{"id":"https://openalex.org/W4391484352","doi":"https://doi.org/10.1007/s11227-023-05884-y","title":"Out of kernel tuning and optimizations for portable large-scale docking experiments on GPUs","display_name":"Out of kernel tuning and optimizations for portable large-scale docking experiments on GPUs","publication_year":2024,"publication_date":"2024-02-02","ids":{"openalex":"https://openalex.org/W4391484352","doi":"https://doi.org/10.1007/s11227-023-05884-y"},"language":"en","primary_location":{"id":"doi:10.1007/s11227-023-05884-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11227-023-05884-y","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11227-023-05884-y.pdf","source":{"id":"https://openalex.org/S32326811","display_name":"The Journal of Supercomputing","issn_l":"0920-8542","issn":["0920-8542","1573-0484"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Supercomputing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s11227-023-05884-y.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055263185","display_name":"Gianmarco Accordi","orcid":"https://orcid.org/0000-0001-8023-2108"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Gianmarco Accordi","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059293847","display_name":"Davide Gadioli","orcid":"https://orcid.org/0000-0002-0143-0737"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Davide Gadioli","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102612803","display_name":"Emanele Vitali","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150043","display_name":"CSC - IT Center for Science (Finland)","ror":"https://ror.org/04m8m1253","country_code":"FI","type":"company","lineage":["https://openalex.org/I4210150043"]},{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["FI","IT"],"is_corresponding":false,"raw_author_name":"Emanele Vitali","raw_affiliation_strings":["CSC - IT Center for Science, Espoo, Finland","Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CSC - IT Center for Science, Espoo, Finland","institution_ids":["https://openalex.org/I4210150043"]},{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085033505","display_name":"Luigi Crisci","orcid":"https://orcid.org/0000-0002-6095-1321"},"institutions":[{"id":"https://openalex.org/I131729948","display_name":"University of Salerno","ror":"https://ror.org/0192m2k53","country_code":"IT","type":"education","lineage":["https://openalex.org/I131729948"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Luigi Crisci","raw_affiliation_strings":["Dipartimento di Informatica, Universit\u00e0 degli studi di Salerno, Salerno, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica, Universit\u00e0 degli studi di Salerno, Salerno, Italy","institution_ids":["https://openalex.org/I131729948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031619277","display_name":"Biagio Cosenza","orcid":"https://orcid.org/0000-0002-8869-6705"},"institutions":[{"id":"https://openalex.org/I131729948","display_name":"University of Salerno","ror":"https://ror.org/0192m2k53","country_code":"IT","type":"education","lineage":["https://openalex.org/I131729948"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Biagio Cosenza","raw_affiliation_strings":["Dipartimento di Informatica, Universit\u00e0 degli studi di Salerno, Salerno, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica, Universit\u00e0 degli studi di Salerno, Salerno, Italy","institution_ids":["https://openalex.org/I131729948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032283822","display_name":"Andrea R. Beccari","orcid":"https://orcid.org/0000-0001-6830-2695"},"institutions":[{"id":"https://openalex.org/I4210140932","display_name":"Domp\u00e9 (Italy)","ror":"https://ror.org/04erezm33","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210140932"]},{"id":"https://openalex.org/I4210141307","display_name":"Farmaceutici Damor (Italy)","ror":"https://ror.org/04cd7aa36","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210141307"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Beccari","raw_affiliation_strings":["Domp\u00e9 Farmaceutici S.p.A, Naples, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Domp\u00e9 Farmaceutici S.p.A, Naples, Italy","institution_ids":["https://openalex.org/I4210141307","https://openalex.org/I4210140932"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077005193","display_name":"Gianluca Palermo","orcid":"https://orcid.org/0000-0001-7955-8012"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gianluca Palermo","raw_affiliation_strings":["Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy","institution_ids":["https://openalex.org/I93860229"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5055263185"],"corresponding_institution_ids":["https://openalex.org/I93860229"],"apc_list":{"value":2390,"currency":"EUR","value_usd":2990},"apc_paid":{"value":2390,"currency":"EUR","value_usd":2990},"fwci":1.3741,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.77918687,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"80","issue":"8","first_page":"11798","last_page":"11815"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9995999932289124,"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9905999898910522,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9815000295639038,"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/computer-science","display_name":"Computer science","score":0.9038108587265015},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6337389945983887},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.5300673842430115},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.48104479908943176}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.9038108587265015},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6337389945983887},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5300673842430115},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.48104479908943176},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/s11227-023-05884-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11227-023-05884-y","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11227-023-05884-y.pdf","source":{"id":"https://openalex.org/S32326811","display_name":"The Journal of Supercomputing","issn_l":"0920-8542","issn":["0920-8542","1573-0484"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Supercomputing","raw_type":"journal-article"},{"id":"pmh:oai:re.public.polimi.it:11311/1260021","is_oa":true,"landing_page_url":"https://hdl.handle.net/11311/1260021","pdf_url":"https://re.public.polimi.it/bitstream/11311/1260021/1/Out%20of%20kernel%20tuning%20and%20optimizations%20for%20portable%20large%e2%80%90scale%20docking%20experiments%20on%20GPUs.pdf","source":{"id":"https://openalex.org/S4306400312","display_name":"Virtual Community of Pathological Anatomy (University of Castilla La Mancha)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79189158","host_organization_name":"University of Castilla-La Mancha","host_organization_lineage":["https://openalex.org/I79189158"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1007/s11227-023-05884-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s11227-023-05884-y","pdf_url":"https://link.springer.com/content/pdf/10.1007/s11227-023-05884-y.pdf","source":{"id":"https://openalex.org/S32326811","display_name":"The Journal of Supercomputing","issn_l":"0920-8542","issn":["0920-8542","1573-0484"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Supercomputing","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.7200000286102295}],"awards":[{"id":"https://openalex.org/G180123996","display_name":null,"funder_award_id":"956137","funder_id":"https://openalex.org/F1100377486","funder_display_name":"European High Performance Computing Joint Undertaking"},{"id":"https://openalex.org/G4155013421","display_name":null,"funder_award_id":"956137","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F1100377486","display_name":"European High Performance Computing Joint Undertaking","ror":null},{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320324039","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4391484352.pdf"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1516402388","https://openalex.org/W1984993578","https://openalex.org/W1993320379","https://openalex.org/W2002555321","https://openalex.org/W2038258350","https://openalex.org/W2042984424","https://openalex.org/W2051838840","https://openalex.org/W2068859599","https://openalex.org/W2107063279","https://openalex.org/W2149381887","https://openalex.org/W2258884006","https://openalex.org/W2306144962","https://openalex.org/W2326224252","https://openalex.org/W2512339600","https://openalex.org/W2578119541","https://openalex.org/W3015498000","https://openalex.org/W3138526880","https://openalex.org/W3195571629","https://openalex.org/W3214514279","https://openalex.org/W3215053647","https://openalex.org/W4206943884","https://openalex.org/W4225270742","https://openalex.org/W4280550952","https://openalex.org/W4285798101","https://openalex.org/W4286655745","https://openalex.org/W4308968707","https://openalex.org/W4366732651","https://openalex.org/W4389955385"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2405661381"],"abstract_inverted_index":{"Abstract":[0],"Virtual":[1],"screening":[2,41,108],"is":[3,31],"an":[4,45,105],"early":[5],"stage":[6],"in":[7,26,35,47,180,192,214],"the":[8,14,19,27,36,48,55,86,96,123,195,202,208],"drug":[9],"discovery":[10],"process":[11],"that":[12,112,146],"selects":[13],"most":[15],"promising":[16],"candidates.":[17],"In":[18,61],"urgent":[20],"computing":[21],"scenario,":[22],"finding":[23,58],"a":[24,39,59,135,148],"solution":[25],"shortest":[28],"time":[29],"frame":[30],"critical.":[32],"Any":[33],"improvement":[34],"performance":[37,162],"of":[38,50,57,92,142],"virtual":[40,107],"application":[42,70],"translates":[43],"into":[44],"increase":[46,160],"number":[49],"candidates":[51],"evaluated,":[52],"thereby":[53],"raising":[54],"probability":[56],"drug.":[60],"this":[62,215],"paper,":[63],"we":[64,67,210],"show":[65,155],"how":[66,156],"can":[68,113,159,198],"improve":[69,95],"throughput":[71],"using":[72],"Out-of-kernel":[73],"optimizations.":[74],"They":[75],"use":[76],"input":[77],"features,":[78],"kernel":[79,87,161],"requirements,":[80],"and":[81,117,182,212],"architectural":[82],"features":[83],"to":[84,94,120,134,173,184],"rearrange":[85],"inputs,":[88],"executing":[89],"them":[90],"out":[91,122],"order,":[93],"computation":[97,124],"efficiency.":[98],"These":[99],"optimizations\u2019":[100],"implementations":[101],"are":[102,132],"designed":[103],"on":[104,115,125],"extreme-scale":[106],"application,":[109,137],"named":[110],"LiGen,":[111],"hinge":[114],"CUDA":[116,181],"SYCL":[118],"kernels":[119],"carry":[121],"modern":[126],"supercomputer":[127],"nodes.":[128],"Even":[129],"if":[130],"they":[131,138],"tailored":[133],"single":[136],"might":[139],"also":[140],"be":[141,199],"interest":[143],"for":[144],"applications":[145],"share":[147],"similar":[149],"design":[150],"pattern.":[151],"The":[152],"experimental":[153],"results":[154],"these":[157],"optimizations":[158],"by":[163,207],"2":[164],"$$\\times$$":[165,175,186],"<mml:math":[166,176,187],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\">":[167,177,188],"<mml:mo>\u00d7</mml:mo>":[168,178,189],"</mml:math>":[169,179,190],",":[170,191],"respectively,":[171],"up":[172,183],"2.2":[174],"1.9":[185],"SYCL.":[193],"Moreover,":[194],"reported":[196,213],"speedup":[197],"achieved":[200],"with":[201],"best-proposed":[203],"parameterization,":[204],"as":[205],"shown":[206],"data":[209],"collected":[211],"manuscript.":[216]},"counts_by_year":[{"year":2024,"cited_by_count":3}],"updated_date":"2026-05-23T08:51:43.019350","created_date":"2025-10-10T00:00:00"}
