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.
>
>
>
> Mark
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