[gmx-users] trajectory file problem

[Anton Feenstra]

David wrote:
> 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.

You can, however, look for the 'magic number' that is written at the
beginning of each frame. The chance for finding it at random is about
one in a TeraByte.


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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