I was successful with building FiPy, the dependancies, and mpi4py, on a Mac and was able to run examples with MPI. I could see multiple cores engage and noticed the improvement in wall time execution. With that success I decided to save some time and purchased the enthought.com single user package and I'm trying to get that to run on a cluster (SUSE Enterprise 64 bit) from within my account (no root). I haven't gone down the route of including Trilinos yet, just the basics for now.
I took examples/parallel.py, took out the Trilinos stuff, and renamed it simple.py. It appears that the MPI part is working, but the parallel and Grid1D is not distributing across the nodes. When I do an mpirun I get: me@cluster% mpirun -np 3 python simple.py mpi4py: processor 0 of 3 :: FiPy: 10 cells on processor 0 of 1 mpi4py: processor 1 of 3 :: FiPy: 10 cells on processor 0 of 1 mpi4py: processor 2 of 3 :: FiPy: 10 cells on processor 0 of 1 The mpirun that is running is from my enthought Python install. I can see that enthought python is built using gcc, but on the cluster I built mpi4py with the Intel compiler. I believe I need to do so to be compatible with the clusters MPI environment and job queue (PBS). (?) The above run was on a development node; not run through PBS. Am I trying to mix apples and organges? Should I build all the stuff, Python, pysparse, etc. with the intel compiler? Should I rebuild mpi4py with gcc? I haven't been able to find any general run-fipy-on-a-cluster advice (but did find how to set the fipy_viewer to dummy). The cluster is well managed and I can change 'module' sets to use mvapich, mpt, mvapich_gcc, mvapich_intel, etc. I have been successful building C/MPI programs and getting them to execute on the cluster, so I not a total nubie to cluster computing... just getting FiPy to run there. What general guidance can you provide vs. what I need to coordinate with my local system admin? Thanks, Bill _______________________________________________ fipy mailing list [email protected] http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
