Re: NAMD disk writes and quota overflow

From: Axel Kohlmeyer (
Date: Thu Jan 08 2009 - 16:19:19 CST

On Thu, 8 Jan 2009, Jeff Forbes wrote:

JF> Hi,


JF> I have found that when disk quota is reached or closely approached,
JF> that NAMD log files become corrupted and sometimes the .dcd files.
JF> The log files will have ^@ characters in them, before the job shuts
JF> down. Often times, the log files will become readable again shortly
JF> before the job shuts down.

JF> Other then more closely monitoring my disk quota, is there anyway to
JF> NAMD to fail on disk write errors without corrupting the files?

no. NAMD knows nothing of this. the kind of corruption you describe
is usually caused by buffering operations of your i/o library and
a networked file system and how they interact with quotas.

since it is rather easy to predict the amount of output created by
a segment of a production run, i would implement a check of available
disk quota before starting a job (and beg for a larger quota ?).


JF> Jeff
JF> Jeffrey G. Forbes, Ph.D.
JF> Muscle Proteomics and Nanotechnology Section
JF> Laboratory of Muscle Biology
JF> National Institute of Arthritis and
JF> Musculoskeletal and Skin Diseases
JF> National Institutes of Health
JF> Department of Health and Human Services
JF> 50 South Drive
JF> Building 50, Room 1139
JF> Bethesda, MD 20892-8024
JF> Voice: 301-451-9535
JF> FAX: 301-402-0009

Axel Kohlmeyer
   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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