[gmx-developers] next Gromacs release

[Carsten Kutzner]

On Jun 12, 2010, at 12:14 PM, Carsten Kutzner wrote:

> Hi,
> 
> I have noticed that with some MPI implementations (Intel MPI, IBM's poe
> and most likely also MPICH2) the g_tune_pme tool sometimes gets
> stuck after having successfully done a part of the test runs. 
> 
> This happens for cases where mdrun (in init_domain_decomposition) cannot 
> find a suitable decomposition and shortly afterwards calls MPI_Abort via
> gmx_fatal. Some (buggy!?) MPI implementations cannot guaratee that all MPI 
> processes are cleanly cancelled after a call to MPI_Abort and in those cases the
> control is never given back to g_tune_pme, which then thinks mdrun is still running. 
> 
> My question is, do we really have to call gmx_fatal when no suitable dd can
> be found? At that point, all MPI processes are still living and we could finish mdrun 
> cleanly with an MPI_Finalize (just as in successful runs), thus omitting the hangs in 
> the tuning utility. I think that also normal mdruns, when unable to find a dd grid,
> would for those MPI's end as zombies until they eventually get killed by the queueing 
> system.
Any comments?

Should I check in a patch?

Carsten


> 
> Carsten
> 
> 
> 
> On Jun 2, 2010, at 11:24 PM, Rossen Apostolov wrote:
> 
>> To all developers,
>> 
>> The new release of Gromacs is coming close. Before releasing the new packages though, in the next couple of weeks until June 15:
>> 
>> * everything in bugzilla should be cleared (David already started exterminating :). If you see a bug that you can fix or help with, please do so.
>> * if there are still any known issues, please file a bug asap or send a patch.
>> * do not add any new features! Berk has some AmberFF stuff but apart from that everything new should wait for the next release
>> * make sure that everything compiles without warnings on all platforms that you have access to
>> 
>> Hopefully all that will be done by the 15th and have a bug-free summer:)
>> 
>> Cheers,
>> Rossen
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> 
> 
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne
> 
> 
> 
> 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne