Hi everybody,
I have installed AMBER 11 on a cluster, which consist os one head node and
50 cluster nodes. My OS is Red Hat enterprise linux. I used openMPI to
compile amber parallel version. On head node and each of the cluster nodes,
I can run msander.MPI on many threads (just on one node). But when I submit
the job on multiple nodes, the many threads were still run on one node,
instead of different nodes. I use PBSPro queue system. Here is my PBS
script:
#!/bin/csh
#PBS -V
#PBS -r n
#PBS -N PAD2_94_Min
#PBS -l select=8:ncpus=8
#PBS -m abe
#PBS -q verylong
#
set WRKDIR=/home/william/Work/PAD4/MD/KP94_PAD2
cd $WRKDIR
nohup mpirun -np 64 sander.MPI -O -i PAD2_KP94_CnsV_10ps.in \
-o PAD2_KP94_CnsV_10ps.out \
-p K94_PAD2.top \
-c K94_PAD2_20K_rst \
-x PAD2_KP94_CnsV_10ps.mdcrd \
-v PAD2_KP94_CnsV_10ps.mdvel \
-e PAD2_KP94_CnsV_10ps.mden \
-r PAD2_KP94_CnsV_10ps.rst \
-inf PAD2_KP94_CnsV_10ps.mdinfo
Does anybody has ideas what went wrong?
Thanks,
William
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Received on Tue Sep 13 2011 - 13:00:04 PDT
