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?
Thanks!
Alex
****
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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