Make sure you don't use a "debug" build of Open MPI. If you use trunk,
the build system detects it and turns on debug by default. It really
kills performance. --disable-debug will remove all those nasty printfs
from the critical path.
You can also run a simple ping-pong test (Netpipe is a good one) to
make sure that the numbers are correct. Based on your processor model,
shared memory latency should be in the .45us, while bandwidth should
reach 9Gbit/s for messages longer than cache.
Aurelien
Le 8 oct. 08 à 17:09, Brian Dobbins a écrit :
Hi guys,
[From Eugene Loh:]
OpenMPI - 25 m 39 s.
MPICH2 - 15 m 53 s.
With regards to your issue, do you have any indication when you get
that 25m39s timing if there is a grotesque amount of time being
spent in MPI calls? Or, is the slowdown due to non-MPI portions?
Just to add my two cents: if this job can be run on less than 8
processors (ideally, even on just 1), then I'd recommend doing so.
That is, run it with OpenMPI and with MPICH2 on 1, 2 and 4
processors as well. If the single-processor jobs still give vastly
different timings, then perhaps Eugene is on the right track and it
comes down to various computational optimizations and not so much
the message-passing that's make a difference. Timings from 2 and 4
process runs might be interesting as well to see how this difference
changes with process counts.
I've seen differences between various MPI libraries before, but
nothing quite this severe either. If I get the time, maybe I'll try
to set up Gromacs tonight -- I've got both MPICH2 and OpenMPI
installed here and can try to duplicate the runs. Sangamesh, is
this a standard benchmark case that anyone can download and run?
Cheers,
- Brian
Brian Dobbins
Yale Engineering HPC
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