[gmx-users] GPU acceleration

[Alex]

Hi Szilárd,

Well, yes, it is an old CPU, but I am actually quite content with the
ns/day performance it churns out on all four cores. I'm looking at
http://manual.gromacs.org/documentation/5.1-beta1/user-guide/environment-variables.html
and it is my understanding that GMXRC needs to be changed to include those
flags, but no recompiling is required. Is that correct?

Thanks,

Alex


On Fri, Jun 5, 2015 at 1:52 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:

> Hi Alex,
>
> That's a quite old CPU so it's hard to tell how fast is it, you'll
> have to try. There are ways to "guesstimate" how fast does your GPU
> have to be to keep up with your CPU cores (hint search for
> GMX_EMULATE_GPU / GMX_NO_NONBONDED on the list).
>
> In any case, unless your CPU is so slow that it balances well with the
> 750Ti, I would strongly recommend that you get a GTX 960 which will
> cost just a bit more, but it will be 1.6-1.8x faster at computing
> non-bonded interactions.
>
>  On Fri, Jun 5, 2015 at 9:08 PM, Alex <nedomacho at gmail.com> wrote:
> > Hi all,
> >
> > We're about to start a bit of a toy project to test GPU-accelerated GMX.
> > What I have here is my old workstation (Dell Precision T3500: Quad-core
> >  Xeon W3530 @ 2.8 GHz, 12 gigs of RAM) running Linux Mint 17.1. The plan
> is
> > to get something like GeForce GTX 750 (
> >
> http://www.amazon.com/GeForce-750Ti-GDDR5-Graphics-GTX750TI-OC-2GD5/dp/B00IB9P1KG/ref=sr_1_3?ie=UTF8&qid=1433529993&sr=8-3&keywords=Nvidia+GTX750
> > )
> > and maybe a new PSU.
> >
> > Questions:
> >
> > 1. With a card like this, how much acceleration (very approximately) can
> we
> > expect in a "standard" simulation (protein+lipid+water, PME
> electrostatics)?
>
> In PME simulations you should see about 3x speedup, more if you are
> lucky and possibly a little less if you are not so lucky with the
> computational workload. What FF are you using?
>
> > 2. Should we put any extra considerations into cooling? We expect
> week-long
> > runs, and I am not sure these cards have this type of hardcore gaming in
> > mind. :)
>
> I don't think so, but it depends how stuffed or dusty is that Dell
> workstation. These Maxwell generation (96x) GPUs run quite cool.
>
> > Any additional comments are highly appreciated. Please keep in mind that
> > this is a toy project to utilize an old workstation.
>
> There is a GPU fan speed issue with desktop NVIDIA cards, the fan
> rotation is limited to 60% and cards can overheat. You can force the
> fan speed higher using nvidia-settings (you'll need an X server
> running, though). For more details you can check slide 28 here:
> https://goo.gl/7DnSri
>
> Cheers,
> --
> Szilárd
>
> > Thank you,
> >
> > Alex
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