Open Access
,
pages 327-336
Early Performance Evaluation of the Hybrid Cluster with Torus Interconnect Aimed at Molecular-Dynamics Simulations
Vladimir V. Stegailov
1, 2, 3
,
Alexander Agarkov
4
,
Sergey Biryukov
4
,
Timur Ismagilov
4
,
Mikhail Khalilov
3
,
Nikolay D. Kondratyuk
1, 2, 3
,
Evgeny Kushtanov
4
,
Dmitry Makagon
4
,
Anatoly Mukosey
4
,
Alexander Semenov
4
,
Alexey Simonov
4
,
A. V. Timofeev
1, 2, 3
,
Vyacheslav Vecher
1, 2
Publication type: Book Chapter
Publication date: 2018-03-22
scimago Q2
SJR: 0.352
CiteScore: 2.4
Impact factor: —
ISSN: 03029743, 16113349, 18612075, 18612083
Abstract
In this paper, we describe the Desmos cluster that consists of 32 hybrid nodes connected by a low-latency high-bandwidth torus interconnect. This cluster is aimed at cost-effective classical molecular dynamics calculations. We present strong scaling benchmarks for GROMACS, LAMMPS and VASP and compare the results with other HPC systems. This cluster serves as a test bed for the Angara interconnect that supports 3D and 4D torus network topologies, and verifies its ability to unite MPP systems speeding-up effectively MPI-based applications. We describe the interconnect presenting typical MPI benchmarks.
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Stegailov V. et al. Early Performance Evaluation of the Hybrid Cluster with Torus Interconnect Aimed at Molecular-Dynamics Simulations // Lecture Notes in Computer Science. 2018. pp. 327-336.
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Stegailov V., Agarkov A., Biryukov S., Ismagilov T., Khalilov M., Kondratyuk N. D., Kushtanov E., Makagon D., Mukosey A., Semenov A., Simonov A., Timofeev A. V., Vecher V. Early Performance Evaluation of the Hybrid Cluster with Torus Interconnect Aimed at Molecular-Dynamics Simulations // Lecture Notes in Computer Science. 2018. pp. 327-336.
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TY - GENERIC
DO - 10.1007/978-3-319-78024-5_29
UR - http://link.springer.com/10.1007/978-3-319-78024-5_29
TI - Early Performance Evaluation of the Hybrid Cluster with Torus Interconnect Aimed at Molecular-Dynamics Simulations
T2 - Lecture Notes in Computer Science
AU - Stegailov, Vladimir V.
AU - Agarkov, Alexander
AU - Biryukov, Sergey
AU - Ismagilov, Timur
AU - Khalilov, Mikhail
AU - Kondratyuk, Nikolay D.
AU - Kushtanov, Evgeny
AU - Makagon, Dmitry
AU - Mukosey, Anatoly
AU - Semenov, Alexander
AU - Simonov, Alexey
AU - Timofeev, A. V.
AU - Vecher, Vyacheslav
PY - 2018
DA - 2018/03/22
PB - Springer Nature
SP - 327-336
SN - 0302-9743
SN - 1611-3349
SN - 1861-2075
SN - 1861-2083
ER -
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@incollection{2018_Stegailov,
author = {Vladimir V. Stegailov and Alexander Agarkov and Sergey Biryukov and Timur Ismagilov and Mikhail Khalilov and Nikolay D. Kondratyuk and Evgeny Kushtanov and Dmitry Makagon and Anatoly Mukosey and Alexander Semenov and Alexey Simonov and A. V. Timofeev and Vyacheslav Vecher},
title = {Early Performance Evaluation of the Hybrid Cluster with Torus Interconnect Aimed at Molecular-Dynamics Simulations},
publisher = {Springer Nature},
year = {2018},
pages = {327--336},
month = {mar}
}