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GPU Acceleration of Four-Site Water Models in LAMMPS
P. 565–573.
Nikolskiy V., Stegailov V.
In this work, a new algorithm was developed for calculating the fourpoint water model TIP4P on graphics accelerators. It was designed as a part of the flexible molecular dynamics modeling package LAMMPS in the library module “GPU”. In this paper we describe two approaches to implement the TIP4P model for GPU: 1) to divide the related computations between CPU and GPU; 2) to compute the interaction fully on the GPU. We verify the program, benchmark and profile it. The achieved speedup of interaction computation is about x7, acceleration of the entire calculation of about 55%.
Plotnikov S., Деева В. В., Тенденции развития науки и образования 2023 № 102-2 С. 113–120
In the scientific article are considered the main technologies of corporate innovative entrepreneurship. Each technology is examined separately, which allows for understanding the purposefulness of using each tool in practice at your company. ...
Added: May 21, 2026
Ismagilov T., Mukosey A., Smirnov F. et al., International Journal of High Performance Computing Applications 2026 Vol. 40 No. 2 P. 240–253
One of the most important aspects of supercomputer development in the post-Moore era is the interconnect technologies that allow one to unite a multitude of processing elements into a well-synchronized computing system. Novel types of supercomputer interconnect require careful benchmarking and compliance with the requirements of modern hardware trends. GPU-based heterogeneous computing is one of ...
Added: May 7, 2026
Afanasiev S., Agakishiev G., Aleksandrov E. et al., Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Нидерланды 2024 Vol. 1065 Article 169532
BM@N (Baryonic Matter at Nuclotron) is the first experiment operating and taking data at the Nuclotron/NICA ion-accelerating complex. The aim of the BM@N experiment is to study interactions of relativistic heavy-ion beams with fixed targets. We present a technical description of the BM@N spectrometer including all its subsystems. ...
Added: November 14, 2024
Yaremenko I., Belyakova Y., Radulov P. et al., Journal of Organic Chemistry 2023 Vol. 88 No. 19 P. 13782–13795
Relief of stereoelectronic frustration drives the acid-catalyzed three-component condensation of β,δ′-triketones with hydrazides and H2O2 to the direction where both nucleophiles and all three electrophilic carbons are involved in the formation of a tricyclic sp3-rich ring system that includes four heteroatoms. The otherwise inaccessible tricyclic N-substituted aminoperoxides are prepared rapidly and selectively from relatively simple ...
Added: October 24, 2023
Pavlov D., Galigerov V., Kolotinskii D. et al., International Journal of High Performance Computing Applications 2024 Vol. 38 No. 1 P. 34–49
Fluid dynamics is a ubiquitous problem that arises in different branches of science and industry. It is usually tackled by numerically solving differential equations on a finite grid. Molecular dynamics was not a feasible tool to approach fluid dynamics until very recently due to its disproportional computational complexity. In this paper we propose a new ...
Added: July 18, 2023
Sorokin P., Chernenko S., Vyatskaya Y., Издательский дом НИУ ВШЭ, 2023.
The report is devoted to the analysis of measures of infrastructural support of student entrepreneurial initiatives in Russian universities. The contribution to the success of the main infrastructure elements of entrepreneurship support was assessed: educational opportunities, business incubator, accelerator, startup studios, communities, etc. The information openness of support measures through the official websites of universities ...
Added: June 13, 2023
Kondratyuk N., Nikolskiy V., Pavlov D. et al., International Journal of High Performance Computing Applications 2021 Vol. 35 No. 4 P. 312–324
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 ...
Added: June 25, 2021
Kuznetsov A., Efremov R., В кн.: Математика. Компьютер. Образование. Тезисы.Вып. 27: Двадцать седьмая международная конференция "Математика. Компьютер. Образование." Симпозиум с международным участием "Биофизика сложных систем, вычислительная и системная биология, молекулярное моделирование".: Ижевск: Ижевский институт компьютерных исследований, 2020. С. 53–54.
Receptor tyrosine kinases form an important class of membrane proteins that regulate cell life cycle and metabolism. Among wide variety of receptors, they have simple structure with single alpha-helix crossing the membrane. This transmembrane domain is functionalm as dimeric state conformation defines active/inactive state of the receptor. The lipid environment can modulate functioning of such ...
Added: February 3, 2020
Stegailov V., Timofeev A., , in: Supercomputing. RuSCDays 2018. Communications in Computer and Information Science, vol 965. Springer, Cham.: Springer, 2019. P. 543–553.
Modern Elbrus-4S and Elbrus-8S processors show floating point performance comparable to the popular Intel processors in the field of high-performance computing. Tasks oriented to take advantage of the VLIW architecture show even greater efficiency on Elbrus processors. In this paper the efficiency of the most popular materials science codes in the field of classical molecular ...
Added: March 10, 2019
Mishra R. K., Kunhi Mohamed A., Geissbühler D. et al., Cement and Concrete Research 2017 Vol. 102 P. 68–89
This paper reviews atomistic force field parameterizations for molecular simulations of cementitious minerals, such as tricalcium silicate (C3S), portlandite (CH), tobermorites (model C-S-H). Computational techniques applied to these materials include classical molecular simulations, density functional theory and energy minimization. Such simulations hold promise to capture the nanoscale mechanisms operating in cementitious materials and guide in ...
Added: November 11, 2017
Nikolskiy V., Vecher V., Stegailov V., , in: Supercomputing. RuSCDays 2016. Communications in Computer and Information Science. Revised Selected Papers.Vol. 687.: Springer, 2016. P. 199–211.
In this paper we consider the efficiency of hybrid systemson-a-chip for high-performance calculations. Firstly, we build Roofline performance models for the systems considered using Empirical Roofline Toolkit and compare the results with the theoretical estimates. Secondly, we use LAMMPS as an example of the molecular dynamic package to demonstrate its performance and efficiency in various ...
Added: May 31, 2017
Vecher V., Nikolskiy V., Stegailov V., , in: Supercomputing. RuSCDays 2016. Communications in Computer and Information Science. Revised Selected Papers.Vol. 687.: Springer, 2016. P. 78–90.
Energy consumption of hybrid systems is an actual problem of modern high-performance computing. The trade-off between power consumption and performance becomes more and more prominent. In this paper, we discuss the energy and power efficiency of two modern hybrid minicomputers Jetson TK1 and TX1. We use the Empirical Roofline Tool to obtain peak performance data ...
Added: May 31, 2017
Norman G., Saitov I., Stegailov V. et al., Contributions to Plasma Physics 2013 Vol. 53 No. 4-5 P. 300–310
Warm dense matter conductivity and reflectivity are investigated by means of density functional theory. Both one- and two-temperature cases are considered. One-temperature mode is related to equilibrium state where temperature of electrons and ions are equal. As an example of one-temperature system xenon plasma is studied. The reflectivity of shock-compressed dense xenon plasma is calculated ...
Added: March 19, 2014