[gmx-users] (no subject)

[Ehsan Moravveji]

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