Early Performance Evaluation of the Hybrid Cluster with Torus Interconnect Aimed at Molecular-Dynamics Simulations

V Stegailov and A Agarkov and S Biryukov and T Ismagilov and M Khalilov and N Kondratyuk and E Kushtanov and D Makagon and A Mukosey and A Semenov and A Simonov and A Timofeev and V Vecher, PARALLEL PROCESSING AND APPLIED MATHEMATICS (PPAM 2017), PT I, 10777, 327-336 (2018).

DOI: 10.1007/978-3-319-78024-5_29

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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