[gmx-users] trajectory file problem

Peter C. Lai sirmoo at cowbert.2y.net
Tue Jan 28 01:56:50 CET 2003

You have filesystem issues. It could either be caused by hardware, or
something buggy with the Linux kernel. It doesn't have anything
to do with gromacs crashing.
You stated that linux is throwing I/O errors at you while
trying to cat or cp the file. That coupled with hdd interrupt
failures listed below suggest that you are actually unable to read
the sector. If an output file just has bad data  (as in having garbage data),
linux should still be happy to cat or cp it even if gromacs is unable to
parse it, but this doesn't appear to be the case.

On Mon, Jan 27, 2003 at 10:08:48AM -0300, Luciane Vieira de Mello wrote:
> 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

Peter C. Lai
University of Connecticut
Dept. of Molecular and Cell Biology
Yale University School of Medicine
SenseLab | Research Assistant

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