[gmx-developers] last days for 5.1

Kutzner, Carsten ckutzne at gwdg.de
Thu Aug 6 13:21:16 CEST 2015


I wanted to quickly report back on tune_pme for 5.1, what are the issues
so we could discuss on how best to proceed.

In principle, tune_pme works, however as a user one may have to set extra
options so that actually tuning can be done.

The issues are:

a) A valid mdrun executable needs to be specified first, see:

b) On GPU nodes, mdrun typically segfaults, due to timers not being reset
at a neighborsearching step, see:
and http://redmine.gromacs.org/issues/1781 

c) One needs to specify -ntomp somevalue, otherwise it is 1 by default
and mdrun refuses to run.

Issue b) is probably the most important one to address, which could be either
done in mdrun or in tune_pme. 
Tune_pme would have to determine from the .tpr what the actual neighborsearching
frequency will be and adjust the counter resetting appropriately.



> On 05 Aug 2015, at 16:45, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Hi
> On Wed, Aug 5, 2015 at 4:30 PM Kutzner, Carsten <ckutzne at gwdg.de> wrote:
> Hi,
> > On 05 Aug 2015, at 16:15, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> >
> > We changed some default behaviour for how mdrun picks things like numbers of cores per rank, etc. Carsten, can you please try a low-key gmx tune_pme run to see we haven’t broken things there?
> Sure - anything particular worth needing a closer look?
> Not that I can think of, but tune_pme does try mdrun's default, and it would be nice to know that that doesn't fail / run slowly / look stupid / parse badly / etc.
> Mark
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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

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