[gmx-users] new i9 processor

Bernhard Reuter b.reuter at uni-kassel.de
Mon Oct 16 15:35:40 CEST 2017

Dear Harry,

you are right for the dual xeon 16 core setup you (and we) use, but for 
the single core i9 setup we made the experience, that we only gained 
between 5-10% of performance by adding a second gpu. This was what I was 
hinting here...

Best Bernhard

Am 16/10/17 um 14:56 schrieb Harry Mark Greenblatt:
> BS”D
> Dear Bernard,
>    Thank you for your reply and info.  Our experience with a second graphics card (when coupled with the appropriate number of cores) is that we garner close to a 100% performance gain.  We have access to nodes on a cluster with 16 cores (2 x E5-2630 v3) + 1 K80 (dual gpu on each card).   If I recall correctly, in our initial tests of those nodes, we compared 8 cores + 1 gpu vs 16 cores + 2gpu’s, and got close to double the performance.  This is also consistent with our performance on our workstations, most of which have a hexacore Xeon coupled to a Geforce GTX 770 (or 970 in more recent versions).  Use of the 16 cores + dual GPU compute nodes gives us close to double the performance relative to the workstations.  I suspect that your dual K40’s are only showing a 5-10% gain over the single Geforce card because the GTX 1080i on your workstations should be significantly faster than the K40 on the nodes.  This is due to the newer architecture (Pascal vs. Kepler), higher core count (3584 vs. 2880), and the higher clock speeds (1480 base vs. 745 base) on the 1080ti.
> I recall a statement by Szilárd once, in some email, about getting very good scaling (i.e., close to linear) with multiple GPU’s.
> Thanks again,
> Harry
> Dear Harry,
> we have several nodes with single i9 7900 decacore processors and one gtx 1080ti each. So far they show very good performance compared with dual 16 core xeon nodes with two K20x and even K40x cards. We reach a performance of >40ns per day for >90000 atoms with the i9 system, compared to 50 ns/day with the dual xeon + dual K40x and 30 ns/day with the dual xeon + dual K20x. So your configuration should easily outrun the xeon setups... since you want to use the 16 core i9 the second gtx you propose might even make sense but mb you should reconsider if the 5-10% speedup with the second card is really worth the buck ...
> Best,
> --------------------------------------------------------------------
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology           harry.greenblatt at weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%40weizmann.ac.il>
> Weizmann Institute of Science        Phone:  972-8-934-6340
> 234 Herzl St.                        Facsimile:   972-8-934-3361
> Rehovot, 7610001
> Israel

Dipl.-Phys. Bernhard Reuter
Theoretical Biophysics Subgroup
Theoretical Physics II
Institute of Physics
University of Kassel
Heinrich-Plett-Str. 40
34132 Kassel, Germany
Tel: +49 561 804 4482
Mobile: +40 152 27331699

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