TY - GEN
T1 - High-performance molecular dynamics simulation for biological and materials sciences
T2 - 2018 IEEE/ACM International Workshop on Performance, Portability and Productivity in HPC, P3HPC 2018
AU - Sedova, Ada
AU - Eblen, John D.
AU - Budiardja, Reuben
AU - Tharrington, Arnold
AU - Smith, Jeremy C.
N1 - Publisher Copyright:
© 2018 IEEE.
PY - 2018/7/2
Y1 - 2018/7/2
N2 - Highly-optimized parallel molecular dynamics programs have allowed researchers to achieve ground-breaking results in biological and materials sciences. This type of performance has come at the expense of portability: A significant effort is required for performance optimization on each new architecture. Using a metric that emphasizes speedup, we assess key accelerating programming components of four different best-performing molecular dynamics programs-GROMACS, NAMD, LAMMPS and CP2K-each having a particular scope of application, for contribution to performance and for portability. We use builds with and without these components, tested on HPC systems. We also analyze the code-bases to determine compliance with portability recommendations. We find that for all four programs, the contributions of the non-portable components to speed are essential to the programs' performances; without them we see a reduction in time-to-solution of a magnitude that is insufferable to domain scientists. This characterizes the performance efficiency that must be approached for good performance portability on a programmatic level, suggesting solutions to this difficult problem, which should come from developers, industry and funding institutions, and possibly new research in programming languages.
AB - Highly-optimized parallel molecular dynamics programs have allowed researchers to achieve ground-breaking results in biological and materials sciences. This type of performance has come at the expense of portability: A significant effort is required for performance optimization on each new architecture. Using a metric that emphasizes speedup, we assess key accelerating programming components of four different best-performing molecular dynamics programs-GROMACS, NAMD, LAMMPS and CP2K-each having a particular scope of application, for contribution to performance and for portability. We use builds with and without these components, tested on HPC systems. We also analyze the code-bases to determine compliance with portability recommendations. We find that for all four programs, the contributions of the non-portable components to speed are essential to the programs' performances; without them we see a reduction in time-to-solution of a magnitude that is insufferable to domain scientists. This characterizes the performance efficiency that must be approached for good performance portability on a programmatic level, suggesting solutions to this difficult problem, which should come from developers, industry and funding institutions, and possibly new research in programming languages.
KW - CUDA-C
KW - SIMD-instructions
KW - heterogenous-architectures
KW - molecular-dynamics
KW - performance-portability
UR - http://www.scopus.com/inward/record.url?scp=85063105896&partnerID=8YFLogxK
U2 - 10.1109/P3HPC.2018.00004
DO - 10.1109/P3HPC.2018.00004
M3 - Conference contribution
AN - SCOPUS:85063105896
T3 - Proceedings of P3HPC 2018: International Workshop on Performance, Portability and Productivity in HPC, Held in conjunction with SC 2018: The International Conference for High Performance Computing, Networking, Storage and Analysis
SP - 1
EP - 13
BT - Proceedings of P3HPC 2018
PB - Institute of Electrical and Electronics Engineers Inc.
Y2 - 16 November 2018
ER -