[gmx-users] trajectory file problem

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 27 15:54:15 CET 2003

On Mon, 2003-01-27 at 14:08, Luciane Vieira de Mello wrote:
> 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.
It's not a coincidence. Since these files are extended all the time by
a  little bit, they ask the operating system for a block to write on. I
don't know what the internal strategy of the OS is when handing out new
blocks, but it seems likely that they would be close physically, i.e. it
is well possible that they would be on the same sector of the disk. What
most likely happened is that you have a bad sector on the disk, or it
may be that your disk is misconfigured by the OS. 

Now if your files are corrupt, there is not much we can do. There is no
repair tool. The shortest way would be to  continue the run from just
before the crash.

If you feel like making a repair tool, you'd have to make something that
reads a binary file and looks for integers with value 1995. In contrast
to what Anton said, the possibility of finding a number like that by
accident is 1/2^32, or one in a billion.
Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 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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