[gmx-users] trajectory file problem

[Luciane Vieira de Mello]

Hi David

Thanks for the mail.  gmxcheck stops at the same point 1.9ns into either
the xtc or trr files.

There are indeed problems in the /var/log/messages file.  A large number
like this

Jan 27 10:00:56 bemtevi kernel: hda: dma_intr: status=0x51 { DriveReady
SeekComplete Error }
Jan 27 10:00:56 bemtevi kernel: hda: dma_intr: error=0x40 {
UncorrectableError }, LBAsect=98790130, sector=78210864
Jan 27 10:00:56 bemtevi kernel: end_request: I/O error, dev 03:03 (hda),
sector 78210864

What does this mean?  A hardware error?  If that were the case, it's a big
coincidence that both trr and xtc have problems 1.9 ns in!  Could ngmx
have crashed at that point while reading both files and left problems of
this kind?  I don't want to rush to blame gromacs but if this is possible
then it's a very serious (potential) bug.

Regards

Luciane


+-------------------------------------------------------------------------+
|                  Dra. Luciane Vieira de Mello Rigden                    |
| e-mail: mello at cenargen.embrapa.br                                       |
| Embrapa Recursos Geneticos e Biotecnologia                              |
| Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
| PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
| 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
+-------------------------------------------------------------------------+



On 24 Jan 2003, 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.
>
>
> >
> >
> > 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                              |
> > | Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
> > | PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
> > | 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
> > +-------------------------------------------------------------------------+
> >
> >
> >
> > _______________________________________________
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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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