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-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ Dne Sat, 19 Feb 2011 04:29:18 +0100 peker milas <pekermilas.gmail.com> napsal/-a: > Hi Brent and Ross, > > I am sorry for my late response but i was terribly sick last week. > This GPU cluster idea is related with the need of pushing the > simulation to higher time scales. I really want to simulate my system > upto a microsecond. Unfortunately, it looks like we will not be able > to start building it right away. You may probably guess that there are > always funding issues. > > On the other hand we needed to have some information about the > hardware. So, thank you so much Ross for enlightening us about > hardware. Also, thank you so much Brent for letting us know about the > other possible ways of simulation, and sharing your ideas. > > best > peker > > > On Fri, Feb 11, 2011 at 8:12 PM, Ross Walker <ross.rosswalker.co.uk> > wrote: >> Hi Peker, >> >>> We are considering putting together a small GPU cluster for running >>> AMBER simulations of some larger biomolecules (~100k atoms). >>> Naturally, there are many decisions to be made and not a whole lot of >>> documentation describing what works. Our budget is <$10k, so our first >>> inclination is to buy four Intel i5s boxes, each with two GPUs >>> connected over Gigabit Ethernet. Have people had good experiences with >>> this sort of setup? In particular, >>> >>> 1) Has anyone had experience using GPUs in an MPI configuration over >>> gigabit ethernet? Is Gigabit Ethernet capable of delivering the >>> bandwidth/latency to keep the cards busy? >> >> The gigabit Ethernet will be fine for mounting a file system, say over >> NFS. >> For MPI communication, to run simulations in parallel it will be >> completely >> useless. For GPU runs in parallel across nodes you need QDR Infiniband >> as a >> minimum. However, you'd be able to run in parallel within a node over >> one or >> more GPUs. >> >>> 2) In the event that gigabit ethernet is insufficient, we have >>> considered purchasing an Infiniband interconnect. This, of course, >> >> Only if you want to run across multiple nodes. If you have multiple >> jobs you >> could always just run them on individual nodes which should be fine. >> >>> would require 3x16 PCIe lanes, which no consumer motherboard I have >>> seen provides. It seems like the most common configuration is one x16 >> >> See: http://www.provantage.com/supermicro-x8dtg-qf~7SUPM39V.htm >> >> Works well with 4 GPUs in one box. All 4 lanes are X16. If you want the >> specs for a complete machine here's an option: >> >> http://www.rosswalker.co.uk/foo.htm >> >>> slot with two x8 slots. This brings us to the question, how much does >>> AMBER rely on GPU-CPU data transfers? Would running two GPUs with 8 >>> lanes each substantially reduce performance? Is there a way we could >>> disable 8 lanes of our current setup for benchmarking purposes? >> >> Running in parallel across multiple GPUs will be poor if you only have >> them >> in x8 slots. It should not affect single GPU runs too much. Maybe 10% >> or so. >> However, for running a single calculation across multiple GPUs then you >> need >> them all in x16 slots. >> >> All the best >> Ross >> >> /\ >> \/ >> |\oss Walker >> >> --------------------------------------------------------- >> | Assistant Research Professor | >> | San Diego Supercomputer Center | >> | Adjunct Assistant Professor | >> | Dept. of Chemistry and Biochemistry | >> | University of California San Diego | >> | NVIDIA Fellow | >> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ | >> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk | >> --------------------------------------------------------- >> >> Note: Electronic Mail is not secure, has no guarantee of delivery, may >> not >> be read every day, and should not be used for urgent or sensitive >> issues. >> >> >> >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > __________ Informace od ESET NOD32 Antivirus, verze databaze 5887 > (20110218) __________ > > Tuto zpravu proveril ESET NOD32 Antivirus. > > http://www.eset.cz > > > -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Feb 18 2011 - 21:00:02 PST