[gmx-users] Dell PowerEdge M710 with Intel Xeon 5667 processor

[Mark Abraham]

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.pall at cbr.su.se>/* wrote:
>
>
>     From: Szilárd Páll <szilard.pall at cbr.su.se>
>     Subject: Re: [gmx-users] Dell PowerEdge M710 with Intel Xeon 5667
>     processor
>     To: "Discussion list for GROMACS users" <gmx-users at 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_7860 at yahoo.com </mc/compose?to=maryam_h_7860 at 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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