[gmx-developers] Performance checklist

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Sat Oct 13 03:34:19 CEST 2012

> I'd like to set up this sort of testing to be automatic and easy, and
> have been using Michael's gear for some other work; ideally, these would
> run via Jenkins. 

I think this would be useful.

> The heavy lifting for 5.0 could break just about
> anything, and my experience of catching problems with feature X not
> working with option Y (e.g. md-vv with v-rescale thermostat in 4.5.x,
> http://redmine.gromacs.org/issues/1000) leads me to the strong opinion
> that a much broader battery of tests is a very sound (overdue?)
> investment. They'd need too much time to run for every commit, but
> catching problems early will be easy and effective with such tests every
> week or two, or when we know a commit is hitting sensitive areas.

Roland and I have been talking about this for a while -- we really do need
something a little more exhaustive to run every week or so.  I assume
redmine would be a good place to put a plan together?  Any thoughts on this,
Swedish people who have most of the infrastructure?

> The main caveat is that Michael's checkensemble tools require Python and
> numpy and to post-process GROMACS output to .xvg. That's fine and good
> for now, but at some point it could prove worthwhile to get
> checkensemble to read .edr files.

I doubt g_energy is the biggest problem timewise, but if it is, then I'd be
happy to work with getting a .edr reading in.  Only one routine would need
to be rewritten.  I assume someone someone somewhere has a python reader for
gromacs .edr files?

> Yes, this is the kind of thing I would also like to see, but AFAICR I am
> yet to hear others' visions for 5.0.

This is something that would be good to start synthesizing.  Perhaps when
4.6 is out the first thing all the developers could do is articulate what
they want to see for 5.0 so we can synthesize all these ideas?  Would
Redmine be the best place for this discussion?

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

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