{"id":"https://openalex.org/W2916682091","doi":"https://doi.org/10.1177/1094342019826667","title":"Angara interconnect makes GPU-based Desmos supercomputer an efficient tool for molecular dynamics calculations","display_name":"Angara interconnect makes GPU-based Desmos supercomputer an efficient tool for molecular dynamics calculations","publication_year":2019,"publication_date":"2019-02-20","ids":{"openalex":"https://openalex.org/W2916682091","doi":"https://doi.org/10.1177/1094342019826667","mag":"2916682091"},"language":"en","primary_location":{"id":"doi:10.1177/1094342019826667","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342019826667","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075717752","display_name":"Vladimir Stegailov","orcid":"https://orcid.org/0000-0002-5349-3991"},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]},{"id":"https://openalex.org/I4210158550","display_name":"Joint Institute for High Temperatures","ror":"https://ror.org/04gns8903","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210158550","https://openalex.org/I4210164537"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Vladimir Stegailov","raw_affiliation_strings":["Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia","National Research University Higher School of Economics, Moscow, Russia"],"raw_orcid":"https://orcid.org/0000-0002-5349-3991","affiliations":[{"raw_affiliation_string":"Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia","institution_ids":["https://openalex.org/I4210158550"]},{"raw_affiliation_string":"National Research University Higher School of Economics, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054773036","display_name":"Ekaterina Dlinnova","orcid":null},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ekaterina Dlinnova","raw_affiliation_strings":["National Research University Higher School of Economics, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Research University Higher School of Economics, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089903901","display_name":"Timur Ismagilov","orcid":"https://orcid.org/0000-0002-7381-5759"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Timur Ismagilov","raw_affiliation_strings":["JSC NICEVT, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"JSC NICEVT, Moscow, Russia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077395612","display_name":"Mikhail Khalilov","orcid":"https://orcid.org/0000-0003-0862-4662"},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Mikhail Khalilov","raw_affiliation_strings":["National Research University Higher School of Economics, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Research University Higher School of Economics, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020060405","display_name":"Nikolay Kondratyuk","orcid":"https://orcid.org/0000-0002-8286-0447"},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]},{"id":"https://openalex.org/I4210158550","display_name":"Joint Institute for High Temperatures","ror":"https://ror.org/04gns8903","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210158550","https://openalex.org/I4210164537"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Nikolay Kondratyuk","raw_affiliation_strings":["Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia","National Research University Higher School of Economics, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia","institution_ids":["https://openalex.org/I4210158550"]},{"raw_affiliation_string":"National Research University Higher School of Economics, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024257676","display_name":"Dmitry Makagon","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dmitry Makagon","raw_affiliation_strings":["JSC NICEVT, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"JSC NICEVT, Moscow, Russia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039635245","display_name":"Alexander Semenov","orcid":"https://orcid.org/0000-0003-4878-6287"},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Alexander Semenov","raw_affiliation_strings":["JSC NICEVT, Moscow, Russia","National Research University Higher School of Economics, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"JSC NICEVT, Moscow, Russia","institution_ids":[]},{"raw_affiliation_string":"National Research University Higher School of Economics, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060138909","display_name":"A. G. Simonov","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alexei Simonov","raw_affiliation_strings":["JSC NICEVT, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"JSC NICEVT, Moscow, Russia","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079495309","display_name":"Grigory Smirnov","orcid":"https://orcid.org/0000-0002-9305-407X"},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]},{"id":"https://openalex.org/I4210158550","display_name":"Joint Institute for High Temperatures","ror":"https://ror.org/04gns8903","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210158550","https://openalex.org/I4210164537"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Grigory Smirnov","raw_affiliation_strings":["Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia","National Research University Higher School of Economics, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia","institution_ids":["https://openalex.org/I4210158550"]},{"raw_affiliation_string":"National Research University Higher School of Economics, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051552685","display_name":"\u0410. \u0412. \u0422\u0438\u043c\u043e\u0444\u0435\u0435\u0432","orcid":"https://orcid.org/0000-0003-1156-893X"},"institutions":[{"id":"https://openalex.org/I118501908","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516","country_code":"RU","type":"education","lineage":["https://openalex.org/I118501908"]},{"id":"https://openalex.org/I4210158550","display_name":"Joint Institute for High Temperatures","ror":"https://ror.org/04gns8903","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210158550","https://openalex.org/I4210164537"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Alexey Timofeev","raw_affiliation_strings":["Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia","National Research University Higher School of Economics, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow, Russia","institution_ids":["https://openalex.org/I4210158550"]},{"raw_affiliation_string":"National Research University Higher School of Economics, Moscow, Russia","institution_ids":["https://openalex.org/I118501908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5075717752"],"corresponding_institution_ids":["https://openalex.org/I118501908","https://openalex.org/I4210158550"],"apc_list":null,"apc_paid":null,"fwci":6.8751,"has_fulltext":false,"cited_by_count":66,"citation_normalized_percentile":{"value":0.97163361,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"33","issue":"3","first_page":"507","last_page":"521"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10829","display_name":"Interconnection Networks and Systems","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.9392406940460205},{"id":"https://openalex.org/keywords/interconnection","display_name":"Interconnection","score":0.7549301385879517},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.7526847720146179},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7509105801582336},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7019720673561096},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.6144859194755554},{"id":"https://openalex.org/keywords/torus","display_name":"Torus","score":0.5580628514289856},{"id":"https://openalex.org/keywords/latency","display_name":"Latency (audio)","score":0.47181427478790283},{"id":"https://openalex.org/keywords/software-deployment","display_name":"Software deployment","score":0.44590699672698975},{"id":"https://openalex.org/keywords/scheduling","display_name":"Scheduling (production processes)","score":0.4244028925895691},{"id":"https://openalex.org/keywords/programming-paradigm","display_name":"Programming paradigm","score":0.41185569763183594},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.36560797691345215},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3397876024246216},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.22389566898345947},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.14892536401748657},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09305959939956665}],"concepts":[{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.9392406940460205},{"id":"https://openalex.org/C123745756","wikidata":"https://www.wikidata.org/wiki/Q1665949","display_name":"Interconnection","level":2,"score":0.7549301385879517},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.7526847720146179},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7509105801582336},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7019720673561096},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.6144859194755554},{"id":"https://openalex.org/C9767117","wikidata":"https://www.wikidata.org/wiki/Q12510","display_name":"Torus","level":2,"score":0.5580628514289856},{"id":"https://openalex.org/C82876162","wikidata":"https://www.wikidata.org/wiki/Q17096504","display_name":"Latency (audio)","level":2,"score":0.47181427478790283},{"id":"https://openalex.org/C105339364","wikidata":"https://www.wikidata.org/wiki/Q2297740","display_name":"Software deployment","level":2,"score":0.44590699672698975},{"id":"https://openalex.org/C206729178","wikidata":"https://www.wikidata.org/wiki/Q2271896","display_name":"Scheduling (production processes)","level":2,"score":0.4244028925895691},{"id":"https://openalex.org/C34165917","wikidata":"https://www.wikidata.org/wiki/Q188267","display_name":"Programming paradigm","level":2,"score":0.41185569763183594},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.36560797691345215},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3397876024246216},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.22389566898345947},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.14892536401748657},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09305959939956665},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1177/1094342019826667","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342019826667","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2956993495","display_name":null,"funder_award_id":"14-50-00124","funder_id":"https://openalex.org/F4320324261","funder_display_name":"National Research University Higher School of Economics"}],"funders":[{"id":"https://openalex.org/F4320323858","display_name":"Far East Branch, Russian Academy of Sciences","ror":"https://ror.org/05t43vz03"},{"id":"https://openalex.org/F4320324261","display_name":"National Research University Higher School of Economics","ror":"https://ror.org/055f7t516"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W170299757","https://openalex.org/W1031578623","https://openalex.org/W1596936080","https://openalex.org/W1810694562","https://openalex.org/W1895692106","https://openalex.org/W1915019682","https://openalex.org/W1981021420","https://openalex.org/W1992432622","https://openalex.org/W1998627866","https://openalex.org/W2002293913","https://openalex.org/W2007395042","https://openalex.org/W2019465613","https://openalex.org/W2034655082","https://openalex.org/W2055564206","https://openalex.org/W2062454596","https://openalex.org/W2062826522","https://openalex.org/W2076198800","https://openalex.org/W2078794610","https://openalex.org/W2079105963","https://openalex.org/W2083222334","https://openalex.org/W2087698390","https://openalex.org/W2099952176","https://openalex.org/W2136141445","https://openalex.org/W2139667204","https://openalex.org/W2146115249","https://openalex.org/W2146351362","https://openalex.org/W2151741062","https://openalex.org/W2159826908","https://openalex.org/W2166379031","https://openalex.org/W2168363974","https://openalex.org/W2407057568","https://openalex.org/W2473383291","https://openalex.org/W2495449080","https://openalex.org/W2501420232","https://openalex.org/W2519398037","https://openalex.org/W2529481803","https://openalex.org/W2530570189","https://openalex.org/W2555578994","https://openalex.org/W2555751324","https://openalex.org/W2586396889","https://openalex.org/W2730740223","https://openalex.org/W2774413277","https://openalex.org/W2952876933","https://openalex.org/W3000662989","https://openalex.org/W3103156673","https://openalex.org/W4238775627","https://openalex.org/W4302391563"],"related_works":["https://openalex.org/W2384867379","https://openalex.org/W4400094300","https://openalex.org/W2329539859","https://openalex.org/W2227905990","https://openalex.org/W2765823764","https://openalex.org/W3214280620","https://openalex.org/W2810598808","https://openalex.org/W2209637120","https://openalex.org/W2073684863","https://openalex.org/W4312120449"],"abstract_inverted_index":{"In":[0],"this":[1],"article,":[2],"we":[3,98],"describe":[4,69],"the":[5,41,70,89,100],"Desmos":[6,34,77,108],"supercomputer":[7,25],"that":[8,44],"consists":[9],"of":[10,107],"32":[11],"hybrid":[12],"nodes":[13],"connected":[14],"by":[15],"a":[16,37],"low-latency":[17],"high-bandwidth":[18],"Angara":[19,42,71],"interconnect":[20,43,72],"with":[21,88],"torus":[22,49],"topology.":[23],"This":[24],"is":[26],"aimed":[27],"at":[28],"cost-effective":[29],"classical":[30],"molecular":[31],"dynamics":[32],"calculations.":[33],"serves":[35],"as":[36],"test":[38],"bed":[39],"for":[40,80,91,104],"supports":[45],"3-D":[46],"and":[47,52,84],"4-D":[48],"network":[50],"topologies":[51],"verifies":[53],"its":[54],"ability":[55],"to":[56],"unite":[57],"massively":[58],"parallel":[59],"programming":[60],"systems":[61],"speeding-up":[62],"effectively":[63],"message-passing":[64],"interface":[65],"(MPI)-based":[66],"applications.":[67],"We":[68],"presenting":[73],"typical":[74],"MPI":[75],"benchmarks.":[76],"benchmarks":[78],"results":[79],"GROMACS,":[81],"LAMMPS,":[82],"VASP":[83],"CP2K":[85],"are":[86],"compared":[87],"data":[90],"other":[92],"high-performance":[93],"computing":[94],"(HPC)":[95],"systems.":[96],"Also,":[97],"consider":[99],"job":[101],"scheduling":[102],"statistics":[103],"several":[105],"months":[106],"deployment.":[109]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":5}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}