<div><br></div><div><br><div class="gmail_quote"><div dir="ltr">On Tue, Aug 14, 2018 at 07:25 Kutzner, Carsten <<a href="mailto:ckutzne@gwdg.de">ckutzne@gwdg.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
> On 14. Aug 2018, at 14:30, Szilárd Páll <<a href="mailto:pall.szilard@gmail.com" target="_blank">pall.szilard@gmail.com</a>> wrote:<br>
> <br>
> 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?<br>
So for an analysis that only needs the data of a single frame,<br>
parallel processing should already work?<br>
<br>
At the moment we wrap the analysis tool by a script<br>
that calls -b begin -e end for N parts, but then<br>
one ends up with N output files, which is a bit <br>
inconvenient.</blockquote><div dir="auto">Hehe, we did the same:</div><div dir="auto"><div><a href="https://github.com/votca/multi_g_rdf">https://github.com/votca/multi_g_rdf</a></div> </div><div dir="auto">A real parallel analyser would be better though!</div><div dir="auto"><br></div><div dir="auto">Christoph </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
Carsten<br>
<br>
<br>
> <br>
> --<br>
> Szilárd<br>
> <br>
> <br>
> On Tue, Aug 14, 2018 at 9:37 AM Kutzner, Carsten <<a href="mailto:ckutzne@gwdg.de" target="_blank">ckutzne@gwdg.de</a>> wrote:<br>
> Hi Roland,<br>
> <br>
> thanks a lot, this seems like a good starting point for building<br>
> an MPI-parallel tool! Is there any specific reason why this <br>
> patch is lying dormant? Any road blocks, or just lack of<br>
> resources?<br>
> <br>
> Best regards,<br>
> Carsten<br>
> <br>
> <br>
> > On 14. Aug 2018, at 01:22, Schulz, Roland <<a href="mailto:roland.schulz@intel.com" target="_blank">roland.schulz@intel.com</a>> wrote:<br>
> > <br>
> > Hi,<br>
> > <br>
> > We done some work on this at UT/ORNL in 2012/13. You find this at <br>
> > <a href="https://gerrit.gromacs.org/c/1316/" rel="noreferrer" target="_blank">https://gerrit.gromacs.org/c/1316/</a> . As far as I know no one has done anything since.<br>
> > <br>
> > Roland<br>
> > <br>
> >> -----Original Message-----<br>
> >> From: <a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a><br>
> >> [mailto:<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>] On<br>
> >> Behalf Of Kutzner, Carsten<br>
> >> Sent: Thursday, August 9, 2018 7:46 AM<br>
> >> To: <<a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a>> GROMACS development <gmx-<br>
> >> <a href="mailto:developers@gromacs.org" target="_blank">developers@gromacs.org</a>><br>
> >> Subject: [gmx-developers] Parallelism in trajectory analysis tools<br>
> >> <br>
> >> Hi,<br>
> >> <br>
> >> what is the status of using any type of parallelism to speed up trajectory<br>
> >> analysis tools?<br>
> >> <br>
> >> I guess OpenMP should be no problem, but what about MPI?<br>
> >> <br>
> >> What are the plans here / what would be preferred in future patches?<br>
> >> <br>
> >> Thanks!<br>
> >> Carsten<br>
> >> <br>
> >> --<br>
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> <br>
> --<br>
> Dr. Carsten Kutzner<br>
> Max Planck Institute for Biophysical Chemistry<br>
> Theoretical and Computational Biophysics<br>
> Am Fassberg 11, 37077 Goettingen, Germany<br>
> Tel. +49-551-2012313, Fax: +49-551-2012302<br>
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--<br>
Dr. Carsten Kutzner<br>
Max Planck Institute for Biophysical Chemistry<br>
Theoretical and Computational Biophysics<br>
Am Fassberg 11, 37077 Goettingen, Germany<br>
Tel. +49-551-2012313, Fax: +49-551-2012302<br>
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