{"updated":"2025-01-22T23:05:45.320146+00:00","metadata":{"_oai":{"id":"oai:ipsj.ixsq.nii.ac.jp:00017858","sets":["934:1074:1079:1081"]},"path":["1081"],"owner":"1","recid":"17858","title":["フラグメント分子軌道法プログラムABINIT - MPにおける2電子積分ルーチンの高速化ならびに並列化と性能評価"],"pubdate":{"attribute_name":"公開日","attribute_value":"2001-08-15"},"_buckets":{"deposit":"98c1013a-e237-453c-959e-b2346cba8084"},"_deposit":{"id":"17858","pid":{"type":"depid","value":"17858","revision_id":0},"owners":[1],"status":"published","created_by":1},"item_title":"フラグメント分子軌道法プログラムABINIT - MPにおける2電子積分ルーチンの高速化ならびに並列化と性能評価","author_link":["0","0"],"item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"フラグメント分子軌道法プログラムABINIT - MPにおける2電子積分ルーチンの高速化ならびに並列化と性能評価"},{"subitem_title":"Improvement, Parallelization and Performance Evaluation of Routines for Electron Repulsion Integrals in Fragment Molecular Orbital Method Program ABINIT - MP","subitem_title_language":"en"}]},"item_keyword":{"attribute_name":"キーワード","attribute_value_mlt":[{"subitem_subject":"並列アプリケーション・グローバルコンピューティング","subitem_subject_scheme":"Other"}]},"item_type_id":"3","publish_date":"2001-08-15","item_3_text_3":{"attribute_name":"著者所属","attribute_value_mlt":[{"subitem_text_value":"株式会社富士総合研究所"},{"subitem_text_value":"国立医薬品食品衛生研究所"},{"subitem_text_value":"大阪府立大学"},{"subitem_text_value":"産業技術総合研究所"}]},"item_3_text_4":{"attribute_name":"著者所属(英)","attribute_value_mlt":[{"subitem_text_value":"Fuji Research Institute Corporation","subitem_text_language":"en"},{"subitem_text_value":"National Institute of Health Science","subitem_text_language":"en"},{"subitem_text_value":"Osaka Prefecture University","subitem_text_language":"en"},{"subitem_text_value":"National Institute of Advanced Industrial Science and Technology","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/17858/files/IPSJ-THPS4209005.pdf"},"date":[{"dateType":"Available","dateValue":"2003-08-15"}],"format":"application/pdf","billing":["billing_file"],"filename":"IPSJ-THPS4209005.pdf","filesize":[{"value":"185.2 kB"}],"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":"6a354f1f-a5d2-4182-885d-89318cd4a92a","displaytype":"detail","licensetype":"license_note","license_note":"Copyright (c) 2001 by the Information Processing Society of Japan"}]},"item_3_creator_5":{"attribute_name":"著者名","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"稲富雄一"},{"creatorName":"中野, 達也"},{"creatorName":"北浦, 和夫"},{"creatorName":"長嶋, 雲兵"}],"nameIdentifiers":[{}]}]},"item_3_creator_6":{"attribute_name":"著者名(英)","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Yuichi, Inadomi","creatorNameLang":"en"},{"creatorName":"Tatsuya, Nakano","creatorNameLang":"en"},{"creatorName":"Kazuo, Kitaura","creatorNameLang":"en"},{"creatorName":"Umpei, Nagashima","creatorNameLang":"en"}],"nameIdentifiers":[{}]}]},"item_3_source_id_9":{"attribute_name":"書誌レコードID","attribute_value_mlt":[{"subitem_source_identifier":"AA11560614","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_description_7":{"attribute_name":"論文抄録","attribute_value_mlt":[{"subitem_description":"Ab initioフラグメント分子軌道（FMO）法は，巨大分子の電子状態計算を目的として北浦ら（Kitaura，1999）によって提唱された計算手法である．従来の方法では分子サイズの4乗に比例していた計算量が，FMO法では2乗に比例するために，大幅に計算時間が短縮できる．このFMO法においても，最も計算時間がかかるのが2電子積分の計算であるため，本研究では高速に2電子積分を行う計算ルーチンを作成し{?abmp}（Nakano，2000）に組み込んで，その性能評価を行った．HITACHI SR8000（512PU$?times$1GB）で計算を行ったところ，2電子積分の計算速度が4倍から7倍向上した．一方，フラグメント（ペア）内の並列化（細粒度並列化）を行った結果，本ルーチンが90?%前後の高い並列化効率を達成していることが分かった．しかしながら，2電子積分の計算速度が速くなったこともあり，計算コストに対する通信速度の重みが増してしまい，SR8000では細粒度並列化による大幅な実行時間の短縮が観測されなかった．","subitem_description_type":"Other"}]},"item_3_description_8":{"attribute_name":"論文抄録(英)","attribute_value_mlt":[{"subitem_description":"Ab initio fragment molecular orbital (FMO) method is a computational technique proposed by Kitaura, et al. (1999) to calculate the electronic structure for large molecule such as polypeptide. The computation cost proportionally to fourth power of the molecular size in the use of conventional method becomes proportional to its square when the FMO method is used, and the FMO method can dramatically shorten the computation time. Since the evaluation of the electron repulsion integrals (ERIs) is still most time-consuming step even in the FMO calculations, we implemented the routines for the fast ERI calculation, embedded them in the ABINIT-MP program (Nakano, 2000) and carried out the performance evaluation of them. As the results of the calculation on the HITACHI SR8000 (512PU x 1GB), the ERI computation speed becomes faster by 4 縲鰀 7 times than original program. On the other hand, the parallel ERI computation (fine-grained parallelization) achieved high parallelization efficiency of more about 90%. However, the weight of the communication cost becomes relatively large to the computation cost because of the shortening of the ERI evaluation time, and the dramatic improvement of the computation time in employing the fine-grained parallelization could not be observed on the SR8000.\"","subitem_description_type":"Other"}]},"item_3_biblio_info_10":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicPageEnd":"35","bibliographic_titles":[{"bibliographic_title":"情報処理学会論文誌ハイパフォーマンスコンピューティングシステム（HPS） "}],"bibliographicPageStart":"28","bibliographicIssueDates":{"bibliographicIssueDate":"2001-08-15","bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"SIG09(HPS3)","bibliographicVolumeNumber":"42"}]},"relation_version_is_last":true,"weko_creator_id":"1"},"created":"2025-01-18T22:50:44.781457+00:00","id":17858,"links":{}}