[gmx-users] GPU acceleration

[Alex]

In that case, I am a bit lost, as I was sure GMXRC needed modification.
:)). Since I never ran anything on GPU and have an mdrun line that looks
like

mdrun -nt 4 -s <tpr> -c <final structure>

what should be added to trigger the behavior you're suggesting? I
understand that it will likely blow up the system, but for the heck of
it...
I am now looking at the stats and see that (NxN QSTab + LJ) and (NxN QSTab
[F]) take up about 86% of all flops in my simulation. Which of those get
offloaded?

Thank you,

Alex


On Fri, Jun 5, 2015 at 2:26 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:

> Hi Alex,
>
> Why do you think GMXRC needs to be changed? You simply need to set
> those env. vars to trigger the GPU code-path - and you will likely
> have to freeze the system, otherwise it will probably not run more
> than a few steps without seeing an explosion. Based on this you'll
> know how fast you can run with GPU offload, but you can also
> guesstimate how fast of a GPU you need (based on the PME+Bonded force
> calculation time + publicly available CUDA kernel performance).
>
> Cheers,
> --
> Szilárd
>
>
> On Fri, Jun 5, 2015 at 10:13 PM, Alex <nedomacho at gmail.com> wrote:
> > 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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