[gmx-users] GPU-accelerated performance

Alex nedomacho at gmail.com
Wed Sep 6 10:58:22 CEST 2017

Hi all,

We just got the new machines that were actually built with Szilárd's 
advice (a while back) and I am doing some preliminary tests. "My" 
machine has two 22-core Xeon E5 CPUs (44 cores / 88 threads total) + 3 
Titan Xp GPUs. So far, I got good test system performance (~11K atoms, 
92 ns/day) from '-nt 36' and running on all GPUs. Further increasing the 
number of threads only reduces performance. The test system is a 
CHARMM-based lipid+water setup, elongated in the Z-direction (6.7 nm x 
6.7 nm x 11.2 nm).Very decent performance (70 ns/day) for 16 CPU cores 
and two GPUs.

Any suggestions on further increase what we can squeeze out of this 
thing for a single simulation? The relevant mdp section is below (CHARMM 
defaults, really). What would you try in your mdrun line?



cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.2
coulombtype             = pme
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2

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