{"id":16682,"date":"2016-11-03T23:05:30","date_gmt":"2016-11-03T21:05:30","guid":{"rendered":"http:\/\/hgpu.org\/?p=16682"},"modified":"2016-11-03T23:30:37","modified_gmt":"2016-11-03T21:30:37","slug":"a-hybrid-algorithm-for-parallel-molecular-dynamics-simulations","status":"publish","type":"post","link":"https:\/\/hgpu.org\/?p=16682","title":{"rendered":"A hybrid algorithm for parallel molecular dynamics simulations"},"content":{"rendered":"<p>This article describes an algorithm for hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-ranged forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with AVX and AVX-2 processors as well as Xeon-Phi co-processors.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>This article describes an algorithm for hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-ranged forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds [&hellip;]<\/p>\n","protected":false},"author":351,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[3,12],"tags":[196,1483,166,112],"class_list":["post-16682","post","type-post","status-publish","format-standard","hentry","category-paper","category-physics","tag-condensed-matter","tag-intel-xeon-phi","tag-materials-science","tag-molecular-dynamics"],"views":2348,"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/16682","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/users\/351"}],"replies":[{"embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=16682"}],"version-history":[{"count":1,"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/16682\/revisions"}],"predecessor-version":[{"id":16686,"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/16682\/revisions\/16686"}],"wp:attachment":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16682"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16682"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16682"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}