[gmx-developers] last days for 5.1

Szilárd Páll pall.szilard at gmail.com
Wed Aug 5 16:48:53 CEST 2015



On Wed, Aug 5, 2015 at 9:15 AM, Mark Abraham <mark.j.abraham at gmail.com>

> 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.

AFAICT there are still a few relatively small issues in redmine, most of
them by me. I'd say at least 1782 and 1784 would be best fixed before
release. I've a draft for the latter in gerrit, but needs a bit more
attention. Will squeeze out some time today to get it ready. May need help
with testing (and this may very well fix the DD+OpenCL issue).

> 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'll try to find some time to read through it. One thing we definitely need
to emphasize is the new PP rank to GPU mapping automation.


> http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 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
> and
> https://gerrit.gromacs.org/#/q/status:open+project:gromacs+branch:release-5-1
> and review as you feel able!
> Cheers,
> Mark
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