[gmx-users] problem of submitting job in HPC
mark.j.abraham at gmail.com
Wed Aug 28 21:52:45 CEST 2013
On Wed, Aug 28, 2013 at 7:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> -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
>> -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?
i.e. by inspecting the top of the .log file, or the output of mdrun -version?
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