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

[Jochen Hub]

Am 29.03.18 um 20:57 schrieb Szilárd Páll:
> 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.

Hi Szilárd,

many thanks, this alrady helps me a lot. Just to get it 100% clear what 
you mean with core-GHz: A 10-core E5-2630v4 with 2.2 GHz would have 22 
core-GHz, right?

Thanks,
Jochen

> 
> 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>
>>> .
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>>> http://cmb.bio.uni-goettingen.de/
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-- 
---------------------------------------------------
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.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
---------------------------------------------------