Re: Not getting good speed up

From: Mauricio Carrillo Tripp (
Date: Thu Mar 03 2005 - 13:44:55 CST

sorry about that stupid mistake, it's building now...

I tried the option +giga (and also +strategy USE_MESH and +strategy USE_GRID)
All of them improved a little the scaling, but not enough though.
It is true that the new cluster is using Rocks, and that's why I want
to compare the
behaviour off all different versions of charm++...
I'll keep you all posted on my findings...

On Thu, 03 Mar 2005 13:34:56 -0600, Gengbin Zheng <> wrote:
> For UDP namd, use command line option: "+giga" which turned on some
> setting (such as UDP window protocol settings) which could speedup the
> performance. You can give it a try.
> I noticed that the OS of your new cluster is Rock. I am not familar with
> it, but I assume it has something different in the way it launch a
> parallel job.
> The error I have when building charm:
> make: *** No rule to make target `charmm++'. Stop.
> -------------------------------------------------
> Charm++ NOT BUILT. Either cd into mpi-linux-icc/tmp and try
> this is because you misspelled charm++ to charmm++.
> Gengbin
> Mauricio Carrillo Tripp wrote:
> >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"
> >>
> >>
> >--incdir="/opt/lam/intel/include"
> >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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