On Sat, May 25, 2013 at 2:16 PM, Broadbent, Richard <richard.broadben...@imperial.ac.uk> wrote: > 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
That sounds like a very imbalanced system for GROMACS, you have essentially 8 GPUs with rather poor PCI-E performance (a board share a single PCI-E bus) and only 12 CPU cores to "drive" the simulation. ~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. That sounds somewhat low if these are all moderately fast CPUs and GPUs. > 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. Indeed. Even two GPUs may be too much - unless the CPU in question is a very high end i7 or E5. Cheers, -- Szilárd > > > 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