[gmx-users] nvcc fatal: 'avx512f': expected a number

Wed Oct 24 11:49:56 CEST 2018

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 <mark.j.abraham at gmail.com>
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 <e.moravveji at gmail.com>
> 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_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
> >
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> >
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> --
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-- 
Kind regards,
Ehsan Moravveji