Hi,
I think the best it would be if you would contact your system
administrator for this but what I see in your script is that you are not
really using properly the MPI command
you should use something like
mpirun -np 4 $AMBERHOME/exec/sander ....
(try to put at the prompter
which mpirun to see the path to the mpi executable)
-np tells mpi how many processors to use and I see you asked for 2 nodes
with 2 processors per node.
The way I know you should ask for processors in a PBS script is to use
#PBS -l ncpus=32
rather than
#PBS -l nodes=2:ppn=2
but that again depends maybe on the local implementation of PBS.
Also are you only asking for 2 minutes CPU time?
#PBS -l cput=00:2:00
two hours would be
#PBS -l cput=02:00:00
Hope this helps,
Ioana
On Wed, 2 Apr 2003, Venkata S Koppuravuri wrote:
> Hi, I am trying to learn how to submit batch job using MPI and PBS to our
> cluster at Wright State University. Below is the script that i have used
> is
>
> ------------
> # AMBER7 Example Batch Script for maxx
> # #PBS -N pti
> #PBS -j oe
> #PBS -m ae
> #PBS -l cput=00:2:00
> #PBS -l nodes=2:ppn=2
> #PBS -S /bin/bash
> set echo
> # set WORK=$HOME/newtest
> set TMPDIR=$HOME/newtemp
> cd $TMPDIR
> #
> set MDIN=min.in
> set MDOUT=min.out
> set PRMTOP=xtop
> set INPCRD=xcrd
> set REFC=xcrd
> set RESTRT=pti.rstrt
> cp $WORK/$MDIN .
> cp $WORK/$PRMTOP .
> cp $WORK/$INPCRD .
> cp $WORK/$REFC .
> #
> /usr/local/bin/mpiexec $AMBERHOME/exe/sander -O -i $MDIN -o $MDOUT -p
> $PRMTOP -c $INPCRD -ref $REFC -r $RESTRT ls -al cp $MDOUT $RESTRT $WORK
>
> ------------------------------------
>
> when i execute it using the command
>
> qsub name.pbs
>
> i am getting the error message
>
> ----------
> mpiexec: Error: get_hosts: pbs_connect: Unknown PBS error 101.
> ----------
>
> can anyone help me what this error means.
>
> Regards
> -Venkat
>
>
>
Received on Wed Apr 02 2003 - 20:53:02 PST
