[gmx-users] info about gpus

[Szilárd Páll]

On Fri, Feb 1, 2019 at 3:30 AM Moir, Michael (MMoir) <MMoir at chevron.com> wrote:
>
> Stephano,
>
> With a motherboard that doesn't split the PCI-E bandwidth, I get a 20% improvement in computation speed with 2 GPUs.

That's on the low side, yo can get 40-60% scaling across two GPUs in
such desktop/workstation use-cases in the current release, but it is
not hassle-free.

> Whether or not you think this is worth the extra $, I leave that up to you!  My system is:  i9-9900K, ASUS WS Z390 Pro motherboard, 2x 1070ti GPUs, 32 MB 3200 MHz RAM.  With my modest system of about 100,000 atoms, I go from 30 ns/day with 1 GPU, to 36 ns/day with 2 GPUs.  -ntmpi 4 -npme 1 -pme gpu -nb gpu, all other combinations of -ntmpi give inferior results with 2 GPUs compared to 1 GPU.

Have you tried to assign as many cores as possible to the PP ranks and
possibly use 5-6 of them (in your case quarter of the cores are not
doing useful stuff as those are assigned to the PME task that's GPU
only)?

>  I am using Gromacs-2019.  It is also important to use the fastest memory you want to afford.  The amount of memory is not important but the speed is.

Memory performance has negligible performance impact on GROMACS
performance as working data sets typically fit in cache. This is
especially true for traditional cluster-based but the a large extent
also the case for a dominant fraction of the workstation / single-node
runs too with a few the notable exceptions:
- AMD Ryzen CPUs are a bit more sensitive but I've not checked by
exactly how much (non-GROMACS benchmarks show ~10% at best for similar
codes)
- depending on the CPU type (cache size) when running >200k atoms on a
single desktop processor (with GPUs, without the threshold is lower)
system memory might improve performance
However, don't expect more than single-digit performance increase even
from the fanciest overclocked gaming memory modules.

Cheers,


> Mike
>
> -----Original Message-----
> From: Moir, Michael (MMoir)
> Sent: Thursday, January 31, 2019 9:44 AM
> To: gmx-users at gromacs.org
> Subject: RE: [**EXTERNAL**] [gmx-users] info about gpus
>
> Stefano,
> I'm investigating that myself.  If your motherboard splits the bandwidth between your PCI-E slots then there is no advantage to having 2 GPUs for a GPU like the 1080.  I have just upgraded to a better motherboard that does not split the  bandwidth but I am not finished my testing.  Going to the 2080 offers a 40% increase in speed over the 1080 in terms of raw computing power but it is unclear that it is worth the extra $.
> Mike
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Stefano Guglielmo
> Sent: Thursday, January 31, 2019 9:14 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [**EXTERNAL**] [gmx-users] info about gpus
>
>  Dear all,
> I am tryin to set a new workstation and I would like to know if there is a
> significant improvement in performance with two gpus (gtx 1080 ti or rtx
> 2080) rather than just one, and eventually with which cpu/ram requisite.
>
> Thanks in advance for any advice and suggestions
> Stefano
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
>
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