[gmx-users] Checking files .xtc .trr .edr

David spoel at xray.bmc.uu.se
Wed Oct 30 10:57:23 CET 2002

On Wed, 2002-10-30 at 00:59, Erik Lindahl wrote:
> Alan Wilter Sousa da Silva wrote:
> >Hi List!
> >
> >	I run GMX in a cluster and some processors write files via NFS.
> >However, the NFS server crashed, stoped for a while and then was rebooted.
> >How could I be sure whether my .xtc .trr and .edr files was, or not,
> >corrupted?  I kept the jobs running.
> >  
> >
> If you use hard NFS mounts (the default, never EVER use soft...) you 
> should be perfectly OK. The client will just continute trying to write 
> until the server comes up again, without dropping any data.
In a perfect world yes, but not with redhat 7.3 for example. We have
lots of weird things going on when our rh73 server goes down. Machines
can not be logged into anymore, the clients hanging on NFS...

> If you are thinking of file system problems, run fsck, and possible test 
> trajectories with gmxcheck. If it gets to the last frame you should 
> probably be ok; I've never seen an error that silently corrupts the data 
> while maintaining the overall structure...
gmxcheck will give you clues indeed.

> Cheers,
> Erik
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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