[gmx-users] mdrun failed

[Mark Abraham]

First, check your install of MPI works on a simple test program. Then,
check that GROMACS cmake picked up the MPI you expected, and that that's
really the one you're using at run time.

Mark


On Thu, May 15, 2014 at 3:28 PM, Albert <mailmd2011 at gmail.com> wrote:

> Hello:
>
> I try to submit Gromacs job with command:
>
> mpirun -np 2 mdrun_mpi -s md.tpr -g -v
>
> but it failed with messages:
>
> --------------------------------------------------------------------------
> It looks like opal_init failed for some reason; your parallel process is
> likely to abort.  There are many reasons that a parallel process can
> fail during opal_init; some of which are due to configuration or
> environment problems.  This failure appears to be an internal failure;
> here's some additional information (which may only be relevant to an
> Open MPI developer):
>
>   opal_shmem_base_select failed
>   --> Returned value -1 instead of OPAL_SUCCESS
> --------------------------------------------------------------------------
> *** An error occurred in MPI_Init
> *** on a NULL communicator
> *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
> ***    and potentially your MPI job)
> [cudaA:5978] Local abort before MPI_INIT completed successfully; not able
> to aggregate error messages, and not able to guarantee that all other
> processes were killed!
>
> --------------------------------------------------------------------------
>
>
> I first compiled openmpi with command:
>
> ./configure --prefix=/soft/openmpi-1.7.5_intel CC=icc F77=ifort FC=ifort
> CXX=icpc
>
> then gromacs-4.6.5 was compiled with command:
>
> env CC=icc F77=ifort CXX=icpc
> CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/openmpi-1.7.5 cmake ..
> -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF
> -DCMAKE_INSTALL_PREFIX=/soft/gromacs-4.6.5 -DGMX_FFT_LIBRARY=mkl
> -DGMX_MPI=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
>
>
>
> thank you very much.
>
> ALbert
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