[gmx-users] problem of submitting job in HPC

[Mark Abraham]

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:
>>
>> 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?

i.e. by inspecting the top of the .log file, or the output of mdrun -version?

Mark