[gmx-developers] trajectory files corrupted

Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu
Fri Jun 22 21:18:12 CEST 2007

On Fri, 22 Jun 2007 mchen2 at mailer.fsu.edu wrote:

> Hi,
>   As the subject, it happened to me several times when the cluster 
> encountering delay writing on running REM MD. The job is finished 
> without any error, but the trajectories are corrupted. Is it possible 
> to enhance data output?


i would first suggest to check your cluster configuration.
what you describe happens a lot, when your nodes and particularly
the file server that you are writing your trajectories to are
not time synchronized. with enhanced caching (for performance
reasons, you can easily run into the situation that the NFS 
client side cannot force flushing of the output, due to the
discrepancies in system time.

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Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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