[gmx-developers] next Gromacs release

[Carsten Kutzner]

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.

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