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

[pbuscemi]

Mirco,

Here are the results for three runs of the million atoms DPPC
===============================8 core 2700x 1080ti ==================================
gmx mdrun -deffnm dppc.md -nb gpu -pme gpu -ntmpi 4 -ntomp 4 -npme 1 -gputasks 0000
Core t (s) Wall t (s) (%)
Time: 5286.270 330.392 1600.0
(ns/day) (hour/ns)
Performance: 5.126 4.682

======================================================================================

On Jan 12 2019, at 5:42 pm, paul buscemi <pbuscemi at q.com> wrote:
>
> Mirco,
> on the modification - nicely done.
> On the system speed, running Maestro-Desmond one core ) the 1080ti is pegged and at usually 90% power. them folks at Schrodinger know what they are doing. So the base speed is apparently sufficient, its some other factor e.g. the work load distribution that is not optimized.
>
> I’ll work with your files tomorrow and let you know how it turns out— thanks
> Have a a great weekend
> Paul
> > On Jan 12, 2019, at 3:11 PM, Wahab Mirco <Mirco.Wahab at chemie.tu-freiberg.de> wrote:
> > Hi Paul,
> > thanks for your reply.
> > On 11.01.2019 23:20, paul buscemi wrote:
> > > Getting the ion and SOL concentration correct in the top is trickier ( for me ) than it should have been, If you happen to reuse both solvate and genion during the build keeping track of the top is like using a digital rubics cube..! The charge the villin was +1 because after I downloaded it from the pdb I removed all other water and ions - it just made pdb2gmx easier to work with.
> > >
> >
> > I simply hand-edited the .gro by making up two ions and put them
> > somewhere near the corners and added a short energy minimization.
> > Then, I added one line in the .top for the ions.
> >
> > > The 1080 scaled nicely with the 1080 ti, these are really nice pieces of hardware. and you are correct, given the choice of increased processors vs faster processors - choose the latter. I have the AMD OC to 4.0 GH and it runs the same model almost as fast as as 32 core AMD at 3.7 GHz.
> > Your system is possibly too slow to saturate the 1080Ti at this small
> > system size. In a much larger system, the lead of the 1080 Ti over the
> > 1080 may possibly reach the theoretical expectation.
> >
> > > I've run 300k DPPC models ( ~300 DPPC molecules ) and they run at ~15 ns/day in NPT. And yes, if you can send the pdb, top, and itps I’t would be interesting to compare the two AMDs.
> >
> > I did upload the stuff here + a readme-file. This system is much too
> > large for a single box + GPU (for productive runs), but maybe in 5 years
> > or so we can watch capillary waves through connected IMD/VMD in real-
> > time ;)
> >
> > => http://suwos.gibtsfei.net/d.dppc.4096.zip
> > Regards
> > Mirco
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