[gmx-users] trajectory file problem

[David]

On Fri, 2003-01-24 at 23:06, Luciane Vieira de Mello wrote:
> Hi
> 
> I already posted a mail reporting that the ngmx visualisation (at least on
> our, Linux) machines only read 1.9ns of a 10ns trajectory.  After this
> the program froze and had to be killed.  Other Gromacs programs didn;t
> seem to have this problem.  Now there's a another issue which I think is
> related.
> 
> Trying to manipulate these files gives us Linux input/output errors.  What
> strikes me is that the errors (when FTPing, copying, splitting - any file
> manipulation) occur around 20% into the file.  In other words be can FTP,
> for example, 20% of the file before we get an error.  What's important is
> that this happens *both* for the xtc and for the trr.  This leads me to
> wonder if ngmx, on crashing, has not left some kind of problem in these
> files at the 20%/1.9ns mark.  Has anyone else seen this?  What could the
> problem be?
> 
> We now have the practical issue of trying to recuperate the trajectories.
> We can get the first 1.9ps but the rest is tricky.  I've just realised
> that I can tail most of the rest of the xtc trajectory (tail
> --bytes=1300m traj.xtc >) but when I try to open it I get
> 
> Fatal error: Magic Number Error in XTC file (read 313737432, should be
> 1995).
> 
> Similarly, I can get the latter part of the trr file.  Then I
> get the error
> 
> trn version:
> Last frame         -1 time    0.000
> WARNING: Incomplete header: nr 0 time 0
> Fatal error:
> Couldn't read time from first frame.

Have you checked your system log files for (/var/log/messages) for file
system errors? I've had problems with EXT3 filesystem, and had to
reinstall my compute cluster, and upgrade the kernel. 
On the gromacs side you could run
gmxcheck -f traj.xtc
to see if the file is OK. You cannot jump in somewhere in the middle and
expect to read it, since the frames do not have the same length.


> 
> 
> Does anyone have any ideas how to solve the problem of the file, or at
> least how to recuperate the maximum possible?
> 
> many thanks in advance
> 
> Luciane
> 
> 
> +-------------------------------------------------------------------------+
> |                  Dra. Luciane Vieira de Mello Rigden                    |
> | e-mail: mello at cenargen.embrapa.br                                       |
> | Embrapa Recursos Geneticos e Biotecnologia                              |
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> 
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel
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