Re: Dell PowerEdge M710 with Intel Xeon 5667 processor

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Hi Jussi,

Many thanks for your email. As you said I am using an old version of Fedora (5) and because there are not many highly experienced linux IT person around, I am hesitating to upgrade it. Currently I am using an 8 node cluster each composed of two dual core Opteron 2212 CPUs. I am managing the cluster, but am not on top it.

Cheers,
Siavoush


From: Jussi Lehtola <[email protected]>
To: [email protected]
Sent: Mon, 17 January, 2011 2:51:08 PM
Subject: Re: Dell PowerEdge M710 with Intel Xeon 5667 processor

On Mon, 17 Jan 2011 01:02:17 -0800 (PST)
Siavoush Dastmalchi <[email protected]> wrote:
> Many thanks for your kind reply. I know that those programs works
> under linux and am currently using them under fedora. What I want to
> know is the suitability of Dell PowerEdge M710 with Intel  Xeon  5667
> processor for parallel computation under linux system.
> By the way, I always have problem with this yum command. Issuing the
> following commands gives me error:
>
> $ yum list "*gromacs*"
> Loading "installonlyn" plugin
> Setting up repositories
> extras
> [1/2] Cannot open/read repomd.xml file for repository: extras
> Cannot find repomd.xml file for extras
> Error: Cannot find repomd.xml file for extras

You must be running an age-old distribution of Fedora. Extras were
merged in Fedora in Fedora 7, that is 2.5 years ago.

GROMACS has been included in Fedora since Fedora 10.

If you're going to run GROMACS only on a single node, then practically
any system should do.

However, if you want to do really parallel runs (more than one node
for a single computation), then you probably have to invest in a decent
interconnect such as InfiniBand, otherwise your parallel performance
will be handicapped by the latencies and slow bandwidth.

You're better off asking what kind of a cluster to buy on a GROMACS
list, http://www.gromacs.org/Support/Mailing_Lists .
--
Jussi Lehtola
Fedora Project Contributor
[email protected]
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