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An exa-scale high-performance molecular dynamics simulation program: MODYLAS.
Yoshimichi Andoh1, Shin-Ichi Ichikawa2, Tatsuya Sakashita3
1National Institute for Materials Science (NIMS), 1-2-1, Sengen, Tsukuba, Ibaraki 305-0047, Japan.
The Journal of Chemical Physics
|May 15, 2023
Summary
A new MODYLAS molecular dynamics (MD) simulation program achieves high performance on the Fugaku supercomputer. Its optimized data transfer and processing enable rapid calculations for large-scale material science research.
Area of Science:
- Computational chemistry
- Materials science
- High-performance computing
Background:
- Molecular dynamics (MD) simulations are crucial for understanding material properties at the atomic level.
- Efficient execution of large-scale MD simulations requires high-performance computing resources and optimized algorithms.
- The Fugaku supercomputer offers unprecedented computational power for scientific research.
Purpose of the Study:
- To develop a high-performance version of the MODYLAS program optimized for the Fugaku supercomputer.
- To evaluate the performance of the modified MODYLAS program for large-scale molecular dynamics simulations.
- To enhance the capabilities of MODYLAS for material research applications.
Main Methods:
- Development of a new minimum transferred data method for reduced data communication.
- Implementation of a data reuse algorithm to enhance on-cache processing.
- Benchmarking the modified MODYLAS program on the Fugaku supercomputer using a system with over 100 million atoms.
Main Results:
- The modified MODYLAS achieved a single MD time-step calculation in 8.5 ms for a system of 101,810,176 atoms.
- Highly efficient communication, single instruction, multiple data (SIMD) processing, and on-cache operations were observed.
- Low cache miss rates (e.g., 2.74% on L1 for direct force calculations) and high SIMD effective instruction rates (e.g., 78.7% for direct force calculations) were achieved.
- The program demonstrated excellent scalability with minimal performance degradation under high parallelization.
Conclusions:
- The enhanced MODYLAS program significantly accelerates large-scale molecular dynamics simulations on the Fugaku supercomputer.
- The developed optimization techniques, including the minimum transferred data method, are effective for high-performance computing environments.
- MODYLAS is now a powerful tool for material research, offering advanced functionalities for free energy calculations and ensemble generation.
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