mrshi...@gmail.com wrote:
What other input might you need for a test set? As a minor developer and a stickler for accuracy, I would be very much interested in the sorts of inputs your looking for, and have some ideas as well.

There's a number of issues listed in the posts in the URLs below, chief among them the absence of a bug-free reference version of GROMACS. The other issues mostly arise because if there's no documentation of what is being tested *for*, it's hard to do maintenance on the test.

There's currently no tests designed for GROMACS in parallel. It's far from clear that there's a suitable reference GROMACS version anyway.

One clear need is a mechanism to permit features to be tested in combination in an automated manner. The set of "complex" tests that already exist are a good start, but they're far from complete. It should be possible to ask a script to test thermostats in (X,Y) with barostats in (W,Z), using -sum/-nosum with the constraint of -npme 0. (This is not at all silly - I spent several weeks this year proving that I'd found a GROMACS bug. It transpired that the problem was with the V-rescale thermostat under -nosum, and I only noticed that because I was using -rerun!) To avoid combinatorial explosion of the reference data, that data would have to be generated at the same time as the test data. Thus the user would need to have installed some known good GROMACS version, and done some "bootstrap" correctness tests of that against supplied reference data, before moving on to more complex cases with user-generated reference data. This requires that the script "know" how to test each feature, so that it can correctly construct reference and test runs. The above example is easy - the script knows that to test a thermostat or barostat, the reference and test .mdp files need to have a certain form, and testing a command line flag is easier still. The script would also need to know how to reject tests of mutually-exclusive features.

In principle, each new feature implemented should be regarded as incomplete until there's a test that functions correctly. This means that the author of the feature needs to designate a GROMACS version that is a suitable reference case (e.g. you can't test V-rescale against a 3.x reference version because it wasn't implemented back then!) That becomes rapidly untenable for a user of the test suite, since they would have to have access to multiple different versions - there'd have to be a web server for providing reference data. There's further complications if testing feature A (whose reference version is 4.0.2) in combination with feature B (whose reference version is 4.0.4). Clearly you'd have to use at least 4.0.4 to generate a reference case for A & B together, and then have to test that A alone in 4.0.4 is correct with respect to 4.0.2.

I don't know how to bring order to this chaos! I do know that the lack of a solution will continue to cost everyone time and money doing broken simulations and chasing bugs.

Mark

> Frankly, the mentions of the test set on the web pages are misleading. gmxtest-4.0.4 doesn't serve its purpose. gmxtest-3.3.3 was useful for GROMACS 3-series installs, I expect, but almost nobody wants to be using GROMACS 3. I've done a bunch of improvements on the publicly-available git version (http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003573.html and http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html), but input is needed from people other than me before a useful test set can be released.
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 > Mark
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