[gmx-users] IO problem on Cray XT3 MPP

Erik Lindahl lindahl at cbr.su.se
Fri Oct 5 22:23:18 CEST 2007


On Oct 5, 2007, at 10:04 PM, David van der Spoel wrote:

> 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  
>> 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.

This has actually been circumvented in the CVS / 3.99 version; we  
still buffer IO while it happens (for performance reasons), but once  
a frame is written we flush the file to make sure everything is  
written out.

In addition, Gromacs will clean up and finish nicely if it receives a  
SIGHUP signal, and finish at the next neighborsearching step if it  
received SIGUSR1.



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