Thanks Christoph.
On Friday, April 20, 2018 at 8:41:41 AM UTC-4, Christoph Junghans wrote:
>
> On Fri, Apr 20, 2018 at 3:35 AM, Salman Zarrini
> <[email protected] <javascript:>> wrote:
> > Dear Votca developers,
> >
> > My Votca calculations are conducted in a cluster which has 82 machines
> each with 16 slots.
> > While the Gromacs can parallel either inter-nodes or intranode, the
> Votca is only multithreaded so that only 16 slots can be used maximally.
> Consequently the Gromacs as the most time consuming part of a IBI-Votca job
> would be limited to 16 slots as well.
> > So, I wonder if there is any possibility to use a higher number of slots
> for at least the Gromacs part of a IBI calculation in such situation?
> Sure nothing prevents you from running VOTCA and gromacs on a
> different number of cores, e.g. using 4 nodes (4*16 cores) for the
> gromacs part (with mpi) and only 1 node (16 cores) for VOTCA's
> csg_stat.
>
Probably doable for the csg_stat by using --nt 16, but how about the
csg_inverse in IBI;
As far as I know, the allocation for running a IBI job (csg_inverse
--options settings.xml) in cluster is addressed by two below commands in
job submission script and setting.xml, respectively.
#$ -pe shm n ## Or other types of parallel environment.
<mdrun>
<command> mpirun -np m gmx_mpi mdrun </command> ### (m =< n)
</mdrun>
The n slots indicated in the job submission script would be assigned to the
both VOTCA and Gromacs commands. Then how can I order to use 4 nodes (4*16
cores) for the gromacs and 1 node (16 cores) for VOTCA (probably the other
way round was much easier in general)? And How VOTCA knows that those 16
cores are all belong to a single node? because if only 1 core from the 16
cores is contributed by another node the VOTCA part crashes.
Thank you.
Regards,
Salman Zarrini
>
> Christoph
>
> > BTW, Votca launches Gromacs directly with "mpirun” now.
> >
> > Regards,
> >
> > Salman Zarrini
> > Department of Chemical Engineering
> > Drexel University
> > Philadelphia, USA
> >
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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