[gmx-users] performance question

[Michael Brunsteiner]

 Dear all,

i just got new hardware, and ran a couple of tests, comparing performance of
the new machine to results from another five years old computer.
I found the outcome (see below) somewhat disappointing, and write to
see if other people got similar results, or if perhaps i overlooked something ...

the test: a system of polymers, ~18000 atoms, MD at ambient conditions
mdp file included below, both computers run linux, the old one ubuntu-12.04
(cuda-5.0), the new one debian-testing (cuda-5.5), both use gromacs 5.0.

old machine:
CPU: Intel(R) Core(TM) i7 CPU 960  @ 3.20GHz, 8 cores
GPU:GeForce GTX 460
Performance: 31.717 ns/day

new machine:
CPU: Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz, 12 cores
GPU:GeForce GTX 780
Performance: 64.072 ns/day

the load balance (both with or without dynamic load balancing) is worse with the new machine
as the GPU is considerbly faster than the CPU, but this still only accounts for something like 20-30%
of the overall speed difference so the new machine appears to be only about twice as fast as the old
one ... is this to be expected? or is there anything i can do to improve its performance??

thanks for any hints/ideas!
michael



mdp file:

integrator               = md
dt                       = 0.002
nsteps                   = 10000
comm-grps                = System
;
nstxout                  = 1000
nstvout                  = 0
nstfout                  = 0
nstlog                   = 1000
nstenergy                = 1000
;
nstlist                  = 20
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.1
cutoff-scheme            = Verlet
;
coulombtype              = PME
rcoulomb                 = 0.9
vdw_type                 = cut-off 
rvdw                     = 0.9
DispCorr                 = EnerPres
;
tcoupl                   = Berendsen
tc-grps                  = System
tau_t                    = 0.2
ref_t                    = 298.0
;
gen-vel                  = yes
gen-temp                 = 240.0
gen-seed                 = -1
continuation             = no
;
Pcoupl                   = berendsen 
Pcoupltype               = isotropic
tau_p                    = 0.5
compressibility          = 1.0e-5
ref_p                    = 1.0
;
constraints              = hbonds