Abstract

Scientific breakthroughs in biomolecular methods and improvements in hardware technology have shifted from a long‐running simulation to a large set of shorter simulations running simultaneously, called an ensemble. In an ensemble, simulations are usually coupled with analyses of data produced by the simulations. In situ methods can be used to analyze large volumes of data generated by scientific simulations at runtime (i.e., simulations and analyses are performed concurrently). In this work, we study the execution of ensemble‐based simulations paired with in situ analyses using in‐memory staging methods. Using an ensemble of molecular dynamics in situ workflows with multiple simulations and analyses, we first show that collecting traditional metrics such as makespan, instructions per cycle, memory usage, or cache miss ratio is not sufficient to characterize complex behaviors of ensembles. We propose a …

Date

September 10, 2023

Authors

Tu Mai Anh Do, Loïc Pottier, Rafael Ferreira da Silva, Silvina Caíno‐Lores, Michela Taufer, Ewa Deelman

Journal

Concurrency and Computation: Practice and Experience

Volume

35

Issue

20

Pages

e7111