[gmx-users] GPU-based workstation

Mon May 27 12:14:51 CEST 2013

On Nvidia benchmarks I've found suggestions of using of the two 6 cores CPU
for systems with the 2 GPU.

Assuming that I'll be using two 680 GTX cards with 256 bits and 4gb ram
(not a profesional nvidia cards like TESLA)
what CPU's could give me the best performance- 1 i7 of 8 cores
or 2 Xeons e5 with 6 cores ? Does it meaningful to use 2 separate CPU's
with several nodes each for the 2 GPU's ?

James

2013/5/26 lloyd riggs <lloyd.riggs at gmx.ch>

>
> 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.
>
> Also, the sim I did on the cluster was 180-190,000 atoms so the exact same
> performance the other person had.
>
> Stephan
>  *Gesendet:* Samstag, 25. Mai 2013 um 15:19 Uhr
> *Von:* "James Starlight" <jmsstarlight at gmail.com>
>
> *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> *Betreff:* Re: Aw: Re: [gmx-users] GPU-based workstation
> 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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