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<div>You can also look at profilling on varied web sites, the high end Nvidia run only slightly better than the 2 year old ones, from an individual point not worth the money yet, but if you have the money? as I've been browsing.</div>
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<div>Also, the sim I did on the cluster was 180-190,000 atoms so the exact same performance the other person had.</div>
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<div>Stephan</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Samstag, 25. Mai 2013 um 15:19 Uhr<br/>
<b>Von:</b> "James Starlight" <jmsstarlight@gmail.com><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> Re: Aw: Re: [gmx-users] GPU-based workstation</div>
<div name="quoted-content">Richard,<br/>
<br/>
thanks for suggestion!<br/>
<br/>
Assuming that I'm using 2 high end GeForce's what performance be better<br/>
<br/>
1) in case of one i7 (4 or 6 nodes ) ?<br/>
<br/>
2) in case of 8 core Xeon like CPU Intel Xeon E5-2650 2.0 GHz / 8core<br/>
<br/>
What properties of MB should take into account primarily for such<br/>
Xenon-based system. Does such MBs support multi-GPU ( I noticed that many<br/>
such MBs lack for PCI)?<br/>
<br/>
James<br/>
<br/>
2013/5/25 Broadbent, Richard <richard.broadbent09@imperial.ac.uk><br/>
<br/>
> I've been running on my Universities GPU nodes these are one E5-xeon<br/>
> (6-cores 12 threads) and have 4 Nvidia 690gtx's. My system is 93 000 atoms<br/>
> of DMF under NVE. The performance has been a little disappointing<br/>
> ~10ns/day. On my home system using a core i5-2500 and a nvidia 560ti I get<br/>
> 5.4ns/day for the same system. On our HPC system using 32 nodes each with 2<br/>
> quad-core xeon processors I get 30-40ns/day.<br/>
><br/>
> I think that to achieve reasonable performance the system has to be<br/>
> balanced between CPU's and GPU's probably getting 2 high end GPU's and a<br/>
> top end xeon E5 or core i7 would be a good choice.<br/>
><br/>
><br/>
> Richard<br/>
><br/>
> From: lloyd riggs <lloyd.riggs@gmx.ch<mailto:lloyd.riggs@gmx.ch>><br/>
> Reply-To: Discussion users <gmx-users@gromacs.org<mailto:<br/>
> gmx-users@gromacs.org>><br/>
> Date: Saturday, 25 May 2013 12:02<br/>
> To: Discussion users <gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>><br/>
> Subject: Aw: Re: [gmx-users] GPU-based workstation<br/>
><br/>
> More RAM the better, and the best I have seen is 4 GPU work station. I<br/>
> can 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<br/>
> is 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<br/>
> 100 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<br/>
> solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say<br/>
> 50 ps eq's....<br/>
><br/>
> Stephan<br/>
><br/>
> Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr<br/>
> Von: "James Starlight" <jmsstarlight@gmail.com<mailto:<br/>
> jmsstarlight@gmail.com>><br/>
> An: "Discussion list for GROMACS users" <gmx-users@gromacs.org<mailto:<br/>
> 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<mailto: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<br/>
> 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,<br/>
> 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<mailto:<br/>
> jmsstarlight@gmail.com>><br/>
> > *An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org<mailto:<br/>
> 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/>
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