[gmx-developers] Verlet kernel testing in 5.1

Roland Schulz roland at utk.edu
Wed Oct 1 00:57:40 CEST 2014


1) Both regressiontests and unit-tests are important. Unit tests won't be
able to find bugs which are in the interplay of different modules. Unit
tests make it *much* easier to narrow down an issue and run many tests
quickly. Thus even if we have a way to run the verlet tests as unit-tests
(which would be awesome) we still needed a regressiontest framework.

2) There are multiple serialization frameworks for C++. The issue has a lot
of overlap with how to communicate complex data structures over MPI. And
also a bit with how to offload those data structures to an accelerator.
Thus it might make sense that we use the same framework for unit tests and
MPI. See http://redmine.gromacs.org/issues/996.

3) I don't think we should move tests from gmxtest.pl to the
mdrun-integrationtests until the later is at least as functional (i.e.
compares output values). And we should decide which way we go sooner rather
than later. I don't think the perl approach is inherently bad. If we
rewrite it partly to make it more extensible it might be a nice long-term


On Tue, Sep 30, 2014 at 3:50 PM, Szilárd Páll <pall.szilard at gmail.com>

> Hi,
> As we aim at removing the group kernels for the next release and
> making the Verlet kernels the only feature-complete non-bonded
> implementation, we will need some form of extensive testing of all
> Verlet kernels. We've discussed things offline today and I'd like to
> summarize some of the conclusions and hopefully get some input on
> which way should we be heading.
> * Build unit tests around the kernels.
> This is probably the most sound way of testing the kernels, but it
> likely requires a lot of work; in particular, with the current code it
> seems to be quite difficult to set up all data structures required for
> search and kernels without calling the entire mdrun and based on
> Mark's experience serializing the data structures will be a pain too
> (although for calling just the kernels only interaction_const_t,
> nbnxn_atomdata_t, nbnxn_pairlist_set_t is needed).
> * Use the mdrun integration test harness
> Can't say much about it as I have admittedly not used it myself.
> However, what's sure is that compared to proper unit tests it requires
> giving up  lightweight-ness. The hardness executes the full mdrun
> without the ability to test just a specific kernel but, just like with
> the gmxtest-based kernel tests, a specially crafted tpr and quite
> likely supporting code changes will be required to exercise only some
> code-paths and kernel versions/flavors.
> * Update gmxtest with Verlet kernel tests
> At the moment a most of the (group) kernel testing functionality is in
> gmxtest. While gmxtest is getting more and more outdated, for the next
> release the regression test suite will surely require a considerable
> amount of attention to at least remove group scheme tests. Having done
> that, not much will be left, which bring up a couple of weakly related
> questions:
> - Will (all) current tests will be migrated to Verlet setup?
> - Will they be kept in gmxtest?
> - ...or most/all will moved all these into some other form of testing?
> If there will, what will that be?
> If gmxtest is kept and tests will get simply migrated from group to
> Verlet setup, it may as well be the least amount of effort to adopt
> the kernel testing procedure used for the group kernels. Of course,
> this will just prolong the life of gmxtest.pl, but it may still be the
> most feasible approach and I believe there has been no consensus on
> whether all testing will be moved into the mdrun integration test
> harness.
> Cheers,
> --
> Szilárd
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