[gmx-developers] last days for 5.1

Mark Abraham mark.j.abraham at gmail.com
Wed Aug 5 16:15:17 CEST 2015

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?

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
and review as you feel able!


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