At the same time, I would emphasize that from a scaling point of view less cores per node is better than lots of cores because processors on the same node share the same network link. Also frequency of CPUs on 2-socket nodes goes higher than 4+-socket configurations.
-- Szilárd On Wed, Jan 19, 2011 at 10:30 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > 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><szilard.p...@cbr.su.se> > * wrote: > > > From: Szilárd Páll <szilard.p...@cbr.su.se> <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><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 <http://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 > > > > -- > > gmx-users mailing list > > gmx-users@gromacs.org<http://mc/compose?to=gmx-users@gromacs.org> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to > > gmx-users-requ...@gromacs.org<http://mc/compose?to=gmx-users-requ...@gromacs.org> > . > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list > gmx-users@gromacs.org<http://mc/compose?to=gmx-users@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to > gmx-users-requ...@gromacs.org<http://mc/compose?to=gmx-users-requ...@gromacs.org> > . > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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