Re: AW: Corrupt dcd files

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu May 12 2011 - 17:20:36 CDT

In an offline discussion we determined that this is 2.7b4, which didn't
check the return value of close() on the DCD file. 2.7 and later do, so
there should at least be an error message if that's the issue.

-Jim

On Thu, 12 May 2011, Norman Geist wrote:

> Hi Marc,
>
> Another question, what kind of filesystem do you use to save your dcd and
> outfiles while namd is running? Is it a nfs source or a local disk?
>
> Let me know.
>
> Best regards
>
> Norman Geist.
>
>
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
> von Marc Baaden
> Gesendet: Mittwoch, 11. Mai 2011 18:16
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: Corrupt dcd files
>
>
> Hi,
>
> I have recently observed a weird behaviour with at least 4 NAMD simulations
> I ran locally on my machine. They all ran to completion but produced corrupt
>
> dcd files. Is this a known issue?
>
> Is there any tool that allows to retrieve as much as possible from such
> dcd files? I have seen hints at using a hex editor, but I thought maybe
> someone has gone through the trouble of writing a tool to do the job..
> . eg is there any magic number or something one can jump to to skip
> the corrupt parts?
>
> Thanks in advance,
> Marc Baaden
>
>
>
> dcdplugin) detected standard 32-bit DCD file of native endianness
> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> dcdplugin) Warning: DCD header claims 4000 frames, file size indicates there
> are actually 3999 frames
> Info) Using plugin dcd for coordinates from file
> /Volumes/apple/bcl1.prod.1.dcd
> dcdplugin) read_dcdstep: corruption or unrecognized file structure
> Info) Coordinate I/O rate 59 frames/sec, 17 MB/sec, 7.5 sec
> Info) Finished with coordinate file /Volumes/apple/bcl1.prod.1.dcd.
> --
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden_at_smplinux.de - http://www.baaden.ibpc.fr
> FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
>
>
>
>

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