Are KNL a good choice for classical MD?

From: Francesco Pietra (
Date: Fri Aug 04 2017 - 15:51:48 CDT

I am carrying out classical all atom MD on a rather large protein system
(3,300,000 atoms). The speed on a NextScale single node (namd1.12
multicore), by choosing

mpirun -perhost 1 -n 1 namd2 +ppn 256 npt-03.conf +pemap 0-63+64+128+192 >

is of 0.5days/ns at ts=1.0fs, rigidbonds water.

This compares with 1.2days/ns, under the same conditions, for a Linux box,
namd1.12 multicore CUDA, with 6cores, 12 hyperthreads, and two GTX-680.

I expected much more from the cluster. Is our cluster unusually slow for
some reasons (compiled mpi with Intel 2017) or are GPUs still the choice
for classical MD?

Thanks for advice

francesco pietra

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