[gmx-users] problem of submitting job in HPC

[Justin Lemkul]

On 8/28/13 12:39 PM, Albert wrote:
> Hello:
>
>   I am trying to use following command to run 4.6.3 in a HPC cluster:
>
> mpiexec -n 32 /opt/gromacs/4.6.3/bin/mdrun_mpi  -dlb yes -v -s md.tpr -x md.xtc
> -o md.trr -g md.log -e md.edr  >& md.info
>
> the 4.5.5 works fine in this machine with command:
>
> mpiexec -n 32 mdrun -nosum -dlb yes -v -s md.tpr -x md.xtc -o md.trr -g md.log
> -e md.edr  >& md.info
>
> the difference is that the option "-nosum" is not available in 4.6.3
>
> but 4.6.3 always failed. It generate a lot of similar files and log
> informations. It looks like use mpiexec evoke serial mdrun.....
>
> Does anybody have any idea?
>

Have you verified that the 4.6.3 mdrun was correctly installed such that it can 
make use of MPI?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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