Benchmarking LAMMPS: Sensitivity to Task Location Under CPU-Based Weak-Scaling

Abstract

This investigation summarizes a set of executions completed

on the supercomputers Stampede at TACC (USA), Helios at IFERC

(Japan), and Eagle at PSNC (Poland), with the molecular dynamics solver

LAMMPS, compiled for CPUs. A communication-intensive benchmark

based on long-distance interactions tackled by the Fast Fourier Transform

operator has been selected to test its sensitivity to rather different patterns

of tasks location, hence to identify the best way to accomplish further

simulations for this family of problems.Weak-scaling tests show that

the attained execution time of LAMMPS is closely linked to the cluster

topology and this is revealed by the varying time-execution observed in

scale up to thousands of MPI tasks involved in the tests. It is noticeable

that two clusters exhibit time saving (up to 61% within the parallelization

range) when the MPI-task mapping follows a concentration pattern over

as few nodes as possible. Besides this result is useful from the user’s standpoint,

it may also help to improve the clusters throughput by, for instance,

adding live-migration decisions in the scheduling policies in those cases

of communication-intensive behaviour detected in characterization tests.

Also, it opens a similar output for a more efficient usage of the cluster from

the energy consumption point of view.