[gmx-users] Results of villin headpiece with AMD 8 core

[Wahab Mirco]

On 11.01.2019 19:55, pbuscemi wrote:
> For those of you considering a workstation build and wonder about AMD processors I have the following results using the included npt and log intro for the villin headpiece in ~ 8000 atoms spc/e. The npt was run from a similar nvt ( 100000 steps ) . The best results were achieved with the simplest command line - letting Gromacs choose threads.
> The system became unstable at dt =0.005 ns step. Note the close correspondence between rcoulomb, rvdw and cutoffswitch. Results compare favorably with the E5-2690+GTX Titan demo
> http://on-demand.gputechconf.com/gtc/2013/webinar/gromacs-kepler-gpus-gtc-express-webinar.pdf (https://link.getmailspring.com/link/1547231722.local-ad2d5ea3-b061-v1.5.2-31660462@getmailspring.com/0?redirect=http%3A%2F%2Fon-demand.gputechconf.com%2Fgtc%2F2013%2Fwebinar%2Fgromacs-kepler-gpus-gtc-express-webinar.pdf&recipient=Z214LXVzZXJzQGdyb21hY3Mub3Jn)
> Core t (s) Wall t (s) (%)
> Time: 112.643 14.080 800.0
> (ns/day) (hour/ns)
> Performance: 1288.622 0.019

Hi Paul,

I couldn't avoid to test this on my R2700X box which has a
GTX 1080 because this allows me to see the difference
to the GTX-1080 Ti. According to your md.log, the boxes
and the OS are very similar, I only had some problems first
to get the old villin benchmark to run with your mdp-file
(I added two chloride ions and changed the solvent to SPC/E
to the original configuration). BTW. you used a rather
large timestep in your test.

So, this would be your 1080 Ti results:

   Number of GPUs detected: 1
   #0: NVIDIA GeForce GTX 1080 Ti, compute cap.: 6.1, ECC: no, stat: comp
   [ ... ]
   starting mdrun [ ... ]
   50000 steps,    210.0 ps.
   Writing final coordinates.
                  Core t (s)   Wall t (s)        (%)
          Time:      112.643       14.080      800.0
                    (ns/day)    (hour/ns)
   Performance:     1288.622        0.019



And this is the run on an almost identical system with
a GTX 1080 Ti (Palit Super-Jetstream):

   Number of GPUs detected: 1
   #0: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC:  no, stat: comp
   [ ... ]
   starting mdrun 'VILLIN in water'
   50000 steps,    210.0 ps.
   Writing final coordinates.
                  Core t (s)   Wall t (s)        (%)
          Time:      147.840       18.480      800.0
                    (ns/day)    (hour/ns)
   Performance:      981.841        0.024


On the (small) villin benchmark, the 1080 Ti would be
about 13% faster than the GTX 1080. The raw SP float power
of the 1080 Ti is about 40% higher than the 1080 (11,340
GFLOPS vs 8,228 GFLOPS) which means a faster processor
could possibly help here.


BTW: I have a large membrane benchmark (DPPC/water, 1.2M atoms,
35x35x13A³ box) which runs at about 3 ns/d on the GTX 1080 with
Parrinello-Rahman semiisotropic coupling, if you'd like to torture
your box I can provide it ;)

Regards

M.