[gmx-users] NVIDIA GTX cards in Rackable servers, how do you do it ?

[Szilárd Páll]

On Tue, Feb 24, 2015 at 2:09 PM, Harry Mark Greenblatt
<harry.greenblatt at weizmann.ac.il> wrote:
> BS"D
>
> Dear David,
>
>
> Hey Harry,
>
> Thanks for the caveat. Carsten Kutzner posted these results a few days ago.
> This is what he said :
>
> I never benchmarked 64-core AMD nodes with GPUs. With a 80 k atoms test
> system using a 2 fs time step I get
> 24 ns/d on 64 AMD   cores 6272
> 16 ns/d on 32 AMD   cores 6380
> 36 ns/d on 32 AMD   cores 6380   with 1x GTX 980
> 40 ns/d on 32 AMD   cores 6380   with 2x GTX 980
> 27 ns/d on 20 Intel cores 2680v2
> 52 ns/d on 20 Intel cores 2680v2 with 1x GTX 980
> 62 ns/d on 20 Intel cores 2680v2 with 2x GTX 980
>
>
> I think 20 Intel cores means 2 x 10 cores each.
>
> Yes, the 2680v2 is a 10 core processor.  The "interference" I mentioned is not apparent across sockets, only within.
>
>
>
>
> But Szilard just mentioned in this same thread :
>
> If you can afford them get the 14/16 or 18 core v3 Haswells, those are
> *really* fast, but a pair can cost as much as a decent car.
>
>
>
> Perhaps he has seen some real results that do not show issues at 16 or 18 cores/socket, in which case they would be advantageous, if one can afford them.  I am only going on what the manager of our cluster mentioned to me in his tests.  But his tests were based on many different software packages, so perhaps Gromacs is less/not affected.

OK, that's an entirely different claim than the one you made
initially. I dare to say that it is dangerous to mix performance
observations of many software packages - especially with that of
GROMACS. However, again, if you have the data, please share it.

--
Szilárd

> Harry
>
>
>
>
>
>
> -------------------------------------------------------------------------
>
> Harry M. Greenblatt
>
> Associate Staff Scientist
>
> Dept of Structural Biology
>
> Weizmann Institute of Science        Phone:  972-8-934-3625
>
> 234 Herzl St.                        Facsimile:   972-8-934-4159
>
> Rehovot, 76100
>
> Israel
>
>
> Harry.Greenblatt at weizmann.ac.il<mailto:Harry.Greenblatt at weizmann.ac.il>
>
>
>
>
>
>
>
> --
> 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.