[gmx-users] IO problem on Cray XT3 MPP

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 5 22:04:45 CEST 2007

vijaya subramanian wrote:
> Hi
> I have been running GROMACS jobs on a 
> Cray XT3 MPP  machine.  I get limited time, 12 hr, for any given run and find that the
> .edr file and .log files do not get written to continuously.  This is ok if the run
> finishes but I lose data everytime the runtime exceeds the 12 hr limit.  The following is the 
> info I got from the sys admn about the issue: The problem with GROMACS looks like it is caused by the way GROMACS
> buffers its IO, which would not be easy for us to fix. Is there a GROMACS
> keyword that you can use to change this?
> Does anyone know of a workaround this problem?  
Of course, you can make the runs so short that they finish in 11:30 h. 
Do also try the -v option to mdrun.

> Thanks
> Vijaya
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David van der Spoel, Ph.D.
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

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