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).
>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> 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://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 -- 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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