On Mon, Oct 1, 2012 at 12:39 PM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Jason,
>
> Thanks. This confirms our conclusion.
> We found no problems on any number of cores that is lower or equal to
> the number of frames to process.
>
OK, then we should fix this to exit cleanly.
Thanks for the report!
Jason
>
> Best,
> Vlad
>
> On 10/01/2012 06:32 PM, Jason Swails wrote:
> > On Mon, Oct 1, 2012 at 12:10 PM, Vlad Cojocaru <
> > vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> >
> >> Dear AMBERs,
> >>
> >> We are experiencing some issues with the parallel version of MMPBSA. We
> >> use AMBER 12 on AMD Opterons (with 12 or 48 cores/node).
> >> In a test with 9 frames to process, we noticed that the parallel MMPBSA
> >> does not run on 12 cores (it hangs at the cpptraj step with no error).
> >> We actually realized that it runs on a number of cores equal or lower
> >> than the number of frames to analyze.
> >>
> >> From this test, we suspect that the number of frames to analyze has to
> >> be a multiple of the number of cores to be used in the parallel MMPBSA
> run.
> >>
> > MMPBSA.py does not support using more processors than you have frames,
> > since it splits the workload by frame. Even though you could potentially
> > scale past nframes by assigning the complex and receptor of the same
> frames
> > to different cores (and this is before trying to call parallel external
> > programs), the gain for such an approach was not worth the cost of
> > programming.
> >
> > MMPBSA.py does handle non-multiple core counts, although it does so
> > naively. For a 10-frame analysis, for instance, 5 cores will run 2
> frames
> > on each core. 6 cores will run 2 frames on 4 of the cores and just 1
> frame
> > on the other 2 (so you see virtually no speed-up relative to 5 cores).
> > Similarly with 9 cores, 1 frame will be run on each of 9 cores, and 2
> > frames will be run on the first core (so again, no speedup from 5 cores).
> > However, it should work.
> >
> > We could not find documentation regarding this issue so I would like to
> >> confirm whether this is a known issue of the parallel MMPBSA.
> >>
> >> Thank you for any clarifications on this issue,
> >>
> > Does MMPBSA.py.MPI stall in parallel when the number of cores is 9 or
> > fewer? Or is it only when nproc>nframes?
> >
> > Thanks!
> > Jason
> >
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cell and Developmental Biology
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 01 2012 - 10:30:02 PDT
