Aw: Re: [gmx-users] GPU-based workstation

[Broadbent, Richard]

I've been running on my Universities GPU nodes these are one E5-xeon (6-cores 12 threads)  and have 4 Nvidia 690gtx's. My system is 93 000 atoms of DMF under NVE.  The performance has been a little disappointing ~10ns/day. On my home system using a core i5-2500 and a nvidia 560ti I get 5.4ns/day for the same system. On our HPC system using 32 nodes each with 2 quad-core xeon processors I get 30-40ns/day.

I think that to achieve reasonable performance the system has to be balanced between CPU's and GPU's probably getting 2 high end GPU's and a top end xeon E5 or core i7 would be a good choice.


Richard

From: lloyd riggs <lloyd.riggs at gmx.ch<mailto:lloyd.riggs at gmx.ch>>
Reply-To: Discussion users <gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>>
Date: Saturday, 25 May 2013 12:02
To: Discussion users <gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>>
Subject: Aw: Re: [gmx-users] GPU-based workstation

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" <jmsstarlight at gmail.com<mailto:jmsstarlight at gmail.com>>
An: "Discussion list for GROMACS users" <gmx-users at gromacs.org<mailto:gmx-users at 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.riggs at gmx.ch<mailto:lloyd.riggs at 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" <jmsstarlight at gmail.com<mailto:jmsstarlight at gmail.com>>
> *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org<mailto:gmx-users at 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
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