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

Reuti reuti at Staff.Uni-Marburg.DE
Mon Sep 12 13:22:00 BST 2011


Am 12.09.2011 um 14:06 schrieb Manhui Wang:

> 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:
>> 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

what do you mean by "mpiexec list", the one from http://www.osc.edu/~djohnson/mpiexec/index.php? Open MPI should work without it.

You tested Open MPI beforehand with a simple mpihello.c?

I remember an issue with the latest version of PBS Pro with either MPICH2 or Open MPI. But as we use SGE I didn't remember the complete discussion about it.

-- Reuti

>> 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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