[gmx-developers] Parallelism in trajectory analysis tools

[Kutzner, Carsten]

> On 14. Aug 2018, at 14:30, Szilárd Páll <pall.szilard at gmail.com> wrote:
> 
> IIRC there did not seem to be enough use cases for parallel analysis  at the time (considering the limitations?), but I'm not sure. Unless I'm remembering incorrectly, only independent per-frame processing was possible, right?
So for an analysis that only needs the data of a single frame,
parallel processing should already work?

At the moment we wrap the analysis tool by a script
that calls -b begin -e end for N parts, but then
one ends up with N output files, which is a bit 
inconvenient.

Carsten


>  
> --
> Szilárd
> 
> 
> On Tue, Aug 14, 2018 at 9:37 AM Kutzner, Carsten <ckutzne at gwdg.de> wrote:
> Hi Roland,
> 
> thanks a lot, this seems like a good starting point for building
> an MPI-parallel tool! Is there any specific reason why this 
> patch is lying dormant? Any road blocks, or just lack of
> resources?
> 
> Best regards,
>   Carsten
> 
> 
> > On 14. Aug 2018, at 01:22, Schulz, Roland <roland.schulz at intel.com> wrote:
> > 
> > Hi,
> > 
> > We done some work on this at UT/ORNL in 2012/13. You find this at 
> > https://gerrit.gromacs.org/c/1316/ . As far as I know no one has done anything since.
> > 
> > Roland
> > 
> >> -----Original Message-----
> >> From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se
> >> [mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On
> >> Behalf Of Kutzner, Carsten
> >> Sent: Thursday, August 9, 2018 7:46 AM
> >> To: <gmx-developers at gromacs.org> GROMACS development <gmx-
> >> developers at gromacs.org>
> >> Subject: [gmx-developers] Parallelism in trajectory analysis tools
> >> 
> >> Hi,
> >> 
> >> what is the status of using any type of parallelism to speed up trajectory
> >> analysis tools?
> >> 
> >> I guess OpenMP should be no problem, but what about MPI?
> >> 
> >> What are the plans here / what would be preferred in future patches?
> >> 
> >> Thanks!
> >>  Carsten
> >> 
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> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa