Dear Dr. Pall! Thank you for your suggestions!
Asumming that I have budget of 5000 $ and I want to build gpu-based desktop on this money. Previously I've used single 4 core i5 with GTX 670 and obtain average 10 ns\day performance for the 70k atoms systems (1.0 cutoffs, no virtual sites , sd integrator). Now I'd like to build system based on 2 hight-end GeForces (e.g like TITAN). Should that system include 2 cpu's for good balancing? (e.g two 6 nodes XEONS with faster clocks for instance could be better for simulations than i7, couldnt it?) What addition properties to the MB should I consider for such system ? James 2013/5/28 lloyd riggs <lloyd.ri...@gmx.ch> > Dear Dr. Pali, > > Thank you, > > Stephan Watkins > > *Gesendet:* Dienstag, 28. Mai 2013 um 19:50 Uhr > *Von:* "Szilárd Páll" <szilard.p...@cbr.su.se> > > *An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org> > *Betreff:* Re: Re: [gmx-users] GPU-based workstation > Dear all, > > As far as I understand, the OP is interested in hardware for *running* > GROMACS 4.6 rather than developing code. or running LINPACK. > > > To get best performance it is important to use a machine with hardware > balanced for GROMACS' workloads. Too little GPU resources will result > in CPU idling; too much GPU resources will lead to the runs being CPU > or multi-GPU scaling bound and above a certain level GROMACS won't be > able to make use of additional GPUs. > > Of course, the balance will depend both on hardware and simulation > settings (mostly the LJ cut-off used). > > An additional factor to consider is typical system size. To reach near > peak pair-force throughput on GPUs you typically need >20k-40k > particles/GPU (depends on the architecture) and throughput drops below > these values. Hence, in most cases it is preferred to use fewer and > faster GPUs rather than more. > > Without knowing the budgdet and indented use of the machine it is hard > to make suggestions, but I would say for a budget desktop box a > quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a > fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well. > If you're considering dual-socket workstations, I suggest you go with > the higher core-count and higher frequency Intel CPUs (6+ cores >2.2 > GHz), otherwise you may not see as much benefit as you would expect > based on the insane price tag (especially if you compare to an i7 > 3939K or its IVB successor). > > Cheers, > -- > Szilárd > > > On Sat, May 25, 2013 at 1:02 PM, lloyd riggs <lloyd.ri...@gmx.ch> wrote: > > 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> > > An: "Discussion list for GROMACS users" <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> > > > >> 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> > >> *An:* "Discussion list for GROMACS users" <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 > >> 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 > >> > > -- > > 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 > -- > 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 > -- 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
