GPU Computing Enabled Linux Computer Cluster

描述（由申请人提供）：电子低温显微镜（cryoEM），特别是单粒子cryoEM，在可实现的分辨率方面取得了巨大的成功。现在可以确定具有高对称性的大型蛋白质组装体的近原子结构，例如二十面体病毒。然而，对于大的低对称性蛋白质复合物，实现类似的分辨率仍然是非常困难的。这部分是因为收集非常大的图像数据集的过程非常繁琐，以及处理如此大的数据集对计算能力的巨大需求。我们已经建立了一个独特的易于操作的电子显微镜系统，专门用于促进这一过程（自动采集软件和一个非常大的格式，8 K x 8 K像素数码相机）。在此申请中，我们寻求资金来建立一个支持GPU计算的计算机集群，以快速处理数据。与电子显微镜系统一起，我们的目标是建立一个集成的cryoEM系统，该系统将克服cryoEM在研究没有高度对称性的大蛋白质复合物时的当前分辨率限制。我们的目标是定期收集和处理105 - 106个粒子图像。 拟议的GPU计算机集群将是一个中等规模的GPU-CPU单元集群，每个服务器级头节点与包含四个Tesla GPU处理器的Nvidia S1070 GPU盒连接。它将专用于cryoEM数据集的快速处理，特别是约100万个粒子图像的超大数据集。建立这样一个GPU计算机集群是实现常规单粒子冷冻电镜测定大分子复合物近原子分辨率结构的关键一步。NIH资助的许多生物医学研究项目，特别是那些需要确定大复合物结构的项目，将受益于这种技术进步。所有开发的软件将免费提供。

DESCRIPTION (provided by applicant): Electron cryomicroscopy (cryoEM), particularly single particle cryoEM, has experienced tremendous successes in term of achievable resolution. It is now possible to determine near atomic structures of large protein assemblies with high symmetry, such as icosahedral virus. However, for large protein complex with low symmetry, achieving the similar resolution is still very difficult. This is partly because of the very tedious process of collecting very large datasets of images, and the tremendous demands of computational power to process such large dataset. We have set up a unique easy-to-operate electron microscope system specifically to facilitate this process (automated acquisition software and a very large format, 8K x 8K pixel digital camera). In this application, we seek funds to set up a GPU computing enabled computer cluster for fast data processing. Together with the electron microscope system, we aim to establish an integrated cryoEM system that will overcome the current resolution limitation of cryoEM in studying large protein complexes without high symmetry. Our goal is to routinely collect and process 105 - 106 particle images. The proposed GPU computer cluster will be a medium sized cluster of GPU-CPU units with each server class headnode connected with the just available Nvidia S1070 GPU box containing four Tesla GPU processors. It will be dedicated for fast processing of cryoEM datasets, particularly very large datasets of ~ 1 million particle images. Establish such a GPU computer cluster is a critical step towards routinely determine near atomic resolution structure of macromolecular complex by single particle cryoEM. Many biomedical research projects funded by NIH, particularly those require structural determination of large complexes; will be benefited from such technological advancement. All developed software will be freely provided.