I may be late with the reply, but here are my 2 cents. If you need a single very fast machine (i.e. maximum single simulation performance), you should get - either a very fast desktop CPU: i7 3930 or for 2x more the 3970 - which, BTW, I think is not worth it ($600-1000) - or 1-2 fast Xeon E5-s - depending on how many and which these will be $1k-2k each.
For a single CPU setup two Titans may be an overkill and (at least with the current code) you may get very little extra performance from using two iso one GPU. With a dual-socket machine (and decently fast CPUs), if you have a large enough input system, two GPUs will work nicely. However, if you care about total simulation throughput and you have multiple simulations to run, I'd suggest that you buy 2-3 machines with the components that give the best ns/day/$: something like i7-4670 or 4770 with GTX 680/770 (or 780). -- Szilárd On Thu, Jun 27, 2013 at 1:01 PM, James Starlight <jmsstarli...@gmail.com> wrote: > 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 -- 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