A GPU Implementation of a Bit-parallel Algorithm for Computing Longest Common Subsequence

• Item type: SIG Technical Reports(1)
• 公開日: 2014-02-24
• タイトル: A GPU Implementation of a Bit-parallel Algorithm for Computing Longest Common Subsequence
• タイトル / 言語: en
• タイトル: A GPU Implementation of a Bit-parallel Algorithm for Computing Longest Common Subsequence
• 言語: eng
• 資源タイプ / 資源タイプ識別子: http://purl.org/coar/resource_type/c_18gh
• 資源タイプ: technical report
• 著者所属: Osaka Prefecture University
• 著者所属: Osaka Prefecture University
• 著者所属(英): en
• 著者所属(英): Osaka Prefecture University
• 著者所属(英): en
• 著者所属(英): Osaka Prefecture University
• 著者名: Katsuya, Kawanami; Noriyuki, Fujimoto
• 著者名(英): Katsuya, Kawanami; Noriyuki, Fujimoto
• 論文抄録 / 内容記述タイプ: Other
• 論文抄録 / 内容記述: The longest common subsequence (LCS for short) for given two strings has various applications, e.g. comparison of DNAs. In the paper, we propose a GPU algorithm to accelerate Hirschberg's LCS algorithm improved with Crochemore et al.'s bit-parallel algorithm. Crochemore et al.'s algorithm includes bitwise logical operators, which can be easily computed in parallel because they have bitwise parallelism. However, Crochemore et al.'s algorithm also includes an operator with less parallelism, i.e. an arithmetic sum. In the paper, we focus on how to implement these operators efficiently in parallel and experimentally show the following results. First, the proposed GPU algorithm with 2.67 GHz Intel Core i7 920 CPU and GeForce GTX 580 GPU runs maximum 15.14 times faster than the bit-parallel CPU algorithm using a single core with 2.67 GHz Intel Xeon X5550 CPU. Next, the proposed GPU algorithm runs maximum 4.09 times faster than the bit-parallel CPU algorithm using four cores with 2.67 GHz Intel Xeon X5550 CPU. Furthermore, the proposed algorithm with GeForce 8800 GTX runs 10.9 to 18.1 times faster than Kloetzli et al.'s existing GPU algorithm with the same GPU.
• 論文抄録(英) / 内容記述タイプ: Other
• 論文抄録(英) / 内容記述: The longest common subsequence (LCS for short) for given two strings has various applications, e.g. comparison of DNAs. In the paper, we propose a GPU algorithm to accelerate Hirschberg's LCS algorithm improved with Crochemore et al.'s bit-parallel algorithm. Crochemore et al.'s algorithm includes bitwise logical operators, which can be easily computed in parallel because they have bitwise parallelism. However, Crochemore et al.'s algorithm also includes an operator with less parallelism, i.e. an arithmetic sum. In the paper, we focus on how to implement these operators efficiently in parallel and experimentally show the following results. First, the proposed GPU algorithm with 2.67 GHz Intel Core i7 920 CPU and GeForce GTX 580 GPU runs maximum 15.14 times faster than the bit-parallel CPU algorithm using a single core with 2.67 GHz Intel Xeon X5550 CPU. Next, the proposed GPU algorithm runs maximum 4.09 times faster than the bit-parallel CPU algorithm using four cores with 2.67 GHz Intel Xeon X5550 CPU. Furthermore, the proposed algorithm with GeForce 8800 GTX runs 10.9 to 18.1 times faster than Kloetzli et al.'s existing GPU algorithm with the same GPU.
• 書誌レコードID / 収録物識別子タイプ: NCID
• 書誌レコードID / 収録物識別子: AN10505667
• 書誌情報: 研究報告数理モデル化と問題解決（MPS）; 巻 2014-MPS-97, 号 12, p. 1-6, 発行日 2014-02-24
• Notice: SIG Technical Reports are nonrefereed and hence may later appear in any journals, conferences, symposia, etc.
• 出版者 / 言語: ja
• 出版者: 情報処理学会