Am 03.04.18 um 16:26 schrieb Szilárd Páll:
On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub <j...@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.abra...@gmail.com>
wrote:
Hi,
On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub <j...@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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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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---------------------------------------------------
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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