Dear all,
I submit my sander.MPI (amber11) job with qsub using the following script:
----
#!/bin/sh
INPUT=sander.in
cat $PBS_NODEFILE
/opt/amber11-ambertools-1.4/
bin/lamboot -d -v $PBS_NODEFILE
echo "mpirun" 1>&2
/opt/amber11-ambertools-1.4/bin/mpirun -np 8
/home_changlab/croberts/local/amber11/bin/sander.MPI -O `cat sa
nder.in`
echo "lamclean" 1>&2
/opt/amber11-ambertools-1.4/bin/lamclean
echo "lamhalt" 1>&2
/opt/amber11-ambertools-1.4/bin/lamhalt
-----
Then I run "top" command, which shows 8 processors are running sander.MPI
about 100%.
But the output says it is running on 1 nodes.
---
| Atom division among processors:
| 0 3128
| Running AMBER/MPI version on 1 nodes
---
And actually it is more than 3 times slower than a sander.MPI (amber10) job
with 4 nodes in the other machine.
---
| Atom division among processors:
| 0 797 1564 2361 3128
| Running AMBER/MPI version on 4 nodes
---
It doesn't show any error message. How can I fix this problem?
*Waiting for some suggestion in this regards.
Myung*
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Received on Fri Jul 22 2011 - 12:00:05 PDT