Re: [gmx-users] nvcc fatal: 'avx512f': expected a number
Dear Mark, Sincere thanks for your swift reply, and apologies for the duplicate message; I realized that my original message had no subject, so, I thought it is more proper to send the message with a meaningful topic; Regarding your comment, I am building GROMACS from source, and without intervention from EasyBuild. In order to be transparent, I also put my full cmake command arguments in the original message as well. Since some other dependencies are installed by EasyBuild as modules, I am setting some of the paths in a compatible way on our system, hence e.g. EBROOTCUDA, etc. To double check your feedback, let me ask the following: I am explicitly setting the flag -DGMX_SIMD='AVX_512'. Is it equivalent to the flag you proposed (-mavx512f), or I have to add the latter to the argument list to cmake, too? Sincere thanks, Ehsan On Wed, Oct 24, 2018 at 10:42 AM Mark Abraham wrote: > Hi, > > You sent this email yesterday. Please be a little more patient. > > Unfortunately, I have no idea how EasyBuild works, and suspect that the > problem lies in the way it is wrapping arguments that then get passed to > nvcc. If you can reproduce this issue with a simple call to cmake with > minimal extra stuff, then we can explore whether there's an issue with the > GROMACS build system. But since -mavx512f is a valid compiler flag that > GROMACS checked was valid before using it, I suspect the problem isn't > ours. > > Mark > > On Wed, Oct 24, 2018 at 9:55 AM Ehsan Moravveji > wrote: > > > Dear GMX users, > > > > I would like to share a difficulty installing GROMACS/2018.3 with you, > > and kindly ask for your wisdom. > > > > I use GCC/6.4.0 on a Linux cluster with CentOS 7.5 kernel and GPU > > nodes equipped with 4 x P100 Nvidia devices. > > > > > > Below is the cmake configuration that I use, followed by the error (in > > boldface font) that I > > receive. I am not sure if there is still an extra flag to set to resolve > > this issue, or some other steps must be taken? > > > > I appreciate your input. > > > > -- > > Kind regards, > > Ehsan Moravveji > > > > ### > > cmake "${cwd}/${dir_src}" \ > > -DGMX_SIMD='AVX_512' \ > > -DBLAS_mkl_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \ > > -DLAPACK_mkl_lapack_LIBRARY="DIR_MKL_LIB/libmkl_sequential.so" \ > > -DBLAS_guide_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \ > > -DCMAKE_C_COMPILER="${GMX_MPICC}" -DCMAKE_CXX_COMPILER="${GMX_MPICXX}" > \ > > -DMPI_C_COMPILER="${GMX_MPICC}" -DMPI_CXX_COMPILER="${GMX_MPICXX}" \ > > -DCMAKE_MPI_C_COMPILER="${GMX_MPICC}" > > -DCMAKE_MPI_CXX_COMPILER="${GMX_MPICXX}" \ > > -DCMAKE_INSTALL_PREFIX="${dir_install}" \ > > -DCMAKE_PREFIX_PATH="${DIR_MKL_LIB}" \ > > -DCMAKE_VERBOSE_MAKEFILE=ON \ > > -DGMX_MPI=ON \ > > -DGMX_GPU=ON \ > > -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF -DEXTRA_CXX_FLAGS="-std=c++11" \ > > -DGMX_USE_NVML=ON -DGMX_BUILD_OWN_FFTW=ON \ > > -DHWLOC_INCLUDE_DIRS="${EBROOTHWLOC}/include" > > -DHWLOC_LIBRARIES="${EBROOTHWLOC}/lib/libhwloc.so" \ > > -DCUDA_HOST_COMPILER="${PATH_NVCC}" > > -DNVML_INCLUDE_DIR="${EBROOTCUDA}/include" \ > > -DNVML_LIBRARY="${EBROOTCUDA}/lib64/stubs/libnvidia-ml.so" \ > > -DCUDA_TOOLKIT_ROOT_DIR="${EBROOTCUDA}" > > -DCUDA_SDK_ROOT_DIR="${EBROOTCUDA}" \ > > -DCUDA_PROPAGATE_HOST_FLAGS=ON -DCUDA_VERBOSE_BUILD=ON \ > > -DGMX_CUDA_TARGET_SM="${SM_VER}" -DGMX_CUDA_TARGET_COMPUTE="${SM_VER}" > \ > > -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF \ > > -DCUDA_CUDART_LIBRARY="${EBROOTCUDA}/lib64/libcudart.so" > > -DCUDA_CUDA_LIBRARY="${EBROOTCUDA}/lib64/libcuda.so" \ > > > > > > > -DCUDA_NVCC_FLAGS="-gencode;arch=compute_${SM_VER},code=compute_${SM_VER};-use_fast_math;-D_FORCE_INLINES" > > \ > > -DGMX_PREFER_STATIC_LIBS=OFF -DGMX_X11=OFF > > > > ### > > > > -- Generating dependency file: > > > > > /work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend > > /software/CUDA/9.2.148/bin/nvcc -M -D__CUDACC__ > > /work/GROMACS/gromacs-2018.3/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu > -o > > > > > /work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nb
[gmx-users] nvcc fatal: 'avx512f': expected a number
Dear GMX users, I would like to share a difficulty installing GROMACS/2018.3 with you, and kindly ask for your wisdom. I use GCC/6.4.0 on a Linux cluster with CentOS 7.5 kernel and GPU nodes equipped with 4 x P100 Nvidia devices. Below is the cmake configuration that I use, followed by the error (in boldface font) that I receive. I am not sure if there is still an extra flag to set to resolve this issue, or some other steps must be taken? I appreciate your input. -- Kind regards, Ehsan Moravveji ### cmake "${cwd}/${dir_src}" \ -DGMX_SIMD='AVX_512' \ -DBLAS_mkl_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \ -DLAPACK_mkl_lapack_LIBRARY="DIR_MKL_LIB/libmkl_sequential.so" \ -DBLAS_guide_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \ -DCMAKE_C_COMPILER="${GMX_MPICC}" -DCMAKE_CXX_COMPILER="${GMX_MPICXX}" \ -DMPI_C_COMPILER="${GMX_MPICC}" -DMPI_CXX_COMPILER="${GMX_MPICXX}" \ -DCMAKE_MPI_C_COMPILER="${GMX_MPICC}" -DCMAKE_MPI_CXX_COMPILER="${GMX_MPICXX}" \ -DCMAKE_INSTALL_PREFIX="${dir_install}" \ -DCMAKE_PREFIX_PATH="${DIR_MKL_LIB}" \ -DCMAKE_VERBOSE_MAKEFILE=ON \ -DGMX_MPI=ON \ -DGMX_GPU=ON \ -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF -DEXTRA_CXX_FLAGS="-std=c++11" \ -DGMX_USE_NVML=ON -DGMX_BUILD_OWN_FFTW=ON \ -DHWLOC_INCLUDE_DIRS="${EBROOTHWLOC}/include" -DHWLOC_LIBRARIES="${EBROOTHWLOC}/lib/libhwloc.so" \ -DCUDA_HOST_COMPILER="${PATH_NVCC}" -DNVML_INCLUDE_DIR="${EBROOTCUDA}/include" \ -DNVML_LIBRARY="${EBROOTCUDA}/lib64/stubs/libnvidia-ml.so" \ -DCUDA_TOOLKIT_ROOT_DIR="${EBROOTCUDA}" -DCUDA_SDK_ROOT_DIR="${EBROOTCUDA}" \ -DCUDA_PROPAGATE_HOST_FLAGS=ON -DCUDA_VERBOSE_BUILD=ON \ -DGMX_CUDA_TARGET_SM="${SM_VER}" -DGMX_CUDA_TARGET_COMPUTE="${SM_VER}" \ -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF \ -DCUDA_CUDART_LIBRARY="${EBROOTCUDA}/lib64/libcudart.so" -DCUDA_CUDA_LIBRARY="${EBROOTCUDA}/lib64/libcuda.so" \ -DCUDA_NVCC_FLAGS="-gencode;arch=compute_${SM_VER},code=compute_${SM_VER};-use_fast_math;-D_FORCE_INLINES" \ -DGMX_PREFER_STATIC_LIBS=OFF -DGMX_X11=OFF ### -- Generating dependency file: /work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend /software/CUDA/9.2.148/bin/nvcc -M -D__CUDACC__ /work/GROMACS/gromacs-2018.3/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu -o /work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend -ccbin /software/CUDA/9.2.148/bin/nvcc -m64 --std c++11 -Dlibgromacs_EXPORTS -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Xcompiler ,\"-mavx512f\",\"-mfma\",\"-fPIC\",\"-O3\",\"-DNDEBUG\",\"-funroll-all-loops\",\"-fexcess-precision=fast\" -gencode arch=compute_60,code=sm_60 -gencode arch=compute_60,code=compute_60 -use_fast_math -gencode arch=compute_60,code=compute_60 -use_fast_math -D_FORCE_INLINES -DNVCC -I/software/CUDA/9.2.148/include -I/work/GROMACS/gromacs-2018.3/src/external/lmfit -I/work/GROMACS/gromacs-2018.3-build/src/contrib/fftw/fftwBuild-prefix/include -I/work/GROMACS/gromacs-2018.3-build/src -I/work/GROMACS/gromacs-2018.3/src/external/thread_mpi/include -I/work/GROMACS/gromacs-2018.3/src -I/software/hwloc/1.11.11-GCCcore-6.4.0/include -I/work/GROMACS/gromacs-2018.3/src/external/tng_io/include -I/work/GROMACS/gromacs-2018.3-build/tng/include*nvcc fatal : 'avx512f': expected a number CMake Error at libgromacs_generated_nbnxn_cuda.cu.o.Release.cmake:219 (message): Error generating /work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda.cu.o* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Dear GMX users, I would like to share a difficulty installing GROMACS/2018.3 with you. I use GCC/6.4.0 on a Linux cluster with CentOS 7.5 kernel and GPU nodes equipped with 4 x P100 Nvidia devices. Below is the cmake configuration that I use, followed by the error that I receive. I am not sure if there is still an extra flag to set to resolve this issue, or some other steps must be taken? I appreciate your input. -- Kind regards, Ehsan Moravveji ### cmake "${cwd}/${dir_src}" \ -DGMX_SIMD='AVX_512' \ -DBLAS_mkl_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \ -DLAPACK_mkl_lapack_LIBRARY="DIR_MKL_LIB/libmkl_sequential.so" \ -DBLAS_guide_LIBRARY="${DIR_MKL_LIB}/libmkl_rt.so" \ -DCMAKE_C_COMPILER="${GMX_MPICC}" -DCMAKE_CXX_COMPILER="${GMX_MPICXX}" \ -DMPI_C_COMPILER="${GMX_MPICC}" -DMPI_CXX_COMPILER="${GMX_MPICXX}" \ -DCMAKE_MPI_C_COMPILER="${GMX_MPICC}" -DCMAKE_MPI_CXX_COMPILER="${GMX_MPICXX}" \ -DCMAKE_INSTALL_PREFIX="${dir_install}" \ -DCMAKE_PREFIX_PATH="${DIR_MKL_LIB}" \ -DCMAKE_VERBOSE_MAKEFILE=ON \ -DGMX_MPI=ON \ -DGMX_GPU=ON \ -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF -DEXTRA_CXX_FLAGS="-std=c++11" \ -DGMX_USE_NVML=ON -DGMX_BUILD_OWN_FFTW=ON \ -DHWLOC_INCLUDE_DIRS="${EBROOTHWLOC}/include" -DHWLOC_LIBRARIES="${EBROOTHWLOC}/lib/libhwloc.so" \ -DCUDA_HOST_COMPILER="${PATH_NVCC}" -DNVML_INCLUDE_DIR="${EBROOTCUDA}/include" \ -DNVML_LIBRARY="${EBROOTCUDA}/lib64/stubs/libnvidia-ml.so" \ -DCUDA_TOOLKIT_ROOT_DIR="${EBROOTCUDA}" -DCUDA_SDK_ROOT_DIR="${EBROOTCUDA}" \ -DCUDA_PROPAGATE_HOST_FLAGS=ON -DCUDA_VERBOSE_BUILD=ON \ -DGMX_CUDA_TARGET_SM="${SM_VER}" -DGMX_CUDA_TARGET_COMPUTE="${SM_VER}" \ -DCUDA_USE_STATIC_CUDA_RUNTIME=OFF \ -DCUDA_CUDART_LIBRARY="${EBROOTCUDA}/lib64/libcudart.so" -DCUDA_CUDA_LIBRARY="${EBROOTCUDA}/lib64/libcuda.so" \ -DCUDA_NVCC_FLAGS="-gencode;arch=compute_${SM_VER},code=compute_${SM_VER};-use_fast_math;-D_FORCE_INLINES" \ -DGMX_PREFER_STATIC_LIBS=OFF -DGMX_X11=OFF ### -- Generating dependency file: /data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend /apps/leuven/skylake/2018a/software/CUDA/9.2.148/bin/nvcc -M -D__CUDACC__ /data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src/gromacs/mdlib/nbnxn_cuda/ nbnxn_cuda.cu -o /data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o.NVCC-depend -ccbin /apps/leuven/skylake/2018a/software/CUDA/9.2.148/bin/nvcc -m64 --std c++11 -Dlibgromacs_EXPORTS -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Xcompiler ,\"-mavx512f\",\"-mfma\",\"-fPIC\",\"-O3\",\"-DNDEBUG\",\"-funroll-all-loops\",\"-fexcess-precision=fast\" -gencode arch=compute_60,code=sm_60 -gencode arch=compute_60,code=compute_60 -use_fast_math -gencode arch=compute_60,code=compute_60 -use_fast_math -D_FORCE_INLINES -DNVCC -I/apps/leuven/skylake/2018a/software/CUDA/9.2.148/include -I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src/external/lmfit -I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src/contrib/fftw/fftwBuild-prefix/include -I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src -I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src/external/thread_mpi/include -I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src -I/apps/leuven/skylake/2018a/software/hwloc/1.11.11-GCCcore-6.4.0/include -I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3/src/external/tng_io/include -I/data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/tng/include nvcc fatal : 'avx512f': expected a number CMake Error at libgromacs_generated_nbnxn_cuda.cu.o.Release.cmake:219 (message): Error generating /data/leuven/sys/x0090231/easybuild/work/GROMACS/gromacs-2018.3-build/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda.cu.o -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.