Re: Not getting good speed up

From: Gengbin Zheng (
Date: Wed Mar 02 2005 - 21:42:39 CST

Hi Mauricio,

With NAMD-tcp version, Charm deoes not compiled on top of MPI, the
communication is based on native TCP socket, that is Charm++ itself
implements its message passing function using TCP sockets.
I can not provide a reason to explain why the scaling is so bad, because
I don't think it should behave like that.
You can do some test running Charm pingpong tests (available at
charm/pgms/converse/pingpong), and see what's the pingpong one way
latency is to compare with MPI.

In fact, I recommend you compile a UDP socket version of charm and NAMD
from source as comparison. (it is net-linux version of charm, and
Linux-i686 version of NAMD).
We have seen NAMD running with good scaling with gigabit ethernet.


Mauricio Carrillo Tripp wrote:

>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.

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