AMBER Archive (2004)

Subject: RE: AMBER: sander gets stuck

From: MURAT CETINKAYA (cetinkayam_at_psu.edu)
Date: Fri Oct 29 2004 - 10:11:15 CDT

Dear Ross Walker,

Thanks for your help. I have realized that I just reached the limit of my quota.
That must be the problem.

Thanks alot,
Murat

On Fri, 29 Oct 2004 07:52:43 +0000, "Ross Walker" wrote:

> 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
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
>
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Murat CETINKAYA
Biomolecular Materials Lab,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
web: www.personal.psu.edu/muc176
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