Angara interconnect makes GPU-based Desmos supercomputer an efficient tool for molecular dynamics calculations
Vladimir Stegailov, Ekaterina Dlinnova, Timur Ismagilov, Mikhail Khalilov, Nikolay Kondratyuk, Dmitry Makagon, Alexander Semenov, A. G. Simonov, Grigory S. Smirnov, А. В. Тимофеев · The International Journal of High Performance Computing Applications · 2019
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.