Dear All,
Have a nice day, I was able to run amber successfully in parallel few
days before using this qsub scrip
#!/bin/tcsh
# This is file Run__amber
#PBS -l nodes=1:ppn=4
#PBS -V
#PBS -N Imtiaz
#PBS -l walltime=00:59:00
set path = (/home/imtiaz/amber10/src/lam-7.1.3
/opt/lam_install_intel/bin/mpirun $path .)
echo "simulation started at" `date`
/opt/lam/7.1.3/bin/lamboot
/opt/lam/7.1.3/bin/mpirun -ssi rpi lamd N sander.MPI -O -i heat.in -o
heat.out -p ras-raf_solvated.prmtop -c min.rst -r
heat.rst -x heat.mdcrd -ref min.rst
echo "simulation ended at" `date`
I am not sure now what happened with the same script when I submit a
qsub job, job is submitted but with no output and no error, even showq
does not show any job running. Our cluster admin is saying that it is
something related to Amber not to the cluster software and hardware
" ran a job for Imtiaz on cluster1 - came back with a walltime error -
that's not a system software/hardware problem."
Please suggest something in this regards
Is there some problem in my qsub script? if yes this was working fine
before as such?
What could be potential problem with wall time?
Here is an example screenshot
[imtiaz.cluster1 amber10]$ qsub -d /home/mis9/amber_cdk2/ 1fin-min -V
413948.cluster1
[imtiaz.cluster1 amber10]$
[imtiaz.cluster1 amber10]$ more Imtiaz.o413948
[imtiaz.cluster1 amber10]$ more Imtiaz.e413948
[imtiaz.cluster1 amber10]$
* both the qsub o and e files related to the job id 413948 are empty
Looking for help and suggestions in this regards
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 29 2010 - 11:30:02 PST
