MICA：充分利用英特尔多集成核心架构（MIC）的快速短读对齐器
MICA: A fast short-read aligner that takes full advantage of Intel Many Integrated Core Architecture (MIC)
摘要：
背景：短读对齐器最近通过利用GPU的大规模并行性获得了很大的速度。GPU的一个崛起的替代品是英特尔MIC;像天河2号这样的超级计算机，目前排名前500，是用48,000个MIC板建造的，提供约55 PFLOPS。MIC的类似CPU的架构允许基于CPU的软件轻松并行化;然而，性能通常不如GPU同行，因为MIC板仅包含约60个核心（而GPU板通常具有超过一千个核心）。结果如下：为了更好地利用支持MIC的计算机进行NGS数据分析，我们开发了一种新的短读比对器MICA，该MICA针对MIC的限制和每个MIC核心内部的额外并行性进行了优化。比对150 bp双端读段的实验表明，使用一个MIC板的MICA比BWA-MEM（使用高端CPU的6核）快4.9倍，比SOAP 3-dp（使用GPU）略快。此外，MICA的简单性允许在一个节点中使用多个MIC板时非常有效地扩展（3个卡比BWA-MEM提供14.1倍的加速）。摘要：MICA可以很容易地被支持MIC的超级计算机用于生产目的。我们已经在天河二号上测试了90个WGS样本（17.47 Tera基）的MICA，这些样本可以在一小时内对齐不到400个节点。MICA具有令人印象深刻的性能，尽管当前的MIC处于开发的初始阶段（下一代MIC已宣布将于2014年底发布）。
英文摘要：
Background: Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alternative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built with 48,000 MIC boards to offer ~55 PFLOPS. The CPU-like architecture of MIC allows CPU-based software to be parallelized easily; however, the performance is often inferior to GPU counterparts as an MIC board contains only ~60 cores (while a GPU board typically has over a thousand cores). Results: To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MICs limitation and the extra parallelism inside each MIC core. Experiments on aligning 150bp paired-end reads show that MICA using one MIC board is 4.9 times faster than the BWA-MEM (using 6-core of a top-end CPU), and slightly faster than SOAP3-dp (using a GPU). Furthermore, MICAs simplicity allows very efficient scale-up when multiple MIC boards are used in a node (3 cards give a 14.1-fold speedup over BWA-MEM). Summary: MICA can be readily used by MIC-enabled supercomputers for production purpose. We have tested MICA on Tianhe-2 with 90 WGS samples (17.47 Tera-bases), which can be aligned in an hour less than 400 nodes. MICA has impressive performance even though the current MIC is at its initial stage of development (the next generation of MIC has been announced to release in late 2014).
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