Re: file writing stopped

From: Nicholas M Glykos (
Date: Wed Apr 14 2010 - 05:01:06 CDT

Just guessing, but: Is the trajectory written on a local disk, or on a
NFS-mounted volume ? If it is NFS, it could be that it has been mounted
with the async option, in which case issuing a 'sync' on both the server
and client side may solve your worries.

On Wed, 14 Apr 2010, francesco oteri wrote:

> Dear NAMD users,
> I'm running 2 simulations of 10ns on 2 different intel quad core PC with
> Ubuntu 9.10 4GB RAM each one, using binary cuda version (CVS 2010-03-26)
> with 2cpu on a "GeForce GTS 250" . The folder containing namd is hosted on a
> server and the 2 pc access to it through NFS.
> I'm experiencing a strange behaviour: though namd seems to run (how
> displayed by top command) after a random number of steps, no data are
> written to disk.
> I've started the simulations 10 days ago and both are still running (
> though should be finished this night) , but the first displayed the problem
> after 1day (around 900000 steps) while the second displayed the problem this
> morning after 4858000 steps.
> I observed that Xorg use 100% of a CPU, but killing it doesn't solve the
> problem; the first simulations shows the problem more often that the second.

          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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