Angara interconnect makes GPU-based Desmos supercomputer an efficient tool for molecular dynamics calculations. (May 2019)

• Record Type: Journal Article
• Authors: Stegailov, Vladimir; Dlinnova, Ekaterina; Ismagilov, Timur; Khalilov, Mikhail; Kondratyuk, Nikolay; Makagon, Dmitry; Semenov, Alexander; Simonov, Alexei; Smirnov, Grigory; Timofeev, Alexey
• Other Names: Mencagli Gabriele guest-editor.; França Felipe MG guest-editor.; Bentes Cristiana Barbosa guest-editor.; Justen Marzulo Leandro Augusto guest-editor.; Lima Pilla Mauricio guest-editor.; Wyrzykowski Roman guest-editor.; Deelman Ewa guest-editor.
• Is Part Of: International journal of high performance computing applications. Volume 33:Number 3(2019)
• Page Start: 507
• Page End: 521
• Publication Date: 2019-05
• Subjects: HPC interconnect -- scalability -- efficiency -- GPU-accelerated software -- atomistic simulations; High performance computing -- Periodicals; Supercomputers -- Periodicals; 004.1105
• DOI: 10.1177/1094342019826667
• Languages: English
• ISSNs: 1094-3420

Abstract

In this article, we describe the Desmos supercomputer that consists of 32 hybrid nodes connected by a low-latency high-bandwidth Angara interconnect with torus topology. This supercomputer is aimed at cost-effective classical molecular dynamics calculations. Desmos serves as a test bed for the Angara interconnect that supports 3-D and 4-D torus network topologies and verifies its ability to unite massively parallel programming systems speeding-up effectively message-passing interface (MPI)-based applications. We describe the Angara interconnect presenting typical MPI benchmarks. Desmos benchmarks results for GROMACS, LAMMPS, VASP and CP2K are compared with the data for other high-performance computing (HPC) systems. Also, we consider the job scheduling statistics for several months of Desmos deployment.