[gmx-developers] bug in 3.2.x not fixed in 3.3.1

[David van der Spoel]

David Mobley wrote:
> Berk,
> 
>> The bug is still in 4.0.4.
>>
>> I would consider it bad practice to use a tpr file with a static
>> box (no pressure coupling) and a rerun trr file with a different
>> sized box for mdrun -rerun.
>> Note that rerunning with a dynamic box would work fine.
> 
> It is sort of bad practice, I suppose, BUT also the documented (if I
> remember correctly) behavior of mdrun -rerun was to use box info from
> the trr file; the gro file was supposed to be basically ignored.
> 
>> But anyhow, I fixed the bug for 4.0.5 and cvs head.
> 
> OK. Is there some reason why this was fixed once but never included in
> the main gromacs releases? It is rather frustrating to go through the
> process of submitting a bugzilla and helping to get the bug fixed only
> to have the same bug come back and get me in a later version of
> gromacs. Is there a way this can be avoided in the future?
> 
By being somewhat more alert from both developer side and user side. 
Apparently I made a patch, which you acknowledged worked. Then someone 
(could well have been me too) closed the bug without any further 
comments. In hindsight this is bad from the developer side.

I propose that whoever closes a bug in the future should comment it such 
that it is clear what has been done. There is also a role for the 
bug-reporter, since he/she get notified when a bug is closed as well, so 
this person could also demand an explanation.

Maybe the bugzilla settings can be changed such that commenting is enforced?



> Thanks,
> David
> 
> 
>> Berk
>>
>>> All,
>>>
>>> There was a very old bug (in 3.3 and 3.2.1) in mdrun -rerun which
>>> caused box size information to be incorrectly read from the gro file
>>> (i.e. starting tpr) rather than the trajectory file. A fixed version
>>> of md.c was developed prior to the release of 3.3.1
>>> (http://bugzilla.gromacs.org/show_bug.cgi?id=26).
>>>
>>> I just established that this fix did NOT make it into the 3.3.1
>>> release. Can someone confirm whether it has made it into subsequent
>>> releases? If not, this bug will still be there...
>>>
>>> Thanks,
>>> David
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>>
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se