{"metadata":{"_oai":{"id":"oai:ipsj.ixsq.nii.ac.jp:00107507","sets":["934:1119:7515:7728"]},"path":["7728"],"owner":"11","recid":"107507","title":["1,024GPUを使用したレプリカ交換分子動力学シミュレーションの並列化"],"pubdate":{"attribute_name":"公開日","attribute_value":"2014-12-16"},"_buckets":{"deposit":"82077d0d-4a8f-4fe5-b7f8-3184ced89673"},"_deposit":{"id":"107507","pid":{"type":"depid","value":"107507","revision_id":0},"owners":[11],"status":"published","created_by":11},"item_title":"1,024GPUを使用したレプリカ交換分子動力学シミュレーションの並列化","author_link":["17596","17595","17592","17597","17590","17591","17593","17594"],"item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"1,024GPUを使用したレプリカ交換分子動力学シミュレーションの並列化"},{"subitem_title":"Parallel Molecular Dynamics Simulation with Replica-exchange Method Using 1,024GPUs","subitem_title_language":"en"}]},"item_keyword":{"attribute_name":"キーワード","attribute_value_mlt":[{"subitem_subject":"[高性能計算] Graphics Processing Unit，CUDA，分子動力学シミュレーション，並列化，レプリカ交換法","subitem_subject_scheme":"Other"}]},"item_type_id":"3","publish_date":"2014-12-16","item_3_text_3":{"attribute_name":"著者所属","attribute_value_mlt":[{"subitem_text_value":"慶應義塾大学"},{"subitem_text_value":"慶應義塾大学"},{"subitem_text_value":"慶應義塾大学"},{"subitem_text_value":"電気通信大学"}]},"item_3_text_4":{"attribute_name":"著者所属(英)","attribute_value_mlt":[{"subitem_text_value":"Keio University","subitem_text_language":"en"},{"subitem_text_value":"Keio University","subitem_text_language":"en"},{"subitem_text_value":"Keio University","subitem_text_language":"en"},{"subitem_text_value":"The University of Electro-Communications","subitem_text_language":"en"}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"jpn"}]},"item_publisher":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"情報処理学会","subitem_publisher_language":"ja"}]},"publish_status":"0","weko_shared_id":-1,"item_file_price":{"attribute_name":"Billing file","attribute_type":"file","attribute_value_mlt":[{"url":{"url":"https://ipsj.ixsq.nii.ac.jp/record/107507/files/IPSJ-TACS0704002.pdf"},"date":[{"dateType":"Available","dateValue":"2016-12-16"}],"format":"application/pdf","billing":["billing_file"],"filename":"IPSJ-TACS0704002.pdf","filesize":[{"value":"1.6 MB"}],"mimetype":"application/pdf","priceinfo":[{"tax":["include_tax"],"price":"660","billingrole":"5"},{"tax":["include_tax"],"price":"330","billingrole":"6"},{"tax":["include_tax"],"price":"0","billingrole":"16"},{"tax":["include_tax"],"price":"0","billingrole":"11"},{"tax":["include_tax"],"price":"0","billingrole":"14"},{"tax":["include_tax"],"price":"0","billingrole":"15"},{"tax":["include_tax"],"price":"0","billingrole":"44"}],"accessrole":"open_date","version_id":"bd3f91bf-73b2-4e67-bb13-7322f25a247c","displaytype":"detail","licensetype":"license_note","license_note":"Copyright (c) 2014 by the Information Processing Society of Japan"}]},"item_3_creator_5":{"attribute_name":"著者名","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"老川, 稔"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"野村, 昴太郎"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"泰岡, 顕治"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"成見, 哲"}],"nameIdentifiers":[{}]}]},"item_3_creator_6":{"attribute_name":"著者名(英)","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Minoru, Oikawa","creatorNameLang":"en"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Kentaro, Nomura","creatorNameLang":"en"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Kenji, Yasuoka","creatorNameLang":"en"}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Tetsu, Narumi","creatorNameLang":"en"}],"nameIdentifiers":[{}]}]},"item_3_source_id_9":{"attribute_name":"書誌レコードID","attribute_value_mlt":[{"subitem_source_identifier":"AA11833852","subitem_source_identifier_type":"NCID"}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourceuri":"http://purl.org/coar/resource_type/c_6501","resourcetype":"journal article"}]},"item_3_source_id_11":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"1882-7829","subitem_source_identifier_type":"ISSN"}]},"item_3_description_7":{"attribute_name":"論文抄録","attribute_value_mlt":[{"subitem_description":"CUDA C/C++言語で記述された，シングルノード向けレプリカ交換分子動力学シミュレーションのソースコードにGPU仮想化ソフトウェアを適用し，マルチノード上のGPUに対応した計算並列化を行った．レプリカ交換法は，分子/原子の最安定状態を効率的に求めるために用いられるシミュレーション手法の1つである．計算の粒度が大きく，計算ノード間の通信が少ないという特徴から，分散計算機環境での並列化に向く．本研究では，GPU仮想化ソフトウェアの機能を利用することで，シングルノード向けのソースコードを改変することなくマルチノード用に再利用した．最大1,024台のGPUを使用して計算速度の並列化効率を計測し，1,024並列時において効率87%の良好な結果を得た．また，効率を低下させる要因について定量的に解析し，特に多並列時においてノード間通信のレイテンシが支配的になることが分かった．","subitem_description_type":"Other"}]},"item_3_description_8":{"attribute_name":"論文抄録(英)","attribute_value_mlt":[{"subitem_description":"We parallelized a molecular dynamics simulation software using single-node GPUs to support multi-node GPUs by applying GPU virtualization tool to CUDA C/C++ program. To obtain the global minimum state of molecules efficiently, we used replica-exchange method, which is suitable for parallel computation since it has large granularity and small communication between nodes. The GPU virtualization software enabled us to use a single-node program to support multi-node calculation without any modification. Parallel efficiency with up to 1,024 GPUs are measured and 87% of efficiency was obtained even with 1,024 GPUs. The main reason of losing efficiency for higher parallelism was quantitatively analyzed and we found it mostly the latency between nodes.","subitem_description_type":"Other"}]},"item_3_biblio_info_10":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicPageEnd":"14","bibliographic_titles":[{"bibliographic_title":"情報処理学会論文誌コンピューティングシステム（ACS）"}],"bibliographicPageStart":"1","bibliographicIssueDates":{"bibliographicIssueDate":"2014-12-16","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"4","bibliographicVolumeNumber":"7"}]},"relation_version_is_last":true,"weko_creator_id":"11"},"id":107507,"updated":"2025-01-21T08:59:30.843336+00:00","links":{},"created":"2025-01-18T23:50:40.928885+00:00"}