[gmx-users] MPI GPU job failed

[jkrieger at mrc-lmb.cam.ac.uk]

The problem is you compiled gromacs with mpi (hence the default _mpi in
your command). You therefore need to set the number of mpi processes
rather than threads. The appropriate command would instead be the
following:

mpirun -np 2 gmx_mpi mdrun -v -s 62.tpr -gpu_id 01

Alternatively you could compile a different gromacs version without mpi.
This should have thread-mpi and openmp by default if you leave out
DGMX_MPI=ON from the cmake command.

Best wishes
James

> Hello:
>
> I try to run command:
>
>
> gmx_mpi mdrun -nt 2 -v -s 62.tpr -gpu_id 01
>
> but it failed with messages:
>
> -------------------------------------------------------
> Program gmx mdrun, VERSION 5.1.3
> Source code file:
> /home/albert/Downloads/gromacs/gromacs-5.1.3/src/programs/mdrun/resource-division.cpp,
> line: 625
>
> Fatal error:
> Setting the total number of threads is only supported with thread-MPI
> and GROMACS was compiled without thread-MPI
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
> -------------------------------------------------------
>
>
>
> On 08/11/2016 06:50 AM, Nikhil Maroli wrote:
>> gmx mdrun -nt X -v -deffnm XXX -gpu_id XYZ
>>
>> What about this?
>>
>> Assign sufficient number of threads
>
> --
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