* Package: sci-chemistry/gromacs-2024.1:0/2024.1 * Repository: gentoo * Maintainer: alexxy@gentoo.org sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 clang cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 custom-cflags doc elibc_glibc fftw gmxapi gmxapi-legacy hwloc kernel_linux openmp python_single_target_python3_11 single-precision threads tng * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox * Using python3.11 to build >>> Unpacking source... >>> Unpacking gromacs-2024.1.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-2024.1/work >>> Unpacking manual-2024.1.pdf to /var/tmp/portage/sci-chemistry/gromacs-2024.1/work unpack manual-2024.1.pdf: file format not recognized. Ignoring. >>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-2024.1/work >>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-2024.1/work/gromacs-2024.1 ... * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2024.1/work/gromacs-2024.1" * Build directory (BUILD_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2024.1/work/gromacs-2024.1_build" * Hardcoded definition(s) removed in src/external/muparser/CMakeLists.txt: * set (CMAKE_BUILD_TYPE Release CACHE STRING "Build type") * Hardcoded definition(s) removed in CMakeLists.txt: * set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation * set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, op >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-2024.1/work/gromacs-2024.1 ... * Configuring for float precision * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2024.1/work/gromacs-2024.1" * Build directory (BUILD_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2024.1/work/gromacs-2024.1_float" cmake -C /var/tmp/portage/sci-chemistry/gromacs-2024.1/work/gromacs-2024.1_float/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DGMX_FFT_LIBRARY=fftw3 -DGMX_USE_LMFIT=EXTERNAL -DGMX_USE_MUPARSER=EXTERNAL -DGMX_EXTERNAL_BLAS=no -DGMX_EXTERNAL_LAPACK=no -DGMX_OPENMP=yes -DGMX_COOL_QUOTES=no -DGMX_USE_TNG=yes -DGMX_BUILD_MANUAL=no -DGMX_HWLOC=yes -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD=AVX2_256 -DGMX_VMD_PLUGIN_PATH=/usr/lib64/vmd/plugins/*/molfile/ -DBUILD_TESTING=no -DGMX_BUILD_UNITTESTS=no -DPYTHON_EXECUTABLE=/usr/bin/python3.11 -DGMX_DOUBLE=OFF -DGMX_MPI=no -DGMX_THREAD_MPI=yes -DGMXAPI=yes -DGMX_INSTALL_LEGACY_API=yes -DGMX_GPU=OFF -DGMX_BINARY_SUFFIX= -DGMX_LIBS_SUFFIX= -DGMX_PYTHON_PACKAGE=no -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/gromacs-2024.1/work/gromacs-2024.1_float/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/gromacs-2024.1/work/gromacs-2024.1 CMake Warning: Ignoring empty string ("") provided on the command line. loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-2024.1/work/gromacs-2024.1_float/gentoo_common_config.cmake -- The C compiler identification is Clang 18.1.2 -- The CXX compiler identification is Clang 18.1.2 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/lib/llvm/18/bin/x86_64-pc-linux-gnu-clang - 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/lib/llvm/18/bin/x86_64-pc-linux-gnu-clang++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test CXX17_COMPILES_SIMPLY -- Performing Test CXX17_COMPILES_SIMPLY - Success -- Found Python3: /var/tmp/portage/sci-chemistry/gromacs-2024.1/temp/python3.11/bin/python3 (found suitable version "3.11.8", minimum required is "3.7") found components: Interpreter Development Development.Module Development.Embed -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) CMake Error at cmake/gmxManageOpenMP.cmake:50 (message): The compiler you are using does not support OpenMP parallelism. This might hurt your performance a lot, in particular with GPUs. Try using a more recent version, or a different compiler. If you don't want to use OpenMP, disable it explicitly with -DGMX_OPENMP=OFF Call Stack (most recent call first): CMakeLists.txt:421 (include) -- Configuring incomplete, errors occurred! * ERROR: sci-chemistry/gromacs-2024.1::gentoo failed (configure phase): * cmake failed * * Call stack: * ebuild.sh, line 136: Called src_configure * environment, line 4573: Called cmake_src_configure * environment, line 1998: Called die * The specific snippet of code: * "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake failed"; * * If you need support, post the output of `emerge --info '=sci-chemistry/gromacs-2024.1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-chemistry/gromacs-2024.1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-chemistry:gromacs-2024.1:20240327-182807.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/gromacs-2024.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-2024.1/temp/environment'. * Working directory: '/var/tmp/portage/sci-chemistry/gromacs-2024.1/work/gromacs-2024.1_float' * S: '/var/tmp/portage/sci-chemistry/gromacs-2024.1/work/gromacs-2024.1'