{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,24]],"date-time":"2025-05-24T05:04:22Z","timestamp":1748063062829},"reference-count":14,"publisher":"World Scientific Pub Co Pte Lt","issue":"04","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Parallel Process. Lett."],"published-print":{"date-parts":[[2009,12]]},"abstract":"<jats:p> This paper presents a parallel system capable of accelerating biological sequence alignment on the graphics processing unit (GPU) grid. The GPU grid in this paper is a desktop grid system that utilizes idle GPUs and CPUs in the office and home. Our parallel implementation employs a master-worker paradigm to accelerate an OpenGL-based algorithm that runs on a single GPU. We integrate this implementation into a screensaver-based grid system that detects idle resources on which the alignment code can run. We also show some experimental results comparing our implementation with three different implementations running on a single GPU, a single CPU, or multiple CPUs. As a result, we find that a single non-dedicated GPU can provide us almost the same throughput as two dedicated CPUs in our laboratory environment, where GPU-equipped machines are ordinarily used to develop GPU applications. In a dedicated environment, the GPU-accelerated code achieves five times higher throughput than the CPU-based code. Furthermore, a linear speedup of 30.7X is observed on a 32-node cluster of dedicated GPUs. We also implement a compute unified device architecture (CUDA) based algorithm to demonstrate further acceleration. <\/jats:p>","DOI":"10.1142\/s0129626409000390","type":"journal-article","created":{"date-parts":[[2009,12,14]],"date-time":"2009-12-14T02:52:15Z","timestamp":1260759135000},"page":"513-533","source":"Crossref","is-referenced-by-count":8,"title":["HARNESSING THE POWER OF IDLE GPUS FOR ACCELERATION OF BIOLOGICAL SEQUENCE ALIGNMENT"],"prefix":"10.1142","volume":"19","author":[{"given":"FUMIHIKO","family":"INO","sequence":"first","affiliation":[{"name":"Graduate School of Information Science and Technology, Osaka University, 1-5 Yamada-oka, Suita, 565-0871 Osaka, Japan"}]},{"given":"YUKI","family":"KOTANI","sequence":"additional","affiliation":[{"name":"Graduate School of Information Science and Technology, Osaka University, 1-5 Yamada-oka, Suita, 565-0871 Osaka, Japan"}]},{"given":"YUMA","family":"MUNEKAWA","sequence":"additional","affiliation":[{"name":"Graduate School of Information Science and Technology, Osaka University, 1-5 Yamada-oka, Suita, 565-0871 Osaka, Japan"}]},{"given":"KENICHI","family":"HAGIHARA","sequence":"additional","affiliation":[{"name":"Graduate School of Information Science and Technology, Osaka University, 1-5 Yamada-oka, Suita, 565-0871 Osaka, Japan"}]}],"member":"219","published-online":{"date-parts":[[2011,11,21]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1109\/JPROC.2008.917757"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1467-8659.2007.01012.x"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1145\/882262.882362"},{"key":"rf5","volume-title":"OpenGL Shading Language","author":"Rost R. 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