sci-chemistry:gromacs-2025.0_beta:20241126-082627.log

sci-chemistry:gromacs-2025.0_beta:20241126-082627.log (text/plain), 24.41 KB, created by Toralf Förster on 2024-11-26 18:46:57 UTC

 * Package:    sci-chemistry/gromacs-2025.0_beta:0/2025.0_beta
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail]
 * USE:        abi_x86_64 amd64 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 custom-cflags doc double-precision elibc_glibc fftw gmxapi hwloc kernel_linux lapack offensive opencl openmp python_single_target_python3_12 single-precision threads tng
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
 * Using python3.12 to build
>>> Unpacking source...
>>> Unpacking gromacs-2025.0-beta.tar.gz to /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work
=== Skipping unpack of manual-2025.0-beta.pdf
>>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta ...
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta_build"
 * Applying gromacs-gcc-15.patch ...
patching file src/gromacs/mdtypes/energyhistory.h
Hunk #1 succeeded at 49 with fuzz 2 (offset 2 lines).
 [ ok ]
 * 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
 * Hardcoded definition(s) removed in src/external/muparser/CMakeLists.txt:
 *    set (CMAKE_BUILD_TYPE Release CACHE STRING "Build type")
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta ...
 * Configuring for float precision
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0_beta_float"
cmake -C /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0_beta_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=yes -DGMX_OPENMP=yes -DGMX_COOL_QUOTES=yes -DGMX_USE_TNG=yes -DGMX_BUILD_MANUAL=no -DGMX_USE_HDF5=off -DGMX_HWLOC=yes -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD=AVX2_256 -DGMX_NNPOT=OFF -DGMX_VMD_PLUGIN_PATH=/usr/lib64/vmd/plugins/*/molfile/ -DBUILD_TESTING=no -DGMX_BUILD_UNITTESTS=no -DPYTHON_EXECUTABLE=/usr/bin/python3.12 -DGMX_DOUBLE=OFF -DGMX_MPI=no -DGMX_THREAD_MPI=yes -DGMXAPI=yes -DGMX_INSTALL_LEGACY_API=no -DGMX_GPU=OPENCL  -DGMX_BINARY_SUFFIX= -DGMX_LIBS_SUFFIX= -DGMX_PYTHON_PACKAGE=no -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0_beta_float/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta
CMake Warning:
  Ignoring empty string ("") provided on the command line.


loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0_beta_float/gentoo_common_config.cmake
-- The C compiler identification is GNU 14.2.1
-- The CXX compiler identification is GNU 14.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc - 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/bin/x86_64-pc-linux-gnu-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/temp/python3.12/bin/python3 (found suitable version "3.12.7", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed
-- Selected GPU FFT library - clFFT
-- 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
-- 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
-- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway.  If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on.
-- Checking for module 'mpi-cxx'
--   Package 'mpi-cxx' not found
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) 
-- Could NOT find MPI (missing: MPI_CXX_FOUND CXX) 
-- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST
-- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success
-- Performing Test HAS_WARNING_NO_CAST_QUAL
-- Performing Test HAS_WARNING_NO_CAST_QUAL - Success
-- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE
-- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success
-- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE
-- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success
-- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT
-- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success
-- Using manually set binary suffix: ""
-- Using manually set library suffix: ""
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version: 
-- Found HWLOC: /usr/lib64/libhwloc.so (found suitable version "2.9.3", minimum required is "1.5")
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- 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 - Success
-- Performing Test C_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test C_mavx2_mfma_COMPILE_WORKS
-- Performing Test C_mavx2_mfma_COMPILE_WORKS - Success
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS - Success
-- Enabling 256-bit AVX2 SIMD instructions using CXX flags:  -mavx2 -mfma
-- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs
-- Performing Test C_march_skylake_avx512_FLAG_ACCEPTED
-- Performing Test C_march_skylake_avx512_FLAG_ACCEPTED - Success
-- Performing Test C_march_skylake_avx512_COMPILE_WORKS
-- Performing Test C_march_skylake_avx512_COMPILE_WORKS - Success
-- Performing Test CXX_march_skylake_avx512_FLAG_ACCEPTED
-- Performing Test CXX_march_skylake_avx512_FLAG_ACCEPTED - Success
-- Performing Test CXX_march_skylake_avx512_COMPILE_WORKS
-- Performing Test CXX_march_skylake_avx512_COMPILE_WORKS - Success
-- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs -  -march=skylake-avx512
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_ 
-- Performing Test _callconv_  - Success
-- GPU support with OpenCL is deprecated. It is still fully supported (and recommended for Apple GPUs). Please use CUDA for running on NVIDIA GPUs and SYCL for running on Intel and AMD GPUs.
-- Looking for CL_VERSION_3_0
-- Looking for CL_VERSION_3_0 - found
-- Found OpenCL: /usr/lib64/libOpenCL.so (found version "3.0")
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Detected build CPU vendor - AMD
-- Detected build CPU brand - AMD Ryzen 9 5950X 16-Core Processor
-- Detected build CPU family - 25
-- Detected build CPU model - 33
-- Detected build CPU stepping - 0
-- Detected build CPU features - aes amd apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4a sse4.1 sse4.2 ssse3
-- 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 - not present
-- Checking for module 'fftw3f'
--   Found fftw3f, version 3.3.10
-- Looking for fftwf_plan_many_dft in /usr/lib64/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib64/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib64/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib64/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib64/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib64/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib64/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib64/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib64/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib64/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- No image conversion possible without ImageMagick
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- 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
-- Found PkgConfig: /usr/bin/x86_64-pc-linux-gnu-pkg-config (found version "2.3.0")
-- Could NOT find clFFT (missing: clFFT_INCLUDE_DIR clFFT_LIBRARY) 
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- 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/include/include (found suitable version "9.0.0", minimum required is "7.0")
-- Performing Test HAS_WARNING_EVERYTHING
-- Performing Test HAS_WARNING_EVERYTHING - Failed
-- 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) (Required is at least version "4.0.0")
-- Could NOT find LATEX (missing: LATEX_COMPILER) 
-- <<< Gentoo configuration >>>
Build type      RelWithDebInfo
Install path    /usr
Compiler flags:
C               -O2 -pipe -march=native -fno-diagnostics-color
C++             -O2 -pipe -march=native -fno-diagnostics-color
Linker flags:
Executable        -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0
Module          -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0
Shared            -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0

-- Configuring done (17.0s)
-- Generating done (0.5s)
-- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0_beta_float
 * Configuring for double precision
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0_beta_double"
cmake -C /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0_beta_double/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=yes -DGMX_OPENMP=yes -DGMX_COOL_QUOTES=yes -DGMX_USE_TNG=yes -DGMX_BUILD_MANUAL=no -DGMX_USE_HDF5=off -DGMX_HWLOC=yes -DGMX_DEFAULT_SUFFIX=off -DGMX_SIMD=AVX2_256 -DGMX_NNPOT=OFF -DGMX_VMD_PLUGIN_PATH=/usr/lib64/vmd/plugins/*/molfile/ -DBUILD_TESTING=no -DGMX_BUILD_UNITTESTS=no -DPYTHON_EXECUTABLE=/usr/bin/python3.12 -DGMX_DOUBLE=ON -DGMX_MPI=no -DGMX_THREAD_MPI=yes -DGMXAPI=yes -DGMX_INSTALL_LEGACY_API=no -DGMX_GPU=OPENCL  -DGMX_BINARY_SUFFIX=_d -DGMX_LIBS_SUFFIX=_d -DGMX_PYTHON_PACKAGE=no -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0_beta_double/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta
CMake Warning:
  Ignoring empty string ("") provided on the command line.


loading initial cache file /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0_beta_double/gentoo_common_config.cmake
-- The C compiler identification is GNU 14.2.1
-- The CXX compiler identification is GNU 14.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc - 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/bin/x86_64-pc-linux-gnu-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python3: /var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/temp/python3.12/bin/python3 (found suitable version "3.12.7", minimum required is "3.9") found components: Interpreter Development Development.Module Development.Embed
-- Selected GPU FFT library - clFFT
-- 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
-- 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
-- GROMACS is being built without library MPI support (-DGMX_MPI=no). However MPI is potentially useful for the gmxapi Python API, so we will search for MPI anyway.  If this causes problems, disable the check with -DCMAKE_DISABLE_FIND_PACKAGE_MPI=on.
-- Checking for module 'mpi-cxx'
--   Package 'mpi-cxx' not found
-- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) 
-- Could NOT find MPI (missing: MPI_CXX_FOUND CXX) 
-- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST
-- Performing Test HAS_WARNING_NO_OLD_STYLE_CAST - Success
-- Performing Test HAS_WARNING_NO_CAST_QUAL
-- Performing Test HAS_WARNING_NO_CAST_QUAL - Success
-- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE
-- Performing Test HAS_WARNING_NO_SUGGEST_OVERRIDE - Success
-- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE
-- Performing Test HAS_WARNING_NO_SUGGEST_DESTRUCTOR_OVERRIDE - Success
-- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT
-- Performing Test HAS_WARNING_NO_ZERO_AS_NULL_POINTER_CONSTANT - Success
-- Using manually set binary suffix: "_d"
-- Using manually set library suffix: "_d"
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version: 
-- Found HWLOC: /usr/lib64/libhwloc.so (found suitable version "2.9.3", minimum required is "1.5")
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- 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 - Success
-- Performing Test C_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test C_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test C_mavx2_mfma_COMPILE_WORKS
-- Performing Test C_mavx2_mfma_COMPILE_WORKS - Success
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED
-- Performing Test CXX_mavx2_mfma_FLAG_ACCEPTED - Success
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS
-- Performing Test CXX_mavx2_mfma_COMPILE_WORKS - Success
-- Enabling 256-bit AVX2 SIMD instructions using CXX flags:  -mavx2 -mfma
-- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs
-- Performing Test C_march_skylake_avx512_FLAG_ACCEPTED
-- Performing Test C_march_skylake_avx512_FLAG_ACCEPTED - Success
-- Performing Test C_march_skylake_avx512_COMPILE_WORKS
-- Performing Test C_march_skylake_avx512_COMPILE_WORKS - Success
-- Performing Test CXX_march_skylake_avx512_FLAG_ACCEPTED
-- Performing Test CXX_march_skylake_avx512_FLAG_ACCEPTED - Success
-- Performing Test CXX_march_skylake_avx512_COMPILE_WORKS
-- Performing Test CXX_march_skylake_avx512_COMPILE_WORKS - Success
-- Detecting flags to enable runtime detection of AVX-512 units on newer CPUs -  -march=skylake-avx512
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED
-- Performing Test _Wno_unused_command_line_argument_FLAG_ACCEPTED - Success
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_ 
-- Performing Test _callconv_  - Success
-- GPU support with OpenCL is deprecated. It is still fully supported (and recommended for Apple GPUs). Please use CUDA for running on NVIDIA GPUs and SYCL for running on Intel and AMD GPUs.
CMake Error at cmake/gmxManageOpenCL.cmake:42 (message):
  OpenCL acceleration is not available in double precision
Call Stack (most recent call first):
  CMakeLists.txt:724 (include)


-- Configuring incomplete, errors occurred!
 * ERROR: sci-chemistry/gromacs-2025.0_beta::gentoo failed (configure phase):
 *   cmake failed
 * 
 * Call stack:
 *     ebuild.sh, line  136:  Called src_configure
 *   environment, line 4637:  Called cmake_src_configure
 *   environment, line 2060:  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-2025.0_beta::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/gromacs-2025.0_beta::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-chemistry:gromacs-2025.0_beta:20241126-082627.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0_beta_double'
 * S: '/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta'