Search
Abstract
Graphical Processor Units (GPUs) are nowadays widely used in all-atom molecular simulations because of the advantage of efficient partitioning of atom pairs between the kernels to compute the contributions to energy and forces, thus enabling the treatment of very large systems. Extension of time- and size-scale of computations is also sought through the development of coarse-grained (CG) models, in which atoms are merged into extended interaction sites. Implementation of CG codes on the GPUs, particularly the multiple-GPU platforms is, however, a challenge due to more complicated potentials and removing the explicit solvent, forcing developers to do interaction- rather than space-domain decomposition. In this paper, we propose a design of a multi-GPU coarse-grained simulator and report the implementation of the heavily coarse-grained physics-based UNited RESidue (UNRES) model of polypeptide chains. By moving all computations to GPUs and keeping the communication with CPUs to a minimum, we managed to achieve almost 5-fold speed-up with 8 A100 GPU accelerators for systems with over 200,000 amino-acid residues, this result making UNRES the best scalable coarse-grained software and enabling us to do laboratory-time millisecond-scale simulations of such cell components as tubulin within days of wall-clock time.
Citations
-
1
CrossRef
-
0
Web of Science
-
1
Scopus
Authors (8)
-
Cezary Czaplewski Dr hab.
-
-
Adam Liwo
-
Adam K. Sieradzan
Cite as
Full text
full text is not available in portal
Keywords
Details
- Category:
- Articles
- Type:
- artykuły w czasopismach
- Published in:
-
COMPUTER PHYSICS COMMUNICATIONS
no. 298,
ISSN: 0010-4655 - Language:
- English
- Publication year:
- 2024
- Bibliographic description:
- Ocetkiewicz K., Czaplewski C., Krawczyk H., Lipska A., Liwo A., Proficz J., Sieradzan A. K., Czarnul P.: Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems// COMPUTER PHYSICS COMMUNICATIONS -, (2024), s.109112-
- DOI:
- Digital Object Identifier (open in new tab) 10.1016/j.cpc.2024.109112
- Sources of funding:
-
- Free publication
- Verified by:
- Gdańsk University of Technology
seen 20 times
Recommended for you
Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
- A. Sieradzan,
- J. Sans‐Duñó,
- E. Lubecka
- + 8 authors