{"_buckets": {"deposit": "dbb5a8af-5d90-4b62-b5c6-4bd4139fcdbc"}, "_deposit": {"created_by": 17, "id": "2000044", "owner": "17", "owners": [17], "owners_ext": {"displayname": "\u56f3\u66f8\u60c5\u5831\u4fc2", "username": "repository"}, "pid": {"revision_id": 0, "type": "depid", "value": "2000044"}, "status": "published"}, "_oai": {"id": "oai:nagoya.repo.nii.ac.jp:02000044", "sets": []}, "author_link": [], "control_number": "2000044", "item_1615768549627": {"attribute_name": "\u51fa\u7248\u30bf\u30a4\u30d7", "attribute_value_mlt": [{"subitem_version_resource": "http://purl.org/coar/version/c_ab4af688f83e57aa", "subitem_version_type": "AM"}]}, "item_1629683748249": {"attribute_name": "\u65e5\u4ed8", "attribute_value_mlt": [{"subitem_date_issued_datetime": "2022-06-05", "subitem_date_issued_type": "Available"}]}, "item_9_biblio_info_6": {"attribute_name": "\u66f8\u8a8c\u60c5\u5831", "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": "\u5185\u5bb9\u8a18\u8ff0", "attribute_value_mlt": [{"subitem_description": "In the era of exascale supercomputers, large\u2010scale, and long\u2010time 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)\u2010communication in the MPI\u2010parallelized fast multipole method (FMM) combined with MD calculations under three\u2010dimensional 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\u2010transferred data (MTD) method, should enable large\u2010scale and long\u2010time MD calculations to be calculated efficiently, under the condition of massive MPI\u2010parallelization on exascale supercomputers.", "subitem_description_language": "en", "subitem_description_type": "Abstract"}]}, "item_9_publisher_32": {"attribute_name": "\u51fa\u7248\u8005", "attribute_value_mlt": [{"subitem_publisher": "Wiley", "subitem_publisher_language": "en"}]}, "item_9_relation_43": {"attribute_name": "\u95a2\u9023\u60c5\u5831", "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": "\u6a29\u5229", "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\u2013 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": "\u53ce\u9332\u7269\u8b58\u5225\u5b50", "attribute_value_mlt": [{"subitem_source_identifier": "0192-8651", "subitem_source_identifier_type": "PISSN"}]}, "item_access_right": {"attribute_name": "\u30a2\u30af\u30bb\u30b9\u6a29", "attribute_value_mlt": [{"subitem_access_right": "open access", "subitem_access_right_uri": "http://purl.org/coar/access_right/c_abf2"}]}, "item_creator": {"attribute_name": "\u8457\u8005", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "Andoh, Yoshimichi", "creatorNameLang": "en"}]}, {"creatorNames": [{"creatorName": "Ichikawa,  Shin\u2010ichi", "creatorNameLang": "en"}]}, {"creatorNames": [{"creatorName": "Sakashita, Tatsuya", "creatorNameLang": "en"}]}, {"creatorNames": [{"creatorName": "Yoshii, Noriyuki", "creatorNameLang": "en"}]}, {"creatorNames": [{"creatorName": "Okazaki, Susumu", "creatorNameLang": "en"}]}]}, "item_files": {"attribute_name": "\u30d5\u30a1\u30a4\u30eb\u60c5\u5831", "attribute_type": "file", "attribute_value_mlt": [{"accessrole": "open_date", "date": [{"dateType": "Available", "dateValue": "2022-06-05"}], "displaytype": "detail", "download_preview_message": "", "file_order": 0, "filename": "JCC_mtd_final.pdf", "filesize": [{"value": "3.8 MB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_free", "mimetype": "application/pdf", "size": 3800000.0, "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": "\u30ad\u30fc\u30ef\u30fc\u30c9", "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": "\u8a00\u8a9e", "attribute_value_mlt": [{"subitem_language": "eng"}]}, "item_resource_type": {"attribute_name": "\u8cc7\u6e90\u30bf\u30a4\u30d7", "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": "\u30bf\u30a4\u30c8\u30eb", "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": ["320/321/322"], "permalink_uri": "http://hdl.handle.net/2237/0002000044", "pubdate": {"attribute_name": "PubDate", "attribute_value": "2021-05-18"}, "publish_date": "2021-05-18", "publish_status": "0", "recid": "2000044", "relation": {}, "relation_version_is_last": true, "title": ["Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations"], "weko_shared_id": -1}