Richard, thanks for suggestion!
Assuming that I'm using 2 high end GeForce's what performance be better 1) in case of one i7 (4 or 6 nodes ) ? 2) in case of 8 core Xeon like CPU Intel Xeon E5-2650 2.0 GHz / 8core What properties of MB should take into account primarily for such Xenon-based system. Does such MBs support multi-GPU ( I noticed that many such MBs lack for PCI)? James 2013/5/25 Broadbent, Richard <richard.broadben...@imperial.ac.uk> > I've been running on my Universities GPU nodes these are one E5-xeon > (6-cores 12 threads) and have 4 Nvidia 690gtx's. My system is 93 000 atoms > of DMF under NVE. The performance has been a little disappointing > ~10ns/day. On my home system using a core i5-2500 and a nvidia 560ti I get > 5.4ns/day for the same system. On our HPC system using 32 nodes each with 2 > quad-core xeon processors I get 30-40ns/day. > > I think that to achieve reasonable performance the system has to be > balanced between CPU's and GPU's probably getting 2 high end GPU's and a > top end xeon E5 or core i7 would be a good choice. > > > Richard > > From: lloyd riggs <lloyd.ri...@gmx.ch<mailto:lloyd.ri...@gmx.ch>> > Reply-To: Discussion users <gmx-users@gromacs.org<mailto: > gmx-users@gromacs.org>> > Date: Saturday, 25 May 2013 12:02 > To: Discussion users <gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>> > Subject: Aw: Re: [gmx-users] GPU-based workstation > > More RAM the better, and the best I have seen is 4 GPU work station. I > can use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is > really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8 > or 10 slot board really holds 8 or 10 GPU's). There's cooling problems > though with GPU's, as on a board there packed, so extra cooling things may > help not blow a GPU, but I would look for good ones (ask around), as its a > video game market and they go for looks even though its in casing? The > external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont > know performance wise, the onboard GPU, the more RAM the marrier...so yes, > normal work stations you can get 4 GPU's for a 300 US$ board, but then the > price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad > is also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests > software, not Gromacs, so would be nice to see performance...for a small > 100 atom molecule and 500 solvent, using just the CPU I get it to run 5-10 > minutes real for 1 ns sim, but tried simple large 800 amino, 25,000 > solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say > 50 ps eq's.... > > Stephan > > Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr > Von: "James Starlight" <jmsstarli...@gmail.com<mailto: > jmsstarli...@gmail.com>> > An: "Discussion list for GROMACS users" <gmx-users@gromacs.org<mailto: > gmx-users@gromacs.org>> > Betreff: Re: [gmx-users] GPU-based workstation > Dear Dr. Watkins! > > Thank you for the suggestions! > > In the local shops I've found only Core i7 with 6 cores (like Core > i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores > than with 4 cores in case of i7 cpu (assuming that I run simulation in > cpu+gpu mode )? > > Also you've mentioned about 4 PCeI MD. Does it means that modern > work-station could have 4 GPU's in one home-like desktop ? According to my > current task I suppose that 2 GPU's would be suitable for my simulations > (assuming that I use typical ASUS MB and 650 Watt power unit). Have > someone tried to use several GPU's on one workstation ? What attributes of > MB should be taken into account for best performance on such multi-gpu > station ? > > James > > 2013/5/25 lloyd riggs <lloyd.ri...@gmx.ch<mailto:lloyd.ri...@gmx.ch>> > > > There's also these, but 1 chip runs 6K US, they can get performance up to > > 2.3 teraflops per chip though double percission...but have no clue about > > integration with GPU's...Intell also sells their chips on PCIe > cards...but > > get only about 350 Gflops, and run 1K US$. > > > > http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor > > http://www.xilinx.com/ > > > > They can design them though to fit a PCIe slot and run about the same, > but > > still need the board, ram etc... > > > > Mostly just to dream about, they say you can order them with radiation > > shielding as well...so... > > > > Stephan Watkins > > > > *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr > > *Von:* "James Starlight" <jmsstarli...@gmail.com<mailto: > jmsstarli...@gmail.com>> > > *An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org<mailto: > gmx-users@gromacs.org>> > > *Betreff:* [gmx-users] GPU-based workstation > > Dear Gromacs Users! > > > > > > I'd like to build new workstation for performing simulation on GPU with > > Gromacs 4.6 native cuda support. > > Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video > > and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system > > with SD integrator) > > > > > > Now I'd like to build multi-gpu wokstation. > > > > My question - How much GPU would give me best performance on the typical > > home-like workstation. What algorithm of Ncidia GPU integration should I > > use (e.g SLI etc) ? > > > > > > Thanks for help, > > > > > > James > > -- > > gmx-users mailing list gmx-users@gromacs.org<mailto: > 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<mailto: > gmx-users-requ...@gromacs.org>. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > > gmx-users mailing list gmx-users@gromacs.org<mailto: > 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<mailto: > gmx-users-requ...@gromacs.org>. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org<mailto: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<mailto: > 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 > -- 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
