{"created":"2021-05-18T04:14:19.097793+00:00","id":2000044,"links":{},"metadata":{"_buckets":{"deposit":"dbb5a8af-5d90-4b62-b5c6-4bd4139fcdbc"},"_deposit":{"created_by":17,"id":"2000044","owner":"17","owners":[17],"owners_ext":{"displayname":"図書情報係","username":"repository"},"pid":{"revision_id":0,"type":"depid","value":"2000044"},"status":"published"},"_oai":{"id":"oai:nagoya.repo.nii.ac.jp:02000044","sets":["320:321:322"]},"author_link":[],"control_number":"2000044","item_1615768549627":{"attribute_name":"出版タイプ","attribute_value_mlt":[{"subitem_version_resource":"http://purl.org/coar/version/c_ab4af688f83e57aa","subitem_version_type":"AM"}]},"item_1629683748249":{"attribute_name":"日付","attribute_value_mlt":[{"subitem_date_issued_datetime":"2022-06-05","subitem_date_issued_type":"Available"}]},"item_9_biblio_info_6":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicIssueDates":{"bibliographicIssueDate":"2021-06-05","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"15","bibliographicPageEnd":"1087","bibliographicPageStart":"1073","bibliographicVolumeNumber":"42","bibliographic_titles":[{"bibliographic_title":"Journal of Computational Chemistry","bibliographic_titleLang":"en"}]}]},"item_9_description_4":{"attribute_name":"内容記述","attribute_value_mlt":[{"subitem_description":"In the era of exascale supercomputers, large‐scale, and long‐time molecular dynamics (MD) calculations are expected to make breakthroughs in various fields of science and technology. Here, we propose a new algorithm to improve the parallelization performance of message passing interface (MPI)‐communication in the MPI‐parallelized fast multipole method (FMM) combined with MD calculations under three‐dimensional periodic boundary conditions. Our approach enables a drastic reduction in the amount of communication data, including the atomic coordinates and multipole coefficients, both of which are required to calculate the electrostatic interaction by using the FMM. In communications of multipole coefficients, the reduction rate of communication data in the new algorithm relative to the amount of data in the conventional one increases as both the number of FMM levels and the number of MPI processes increase. The aforementioned rate increase could exceed 50% as the number of MPI processes becomes larger for very large systems. The proposed algorithm, named the minimum‐transferred data (MTD) method, should enable large‐scale and long‐time MD calculations to be calculated efficiently, under the condition of massive MPI‐parallelization on exascale supercomputers.","subitem_description_language":"en","subitem_description_type":"Abstract"}]},"item_9_publisher_32":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"Wiley","subitem_publisher_language":"en"}]},"item_9_relation_43":{"attribute_name":"関連情報","attribute_value_mlt":[{"subitem_relation_type":"isVersionOf","subitem_relation_type_id":{"subitem_relation_type_id_text":"https://doi.org/10.1002/jcc.26524","subitem_relation_type_select":"DOI"}}]},"item_9_rights_12":{"attribute_name":"権利","attribute_value_mlt":[{"subitem_rights":"\"This is the peer reviewed version of the following article: [Andoh, Y, Ichikawa, S, Sakashita, T, Yoshii, N, Okazaki, S. Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations. J Comput Chem. 2021; 42: 1073– 1087. https://doi.org/10.1002/jcc.26524], which has been published in final form at [https://doi.org/10.1002/jcc.26524]. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.\"","subitem_rights_language":"en"}]},"item_9_source_id_7":{"attribute_name":"収録物識別子","attribute_value_mlt":[{"subitem_source_identifier":"0192-8651","subitem_source_identifier_type":"PISSN"}]},"item_access_right":{"attribute_name":"アクセス権","attribute_value_mlt":[{"subitem_access_right":"open access","subitem_access_right_uri":"http://purl.org/coar/access_right/c_abf2"}]},"item_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Andoh, Yoshimichi","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Ichikawa,  Shin‐ichi","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Sakashita, Tatsuya","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Yoshii, Noriyuki","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Okazaki, Susumu","creatorNameLang":"en"}]}]},"item_files":{"attribute_name":"ファイル情報","attribute_type":"file","attribute_value_mlt":[{"accessrole":"open_date","date":[{"dateType":"Available","dateValue":"2022-06-05"}],"displaytype":"detail","filename":"JCC_mtd_final.pdf","filesize":[{"value":"3.8 MB"}],"format":"application/pdf","licensetype":"license_note","mimetype":"application/pdf","url":{"objectType":"fulltext","url":"https://nagoya.repo.nii.ac.jp/record/2000044/files/JCC_mtd_final.pdf"},"version_id":"cb885661-f0b5-419b-9b5d-33cd0ee00c9d"}]},"item_keyword":{"attribute_name":"キーワード","attribute_value_mlt":[{"subitem_subject":"efficient MPI communication","subitem_subject_scheme":"Other"},{"subitem_subject":"exascale supercomputers","subitem_subject_scheme":"Other"},{"subitem_subject":"fast multipole method","subitem_subject_scheme":"Other"},{"subitem_subject":"molecular dynamics calculation","subitem_subject_scheme":"Other"},{"subitem_subject":"MPI parallelization","subitem_subject_scheme":"Other"}]},"item_language":{"attribute_name":"言語","attribute_value_mlt":[{"subitem_language":"eng"}]},"item_resource_type":{"attribute_name":"資源タイプ","attribute_value_mlt":[{"resourcetype":"journal article","resourceuri":"http://purl.org/coar/resource_type/c_6501"}]},"item_title":"Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations","subitem_title_language":"en"}]},"item_type_id":"40001","owner":"17","path":["322"],"pubdate":{"attribute_name":"PubDate","attribute_value":"2021-05-18"},"publish_date":"2021-05-18","publish_status":"0","recid":"2000044","relation_version_is_last":true,"title":["Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations"],"weko_creator_id":"17","weko_shared_id":-1},"updated":"2023-01-16T05:09:31.754636+00:00"}