> Installing existing package /packages/All/blas-3.12.1.pkg [pkg-builder.dan.net.uk] Installing blas-3.12.1... [pkg-builder.dan.net.uk] `-- Installing gcc13-13.3.0_2... [pkg-builder.dan.net.uk] | `-- Installing binutils-2.44,1... [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.7... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.10.0,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.10.0,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.7: .......... done [pkg-builder.dan.net.uk] | `-- Extracting binutils-2.44,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | | `-- Installing mpfr-4.2.2,1... [pkg-builder.dan.net.uk] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] `-- Extracting gcc13-13.3.0_2: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) [pkg-builder.dan.net.uk] Extracting blas-3.12.1: ..... done ===== Message from gcc13-13.3.0_2: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> gromacs-2025.0_1 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> Returning to build of gromacs-2025.0_1 ===> gromacs-2025.0_1 depends on shared library: liblapack.so - not found ===> Installing existing package /packages/All/lapack-3.12.1.pkg [pkg-builder.dan.net.uk] Installing lapack-3.12.1... [pkg-builder.dan.net.uk] Extracting lapack-3.12.1: .......... done ===> gromacs-2025.0_1 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) ===> Returning to build of gromacs-2025.0_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for gromacs-2025.0_1 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/science/gromacs/work/.build -- The C compiler identification is Clang 18.1.6 -- The CXX compiler identification is Clang 18.1.6 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/local/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test HAVE_CRAY_MACRO -- Performing Test HAVE_CRAY_MACRO - Failed -- Performing Test CXX17_COMPILES_SIMPLY -- Performing Test CXX17_COMPILES_SIMPLY - Success -- Found Python3: /usr/local/bin/python3.11 (found suitable version "3.11.12", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp=libomp (found version "5.1") -- Found OpenMP_CXX: -fopenmp=libomp (found version "5.1") -- Found OpenMP: TRUE (found version "5.1") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_WARN_NO_RESERVED_IDENTIFIER -- Performing Test CXXFLAGS_WARN_NO_RESERVED_IDENTIFIER - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file pwd.h -- Looking for include file pwd.h - found -- Looking for include file dirent.h -- Looking for include file dirent.h - found -- Looking for include file time.h -- Looking for include file time.h - found -- Looking for include file sys/time.h -- Looking for include file sys/time.h - found -- Looking for include file io.h -- Looking for include file io.h - not found -- Looking for include file sched.h -- Looking for include file sched.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Checking for _mm_malloc() -- Checking for _mm_malloc() - supported -- Looking for posix_memalign -- Looking for posix_memalign - found -- Looking for memalign -- Looking for memalign - not found -- Torch not found. Neural network potential support will be disabled. -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Looking for HWLOC -- Looking for hwloc_topology_init -- Looking for hwloc_topology_init - found -- hwloc version: -- Found HWLOC: /usr/local/lib/libhwloc.so (found suitable version "2.11.2", minimum required is "1.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test TEST_ATOMICS -- Performing Test TEST_ATOMICS - Success -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Failed -- SIMD instructions disabled -- Performing Test _callconv___vectorcall -- Performing Test _callconv___vectorcall - Success -- Checking for GCC x86 inline asm -- Checking for GCC x86 inline asm - supported -- Detected build CPU vendor - Intel -- Detected build CPU brand - Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz -- Detected build CPU family - 6 -- Detected build CPU model - 79 -- Detected build CPU stepping - 0 -- Detected build CPU features - aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma intel lahf mmx msr nonstop_tsc pcid pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic -- Checking for 64-bit off_t -- Checking for 64-bit off_t - present -- Checking for fseeko/ftello -- Checking for fseeko/ftello - present -- Checking for SIGUSR1 -- Checking for SIGUSR1 - found -- Checking for pipe support -- Checking for system XDR support -- Checking for system XDR support - present -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Looking for fftw_plan_many_dft in /usr/local/lib/libfftw3.so -- Looking for fftw_plan_many_dft in /usr/local/lib/libfftw3.so - found -- Looking for fftw_plan_many_dft_r2c in /usr/local/lib/libfftw3.so -- Looking for fftw_plan_many_dft_r2c in /usr/local/lib/libfftw3.so - found -- Looking for fftw_plan_many_dft_c2r in /usr/local/lib/libfftw3.so -- Looking for fftw_plan_many_dft_c2r in /usr/local/lib/libfftw3.so - found -- Looking for fftw_have_simd_sse in /usr/local/lib/libfftw3.so -- Looking for fftw_have_simd_sse in /usr/local/lib/libfftw3.so - not found -- Looking for fftw_have_sse in /usr/local/lib/libfftw3.so -- Looking for fftw_have_sse in /usr/local/lib/libfftw3.so - not found -- Looking for fftw_have_simd_sse2 in /usr/local/lib/libfftw3.so -- Looking for fftw_have_simd_sse2 in /usr/local/lib/libfftw3.so - found -- Using external FFT library - FFTW3 -- Found BLAS: /usr/local/lib/libblas.so -- Found LAPACK: /usr/local/lib/liblapack.so -- No image conversion possible without ImageMagick -- Performing Test HAS_WARNING_EVERYTHING -- Performing Test HAS_WARNING_EVERYTHING - Success -- Performing Test HAS_WARNING_NO_CPLUSPLUS98_COMPAT -- Performing Test HAS_WARNING_NO_CPLUSPLUS98_COMPAT - Success -- Performing Test HAS_WARNING_NO_CPLUSPLUS98_COMPAT_PEDANTIC -- Performing Test HAS_WARNING_NO_CPLUSPLUS98_COMPAT_PEDANTIC - Success -- Performing Test HAS_WARNING_NO_RETURN_STD_MOVE_IN_CPLUSPLUS11 -- Performing Test HAS_WARNING_NO_RETURN_STD_MOVE_IN_CPLUSPLUS11 - Failed -- Performing Test HAS_WARNING_NO_SOURCE_USED_OPENMP -- Performing Test HAS_WARNING_NO_SOURCE_USED_OPENMP - Success -- Performing Test HAS_WARNING_NO_CPLUSPLUS17_EXTENSIONS -- Performing Test HAS_WARNING_NO_CPLUSPLUS17_EXTENSIONS - Success -- Performing Test HAS_WARNING_NO_DOCUMENTATION_UNKNOWN_COMMAND -- Performing Test HAS_WARNING_NO_DOCUMENTATION_UNKNOWN_COMMAND - Success -- Performing Test HAS_WARNING_NO_COVERED_SWITCH_DEFAULT -- Performing Test HAS_WARNING_NO_COVERED_SWITCH_DEFAULT - Success -- Performing Test HAS_WARNING_NO_SWITCH_ENUM -- Performing Test HAS_WARNING_NO_SWITCH_ENUM - Success -- Performing Test HAS_WARNING_NO_SWITCH_DEFAULT -- Performing Test HAS_WARNING_NO_SWITCH_DEFAULT - Success -- Performing Test HAS_WARNING_NO_EXTRA_SEMI_STMT -- Performing Test HAS_WARNING_NO_EXTRA_SEMI_STMT - Success -- Performing Test HAS_WARNING_NO_WEAK_VTABLES -- Performing Test HAS_WARNING_NO_WEAK_VTABLES - Success -- Performing Test HAS_WARNING_NO_SHADOW -- Performing Test HAS_WARNING_NO_SHADOW - Success -- Performing Test HAS_WARNING_NO_PADDED -- Performing Test HAS_WARNING_NO_PADDED - Success -- Performing Test HAS_WARNING_NO_RESERVED_ID_MACRO -- Performing Test HAS_WARNING_NO_RESERVED_ID_MACRO - Success -- Performing Test HAS_WARNING_NO_DOUBLE_PROMOTION -- Performing Test HAS_WARNING_NO_DOUBLE_PROMOTION - Success -- Performing Test HAS_WARNING_NO_EXIT_TIME_DESTRUCTORS -- Performing Test HAS_WARNING_NO_EXIT_TIME_DESTRUCTORS - Success -- Performing Test HAS_WARNING_NO_GLOBAL_CONSTRUCTORS -- Performing Test HAS_WARNING_NO_GLOBAL_CONSTRUCTORS - Success -- Performing Test HAS_WARNING_NO_DOCUMENTATION -- Performing Test HAS_WARNING_NO_DOCUMENTATION - Success -- Performing Test HAS_WARNING_NO_FORMAT_NONLITERAL -- Performing Test HAS_WARNING_NO_FORMAT_NONLITERAL - Success -- Performing Test HAS_WARNING_NO_USED_BUT_MARKED_UNUSED -- Performing Test HAS_WARNING_NO_USED_BUT_MARKED_UNUSED - Success -- Performing Test HAS_WARNING_NO_FLOAT_EQUAL -- Performing Test HAS_WARNING_NO_FLOAT_EQUAL - Success -- Performing Test HAS_WARNING_CONDITIONAL_UNINITIALIZED -- Performing Test HAS_WARNING_CONDITIONAL_UNINITIALIZED - Success -- Performing Test HAS_WARNING_NO_CONVERSION -- Performing Test HAS_WARNING_NO_CONVERSION - Success -- Performing Test HAS_WARNING_NO_DISABLED_MACRO_EXPANSION -- Performing Test HAS_WARNING_NO_DISABLED_MACRO_EXPANSION - Success -- Performing Test HAS_WARNING_NO_UNUSED_MACROS -- Performing Test HAS_WARNING_NO_UNUSED_MACROS - Success -- Performing Test HAS_WARNING_NO_UNSAFE_BUFFER_USAGE -- Performing Test HAS_WARNING_NO_UNSAFE_BUFFER_USAGE - Success -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT -- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success -- Performing Test HAS_WARNING_NO_GNU_ZERO_VARIADIC_MACRO_ARGUMENTS -- Performing Test HAS_WARNING_NO_GNU_ZERO_VARIADIC_MACRO_ARGUMENTS - Success -- Performing Test HAS_WARNING_NO_UNUSED_MEMBER_FUNCTION -- Performing Test HAS_WARNING_NO_UNUSED_MEMBER_FUNCTION - Success -- Found Python: /usr/local/bin/python3.11 (found version "3.11.12") found components: Interpreter -- Performing Test HAVE_NO_DEPRECATED_COPY -- Performing Test HAVE_NO_DEPRECATED_COPY - Success -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION -- Performing Test HAVE_NO_IMPLICIT_INT_FLOAT_CONVERSION - Success -- Performing Test HAS_NO_STRINGOP_TRUNCATION -- Performing Test HAS_NO_STRINGOP_TRUNCATION - Failed -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT -- Performing Test HAS_WARNING_NO_CAST_FUNCTION_TYPE_STRICT - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_UNUSED_PARAMETER -- Performing Test HAS_NO_UNUSED_PARAMETER - Success -- Performing Test HAS_NO_MISSING_DECLARATIONS -- Performing Test HAS_NO_MISSING_DECLARATIONS - Success -- Performing Test HAS_NO_NULL_CONVERSIONS -- Performing Test HAS_NO_NULL_CONVERSIONS - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Performing Test HAS_WARNING_NO_DEPRECATED_NON_PROTOTYPE -- Performing Test HAS_WARNING_NO_DEPRECATED_NON_PROTOTYPE - Success -- Performing Test LMFIT_LINKS_OK -- Performing Test LMFIT_LINKS_OK - Success -- Found Lmfit: /usr/local/include (found suitable version "9.0.0", minimum required is "7.0") -- Looking for dlopen -- Looking for dlopen - found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "4.0.0") -- Could NOT find LATEX (missing: LATEX_COMPILER) -- Configuring done (18.9s) -- Generating done (0.8s) CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_COLOR_MAKEFILE CMAKE_MODULE_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED Python_ADDITIONAL_VERSIONS -- Build files have been written to: /wrkdirs/usr/ports/science/gromacs/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for gromacs-2025.0_1 [ 0% 1/1015] cd /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0 && /usr/local/bin/cmake -D PYTHON_EXECUTABLE=/usr/local/bin/python3.11 -D PROJECT_VERSION=2025.0 -D PROJECT_SOURCE_DIR=/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0 -D VERSION_CMAKEIN=/wrkdirs/usr/ports/science/gromacs/work/.build/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/wrkdirs/usr/ports/science/gromacs/work/.build/VersionInfo.cmake -D VERSION_STRING_OF_FORK= -P /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake [ 0% 2/1015] /usr/local/libexec/ccache/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/include -I/wrkdirs/usr/ports/science/gromacs/work/.build/src/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/external/thread_mpi/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -fPIC -Wno-reserved-identifier 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src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -MF src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o.d -o src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/external/thread_mpi/src/atomic.cpp [ 0% 5/1015] /usr/local/libexec/ccache/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/include -I/wrkdirs/usr/ports/science/gromacs/work/.build/src/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/external/thread_mpi/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -fPIC -Wno-reserved-identifier -Wno-missing-field-initializers -MD -MT src/gromacs/CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -MF 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/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/external -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -Wno-reserved-identifier -Wno-missing-field-initializers -MD -MT src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -MF src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o.d -o src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/programs/mdrun/nonbonded_bench.cpp [ 99% 1013/1015] /usr/local/libexec/ccache/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/include -I/wrkdirs/usr/ports/science/gromacs/work/.build/src/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/api/legacy/include -I/wrkdirs/usr/ports/science/gromacs/work/.build/api/legacy/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/gromacs/utility/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/external -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -MF src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o.d -o src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/programs/gmx.cpp [ 99% 1014/1015] /usr/local/libexec/ccache/c++ -DGMX_DOUBLE=1 -DTMPI_USE_VISIBILITY -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/include -I/wrkdirs/usr/ports/science/gromacs/work/.build/src/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/api/legacy/include -I/wrkdirs/usr/ports/science/gromacs/work/.build/api/legacy/include -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src -I/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/gromacs/utility/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/external/thread_mpi/include -isystem /usr/local/include -isystem /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/external -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -std=c++17 -MD -MT src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -MF src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o.d -o src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o -c /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/src/programs/legacymodules.cpp [100% 1015/1015] : && /usr/local/libexec/ccache/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -L/usr/local/lib -fstack-protector-strong -Xlinker --dependency-file=src/programs/CMakeFiles/gmx.dir/link.d src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o src/programs/CMakeFiles/gmx_objlib.dir/legacymodules.cpp.o src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o src/programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o bin/gmx_d -Wl,-rpath,"\$ORIGIN/../lib" lib/libgromacs_d.so.10.0.0 /usr/lib/libm.so /usr/lib/libomp.so && : =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gromacs-2025.0_1 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for gromacs-2025.0_1 ===> Generating temporary packing list [ 7% 1/14] cd /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0 && /usr/local/bin/cmake -D PYTHON_EXECUTABLE=/usr/local/bin/python3.11 -D PROJECT_VERSION=2025.0 -D PROJECT_SOURCE_DIR=/wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0 -D VERSION_CMAKEIN=/wrkdirs/usr/ports/science/gromacs/work/.build/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/wrkdirs/usr/ports/science/gromacs/work/.build/VersionInfo.cmake -D VERSION_STRING_OF_FORK= -P /wrkdirs/usr/ports/science/gromacs/work/gromacs-2025.0/cmake/gmxGenerateVersionInfoWithoutGit.cmake [ 50% 2/2] cd /wrkdirs/usr/ports/science/gromacs/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/gromacs/COPYING -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/gromacs/template/CMakeLists.txt -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/gromacs/template/README -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/gromacs/template/template.cpp -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/gromacs/template/Makefile.pkg -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/gromacs/template/cmake/FindGROMACS.cmake -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/gromacs/README.tutor -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/gromacs/README_FreeEnergyModifications.txt -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/gromacs/top -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/gromacs/top/ffG45a3.itp -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/gromacs/top/surface.dat -- Installing: 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Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-mdrun.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-convert-tpr.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-analyze.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-clustsize.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-energy.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-tune_pme.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-solvate.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-nmr.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-mdmat.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-dos.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-convert-trj.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-densmap.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-rotacf.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-genrestr.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-trjorder.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-sigeps.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-gyrate-legacy.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-spol.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-report-methods.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-helixorient.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-disre.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-filter.1 -- Installing: /wrkdirs/usr/ports/science/gromacs/work/stage/usr/local/share/man/man1/gmx-velacc.1 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-05-02T09:31:21+0000' 'PKG_NOTE_ports_top_git_hash=5529c5919b' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=abc07dd3b2' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for gromacs-2025.0_1 ===> Building gromacs-2025.0_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for gromacs-2025.0_1 build of science/gromacs | gromacs-2025.0_1 ended at Fri May 2 11:11:10 BST 2025 build time: 00:39:49