,
volume 35
,
issue 4
,
pages 312-324
GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP
Nikolay D. Kondratyuk
1, 2, 3
,
Nikolay Kondratyuk
1, 2, 3
,
Vsevolod Nikolskiy
1, 3
,
Daniil Pavlov
1, 2
,
Vladimir V. Stegailov
1, 2, 3
Publication type: Journal Article
Publication date: 2021-04-19
scimago Q1
wos Q2
SJR: 1.051
CiteScore: 7.4
Impact factor: 2.5
ISSN: 10943420, 17412846
Hardware and Architecture
Software
Theoretical Computer Science
Abstract
Classical molecular dynamics (MD) calculations represent a significant part of the utilization time of high-performance computing systems. As usual, the efficiency of such calculations is based on an interplay of software and hardware that are nowadays moving to hybrid GPU-based technologies. Several well-developed open-source MD codes focused on GPUs differ both in their data management capabilities and in performance. In this work, we analyze the performance of LAMMPS, GROMACS and OpenMM MD packages with different GPU backends on Nvidia Volta and AMD Vega20 GPUs. We consider the efficiency of solving two identical MD models (generic for material science and biomolecular studies) using different software and hardware combinations. We describe our experience in porting the CUDA backend of LAMMPS to ROCm HIP that shows considerable benefits for AMD GPUs comparatively to the OpenCL backend.
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Total citations:
79
Citations from 2025:
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(27.85%)
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Kondratyuk N. et al. GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP // International Journal of High Performance Computing Applications. 2021. Vol. 35. No. 4. pp. 312-324.
GOST all authors (up to 50)
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Kondratyuk N. D., Kondratyuk N., Nikolskiy V., Pavlov D., Stegailov V. GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP // International Journal of High Performance Computing Applications. 2021. Vol. 35. No. 4. pp. 312-324.
Cite this
RIS
Copy
TY - JOUR
DO - 10.1177/10943420211008288
UR - http://journals.sagepub.com/doi/10.1177/10943420211008288
TI - GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP
T2 - International Journal of High Performance Computing Applications
AU - Kondratyuk, Nikolay D.
AU - Kondratyuk, Nikolay
AU - Nikolskiy, Vsevolod
AU - Pavlov, Daniil
AU - Stegailov, Vladimir V.
PY - 2021
DA - 2021/04/19
PB - SAGE
SP - 312-324
IS - 4
VL - 35
SN - 1094-3420
SN - 1741-2846
ER -
Cite this
BibTex (up to 50 authors)
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@article{2021_Kondratyuk,
author = {Nikolay D. Kondratyuk and Nikolay Kondratyuk and Vsevolod Nikolskiy and Daniil Pavlov and Vladimir V. Stegailov},
title = {GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP},
journal = {International Journal of High Performance Computing Applications},
year = {2021},
volume = {35},
publisher = {SAGE},
month = {apr},
url = {http://journals.sagepub.com/doi/10.1177/10943420211008288},
number = {4},
pages = {312--324},
doi = {10.1177/10943420211008288}
}
Cite this
MLA
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Kondratyuk, Nikolay, et al. “GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP.” International Journal of High Performance Computing Applications, vol. 35, no. 4, Apr. 2021, pp. 312-324. http://journals.sagepub.com/doi/10.1177/10943420211008288.