------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for gromacs-2023.1: ATLAS=off: Use ATLAS for BLAS and LAPACK FLOAT=off: Use single instead of double precision LEGACY=on: Install legacy API 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 3 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- F77="gfortran12" F90="gfortran12" FC="gfortran12" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc12" 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/python3.9" BLA_VENDOR="Generic" XDG_DATA_HOME=/construction/science/gromacs XDG_CONFIG_HOME=/construction/science/gromacs XDG_CACHE_HOME=/construction/science/gromacs/.cache HOME=/construction/science/gromacs TMPDIR="/tmp" PATH=/construction/science/gromacs/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/gromacs/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- F77="gfortran12" F90="gfortran12" FC="gfortran12" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc12" PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/science/gromacs XDG_CONFIG_HOME=/construction/science/gromacs XDG_CACHE_HOME=/construction/science/gromacs/.cache HOME=/construction/science/gromacs TMPDIR="/tmp" PATH=/construction/science/gromacs/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/gromacs/.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 CCVER=gcc80 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" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc12 -L/usr/local/lib/gcc12 -B/usr/local/bin -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS=" -pipe -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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/science/gromacs/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- ATLAS="@comment " NO_ATLAS="" FLOAT="@comment " NO_FLOAT="" SUFFIX_D="_d" LEGACY="" NO_LEGACY="@comment " MPICH="@comment " NO_MPICH="" NOMP="@comment " NO_NOMP="" OPENCL="@comment " NO_OPENCL="" OPENMP="" NO_OPENMP="@comment " OPENMPI="@comment " NO_OPENMPI="" SIMD="@comment " NO_SIMD="" THREAD_MPI="" NO_THREAD_MPI="@comment " SUFFIX_MPI="" X11="" NO_X11="@comment " CMAKE_BUILD_TYPE="release" GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 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/5.32 PROFILE="@comment " DOCSDIR="share/doc/gromacs" EXAMPLESDIR="share/examples/gromacs" DATADIR="share/gromacs" WWWDIR="www/gromacs" ETCDIR="etc/gromacs" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- ATLAS="@comment " NO_ATLAS="" FLOAT="@comment " NO_FLOAT="" LEGACY="" NO_LEGACY="@comment " MPICH="@comment " NO_MPICH="" NOMP="@comment " NO_NOMP="" OPENCL="@comment " NO_OPENCL="" OPENMP="" NO_OPENMP="@comment " OPENMPI="@comment " NO_OPENMPI="" SIMD="@comment " NO_SIMD="" THREAD_MPI="" NO_THREAD_MPI="@comment " X11="" NO_X11="@comment " PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/icu-73.2,1.pkg Installing /packages/All/boost-libs-1.82.0_1.pkg ===== Message from boost-libs-1.82.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/libuv-1.46.0.pkg Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/rhash-1.4.3.pkg Installing /packages/All/pkg-1.19.2.pkg Installing /packages/All/liblz4-1.9.4,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/zstd-1.5.5.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libarchive-3.6.2,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/ncurses-6.4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/cmake-core-3.26.1_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gmp-6.2.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/mpfr-4.2.0_1,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/mpc-1.3.1_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/binutils-2.40_4,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/gcc12-12.2.0_6.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from gcc12-12.2.0_6: -- 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/gcc12 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/pkgconf-1.8.1,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libffi-3.4.4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/mpdecimal-2.5.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/readline-8.2.1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/python39-3.9.17.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required ===== Message from python39-3.9.17: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 Installing /packages/All/perl5-5.32.1_3.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libICE-1.1.0_1,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libSM-1.2.3,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXau-1.0.9.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/xorgproto-2022.1_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXdmcp-1.1.3.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libxcb-1.15_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libX11-1.8.6,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libXext-1.3.4,1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/ccache-3.7.12_4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required 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 gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) create symlink for gcc12 create symlink for gcc12 (world) create symlink for g++12 create symlink for g++12 (world) create symlink for cpp12 create symlink for cpp12 (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. Installing /packages/All/fftw3-3.3.10_3.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/libxml2-2.10.4.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/blas-3.11.0_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required Installing /packages/All/lapack-3.11.0_1.pkg pkg: Repository Avalon cannot be opened. 'pkg update' required UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:22 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> gromacs-2023.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> gromacs-2023.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gromacs-2023.1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> gromacs-2023.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gromacs-2023.1 for building => SHA256 Checksum OK for gromacs-2023.1.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> gromacs-2023.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gromacs-2023.1 for building ===> Extracting for gromacs-2023.1 ===> gromacs-2023.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gromacs-2023.1 for building => SHA256 Checksum OK for gromacs-2023.1.tar.gz. Extracted Memory Use: 141.69M SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for gromacs-2023.1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> gromacs-2023.1 depends on package: boost-libs>=1.44 - found ===> gromacs-2023.1 depends on file: /usr/local/bin/cmake - found ===> gromacs-2023.1 depends on executable: gfortran12 - found ===> gromacs-2023.1 depends on package: pkgconf>=1.3.0_1 - found ===> gromacs-2023.1 depends on file: /usr/local/bin/python3.9 - found ===> gromacs-2023.1 depends on file: /usr/local/bin/as - found ===> gromacs-2023.1 depends on package: perl5>=5.32.r0<5.33 - found ===> gromacs-2023.1 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> gromacs-2023.1 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found ===> gromacs-2023.1 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> gromacs-2023.1 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> gromacs-2023.1 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> gromacs-2023.1 depends on shared library: libfftw3.so - found (/usr/local/lib/libfftw3.so) ===> gromacs-2023.1 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) ===> gromacs-2023.1 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> gromacs-2023.1 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> gromacs-2023.1 depends on package: boost-libs>=1.44 - found ===> gromacs-2023.1 depends on file: /usr/local/bin/cmake - found ===> gromacs-2023.1 depends on executable: gfortran12 - found ===> gromacs-2023.1 depends on package: pkgconf>=1.3.0_1 - found ===> gromacs-2023.1 depends on file: /usr/local/bin/python3.9 - found ===> gromacs-2023.1 depends on file: /usr/local/bin/as - found ===> gromacs-2023.1 depends on package: perl5>=5.32.r0<5.33 - found ===> gromacs-2023.1 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> gromacs-2023.1 depends on file: /usr/local/libdata/pkgconfig/sm.pc - found ===> gromacs-2023.1 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> gromacs-2023.1 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> gromacs-2023.1 depends on file: /usr/local/bin/ccache - found ===> gromacs-2023.1 depends on shared library: libfftw3.so - found (/usr/local/lib/libfftw3.so) ===> gromacs-2023.1 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) ===> gromacs-2023.1 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so) ===> gromacs-2023.1 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) ===> Configuring for gromacs-2023.1 ===> Performing out-of-source build /bin/mkdir -p /construction/science/gromacs/.build -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- 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 CMake Warning at cmake/gmxPythonDiscovery.cmake:51 (message): Specifying FindPython3 artifacts may complicate consistent Python detection in projects bundled with GROMACS. See https://cmake.org/cmake/help/latest/module/FindPython3.html#artifacts-specification Call Stack (most recent call first): CMakeLists.txt:95 (include) -- Found Python3: /usr/local/bin/python3.9 (found suitable version "3.9.17", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CFLAGS_EXCESS_PREC -- Performing Test CFLAGS_EXCESS_PREC - Success -- Performing Test CFLAGS_COPT -- Performing Test CFLAGS_COPT - Success -- Performing Test CFLAGS_NOINLINE -- Performing Test CFLAGS_NOINLINE - Success -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS -- Performing Test CXXFLAGS_WARN_NO_MISSING_FIELD_INITIALIZERS - Success -- Performing Test CXXFLAGS_EXCESS_PREC -- Performing Test CXXFLAGS_EXCESS_PREC - Success -- Performing Test CXXFLAGS_COPT -- Performing Test CXXFLAGS_COPT - Success -- Performing Test CXXFLAGS_NOINLINE -- Performing Test CXXFLAGS_NOINLINE - Success CMake Error at cmake/gmxTestCompilerProblems.cmake:69 (message): GCC version 9 or later required. Earlier versions don't have full C++17 support. Call Stack (most recent call first): CMakeLists.txt:403 (gmx_test_compiler_problems) -- Configuring incomplete, errors occurred! *** Error code 1 Stop. make[1]: stopped in /xports/science/gromacs *** Error code 1 Stop. make: stopped in /xports/science/gromacs FAILED 00:00:06