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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.<\/jats:p>","DOI":"10.1177\/1094342019826667","type":"journal-article","created":{"date-parts":[[2019,2,20]],"date-time":"2019-02-20T22:17:58Z","timestamp":1550701078000},"page":"507-521","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":58,"title":["Angara interconnect makes GPU-based Desmos supercomputer an efficient tool for molecular dynamics calculations"],"prefix":"10.1177","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5349-3991","authenticated-orcid":false,"given":"Vladimir","family":"Stegailov","sequence":"first","affiliation":[{"name":"Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia"},{"name":"National Research University Higher School of Economics, Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ekaterina","family":"Dlinnova","sequence":"additional","affiliation":[{"name":"National Research University Higher School of Economics, Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Timur","family":"Ismagilov","sequence":"additional","affiliation":[{"name":"JSC NICEVT, Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikhail","family":"Khalilov","sequence":"additional","affiliation":[{"name":"National Research University Higher School of Economics, Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikolay","family":"Kondratyuk","sequence":"additional","affiliation":[{"name":"Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia"},{"name":"National Research University Higher School of Economics, Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dmitry","family":"Makagon","sequence":"additional","affiliation":[{"name":"JSC NICEVT, Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Semenov","sequence":"additional","affiliation":[{"name":"National Research University Higher School of Economics, Moscow, Russia"},{"name":"JSC NICEVT, Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexei","family":"Simonov","sequence":"additional","affiliation":[{"name":"JSC NICEVT, Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Grigory","family":"Smirnov","sequence":"additional","affiliation":[{"name":"Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia"},{"name":"National Research University Higher School of Economics, Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexey","family":"Timofeev","sequence":"additional","affiliation":[{"name":"Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia"},{"name":"National Research University Higher School of Economics, Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2019,2,20]]},"reference":[{"key":"bibr1-1094342019826667","doi-asserted-by":"crossref","unstructured":"Abraham MJ, Murtola T, Schulz R, et al. 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