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

Mark Abraham mark.j.abraham at gmail.com
Wed Mar 28 04:31:58 CEST 2018


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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