Re: qsub on a linux cluster

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Jul 14 2006 - 10:38:06 CDT

Hej san Per,

In some cases the queueing system will not know the path to the second
command executable which in this case is namd2.

Try full paths to both charmrun and namd2 in the script.

Also, double check that NUMPROCS is actually interpreted correctly.

MVH
Brian

On Fri, 14 Jul 2006, Per Jr. Greisen wrote:

> Hey,
>
> I am trying to run namd on a linux cluster and have looked at the namdwiki
> but cannot get the script working correctly; i Have made the file
> specifying which nodes to use - anybody has experience for running on
> linux clusters?
>
> Thanks
>
> #!/bin/csh -f
>
> # Name of the job
> #$ - N NAMD_test
> # Execute from the current directory
> #$ -cwd
>
> # Error logs
> #$ -e ./
> #$ -o ./
>
> set NODES = 'cat $HOST_FILE'
> set NODELIST = $TMPDIR/namd2.nodelist
> echo group main >! $NODELIST
>
> foreach node ( $nodes )
> echo host $node >> $NODELIST
> end
>
> @ NUMPROCS = 1* $#NODES
>
> #$ -e namd-job.errout
> charmrun namd2 +p$NUMPROCS ++nodelist $NODELIST minimization.conf > data.log
>
>
> --
> Best Regards
>
> Per Jr. Greisen
>
>

************************************************
   Brian Bennion, Ph.D.
   Biosciences Directorate
   Lawrence Livermore National Laboratory
   P.O. Box 808, L-446 bennion1_at_llnl.gov
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