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Linear-scaling self-consistent field calculations based on divide-and-conquer method using resolution-of-identity approximation on graphical processing units
Graphical processing units (GPUs) are emerging in computational chemistry to include Hartree−Fock (HF) methods and electron‐correlation theories. However, ab initio calculations of large molecules face technical difficulties such as slow memory access between central processing unit and GPU and othe...
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Published in: | Journal of computational chemistry 2015-01, Vol.36 (3), p.164-170 |
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container_title | Journal of computational chemistry |
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creator | Yoshikawa, Takeshi Nakai, Hiromi |
description | Graphical processing units (GPUs) are emerging in computational chemistry to include Hartree−Fock (HF) methods and electron‐correlation theories. However, ab initio calculations of large molecules face technical difficulties such as slow memory access between central processing unit and GPU and other shortfalls of GPU memory. The divide‐and‐conquer (DC) method, which is a linear‐scaling scheme that divides a total system into several fragments, could avoid these bottlenecks by separately solving local equations in individual fragments. In addition, the resolution‐of‐the‐identity (RI) approximation enables an effective reduction in computational cost with respect to the GPU memory. The present study implemented the DC‐RI‐HF code on GPUs using math libraries, which guarantee compatibility with future development of the GPU architecture. Numerical applications confirmed that the present code using GPUs significantly accelerated the HF calculations while maintaining accuracy. © 2014 Wiley Periodicals, Inc.
The graphical processing units (GPU) implementations were performed for accelerating the Hartree–Fock (HF) calculations by combining the linear‐scaling divide‐and‐conquer (DC) method with the effective resolution‐of‐the‐identity (RI) technique. The speedups of DC‐RI‐HF on GPU compared with standard HF increased with increasing molecular size because of the sparse density matrix and local diagonalization by the DC method. |
doi_str_mv | 10.1002/jcc.23782 |
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The graphical processing units (GPU) implementations were performed for accelerating the Hartree–Fock (HF) calculations by combining the linear‐scaling divide‐and‐conquer (DC) method with the effective resolution‐of‐the‐identity (RI) technique. The speedups of DC‐RI‐HF on GPU compared with standard HF increased with increasing molecular size because of the sparse density matrix and local diagonalization by the DC method.</description><identifier>ISSN: 0192-8651</identifier><identifier>EISSN: 1096-987X</identifier><identifier>DOI: 10.1002/jcc.23782</identifier><identifier>PMID: 25392975</identifier><identifier>CODEN: JCCHDD</identifier><language>eng</language><publisher>United States: Blackwell Publishing Ltd</publisher><subject>Approximation ; Central processing units ; Cost reduction ; CPUs ; Libraries ; Molecular chemistry ; Numerical analysis</subject><ispartof>Journal of computational chemistry, 2015-01, Vol.36 (3), p.164-170</ispartof><rights>2014 Wiley Periodicals, Inc.</rights><rights>Copyright Wiley Subscription Services, Inc. Jan 30, 2015</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4572-f69eea442a88eb8bef2182c9377a567a7a38ef512a71a78c18bafa0b9ab5a4c33</citedby><cites>FETCH-LOGICAL-c4572-f69eea442a88eb8bef2182c9377a567a7a38ef512a71a78c18bafa0b9ab5a4c33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25392975$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yoshikawa, Takeshi</creatorcontrib><creatorcontrib>Nakai, Hiromi</creatorcontrib><title>Linear-scaling self-consistent field calculations based on divide-and-conquer method using resolution-of-identity approximation on graphical processing units</title><title>Journal of computational chemistry</title><addtitle>J. Comput. Chem</addtitle><description>Graphical processing units (GPUs) are emerging in computational chemistry to include Hartree−Fock (HF) methods and electron‐correlation theories. However, ab initio calculations of large molecules face technical difficulties such as slow memory access between central processing unit and GPU and other shortfalls of GPU memory. The divide‐and‐conquer (DC) method, which is a linear‐scaling scheme that divides a total system into several fragments, could avoid these bottlenecks by separately solving local equations in individual fragments. In addition, the resolution‐of‐the‐identity (RI) approximation enables an effective reduction in computational cost with respect to the GPU memory. The present study implemented the DC‐RI‐HF code on GPUs using math libraries, which guarantee compatibility with future development of the GPU architecture. Numerical applications confirmed that the present code using GPUs significantly accelerated the HF calculations while maintaining accuracy. © 2014 Wiley Periodicals, Inc.
The graphical processing units (GPU) implementations were performed for accelerating the Hartree–Fock (HF) calculations by combining the linear‐scaling divide‐and‐conquer (DC) method with the effective resolution‐of‐the‐identity (RI) technique. The speedups of DC‐RI‐HF on GPU compared with standard HF increased with increasing molecular size because of the sparse density matrix and local diagonalization by the DC method.</description><subject>Approximation</subject><subject>Central processing units</subject><subject>Cost reduction</subject><subject>CPUs</subject><subject>Libraries</subject><subject>Molecular chemistry</subject><subject>Numerical analysis</subject><issn>0192-8651</issn><issn>1096-987X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><recordid>eNp1kcFu1DAURS0EoqWw4AeQJTawcBvbcews0QAD1QgQKio768V5aT1knMFOoPMx_CvOTNsFEisv3rnHfr6EPOfFKS8KcbZ27lRIbcQDcsyLumK10d8fkuOC14KZSvEj8iSldVEUUlXlY3IklKxFrdUx-bPyASGy5KD34Yom7DvmhpB8GjGMtPPYtzQP3dTD6POANpCwpUOgrf_lW2QQ2jnxc8JINzheDy2d0uyKmIZ-mkNs6FhGw-jHHYXtNg43frPXzZ6rCNtrn--geeAw7cNT8GN6Sh510Cd8dnuekG_v310sPrDV5-XHxZsVc6XSgnVVjQhlKcAYbEyDneBGuFpqDarSoEEa7BQXoDlo47hpoIOiqaFRUDopT8irgzc_IO-RRrvxyWHfQ8BhSpZXJRfzb6qMvvwHXQ9TDPl1M6VkWRpVZ-r1gXJxSCliZ7cxbxx3lhd27szmzuy-s8y-uDVOzQbbe_KupAycHYDfvsfd_032fLG4U7JDYm7x5j4B8YettNTKXn5a2uXlxdcv5nxp38q_0Ge0Ng</recordid><startdate>20150130</startdate><enddate>20150130</enddate><creator>Yoshikawa, Takeshi</creator><creator>Nakai, Hiromi</creator><general>Blackwell Publishing Ltd</general><general>Wiley Subscription Services, Inc</general><scope>BSCLL</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>JQ2</scope><scope>7X8</scope></search><sort><creationdate>20150130</creationdate><title>Linear-scaling self-consistent field calculations based on divide-and-conquer method using resolution-of-identity approximation on graphical processing units</title><author>Yoshikawa, Takeshi ; Nakai, Hiromi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4572-f69eea442a88eb8bef2182c9377a567a7a38ef512a71a78c18bafa0b9ab5a4c33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Approximation</topic><topic>Central processing units</topic><topic>Cost reduction</topic><topic>CPUs</topic><topic>Libraries</topic><topic>Molecular chemistry</topic><topic>Numerical analysis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yoshikawa, Takeshi</creatorcontrib><creatorcontrib>Nakai, Hiromi</creatorcontrib><collection>Istex</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Computer Science Collection</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of computational chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yoshikawa, Takeshi</au><au>Nakai, Hiromi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Linear-scaling self-consistent field calculations based on divide-and-conquer method using resolution-of-identity approximation on graphical processing units</atitle><jtitle>Journal of computational chemistry</jtitle><addtitle>J. Comput. Chem</addtitle><date>2015-01-30</date><risdate>2015</risdate><volume>36</volume><issue>3</issue><spage>164</spage><epage>170</epage><pages>164-170</pages><issn>0192-8651</issn><eissn>1096-987X</eissn><coden>JCCHDD</coden><abstract>Graphical processing units (GPUs) are emerging in computational chemistry to include Hartree−Fock (HF) methods and electron‐correlation theories. However, ab initio calculations of large molecules face technical difficulties such as slow memory access between central processing unit and GPU and other shortfalls of GPU memory. The divide‐and‐conquer (DC) method, which is a linear‐scaling scheme that divides a total system into several fragments, could avoid these bottlenecks by separately solving local equations in individual fragments. In addition, the resolution‐of‐the‐identity (RI) approximation enables an effective reduction in computational cost with respect to the GPU memory. The present study implemented the DC‐RI‐HF code on GPUs using math libraries, which guarantee compatibility with future development of the GPU architecture. Numerical applications confirmed that the present code using GPUs significantly accelerated the HF calculations while maintaining accuracy. © 2014 Wiley Periodicals, Inc.
The graphical processing units (GPU) implementations were performed for accelerating the Hartree–Fock (HF) calculations by combining the linear‐scaling divide‐and‐conquer (DC) method with the effective resolution‐of‐the‐identity (RI) technique. The speedups of DC‐RI‐HF on GPU compared with standard HF increased with increasing molecular size because of the sparse density matrix and local diagonalization by the DC method.</abstract><cop>United States</cop><pub>Blackwell Publishing Ltd</pub><pmid>25392975</pmid><doi>10.1002/jcc.23782</doi><tpages>7</tpages></addata></record> |
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subjects | Approximation Central processing units Cost reduction CPUs Libraries Molecular chemistry Numerical analysis |
title | Linear-scaling self-consistent field calculations based on divide-and-conquer method using resolution-of-identity approximation on graphical processing units |
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