[gmx-developers] last days for 5.1

Alexey Shvetsov alexxy at omrb.pnpi.spb.ru
Wed Aug 5 19:20:38 CEST 2015


Mark Abraham писал 05-08-2015 17:15:
> Hi all,
> I know we're all keen to get 5.1 shipped and move on to new work, so I
> thought I'd list the things I know would be good to get done so we can
> feel happy about shipping the real release, e.g. early next week. Then
> you can get some brain-share from me for new and exciting things ;-)
> Performance regression testing - I've done some manual testing here,
> things look fine (several issues flagged by Szilard over the lifetime
> of 5.1 have all been resolved, one way or another) but there are a few
> things left I want to check.
> I'll re-run some ensemble-checking tests on a range of hardware. This
> is important to do with all the bells and whistles on/default, because
> we have to disable some of those for the regression testing to work
> reliably.
> I will also try re-run a battery of free-energy tests we ran while
> fixing issues just before 5.0. Nothing should have changed, but we may
> as well find out.
> I've checked the build on BlueGene/Q (found a few issues now on gerrit
> or redmine, some solved already), and will check it on a few GPU
> clusters. Erik can you check in on K, please?
> We need to add some mdrun-time check that does not try to run (AMD?)
> OpenCL kernels with MacOS 10.3 (but only the necessary combo should be
> prohibited, and preferably not all of mdrun). A cmake-time warning for
> that combo would also be nice.
> 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?
> There's a few TODOs in docs/user-guide/mdrun-performance.rst that I'd
> like to deal with (and a couple of pages to add), so that
> version-specific information isn't living on a wiki page with
> switch(version). Szilard, are there things that you'd like to add for
> running with GPUs?

I can add some info here about running native mode on Xeon Phi (e.g. 
best mpi ranks/openmp threads ration and so on)

> http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 [1]
> is starting to leak a bit, because we have changes for 5.0 and
> probably some changes for 5.1 that would need similar documentation,
> and some of those areas overlap (IIRC gmx distance and gmx pairlist?).
> So I'll have a think about what we can do better here. Thoughts,
> anyone?
> Anything I've forgotten?
> Otherwise, please keep an eye on
> https://gerrit.gromacs.org/#/q/status:open+project:gromacs+branch:release-5-0
> [2] and
> https://gerrit.gromacs.org/#/q/status:open+project:gromacs+branch:release-5-1
> [3] and review as you feel able!
> Cheers,
> Mark
> Links:
> ------
> [1] http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
> [2]
> https://gerrit.gromacs.org/#/q/status:open+project:gromacs+branch:release-5-0
> [3]
> https://gerrit.gromacs.org/#/q/status:open+project:gromacs+branch:release-5-1

Best Regards,
Alexey 'Alexxy' Shvetsov, PhD
Department of Molecular and Radiation Biophysics
FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
Leningrad region, Gatchina, Russia
mailto:alexxyum at gmail.com
mailto:alexxy at omrb.pnpi.spb.ru

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