Re: how should I run NAMD on parallel platform?

From: Gengbin Zheng (
Date: Thu Dec 18 2003 - 02:40:16 CST


For Linux cluster there are various ways of using them for NAMD, largely
depending on how you manage the cluster and what communication hardware
you have. These are some of the choices:

1. you can build NAMD and its communication library Charm++
*directly* using sockets (UDP or TCP) or specialized fast communication
hardware like Myrinet. Charm++ provides a charmrun utility for these
versions to start a parallel program onto the compute nodes.

2. you can also build NAMD and Charm++ using MPI which is Message
Passing Interface standard which takes care of almost everything
regarding to the low level communication. MPI version of NAMD due to the
fact of extra layer in NAMD/Charm++/MPI/Hardware, it normally is slower
than the previous implementation of Charm++ directly on top of hardware.
However, MPI version is considered more stable. To run a MPI version of
NAMD, MPI provides a mpirun utility program to do so.

3. If you want easy management of a cluster, you can also build a
Beowulf style cluster for example Scyld or Clustermatic. You can find
their information on the web. For the point view of NAMD/Charm++, there is
no difference in running a parallel NAMD job in case of MPI is used, or
just need a specialized version of charmrun that knows how to start a job
on these environment.

 In general, the philosophy of Charm++ and NAMD is that they should be
able to run on whatever hardware and parallel enironment you have.

 Our NAMD website has binary distributions for a large varieties
of platforms including pc linux that you can quickly try out on your cluster.
Please let us know if you have further question,


On Thu, 18 Dec 2003, wrote:

> Dear sir,
> Our lab has a cluster of 10 PCs with Linux. I want to run NAMD on parallel
> platform. I see in the userguide of NAMD program that a parallel program MPI is
> needed. I also see in the website of NAMD "how to build your own cluster" that
> Clustermatic is needed.
> I am not good at PCs with Linux. Could you please tell me in detail how should
> I run NAMD on parallel platform? I will be very appreciated with your
> information.

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