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

Tue Apr 3 17:10:11 CEST 2018

Am 03.04.18 um 16:26 schrieb Szilárd Páll:
> On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub <jhub at gwdg.de> wrote:
>>
>>
>> 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?
> 
> Yes, that's what I was referring to; note that a 2630v4 won't be
> running at a 2.2 GHz base clock if you run AVX code ;)

Okay, I didn't know this. What would be the base clock instead with AVX 
code?

> 
>> 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>
>>>>> .
>>>>> Phone: +49-551-39-14189 <+49%20551%203914189>
>>>>> http://cmb.bio.uni-goettingen.de/
>>>>> ---------------------------------------------------
>>>>> --
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>>>>
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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/
>> ---------------------------------------------------
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>> Gromacs Users mailing list
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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/
---------------------------------------------------