Multithreaded parallelization of the energy and analytic gradient in the fragment molecular orbital method

Mironov Vladimir; Alexeev Yuri; Fedorov Dmitri G.

摘要

Abstract >The fragment molecular orbital method in GAMESS is parallelized in a multithreaded OpenMP implementation combined with the MPI version of the two‐level generalized distributed data interface. The energy and analytic gradient in gas phase and the polarizable continuum model of solvation are parallelized in this hybrid three‐level scheme, achieving a large memory footprint reduction and a high parallel efficiency on Intel Xeon Phi processors. The parallel efficiency is demonstrated on the Stampede2 and Theta supercomputers using up to 2048 nodes (262?144 threads). </abstract> </span> <span class="z_kbtn z_kbtnclass hoverxs" style="display: none;">展开▼</span> </div> <div class="translation abstracttxt"> <span class="zhankaihshouqi fivelineshidden" id="abstract"> <span>机译：</span><Abstract Type =“Main”XML：Lang =“en”> <标题类型=“main”>抽象</ title> >游戏中的片段分子轨道方法在多线程的OpenMP实现中并行化与MPI版本相结合两个级别广泛的分布式数据接口。气相中的能量和分析梯度和可极化的连续体溶剂化模型在这种混合三级方案中并行化，在英特尔Xeon Phi处理器上实现了大的内存占用减少和高并行效率。使用多达2048个节点（262×144线程），在Stampede2和Theta超级计算机上演示了并行效率。</ p> </ abstract> </span> <span class="z_kbtn z_kbtnclass hoverxs" style="display: none;">展开▼</span> </div> </div> <div class="record"> <h2 class="all_title" id="enpatent33" >著录项</h2> <ul> <li> <span class="lefttit">来源</span> <div style="width: 86%;vertical-align: text-top;display: inline-block;"> <a href='/journal-foreign-21753/'>《International Journal of Quantum Chemistry》</a> <b style="margin: 0 2px;">|</b><span>2019年第12期</span><b style="margin: 0 2px;">|</b><span>共14页</span> </div> </li> <li> <div class="author"> <span class="lefttit">作者</span> <p id="fAuthorthree" class="threelineshidden zhankaihshouqi"> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Mironov Vladimir&option=202" target="_blank" rel="nofollow">Mironov Vladimir;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Alexeev Yuri&option=202" target="_blank" rel="nofollow">Alexeev Yuri;</a> <a href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=Fedorov Dmitri G.&option=202" target="_blank" rel="nofollow">Fedorov Dmitri G.;</a> </p> <span class="z_kbtnclass z_kbtnclassall hoverxs" id="zkzz" style="display: none;">展开▼</span> </div> </li> <li> <div style="display: flex;"> <span class="lefttit">作者单位</span> <div style="position: relative;margin-left: 3px;max-width: 639px;"> <div class="threelineshidden zhankaihshouqi" id="fOrgthree"> <p>Department of ChemistryLomonosov Moscow State UniversityMoscow Russia;</p> <p>Computational Science DivisionArgonne National LaboratoryArgonne Illinois;</p> <p>Research Center for Computational Design of Advanced Functional Materials (CD‐FMat)National Institute of Advanced Industrial Science and TechnologyTsukuba Japan;</p> </div> <span class="z_kbtnclass z_kbtnclassall hoverxs" id="zhdw" style="display: none;">展开▼</span> </div> </div> </li> <li > <span class="lefttit">收录信息</span> <span style="width: 86%;vertical-align: text-top;display: inline-block;"></span> </li> <li> <span class="lefttit">原文格式</span> <span>PDF</span> </li> <li> <span class="lefttit">正文语种</span> <span>eng</span> </li> <li> <span class="lefttit">中图分类</span> <span><a href="https://www.zhangqiaokeyan.com/clc/1186.html" title="物理化学（理论化学）、化学物理学">物理化学（理论化学）、化学物理学;</a></span> </li> <li class="antistop"> <span class="lefttit">关键词</span> <p style="width: 86%;vertical-align: text-top;"> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=DDI&option=203" rel="nofollow">DDI;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=FMO&option=203" rel="nofollow">FMO;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=GAMESS&option=203" rel="nofollow">GAMESS;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=MPI&option=203" rel="nofollow">MPI;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=OpenMP&option=203" rel="nofollow">OpenMP;</a> <a style="color: #3E7FEB;" href="/search.html?doctypes=4_5_6_1-0_4-0_1_2_3_7_9&sertext=parallelization&option=203" rel="nofollow">parallelization;</a> </p> <div class="translation"> 机译：DDI;FMO;游戏;MPI;OPENMP;并行化; </div> </li> </ul> </div> </div> <div class="literature cardcommon"> <div class="similarity "> <h3 class="all_title" id="enpatent66">相似文献</h3> <div class="similaritytab 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