Angara interconnect makes GPU-based Desmos supercomputer an efficient tool for molecular dynamics calculations

V Stegailov and E Dlinnova and T Ismagilov and M Khalilov and N Kondratyuk and D Makagon and A Semenov and A Simonov and G Smirnov and A Timofeev, INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 33, 507-521 (2019).

DOI: 10.1177/1094342019826667

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.

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