[gmx-users] GPU-based workstation

[James Starlight]

Back to my question
I want to build gpu-based workstation based onto 2 titans geforces.

My current budget allow me only hight-end  6nodes core i 7-3930  and MB
with 5 PCI-E (like Asus rampage IV series). Would this system be balanced
with two GPUs ? Should I use two 6-8 nodes XEONS instead of i7?

James

2013/5/29 James Starlight <jmsstarlight at gmail.com>

> 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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>
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