[gmx-users] Installation problem on CRAY XC40----Gromacs-5.0.4

[Szilárd Páll]

Hi,

You may want to read the Cray docs before attempting to compile on the
machine. You need to use the compiler wrappers (cc/CC) if you want to
run on the compute nodes and I suggest that you just use gcc 4.8/4.9
which will be both compatible with nvcc and faster.

Cheers,
--
Szilárd


On Mon, Mar 30, 2015 at 4:13 PM, Satyabrata Das <satyabratad04 at gmail.com> wrote:
> Dear All,
> I am trying to install Gromacs-5.0.4 on cray XC40 by using following
> combinations:
>
> (cmake-3.2.1 is compiled by myself, OS is Suse Linux X86_64)
>
> Combination 1: INTEL 15.0/13.0 , MKL / FFTW and MPI (Cray-MPICH-7.0.5)
>
> set FLAGS="-dynamic -O3 -funroll-loops"
>
> cmake .. -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DGMX_MPI=on
> -DGMX_OPENMP=on -DGMX_GPU=off
> -DCMAKE_INSTALL_PREFIX=/gromacs-5.0.4/intel-mkl-mpi -DGMX_FFT_LIBRARY=mkl
> -DGMX_DOUBLE=off -DGMX_BUILD_UNITTESTS=ON -DGMX_X11=off
> -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS"
> -DCMAKE_PREFIX_PATH=/opt/cray/mpt/7.0.5/gni/mpich2-intel/140/lib:/opt/cray/mpt/7.0.5/gni/mpich2-intel/140/include:/opt/cray/mpt/7.0.5/gni/bin
>
> It is showing the following error:
>
> -- MPI is not compatible with thread-MPI. Disabling thread-MPI.
> -- Could NOT find MPI_C (missing:  MPI_C_LIBRARIES MPI_C_INCLUDE_PATH)
> -- Could NOT find MPI_CXX (missing:  MPI_CXX_LIBRARIES
> MPI_CXX_INCLUDE_PATH)
> CMake Error at cmake/gmxManageMPI.cmake:150 (message):
>   MPI support requested, but no MPI compiler found.  Either set the
>   C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc), or
>   set the variables reported missing for MPI_C above.
> Call Stack (most recent call first):
>   CMakeLists.txt:464 (include)
>
>
> -- Configuring incomplete, errors occurred!
>
> Combination 2: INTEL 15.0/13.0, MKL / FFTW and MPI (Cray-MPICH-7.0.5),
> CUDA(cudatoolkit/5.5.22)
>
> It is showing the following error:
> [  0%] Building NVCC (Device) object
> src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_pmalloc_cuda.cu.o
> In file included from
> /opt/nvidia/cudatoolkit/5.5.22-1.0502.7944.3.1/include/cuda_runtime.h(59),
>                  from
> /home/proj/14/physatya/c40/gromacs-5.0.4/src/gromacs/gmxlib/cuda_tools/
> pmalloc_cuda.cu(0):
> /opt/nvidia/cudatoolkit/5.5.22-1.0502.7944.3.1/include/host_config.h(72):
> error: #error directive: -- unsupported ICC configuration! Only ICC 12.1 on
> Linux x86_64 is supported!
>   #error -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 is
> supported!
>    ^
>
> CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message):
>   Error generating
>
> /home/proj/14/physatya/c40/gromacs-5.0.4/build1/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
>
>
> make[2]: ***
> [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/cuda_tools_generated_pmalloc_cuda.cu.o]
> Error 1
> make[1]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
> Error 2
> make: *** [all] Error 2
>
>
> I have tried with GNU PrgEnv also, but unable to install. Kindly help.
>
> With best regards,
>
> Satyabrata Das
> --
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