[gmx-developers] regression tests - git failing?

[Berk Hess]

Mark Abraham wrote:
>
> On 08/07/09, *Berk Hess *<hess at cbr.su.se> wrote:
>> Mark Abraham wrote:
>> > Michael Shirts wrote:
>> >> Hi, guys-
>> >>
>> >> I just pulled the latest git directory to see how my own changes were
>> >> faring on the regression tests -- I got the following failures.
>> >>
>> >> single precision:
>> >> Testing aminoacids . . . FAILED. Check checkpot.out (      35 errors),
>> >> checkvir.out (402 errors) files in aminoacids
>> >>
>> >> double precision:
>> >> Testing aminoacids . . . FAILED. Check checkpot.out (      35 errors),
>> >> checkvir.out (402 errors) files in aminoacids
>> >> N      Reference   This test
>> >>   10    -39.0984    -32.3783
>> >>   11    -39.0984    -32.3783
>> >>   12    -93.8123    -75.8899
>> >>   13    -93.8123    -75.8899
>> >>   21    -11007.5    -9914.46
>> >> There were 5 differences in final energy with the reference file
>> >> All 45 pdb2gmx tests PASSED
>> >> pdb2gmx tests FAILED
>> >>
>> >> Now that we have a good regression test set that runs in just a few
>> >> minutes, and have public git repositories that make it easier to share
>> >> beta code, I'm wondering if it would make sense to ask that commits to
>> >> the main repository pass the regression tests -- this would make it
>> >> easier to locate problems and eliminate many coding errors.
>> >
>> > There is a current problem with a handful of the regression tests
>> > inasmuch as the reference values are still computed with a 3.3.2
>> > version (IIRC). These manifest as a checkvir issue. I haven't
>> > committed the time to solving it, though as I did the last fixes to
>> > the regression tests, I probably should.
>> >
>> > Mark
>> This is due a change in the Berendsen (and v-rescale) termostat I made.
>> The velocties at t-dt/2 are now scaled iso at t+dt/2, this provides much
>> better energy conservation
>> with the v-rescale thermostat.
>>
>> I guess the best solution would be to remove temperature coupling in all
>> test sets that are
>> not intended to test temperature coupling. (also Berendsen is not the
>> right algorithm to test).
>> We would probably want the initial temperature to be around 300 K.
>> The references could still be made with 3.3 to keep the test sets
>> backwards compatible.
>
> OK, I can do that.
>
> 1) Generate reference data with 3.3.3 with .mdp options that 4.x can
> reproduce, i.e. largely without T-coupling and with suitable grid
> search options.
>
> 2) Generate a v-rescaling test with 4.0.5, and note that failure will
> be expected if testing with 3.3.x
>
> Any other gotchas?
>
> Mark
Note that the problems mailed by Michael were with the current git version.
I still get several failures in the complex directory due to the virial
with GMX 4.0.

In 4.1 I also just changed the twin-range integrator to a Trotter
integrator.
With only LJ twin-range results will differ very little from before, but
with
reaction-field twin-range the effects are large. I don't know if the are
twin0-range tests.

Thanks a lot,

Berk