Not getting good speed up

From: Mauricio Carrillo Tripp (
Date: Wed Mar 02 2005 - 16:37:18 CST


Some time ago I started using NAMD on a 16 node cluster
with good results. I downloaded the executables (tcp version,
the recomended one for gigabit network) and everything
ran smoothly. The speed up was good (see Fig 1 at,
although maybe it could be improved, which takes me two the real
issue: we got a new cluster, I did the same as before, but
I noticed that the simulations were running a lot slower.
I did the same analysis as I did with the old cluster
and I found that the speed up was just terrible. I tried the other
executable version of NAMD2.5 and things went a little better
but not quite as good as I know the could've been (see Fig 2 at
I also found a big difference between MPICH and LAM/MPI. The
latter is the only MPI library installed in the old cluster.
So, these results clearly show that the problem lays in the communication
(cpu speed up is good)
and they suggest that charm++ is behaving as MPICH (or worst),
but I don't know the details of how charm++ works, i.e., does it
rely on the MPI libraries? if so, how can I tell it which one to use?
If not, how can I optimize its performance? (Is there a way to measure
it in a similar way as NetPIPE does?). I would like to take the maximum
advantage when running on 32 processors...

Any advice will be appreciated. Thanks.

Mauricio Carrillo Tripp, PhD
Department of Chemistry
Wabash College

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