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

[James Starlight]

Richard,

thanks for suggestion!

Assuming that I'm using 2 high end GeForce's what performance be better

1) in case of one i7 (4 or 6 nodes ) ?

2) in case of 8 core Xeon like  CPU Intel Xeon E5-2650 2.0 GHz / 8core

What properties of MB should take into account primarily for such
Xenon-based system. Does such MBs support multi-GPU ( I noticed that many
such MBs lack for PCI)?

James

2013/5/25 Broadbent, Richard <richard.broadbent09 at imperial.ac.uk>

> 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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