Hi Cihan,
> Greetings AMBER community,
>
> I have a problem with AMBER. It fails to write the restart file every
> ntwr steps. I have tested this on our cluster with two different
> compilations using different compilers (gnu compilers and intel
> compilers) which failed to write restart files.
>
> Do you know what may have caused this? If the problem is not clear what
> should i provide in the next mail?
When you say AMBER what exactly do you mean? Version 10? Do you mean sander or pmemd and I assume you mean running in parallel?
It would be useful to have more information including what your input file, job submission script and output file look like. Are you seeing no file written at all? Or the file created by of zero bytes? Also when the job runs to completion do you get a restart file?
One problem that might occur could be the way the file system is setup on your cluster. It is possible that the information is not being flushed to disk so while sander/pmemd is writing the restart file it simply isn't being flushed from the disk cache. However, when a job runs successfully and the final restart file gets closed you should see the final restart file. If you are not then there is something more complex at play.
Do the test cases pass? (in parallel?)
All the best
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
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Received on Wed Jan 13 2010 - 14:00:02 PST
