[gmx-users] corrupt trr file?
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jul 25 12:45:27 CEST 2006
Samantha Kaye wrote:
> The files are over 2gb and I'm using gromacs 3.3 on a linux cluster with amd64's (is that enough info? let me know if you need more).
> The only frame info I get is counting through the frames being checked until it gets to the last (corrupt) one at 4550.
> Thanks for your help David. It's appreciated.
Magic number errors can be caused by flaky hardware or software, e.g.
intermittent NFS failures (or temporary full disks) sometimes corrupt
files without crashing. Is the 910 ps problem reproducible? You could
restart the calculation from the same tpr file and see if the problem
reoccurs. Since MD is deterministic it should give the same result.
> In message <44C5C7BD.1080109 at xray.bmc.uu.se> Discussion list for GROMACS users <gmx-users at gromacs.org> writes:
>> Samantha Kaye wrote:
>>> When I tried to cat the results of that continuation file (started from 4500) it also has a magic number error at frame 910 (which is now in the second file) so I will try to truncate my trr file as suggested.
>> did you say what platform this is? are the files larger than 2Gb?
>>> One further question, how do I get gmxcheck to tell me this? I don't get any output other than the error message. Is there a verbose option in there somewhere? At the moment I'm just running gmxcheck -f file.trr
>> It should say how many frames there are etc. but maybe not if it crashes...
>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>> phone: 46 18 471 4205 fax: 46 18 511 755
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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