Re: how should I run NAMD on parallel platform?

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Dec 18 2003 - 13:27:24 CST

Hi,

The instructions on the web site are for Clustermatic 3. We've just
installed a test cluster with Clustermatic 4. It's not binary compatible.

One of the main changes is that the "beowulf" directories have been
renamed to "clustermatic".

-Jim

On Thu, 18 Dec 2003, wrote:

> 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 <gzheng_at_ks.uiuc.edu>
> >Reply-To:
> >To: yxiong_at_mail.ccnu.edu.cn
> >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
> 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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