[gmx-developers] Performance checklist

David van der Spoel spoel at xray.bmc.uu.se
Sat Oct 13 13:02:38 CEST 2012

On 2012-10-13 05:04, Mark Abraham wrote:
> On 13/10/2012 12:34 PM, Shirts, Michael (mrs5pt) wrote:
>>> 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?
> I did have a look around recently, but mostly there was a number of stub
> projects that didn't seem to have gone anywhere. :-)
If something this would be good to add to libxdrfile, which will 
probably be incorporated into OpenBabel soon (I'm talking to these guys) 
and babel has a python interface. It's a bit of a detour though :).

>>> 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?
> People who have perspectives of interest are more likely to find the
> thread here, I think.
> Mark

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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