[molpro-user] Molpro 2006.1 on cluster with infiniband

Jyh-Shyong Ho c00jsh00 at nchc.org.tw
Mon Jan 8 02:01:30 GMT 2007


I  got an Infiniband /OpenIB version of GA library and built Molpro2006.1
on our Opteron cluster.  However, I don't know how to set the
WRAPPER-mpi varibale correctly in order to run parallel Molpro job
under TORQUE environment.  Perhaps someone can provide me some help?

Normall, the command to run an MPI job over Infiniband interconnect on our
cluster is

/opt/mvapich/pathscale/bin/mpirun_rsh -ssh -hostfile $PBS_NODEFILE  -np 
$nproc $executable

Where $PBS_NODEFILE is a temporary file which include the names of nodes 
by TORQUE for this job.  $nproc is the number of processors required.

I defined WRAPPER_mpi in file CONFIG as
WRAPPER_mpi="/opt/mvapich/pathscale/bin/mpirun_rsh \-ssh"
since both $PBS_NODEFILE and $nproc variables cannot be defined during
the compilation. 

I am not able to run the compiled Molpro2006.1 with  command in a TORQUE 
script file

/opt/chem/molpro/bin/molpro -n$NCPU -d$JOBDIR $JOB.com

I always got an error message:

Cannot find MPIRUN machine file for machine ch_gen2 and architecture LINUX .
(No device specified)

Which means that the machine list in file $PBS_NODEFILE  was not read.

Any suggestion on how to solve this problem?

Jyh-Shyong Ho, Ph.D.
Research Scientist
National Center for High Performance Computing
Hsinchu, Taiwan, ROC

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