VMD-L Mailing List

From: Bogdan Costescu (bogdan.costescu_at_iwr.uni-heidelberg.de)
Date: Sat Jan 03 2004 - 10:07:49 CST

On Fri, 2 Jan 2004, Mauricio C. Tripp wrote:

> I'm sorry, something definitely went wrong with charmm, in the output
> file it skiped 69 output steps and there's garbage in its place (as if
> the file was binary) and it corresponds to where VMD finds the error
> format.

I would suspect more a hardware problem (e.g. memory or disk failure) or a
low level network problem (if files were written to NFS mounted
directory).

> After that everything seems fine, so it is like if charmm did something
> wrong while writing to files for a while and then came back to normal...

... and this confirms what I wrote above. Could you check if the size of
the "bad" trajectory part is a power of two ? Does it have a constant
content ?

> have you heard anything like that before?

I did experience such corruption with some older (2.2) Linux kernels that
had some NFS problems. People on the Linux NFS development list have
reported silent data corruption when using NFS in combination with some
Intel network cards; those did not appear anymore in a while so it might
have been an issue that could be fixed in software (=driver). 

-- 
Bogdan Costescu
IWR - Interdisziplinaeres Zentrum fuer Wissenschaftliches Rechnen
Universitaet Heidelberg, INF 368, D-69120 Heidelberg, GERMANY
Telephone: +49 6221 54 8869, Telefax: +49 6221 54 8868
E-mail: Bogdan.Costescu_at_IWR.Uni-Heidelberg.De