With the same setup, we've been able to run just fine across different
nodes.
Look at the options that exist for mpirun -- I'm guessing it's not getting
the proper machinefile or nodefile (I'm not an expert in this), so it
doesn't know to start threads on multiple machines.
If your cluster has PBS, then that often takes care of it for you, but
possibly not. Try reading through some of the OpenMPI documentation to see
if it gives you any leads (or see your system administrator for some
advice). It may also be worth testing to see if you can reproduce this
behavior with other MPI programs compiled the same way.
Good luck!
Jason
2011/1/12 Jesper Sørensen <lists.jsx.dk>
> Hello,
>
>
>
> I have installed MMPBSA.py on our cluster and the parallel versions works
> well on a single node using all 8 CPU’s.
>
> However, once I perform a calculation using several nodes, it only starts
> on
> the master-node leaving the other nodes running nothing.
>
>
>
> I am using the following versions of programs
>
> Amber 11 with all patches
>
> AmberTools 1.4 with all patches
>
> Mpi4py-1.2.2
>
> ActivePython 2.7.1.3
>
> OpenMPI 1.4.1
>
> mmpbsa_py (downloaded from the tutorial website) with all patches
>
>
>
> I have tried running the calculation on nodes using either Ethernet or
> infiniband, but the error occurs using both setups.
>
>
>
> All suggestions are appreciated.
>
>
>
> Best regards,
>
>
>
> Jesper Soerensen
>
> Ph.D. Student
>
> Department of Chemistry
>
> Aarhus University, Denmark
>
> jes.chem.au.dk
>
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jan 12 2011 - 10:30:03 PST
