[gmx-users] MPI GPU job failed

[Mark Abraham]

Hi,

Configuration of MPI also happens when mpirun acts. You need to have set
things up so that those two ranks are assigned to hardware the way you
want. Your output looks like there are two processes, but that they aren't
organised by mpirun to know to talk to each other.

Mark

On Thu, 11 Aug 2016 15:22 Albert <mailmd2011 at gmail.com> wrote:

> well, here is the command line I used for compiling:
>
>
> env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90
> CMAKE_PREFIX_PATH=/soft/gromacs/fftw-3.3.4:/soft/intel/impi/5.1.3.223
> cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF
> -DCMAKE_INSTALL_PREFIX=/soft/gromacs/5.1.3_intel -DGMX_MPI=ON
> -DGMX_GPU=ON -DGMX_PREFER_STATIC_LIBS=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
>
> here is my cshrc:
>
> source /soft/intel/bin/compilervars.csh intel64
> source /soft/intel/impi/5.1.3.223/bin64/mpivars.csh
> set path=(/soft/intel/impi/5.1.3.223/intel64/bin $path)
> setenv CUDA_HOME /usr/local/cuda
> setenv MKL_HOME /soft/intel/mkl/
> setenv LD_LIBRARY_PATH
>
> /soft/intel/compilers_and_libraries_2016.3.223/linux/mpi/lib64:/usr/local/cuda/lib64:/soft/intel/lib/intel64:/soft/intel/lib/ia32:/soft/intel/mkl/lib/intel64:/soft/intel/mkl/lib/ia32:{$LD_LIBRARY_PATH}
>
>
> It should build with MPI support with above settings. Does it?
>
>
>
>
> On 08/11/2016 04:18 PM, Szilárd Páll wrote:
> > PPS: given the double output (e.g. "Reading file 61.tpr, ...") it's
> > even more likely that you're using a non-PI build.
> >
> > BTW, looks like you had the same issue about two years ago:
> >
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-September/092046.html
>
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