Re: NAMD infiniband performance

From: Axel Kohlmeyer (
Date: Tue May 19 2009 - 10:00:11 CDT

On Tue, 2009-05-19 at 09:56 -0400, Guanglei Cui wrote:
> Hi Lev,

dear guanglei,

> Thanks for the reply. I have not tried to compile Charm++ with any MPI
> implementations, and been using the net- option. Is there any
> advantage of using MPI (just any MPI)vs. using the net- option?

yes there is an advantage. the net version always uses tcp/ip,
which has a high communication overhead. now for a small number
of nodes or a large system this does not matter much, as NAMD
can hide communication latencies through the ingenuity of charm++
over plain MPI. however, if you have an infiniband network, the
low latency that the infiniband communication offers, is only
available if you use a charm++ installation that uses MPI for
lowlevel communication or even the ibverbs layer directly.

the difference between the two approaches will be larger the
more nodes you can use in your tests. the net version will scale
out _much_ faster than the custom compile.


> Best regards,
> Guanglei
> On Tue, May 19, 2009 at 2:31 AM, Lev Lafayette <> wrote:
> > Hi Guanglei,
> >
> > Although I am no NAMD expert, I would suggest compiling from source and creating an application. As a binary you probably won't be picking up the performance benefits, which should be determined by whatever you're using as message parsing interface (OpenMPI?). Then you should seem some real gains.
> >
> > All the best,
> >
> > --
> > Lev Lafayette (03) 9925 4909, Systems Administrator, Victorian Partnership for Advanced Computing
> > "If you are sending a reply to a message or a posting be sure you summarize the original at the top of the message, or include just enough text of the original to give a context. This will make sure readers understand when they start to read your response."
> > RFC 1855
> >
> >

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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