[gmx-users] problem of submitting job in HPC
jalemkul at vt.edu
Wed Aug 28 19:06:18 CEST 2013
On 8/28/13 12:39 PM, Albert wrote:
> 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 A. Lemkul, Ph.D.
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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