Decreasing performance of cluster running FEP

From: Francesco Pietra (
Date: Wed Jul 11 2018 - 00:29:51 CDT

I am observing a marked decrease in the performance of a NextScale cluster
running a FEP for protein-ligand, previously equilibrated for over 100ns.
No such problems when running MD equilibration on the same system. Code
NAMD 2.12, ad hoc compilation in house with Intel 2016 (NAMD2.12, compiled
on more recent Intel, available as module at the cluster, proved unable to
run a FEP)

The system is made of ca 460 residues in water, FEP 0.2-1.0 lambda 0.025
(32 windows), preeq 175,000/numSteps 750,000, ts=1.0fs.
FEP on 4 nodes/144core (optimal for scaling) starts with 0.0078/step
performance until window 3. Thereafter 0.014/step until window 5,
thereafter 0.021 until present window 9. The ligand, under modest
r/angle/dih colvars, remains in place with no detectable rotation or
distortion. Slowdown is such that it becomes extremely expensive carrying
out a FEP, even if divided in two sectors like now. same problems for FEP

I observed the same problem when running FEP on the ligand alone in water
on one node /36 core.

In all cases, letting the code writing on disk less frequently did not help.

These are problems that are being observed since the start of this projet,
a few months ago.

Thanks for advice.

francesco pietra

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