On 20/01/2011 3:33 AM, Maryam Hamzehee wrote:
Dear Szilárd,
Many thanks for your reply. I've got following reply from my question
from Linux-PowerEdge mailing list. I was wondering which one applies
to GROMACS parallel computation (I mean CPU bound, disk bound, etc).
In serial, GROMACS is very much CPU-bound, and a lot of work has gone
into making the most of the CPU. In parallel, that CPU-optimization work
is so effective that smallish packets of information have to be
transferred regularly without much possibility of effectively
overlapping communication and computation, and so a low-latency
communication network is essential in order to continue making effective
use of all the CPUs. Something like Infiniband or NUMAlink is definitely
required.
Mark
>There shouldn't be any linux compatibility issues with any PowerEdge
>system. At Duke we have a large compute cluster using a variety of
>PowerEdge blades (including M710's) all running on linux.
>What interconnect are you using? And are your jobs memory bound, cpu
>bound, disk bound, or network bound?
>If your computation is more dependent on the interlink and communication
>between the nodes, its more important to worry about your interconnect.
>If Inter-node communication is highly important, you may also want to
>consider something like the M910. The M910 can be configured with 4
>8-core CPUs, thus giving you 32 NUMA-connected cores. Or 64 logical
>processors if your job is one that can benefit from HT. Note that when
>going with more cores-per chip, your max clockrate tends to be lower.
>As such, its really important to know how your jobs are bound so that
>you can order a cluster configuration that'll be best for that job.
Cheers, Maryam
--- On *Tue, 18/1/11, Szilárd Páll /<szilard.p...@cbr.su.se>/* wrote:
From: Szilárd Páll <szilard.p...@cbr.su.se>
Subject: Re: [gmx-users] Dell PowerEdge M710 with Intel Xeon 5667
processor
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Received: Tuesday, 18 January, 2011, 10:31 PM
Hi,
Although the question is a bit fuzzy, I might be able to give you a
useful answer.
>From what I see on the whitepaper of the Poweredge m710 baldes, among
other (not so interesting :) OS-es, Dell provides the options of Red
Had or SUSE Linux as factory installed OS-es. If you have any of
these, you can rest assured that Gromacs will run just fine -- on a
single node.
Parallel runs are little bit different story and depends on the
interconnect. If you have Infiniband, than you'll have a very good
scaling over multiple nodes. This is true especially if it's the I/O
cards are the Mellanox QDR-s.
Cheers,
--
Szilárd
On Tue, Jan 18, 2011 at 4:48 PM, Maryam Hamzehee
<maryam_h_7...@yahoo.com </mc/compose?to=maryam_h_7...@yahoo.com>>
wrote:
>
> Dear list,
>
> I will appreciate it if I can get your expert opinion on doing
parallel computation (I will use GROMACS and AMBER molecular
mechanics packages and some other programs like CYANA, ARIA and
CNS to do structure calculations based on NMR experimental data)
using a cluster based on Dell PowerEdge M710 with Intel Xeon 5667
processor architecture which
> apparently each blade has two quad-core cpus. I was wondering if
I can get some information about LINUX compatibility and parallel
computation on this system.
> Cheers,
> Maryam
>
> --
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