[gmx-users] Number of Xeon cores per GTX 1080Ti

Szilárd Páll pall.szilard at gmail.com
Thu Mar 29 20:57:28 CEST 2018


Hi Jochen,

For that particular benchmark I only measured performance with
1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy
to do the runs on all possible core counts with increments of 1, but
that won't tell a whole lot more than what the performance is of a run
using a E5-2620 v4 CPU (with some GPUs) on a certain core count. Even
extrapolating from that 2620 to a E5-2630 v4 and expecting to get a
good estimate is tricky (given that the latter has 25% more cores for
the same TDP!), let alone to any 26xxv4 CPU or the current-gen Skylake
chips which have different performance characteristics.

As Mark notes, there are some mdp option as well as some system
charateristics that will have a strong influence on performance -- if
tens of % is something you consider "strong" (some users are fine to
be within a 2x ballpark :).

What's worth considering is to try to avoid ending up strongly CPU or
GPU bound from start. That may admittedly could be a difficult task
you would run e.g. both biased MD with large pull groups and all-bonds
constraints with Amber FF on large-ish (>100k) systems as well as
vanilla MD with CHARMM FF with small-ish (<25k) systems. On the same
hardware the former will be more prone to be CPU-bound while the
latter will have relatively more GPU-heavy workload.

There are many factors that influence the performance of a run and
therefore giving a the one right answer to your question is not really
possible. What can say is that 7-10 "core-GHz" per fast Pascal GPU is
generally sufficient for "typical" protein simulations to run at >=85%
of peak.

Cheers,
--
Szilárd


On Wed, Mar 28, 2018 at 4:31 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Hi,
>
> On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub <jhub at gwdg.de> wrote:
>
>> Dear Gromacs community, dear Mark,
>>
>> Mark showed in the webinar today that having more than 8 Xeon E5-26XXv4
>> cores does not help when using a GTX 1080Ti and PME on the GPU.
>>
>
> ... for that particular simulation system.
>
>
>> Unfortunately, there were no data points between 4 and 8 CPU cores,
>> hence it was not clear at which #cores the performance actually levels
>> off. With a GTX 1080 (not Ti) I once found that having more than 5 Xeon
>> cores does not help, if not having UB potentials, but I don't have a
>> 1080Ti at hand to test for that.
>>
>
> Those data points may not have been run. Szilard might have the data - this
> was GLIC 2fs comparing 1080 with 1080Ti from the recent plots he shared.
>
>
>> So my questions are:
>>
>> - At which number of E5-26XXv4 cores does the performance for common
>> systems level off with a 1080Ti for your test system (GLIC)?
>>
>> - Does the answer depend strongly on the mdp settings (in particular on
>> the LJ cutoff)?
>>
>
> Longer LJ cutoff (e.g. from different forcefields) will certainly require
> more non-bonded work, so then fewer CPU cores would be needed to do the
> remaining non-offloaded work. However any sweet spot for a particular .tpr
> would be highly dependent on other effects, such as the ratio of solvent
> (which typically has less LJ and simpler update) to solute, or the density
> of dihedral or U-B interactions. And doing pulling or FEP is very different
> again. The sweet spot for the next project will be elsewhere, sadly.
>
> This would help us a lot when choosing the appropriate CPU for a 1080Ti.
>>
>> Many thanks for any suggestions,
>> Jochen
>>
>> --
>> ---------------------------------------------------
>> Dr. Jochen Hub
>> Computational Molecular Biophysics Group
>> Institute for Microbiology and Genetics
>> Georg-August-University of Göttingen
>> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
>> <https://maps.google.com/?q=Justus-von-Liebig-Weg+11,+37077+G%C3%B6ttingen,+Germany&entry=gmail&source=g>
>> .
>> Phone: +49-551-39-14189 <+49%20551%203914189>
>> http://cmb.bio.uni-goettingen.de/
>> ---------------------------------------------------
>> --
>> 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.


More information about the gromacs.org_gmx-users mailing list