[gmx-users] MD workstation

[Hadházi Ádám]

2014-10-17 11:47 GMT+10:00 lloyd riggs <lloyd.riggs at gmx.ch>:

>
> Is there any progress in openCL versions of Gromacs, as it is listed on
> the developer site?  Just askin.  One thing I ran across is one can get
> integrated GPU arrays on a board if you find say Russian board designs from
> China for about the same price with 10x the computational speed, but the
> boards would be largly OpenCL dependent.
>
> Stephan Watkins
>  *Gesendet:* Donnerstag, 16. Oktober 2014 um 20:21 Uhr
> *Von:* "Szilárd Páll" <pall.szilard at gmail.com>
> *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> *Betreff:* Re: [gmx-users] MD workstation
> On Thu, Oct 16, 2014 at 3:35 PM, Hadházi Ádám <hadadam at gmail.com> wrote:
> > May I ask why your config is better than e.g.
> >
> > 2x Intel Xeon E5-2620 CPUs (2x$405)
> > 4x GTX 970(4x $330)
> > 1x Z9PE-D8 WS ($449)
> > 64 GB DDR3 ($600)
> > PSU 1600W, ($250)
> > standard 2TB 5400rpm drive, ($85)
> > total: (~$3500)
>
> Mirco's suggested setup will give much higher *aggregate* simulation
> throughput. GROMACS uses both CPUs and GPUs and requires a balanced
> resource mix to run efficiently (less so if you don't use PME). The
> E5-2620 is rather slow and it will be a good match for a single GTX
> 970, perhaps even a 980, but it will be the limiting factor with two
> GPUs per socket.
>

Maybe this is not the best forum for this question, but I also plan to use
AMBER and Desmond for MD/FEP purposes.
Question: Is the recommended 4x1 node config the best setup for these 2
other software too?

>
> > As for your setup...can I use that 4 nodes in parallel for 1 long
> > simulation or 1 FEP job?
>
> Not without a fast network.
>
What would be a fast network? How should I connect them?
Is 8GB memory really enough/node?

>
> > What are the weak points of my workstation?
>
> The CPU. Desktop IVB-E or HSW-E (e.g. i7 49XX, 59XX) will give much
> better performance per buck.
>
> Also note:
> * your smaller 25k MD setup will not scale across multiple GPUs;
> * in FEP runs you, by sharing a GPU between multiple runs you can
> increase the aggregate throughput by quite a lot!
>
> Do you mean, by sharing 1 GPU between multiple FEP runs, or  by sharing
more GPUs between multiple FEP runs?

We have an access to a server having multiple nodes... both of them
possesses 4x Intel X5675 (3.07GHz) CPU (each 6 cores) and 6x NVIDIA Tesla
M2070 GPU). Total: 2 x (24 cores and 6 GPU).
Question: Is this a good construction for MD/FEP?

Regards,
Ádám

> Cheers,
> --
> Szilárd
>
> > Best,
> > Adam
> >
> >
> > 2014-10-16 23:00 GMT+10:00 Mirco Wahab <
> mirco.wahab at chemie.tu-freiberg.de>:
> >
> >> On 16.10.2014 14:38, Hadházi Ádám wrote:
> >>
> >>> Dear GMX Stuff and Users,
> >>>>> I am planning to buy a new MD workstation with 4 GPU (GTX 780 or 970)
> >>>>> or 3
> >>>>> GPU (GTX 980) for 4000$.
> >>>>> Could you recommend me a setup for this machine?
> >>>>> 1 or 2 CPU is necessary? 32/64 GB memory? Cooling? Power?
> >>>>>
> >>>>
> >>>> - What system (size, type, natoms) do you plan to simulate?
> >>>>
> >>>> - Do you have to run *only one single simulation* over long time
> >>>> or *some similar simulations* with similar parameters?
> >>>>
> >>>
> >>> The systems are kind of mix:
> >>> MD:
> >>> smallest system: 25k atoms, spc/tip3p, 2fs/4fs, NPT, simulation time:
> >>> 500-1000ns
> >>> biggest system: 150k atoms, spc/tip3p, 2fs/4fs, NPT, simulation time:
> >>> 100-1000ns
> >>> FEP (free energy perturbation): ligand functional group mutation
> >>> 25k-150k atoms, in complex and in water simulations, production
> >>> simulation:
> >>> 5ns for each lambda window (number of windows: 12)
> >>>
> >>
> >> In this situation, I'd probably use 4 machines for $1000 each,
> >> putting in each:
> >> - consumer i7/4790(K), $300
> >> - any 8GB DDR3, $75-$80
> >> - standard Z97 board, $100
> >> - standard PSU 450W, $40
> >> - standard 2TB 5400rpm drive, $85
> >>
> >> the rest of the money (4 x $395), I'd use for 4 graphics
> >> cards, probably 3 GTX-970 ($330) and one GTX-980 ($550) -
> >> depending on availability, the actual prices, and
> >> your detailed budget.
> >>
> >> YMMV,
> >>
> >>
> >> Regards
> >>
> >> M.
> >>
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