Re: how should I run NAMD on parallel platform?

Date: Thu Dec 18 2003 - 04:40:58 CST

Dear sir,
Thank you for your clear explanation.
I am trying the third way you mentioned.
I had installed Clustermatic 4 and get the following information:
Preparing... ########################################### [100%]
        package kernel-2.4.22-1.2115.nptl (which is newer than kernel-2.4.22-cm36)
is already installed
        package kernel-doc-2.4.22-1.2115.nptl (which is newer than
kernel-doc-2.4.22-cm36) is already installed
        package kernel-smp-2.4.22-1.2115.nptl (which is newer than
kernel-smp-2.4.22-cm36) is already installed
        package kernel-source-2.4.22-1.2115.nptl (which is newer than
kernel-source-2.4.22-cm36) is already installed
However, as the "how to build your own cluster" in the website of NAMD said, I
need modify the /etc/beowulf/config, but I can't find this file.Could you please
tell me the reason?

>From: Gengbin Zheng <>
>Subject: Re: namd-l: how should I run NAMD on parallel platform?
> Hi,
> 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,
> Gengbin
> 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
> > needed. I also see in the website of NAMD "how to build your own cluster"
> > Clustermatic is needed.
> > I am not good at PCs with Linux. Could you please tell me in detail how
> > I run NAMD on parallel platform? I will be very appreciated with your
> > information.
> >
> >
> >

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