Malleable Molecular Dynamics Simulations with GROMACS and DMR

Abstract

Static resource allocations in high-performance computing (HPC) lead to inefficiencies for time-varying workloads, causing idle resources, queue delays, and higher node-hour costs. The Dynamic Management of Resources (DMR) middleware enables MPI process malleability in Slurm via a simple API decoupled from scheduler internals. In this work, we integrate DMR into the GROMACS molecular dynamics engine to obtain a malleable variant that can dynamically adapt its MPI process count by combining communication-efficiency-aware reconfiguration with GROMACS' native checkpoint/restart mechanism. We evaluate this design on the MareNostrum~5 supercomputer, comparing dynamic runs against static executions and quantifying reconfiguration overheads, time-to-solution, and node-hour savings for bursty GROMACS workloads.