Re: Not getting good speed up

From: Mauricio Carrillo Tripp (
Date: Thu Mar 03 2005 - 13:16:24 CST

Hi Gengbin, thanks for your answer. I did the comparison you recommend,
TCP vs UDP (I didn't compile from source though, I used the
executables NAMD supplies). The results are on Fig 2 at
Indeed, I get an increase in performance but not good enough.
Using the TCP version on the old cluster (lg66) did show good scaling,
but that's not the case for the new cluster (lgrocks).
Any ideas why is this, anybody?

I'm trying to compile different versions of charm++ (gcc, intel, tcp,
udp, mpi), to compare them using converse/pingpong,
although I'm having trouble building the mpi version,
I haven't found an example on how to do it, and all I get is:

>./build charmm++ mpi-linux icc --libdir="/opt/lam/intel/lib"
Selected Compiler: icc
Selected Options:
Copying src/scripts/Makefile to mpi-linux-icc/tmp
Soft-linking over bin
Soft-linking over lib
Soft-linking over lib_so
Soft-linking over include
Soft-linking over tmp
Generating mpi-linux-icc/tmp/
Performing 'make charmm++ OPTS=' in mpi-linux-icc/tmp
make: *** No rule to make target `charmm++'. Stop.
Charm++ NOT BUILT. Either cd into mpi-linux-icc/tmp and try

any help will be appreciated!

Thanks again.

On Wed, 02 Mar 2005 21:42:39 -0600, Gengbin Zheng <> wrote:
> 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.
> Gengbin
> Mauricio Carrillo Tripp wrote:
> >Hi,
> >
> >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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