Optimization of LAMMPS

Abstract

The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code is part of the Department of Defense High Performance Computing Modernization Program (HPCMP) technology insertion (TI) benchmarking suite of applications. As a component of the TI benchmarking applications, LAMMPS is a significant contributor to Computational Chemistry and Materials Science requirements within the DoD. Ensuring its optimal performance on HPCMP resources is a high priority. The CCM-KY5-003 User Productivity Enhancements and Technology Transfer (PET) project was created to profile and optimize LAMMPS to improve its performance and efficiency on two HPCMP assets, Eagle (Altix 3700) and JVN(Linux Cluster). Profiling efforts were completed on Eagle using the Tuning and Analysis Utilities (TAU) application in conjunction with the Performance Application Programming Interface (PAPI). The time and hardware counter data was analyzed with ParaProf and PerfExplorer, while the trace data was automatically analyzed by the Kit for Objective Judgment and Knowledge-based Detection of Performance Bottlenecks (KOJAK). The profiling effort used three different model systems, where each uses a different physical potential. Several opportunities for performance improvement were identified in the critical portions of the code, such as loop-static branching conditions, multi-dimensional C-arrays and redundant integer, and floating-point operations. In addition to algorithmic changes, compiler options and machine-specific instructions were also investigated. The performance of the code increased from 1.3x to 3.5x on Eagle and 1.2x to 1.8x on JVN depending on the physical potential employed