[gmx-users] GPU-based workstation

Wed May 29 07:02:04 CEST 2013

Dear Dr. Pall!

Thank you for your suggestions!

Asumming that I have budget of 5000 $ and I want to build gpu-based desktop
on this money.

Previously I've used single 4 core i5 with GTX 670 and obtain average 10
ns\day performance for the 70k atoms systems (1.0 cutoffs, no virtual sites
, sd integrator).

Now I'd like to build system based on 2 hight-end GeForces (e.g like TITAN).
Should that system include 2 cpu's for good balancing? (e.g two 6 nodes
XEONS with faster clocks for instance could be better for simulations than
i7, couldnt it?)

What addition properties to the MB should I consider for such system ?

James

2013/5/28 lloyd riggs <lloyd.riggs at gmx.ch>

> Dear Dr. Pali,
>
> Thank you,
>
> Stephan Watkins
>
> *Gesendet:* Dienstag, 28. Mai 2013 um 19:50 Uhr
> *Von:* "Szilárd Páll" <szilard.pall at cbr.su.se>
>
> *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> *Betreff:* Re: Re: [gmx-users] GPU-based workstation
> Dear all,
>
> As far as I understand, the OP is interested in hardware for *running*
> GROMACS 4.6 rather than developing code. or running LINPACK.
>
>
> To get best performance it is important to use a machine with hardware
> balanced for GROMACS' workloads. Too little GPU resources will result
> in CPU idling; too much GPU resources will lead to the runs being CPU
> or multi-GPU scaling bound and above a certain level GROMACS won't be
> able to make use of additional GPUs.
>
> Of course, the balance will depend both on hardware and simulation
> settings (mostly the LJ cut-off used).
>
> An additional factor to consider is typical system size. To reach near
> peak pair-force throughput on GPUs you typically need >20k-40k
> particles/GPU (depends on the architecture) and throughput drops below
> these values. Hence, in most cases it is preferred to use fewer and
> faster GPUs rather than more.
>
> Without knowing the budgdet and indented use of the machine it is hard
> to make suggestions, but I would say for a budget desktop box a
> quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a
> fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well.
> If you're considering dual-socket workstations, I suggest you go with
> the higher core-count and higher frequency Intel CPUs (6+ cores >2.2
> GHz), otherwise you may not see as much benefit as you would expect
> based on the insane price tag (especially if you compare to an i7
> 3939K or its IVB successor).
>
> Cheers,
> --
> Szilárd
>
>
> On Sat, May 25, 2013 at 1:02 PM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:
> > 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>
> > An: "Discussion list for GROMACS users" <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>
> >
> >> 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>
> >> *An:* "Discussion list for GROMACS users" <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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