[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:
> 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.
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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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