In this paper, we present an all-core implementation of Burrows Wheeler Compression algorithm that exploits all computing resources on a system. Our focus is to provide significant benefit to everyday users on common end-to-end applications by exploiting the parallelism of multiple CPU cores and many-core GPU on their machines. The all-core framework is suitable for problems that process large files or buffers in blocks. We consider a system to be made up of compute stations and use a work-queue to dynamically divide the tasks among them. Each compute station uses an implementation that optimally exploits its architecture. We develop a fast GPU BWC algorithm by extending the state-of-the-art GPU string sort to efficiently perform BWT step of BWC. Our hybrid BWC implementation achieves a 2.9x speedup over the best CPU implementation. Our all-core framework allows concurrent processing of blocks by both GPU and all available CPU cores. We achieve a 3.06x speedup by using all CPU cores and a 4.87x speedup using the GPU also in the all-core framework. Our approach will scale to the number and type of computing resources on a system.<\/p>\n","protected":false},"excerpt":{"rendered":"
In this paper, we present an all-core implementation of Burrows Wheeler Compression algorithm that exploits all computing resources on a system. Our focus is to provide significant benefit to everyday users on common end-to-end applications by exploiting the parallelism of multiple CPU cores and many-core GPU on their machines. The all-core framework is suitable for […]<\/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":[36,11,89,3],"tags":[1787,832,1782,14,20,234,974,964,176,1506],"class_list":["post-11879","post","type-post","status-publish","format-standard","hentry","category-algorithms","category-computer-science","category-nvidia-cuda","category-paper","tag-algorithms","tag-compression","tag-computer-science","tag-cuda","tag-nvidia","tag-nvidia-geforce-gtx-280","tag-nvidia-geforce-gtx-580","tag-nvidia-quadro-fx-3700","tag-package","tag-thrust"],"views":3326,"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/11879","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=11879"}],"version-history":[{"count":0,"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/11879\/revisions"}],"wp:attachment":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=11879"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=11879"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=11879"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}