In drug discovery, molecular docking is the task in charge of estimating the position of a molecule when interacting with the docking site. This task is usually used to perform screening of a large library of molecules, in the early phase of the process. Given the amount of candidate molecules and the complexity of the application, this task is usually performed using High-Performance Computing (HPC) platforms. In modern HPC systems, heterogeneous platforms provide a better throughput with respect to homogeneous platforms. In this work, we ported and optimized a molecular docking application to a heterogeneous system, with one or more GPU accelerators, leveraging a hybrid OpenMP and OpenACC approach. We prove that our approach has a better exploitation of the node compared to pure CPU\/GPU data splitting approaches, reaching a throughput improvement up to 36% while considering the same computing node.<\/p>\n","protected":false},"excerpt":{"rendered":"
In drug discovery, molecular docking is the task in charge of estimating the position of a molecule when interacting with the docking site. This task is usually used to perform screening of a large library of molecules, in the early phase of the process. Given the amount of candidate molecules and the complexity of the […]<\/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":[11,89,3],"tags":[1782,14,452,1682,1588,242,20,1321,252,1740],"class_list":["post-18730","post","type-post","status-publish","format-standard","hentry","category-computer-science","category-nvidia-cuda","category-paper","tag-computer-science","tag-cuda","tag-heterogeneous-systems","tag-hpc","tag-molecular-docking","tag-mpi","tag-nvidia","tag-openacc","tag-openmp","tag-tesla-k80"],"views":2482,"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/18730","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=18730"}],"version-history":[{"count":0,"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/18730\/revisions"}],"wp:attachment":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=18730"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=18730"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=18730"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}