AMBER Archive (2004)

Subject: RE: AMBER: sander gets stuck

From: Ross Walker (
Date: Fri Oct 29 2004 - 09:52:43 CDT

Dear Murat

> However for this system, my output files always get stuck at
> 220ps and I found
> the following message in my computer nodes:
> FLUSH--FAILED:: Stale NFS file handle
> FLUSH--FAILED:: Stale NFS file handle
> Input/Output Error 173: unknown error

How big is your mdcrd file at this point? What architecture are you running
this on? If it is 32bit then you could be hitting the 2GB file limit. If so
split your job up into 200ps chunks.

You also might be hitting your quota, or filling the filesystem, or some
maximum filesize limit in the NFS implementation. Writing a sander output
over NFS is probably not a good idea anyway, if you can write to a local
drive and copy it over when you are done.

Check the above scenarios and if you still have problems email me back.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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