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IIBMP2014 Lightning Talk - MEGADOCK 4.0

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第3回生命医薬情報学連合大会のライトニングトークのスライドです.
http://iibmp2014.castle104.com/#!_/presentations/11648

Veröffentlicht in: Software
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IIBMP2014 Lightning Talk - MEGADOCK 4.0

  1. 1. MEGADOCK 4.0 an ultra-high-performance protein-protein docking software for heterogeneous supercomputers 1T1-35 (G-06) 大上雅史,下田雄大,鈴木脩司,松崎由理,石田貴士,秋山泰(東工大・情報理工) I I B M P 2 0 1 4 タンパク質ドッキングを1日で100万ペア計算するよ^^ タンパク質ドッキングって何? 2つのタンパク構造から複合体構造を予測する計算のこと なんで1日に100万ペア? タンパク質間相互作用(PPI)ネットワークの予測や、アン サンブルドッキングとかに気軽に応用できるようにする ためには、そのくらい速い計算が必要なんだ。 へぇ、どうやってやるの? GPUスパコンを使うよ
  2. 2. MEGADOCK 4.0 大上雅史 MPI, OpenMP, and CUDA Hybrid Parallelization 東工大TSUBAME 2.5のGPU(1ノードあたり3枚)を全て活用 1ノードフル利用で 84倍高速化 (12CPUコアに対して9.4倍) 1T1-35 (G-06) 世界第13位(2.8 PetaFlops) 17,984 CPUコア,4,258 GPU 1ノード:12CPUコア+3GPU 並列化効率 強スケーリング 97%以上を達成 単一ノードでのGPUによる高速化 複数ノードでの並列化効率
  3. 3. MEGADOCK 4.0 大上雅史1T1-35 (G-06) で、結局100万ペアのドッキングは何時間でできたの? 論文Open Access! ツールOpen Source! www.bi.cs.titech.ac.jp/megadock ノートPCからTSUBAMEまで! I I B M P 2 0 1 4 TSUBAME 2.5の420ノード利用でおよそ12時間だったよ Binding Partner Recognition Test Chemotaxis Pathway Analysis Human Apoptosis Pathway Analysis

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