[gmx-users] GPU acceleration

[Szilárd Páll]

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
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> > * For (un)subscribe requests visit
>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.