Thank you Mirco and Szilard, With regards to the GPU system, I have decided on a Xeon E5-1650 v2 system with GEForce GTX -780 Ti GPU for equilibration and production runs with small systems. But for large systems or REMD simulations, I am a bit skeptical on banking on GPU systems. Any pointers as to what would be the minimum configuration required for REMD simulations on say a 50 K atom protein sampled for 100 different temperatures? I am open to all possible options in this regard (obviously a little cost effectiveness does not harm ). Also, would investing in a *good* 40 Gigabit ethernet network ensure good performance if we later plan to more nodes to the cluster.
Regards, Abhishek On Tue, Aug 5, 2014 at 5:46 PM, Szilárd Páll <pall.szil...@gmail.com> wrote: > Hi, > > You need fast network to parallelize across multiple nodes. 1 Gb > ethernet won't work well and even even 10/40 Gb ethernet needs to be > of good quality; you'd likely need to buy separate adapters, the > on-board ones won't perform well. I posted some links to the list > related to this a fed days ago. > > The AMD FX dekstop hardware you mention is OK, but I'm not sure that > it's gives the best performance/price. If you find (very) discounted > Sandy Bridge-E (i7 3930K) or the cheaper Haswells like i5 4670 may > actually provide better prerformance for the money. Ivy Bridge-E or > Haswell-E as Mirco suggests are the best single-socket workstation > options, but those are/will be pretty expensive. > > Finally, unless you have a good reason not to, you should not just > consider GPUs, but consider what CPU/platform works best with GPUs. > > Cheers, > -- > Szilárd > > > On Tue, Aug 5, 2014 at 7:01 AM, Abhishek Acharya > <abhi117acha...@gmail.com> wrote: > > Hello gromacs users, > > I am planning on investing in a beowulf cluster with 6 nodes (48 cores) > each with AMD Fx 8350 processor, 8 GB memory connected by 1 Gigabit > Ethernet switch. Although I plan to add more cores to this cluster later > on, what is the max performance expected from the current specs for a > 100,000 atom simulation box ? Also, is it better to invest in a single 48 > core server ? The cluster system can be set up at almost half the price of > a 48 core server, but do we lose out on performance in the process?? > > > > Regards, > > > > Abhishek Acharya > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Abhishek Acharya Senior Research Fellow Gene Regulation Laboratory National Institute of Immunology -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.