AMBER Archive (2004)

Subject: Re: AMBER: Amber job submission using PBS

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Thu Sep 23 2004 - 12:59:00 CDT

> > node001
> > node002
> > node004
> > node007
> > /var/spool/PBS/mom_priv/jobs/9355.sched.SC: -machinefile: command not found
> > /var/spool/PBS/mom_priv/jobs/9355.sched.SC: -O: command not found

Regarding the PBS problems, a very good way to debug these is to attempt
to run the job interatively in the queue.

qsub -I -l nodes=2:ppn=2,walltime=1:00:00 -q normal

Then if this starts up, you will be on the first node of the assigned
$PBS_NODEFILE list.

Then you can try doing each of the commands by hand.

 cd /home2/e953kks/amber8/test/4096wat
 set mpich_run = "/opt/mpich/1.2.5..10/gm-2.0.12-2.4.20-28.7smp-i686/smp/gnu/ssh/bin//mpirun"
 set sander = "/home2/e953kks/amber8/exe/sander"

 $mpich_run -machinefile $PBS_NODEFILE -np 4 $sander -O -i gbin -c eq1.x -o mdout.test

Sometimes with mpich versions I've had trouble in the past if the
executable to run is not in/out of the current directory, i.e. the paths
get messed up so it thinks your job is running out of the path where your
exe is.

So, try

cp -p /home2/e953kks/amber8/exe/sander .

$mpich_run -machinefile $PBS_NODEFILE -np 4 ./sander -O -i gbin -c eq1.x -o mdout.test

The interactive testing in the queue is a very nice way to go...

Good luck,

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu