[gmx-users] AMD 32 core TR

[pbuscemi at q.com]

Dear users,

 

I had trouble getting suitable performance from an AMD 32 core TR.  By
updating  all the cuda drivers and runtime to v10  and using gcc,g++ -6 from
v5  -- I did try gcc-7 but Cuda 10 did not appreciate the attempt  --  and
in particular removing  CUDA v7 runtime.), I was able to improve a 300k atom
nvt run from 8 ns/day to 26 ns/day .  I replicated  as far as possible the
Gromacs ADH benchmark with 137000 atoms-spc/e.  I could achieve an md of
49.5 ns/day. I do not have a firm grasp if this is respectable or not (
comments ? )  but appears at least ok.   The input command was simply mdrun
ADH.md   -nb gpu  -pme gp   ( and not using -ntomp or ntmpi which in my
hands degraded performance ) .   To run the ADH  I replaced the two ZN ions
in  ADH file from PDB ( 2ieh.pdb ) with CA ions  since ZN was not found in
the OPLS data base in using pdb2gmx.

 

The points being ( 1) Gromacs appears reasonably happy with  the 8 core and
32 core Ryzen although ( again in my hands ) for these  smallish systems
there is only about a 10% improvement between the two, and  (2) , as often
suggested in the Gromacs literature, use the latest drivers possible