Back to my question I want to build gpu-based workstation based onto 2 titans geforces.
My current budget allow me only hight-end 6nodes core i 7-3930 and MB with 5 PCI-E (like Asus rampage IV series). Would this system be balanced with two GPUs ? Should I use two 6-8 nodes XEONS instead of i7? James 2013/5/29 James Starlight <jmsstarli...@gmail.com> > 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
