About the performance of RAMD

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Nov 10 2017 - 10:55:42 CST


I have been using pretty much RAMD with small proteins, particularly on a
small Linux box with 6 cores and two GPUs. The loss of performance from MD
to RAMD was very limited, with namd2.12 or previous versions.

With larger systems (ca 300000 atoms) the corresponding loss of performance
is six on the above hardware.

With clusters based on CPUs, like a nextscale, the loss of performance with
the above system of 300000 atoms is so high as to prevent using small
accelerations. With four nodes (144 cores) the loss of performance is 36.
Four nodes become somewhat slower than two nodes.

Has any remedy been invented for ramd tcl? Could ramd be run (with
successful performance) on a single node by loading everything to /dev/smh?

Thanks for advice

francesco pietra

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