{"id":"https://openalex.org/W4381586533","doi":"https://doi.org/10.1145/3592979.3593403","title":"Lessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation","display_name":"Lessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation","publication_year":2023,"publication_date":"2023-06-26","ids":{"openalex":"https://openalex.org/W4381586533","doi":"https://doi.org/10.1145/3592979.3593403"},"language":"en","primary_location":{"id":"doi:10.1145/3592979.3593403","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3592979.3593403","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Platform for Advanced Scientific Computing Conference","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2306.11544","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092230963","display_name":"Marc Clasc\u00e0","orcid":"https://orcid.org/0000-0002-5963-6658"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Marc Clasc\u00e0","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0002-5963-6658","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082933794","display_name":"Marta Garc\u00eda-Gasulla","orcid":"https://orcid.org/0000-0003-3682-9905"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Marta Garcia-Gasulla","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0003-3682-9905","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051818233","display_name":"Arnau Montagud","orcid":"https://orcid.org/0000-0002-7696-1241"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Arnau Montagud","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0002-7696-1241","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066796940","display_name":"Jos\u00e9 Carbonell\u2010Caballero","orcid":"https://orcid.org/0000-0002-9170-0533"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Carbonell Caballero","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0002-9170-0533","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015217651","display_name":"Alfonso Valencia","orcid":"https://orcid.org/0000-0002-8937-6789"},"institutions":[{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Alfonso Valencia","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain","ICREA, Pg. Llu\u00eds Companys 23, Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0002-8937-6789","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"ICREA, Pg. Llu\u00eds Companys 23, Barcelona, Spain","institution_ids":["https://openalex.org/I11932220"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9921000003814697,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9921000003814697,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10492","display_name":"Microtubule and mitosis dynamics","score":0.9908999800682068,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9865000247955322,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.825822114944458},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7880197763442993},{"id":"https://openalex.org/keywords/locality","display_name":"Locality","score":0.7520802021026611},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6187993288040161},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5225234031677246},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.47099679708480835},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.4660407602787018},{"id":"https://openalex.org/keywords/program-optimization","display_name":"Program optimization","score":0.4106609523296356},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3906277120113373},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10098785161972046}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.825822114944458},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7880197763442993},{"id":"https://openalex.org/C2779808786","wikidata":"https://www.wikidata.org/wiki/Q6664603","display_name":"Locality","level":2,"score":0.7520802021026611},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6187993288040161},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5225234031677246},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.47099679708480835},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.4660407602787018},{"id":"https://openalex.org/C139571649","wikidata":"https://www.wikidata.org/wiki/Q1156793","display_name":"Program optimization","level":3,"score":0.4106609523296356},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3906277120113373},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10098785161972046},{"id":"https://openalex.org/C169590947","wikidata":"https://www.wikidata.org/wiki/Q47506","display_name":"Compiler","level":2,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/3592979.3593403","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3592979.3593403","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Platform for Advanced Scientific Computing Conference","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:2306.11544","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2306.11544","pdf_url":"https://arxiv.org/pdf/2306.11544","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:upcommons.upc.edu:2117/403351","is_oa":true,"landing_page_url":"https://arxiv.org/abs/2306.11544","pdf_url":"https://upcommons.upc.edu/bitstreams/4b1d2746-cec0-49b3-9d5f-fca90abf8de3/download","source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Conference lecture"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2306.11544","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2306.11544","pdf_url":"https://arxiv.org/pdf/2306.11544","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"score":0.4099999964237213,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4381586533.pdf"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W114182254","https://openalex.org/W1893942944","https://openalex.org/W1950832899","https://openalex.org/W1955228981","https://openalex.org/W1967961367","https://openalex.org/W1988888548","https://openalex.org/W2014579090","https://openalex.org/W2091894263","https://openalex.org/W2099772777","https://openalex.org/W2119410416","https://openalex.org/W2124677924","https://openalex.org/W2139745270","https://openalex.org/W2141204041","https://openalex.org/W2154599522","https://openalex.org/W2160135160","https://openalex.org/W2551375131","https://openalex.org/W2591529598","https://openalex.org/W2691733701","https://openalex.org/W2759285908","https://openalex.org/W2795780752","https://openalex.org/W2911948847","https://openalex.org/W2914651956","https://openalex.org/W2949797623","https://openalex.org/W2951856423","https://openalex.org/W2953317739","https://openalex.org/W2969609976","https://openalex.org/W2995326322","https://openalex.org/W3011439212","https://openalex.org/W3012553271","https://openalex.org/W3025498066","https://openalex.org/W3043480970","https://openalex.org/W3148709032","https://openalex.org/W3199089929","https://openalex.org/W3200584885","https://openalex.org/W3203423444","https://openalex.org/W4205879534","https://openalex.org/W4226048073","https://openalex.org/W4388035307"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2013643406","https://openalex.org/W2027972911","https://openalex.org/W2157978810","https://openalex.org/W2597809628","https://openalex.org/W4311687867"],"abstract_inverted_index":{"This":[0],"work":[1],"presents":[2],"a":[3,10,31],"comprehensive":[4],"performance":[5,22],"analysis":[6,23],"and":[7,24,30,63,74],"optimization":[8],"of":[9,36,44],"multiscale":[11],"agent-based":[12],"cellular":[13],"simulation.":[14],"The":[15,34],"optimizations":[16],"applied":[17],"are":[18],"guided":[19],"by":[20,47],"detailed":[21],"include":[25],"memory":[26],"management,":[27],"load":[28],"balance,":[29],"locality-aware":[32],"parallelization.":[33],"outcome":[35],"this":[37],"paper":[38],"is":[39],"not":[40],"only":[41],"the":[42,48,54,60,80],"speedup":[43],"2.4x":[45],"achieved":[46],"optimized":[49],"version":[50],"with":[51],"respect":[52],"to":[53,71],"original":[55],"PhysiCell":[56],"code,":[57],"but":[58],"also":[59],"lessons":[61],"learned":[62],"best":[64],"practices":[65],"when":[66],"developing":[67],"parallel":[68],"HPC":[69],"codes":[70],"obtain":[72],"efficient":[73],"highly":[75],"performant":[76],"applications,":[77],"especially":[78],"in":[79],"computational":[81],"biology":[82],"field.":[83]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
