[molpro-user] parallel molpro and PBSPro on more than 1 node

Manhui Wang wangm9 at cardiff.ac.uk
Mon Sep 12 13:06:34 BST 2011

Dear Ulrike,

There is some problem when running molpro with openmpi/infiniband on 
multinodes, and the internal reason is still unknown (you may have  seen 
there are a number of options when building and running OpenMPI, it 
might help by adjusting these options). However, with mvapich2 or 
intelmpi over infiniband, molpro runs well. I regularly run molpro jobs 
with mvapich2/Infiniband  via PBSPro (pbs_version = PBSPro_10.0.0.82981) 
on multinodes, and it always works fine. Instead of using the extra MPI 
parallel job launcher Mpiexec, I simply submit the Molpro job using a 
rather simple job script like:
#PBS -l select=4:ncpus=8:mpiprocs=8
#PBS -l place=scatter
#PBS -l walltime=02:00:00
#PBS -N Molprojob


NPROCS=`wc -l $PBS_NODEFILE | awk '{ print $1 }'`


echo "Running Molpro job:"

./bin/molpro -n $NPROCS testjobs/h2o_vdz.test

echo "All Done."

Best wishes,

On 09/09/11 14:45, Ulrike Nitzsche wrote:
> Hello,
> I'm asking for help in the following situation:
> We would like to use molpro (2010.1pl23) on a cluster running
> PBSPro_10.4.5.110853. The connections are done over infiniband.
> Usually we use the openmpi implementation for parallel computing without
> any problem. I tried to compile molpro both with openmpi-1.4.3 and the
> beta version openmpi-1.5.4 as well. In both cases the error reported in
> this post:
> http://www.molpro.net/pipermail/molpro-user/2011-May/004382.html
> and an unexpected "eating of memory" for the parallel benchmarks is
> observed when jobs run on more than 1 node.
> As suggested I tried the compilation with mvapich2 (again with stable 1.6
> and the beta 1.7rc1) and an interactive mpiexec of the jobs is running fine -
> no finalizing problem, no memory problem.
> But: mvapich2 is only running up to PBSPro version 7 (that's the state more
> than 5 years ago). Of course I asked for help at the mpiexec mailing list
> and at PBSPro too. Up to now without any hints. Therefore I asked here on the
> application mailing list:
> 1. Is there any report about running molpro with openmpi and infiniband on
>     more than 1 node? If not - are there any ideas about the internal problems?
> 2. Is there any report about molpro with mvapich2 and PBSPro version 8 and
>     above using the select-syntax to submit a job?
> 3. Any other ideas how to get molpro running in parallel on several hosts
>     under the control of PBSPro?
> Thanks in advance for your help,
> Ulrike Nitzsche

Manhui  Wang
School of Chemistry, Cardiff University,
Main Building, Park Place,
Cardiff CF10 3AT, UK

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