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<div>Dear Dr. Pali,</div>
<div> </div>
<div>Thank you,</div>
<div> </div>
<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Dienstag, 28. Mai 2013 um 19:50 Uhr<br/>
<b>Von:</b> "Szilárd Páll" <szilard.pall@cbr.su.se><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> Re: Re: [gmx-users] GPU-based workstation</div>
<div name="quoted-content">Dear all,<br/>
<br/>
As far as I understand, the OP is interested in hardware for *running*<br/>
GROMACS 4.6 rather than developing code. or running LINPACK.<br/>
<br/>
<br/>
To get best performance it is important to use a machine with hardware<br/>
balanced for GROMACS' workloads. Too little GPU resources will result<br/>
in CPU idling; too much GPU resources will lead to the runs being CPU<br/>
or multi-GPU scaling bound and above a certain level GROMACS won't be<br/>
able to make use of additional GPUs.<br/>
<br/>
Of course, the balance will depend both on hardware and simulation<br/>
settings (mostly the LJ cut-off used).<br/>
<br/>
An additional factor to consider is typical system size. To reach near<br/>
peak pair-force throughput on GPUs you typically need >20k-40k<br/>
particles/GPU (depends on the architecture) and throughput drops below<br/>
these values. Hence, in most cases it is preferred to use fewer and<br/>
faster GPUs rather than more.<br/>
<br/>
Without knowing the budgdet and indented use of the machine it is hard<br/>
to make suggestions, but I would say for a budget desktop box a<br/>
quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a<br/>
fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well.<br/>
If you're considering dual-socket workstations, I suggest you go with<br/>
the higher core-count and higher frequency Intel CPUs (6+ cores >2.2<br/>
GHz), otherwise you may not see as much benefit as you would expect<br/>
based on the insane price tag (especially if you compare to an i7<br/>
3939K or its IVB successor).<br/>
<br/>
Cheers,<br/>
--<br/>
Szilárd<br/>
<br/>
<br/>
On Sat, May 25, 2013 at 1:02 PM, lloyd riggs <lloyd.riggs@gmx.ch> wrote:<br/>
> More RAM the better, and the best I have seen is 4 GPU work station. I can<br/>
> use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is<br/>
> really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8<br/>
> or 10 slot board really holds 8 or 10 GPU's). There's cooling problems<br/>
> though with GPU's, as on a board there packed, so extra cooling things may<br/>
> help not blow a GPU, but I would look for good ones (ask around), as its a<br/>
> video game market and they go for looks even though its in casing? The<br/>
> external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont<br/>
> know performance wise, the onboard GPU, the more RAM the marrier...so yes,<br/>
> normal work stations you can get 4 GPU's for a 300 US$ board, but then the<br/>
> price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad is<br/>
> also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests<br/>
> software, not Gromacs, so would be nice to see performance...for a small 100<br/>
> atom molecule and 500 solvent, using just the CPU I get it to run 5-10<br/>
> minutes real for 1 ns sim, but tried simple large 800 amino, 25,000 solvent<br/>
> eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps<br/>
> eq's....<br/>
><br/>
> Stephan<br/>
><br/>
> Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr<br/>
> Von: "James Starlight" <jmsstarlight@gmail.com><br/>
> An: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
> Betreff: Re: [gmx-users] GPU-based workstation<br/>
> Dear Dr. Watkins!<br/>
><br/>
> Thank you for the suggestions!<br/>
><br/>
> In the local shops I've found only Core i7 with 6 cores (like Core<br/>
> i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores<br/>
> than with 4 cores in case of i7 cpu (assuming that I run simulation in<br/>
> cpu+gpu mode )?<br/>
><br/>
> Also you've mentioned about 4 PCeI MD. Does it means that modern<br/>
> work-station could have 4 GPU's in one home-like desktop ? According to my<br/>
> current task I suppose that 2 GPU's would be suitable for my simulations<br/>
> (assuming that I use typical ASUS MB and 650 Watt power unit). Have<br/>
> someone tried to use several GPU's on one workstation ? What attributes of<br/>
> MB should be taken into account for best performance on such multi-gpu<br/>
> station ?<br/>
><br/>
> James<br/>
><br/>
> 2013/5/25 lloyd riggs <lloyd.riggs@gmx.ch><br/>
><br/>
>> There's also these, but 1 chip runs 6K US, they can get performance up to<br/>
>> 2.3 teraflops per chip though double percission...but have no clue about<br/>
>> integration with GPU's...Intell also sells their chips on PCIe cards...but<br/>
>> get only about 350 Gflops, and run 1K US$.<br/>
>><br/>
>> <a href="http://en.wikipedia.org/wiki/Field-programmable_gate_array" target="_blank">http://en.wikipedia.org/wiki/Field-programmable_gate_array</a> and vendor<br/>
>> <a href="http://www.xilinx.com/" target="_blank">http://www.xilinx.com/</a><br/>
>><br/>
>> They can design them though to fit a PCIe slot and run about the same, but<br/>
>> still need the board, ram etc...<br/>
>><br/>
>> Mostly just to dream about, they say you can order them with radiation<br/>
>> shielding as well...so...<br/>
>><br/>
>> Stephan Watkins<br/>
>><br/>
>> *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr<br/>
>> *Von:* "James Starlight" <jmsstarlight@gmail.com><br/>
>> *An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
>> *Betreff:* [gmx-users] GPU-based workstation<br/>
>> Dear Gromacs Users!<br/>
>><br/>
>><br/>
>> I'd like to build new workstation for performing simulation on GPU with<br/>
>> Gromacs 4.6 native cuda support.<br/>
>> Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video<br/>
>> and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system<br/>
>> with SD integrator)<br/>
>><br/>
>><br/>
>> Now I'd like to build multi-gpu wokstation.<br/>
>><br/>
>> My question - How much GPU would give me best performance on the typical<br/>
>> home-like workstation. What algorithm of Ncidia GPU integration should I<br/>
>> use (e.g SLI etc) ?<br/>
>><br/>
>><br/>
>> Thanks for help,<br/>
>><br/>
>><br/>
>> James<br/>
>> --<br/>
>> gmx-users mailing list gmx-users@gromacs.org<br/>
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>><br/>
>> --<br/>
>> gmx-users mailing list gmx-users@gromacs.org<br/>
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>><br/>
> --<br/>
> gmx-users mailing list gmx-users@gromacs.org<br/>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br/>
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><br/>
> --<br/>
> gmx-users mailing list gmx-users@gromacs.org<br/>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br/>
> * Please search the archive at<br/>
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--<br/>
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