用SpiniFEL进行单粒子成像实验的三维结构测定的标度和加速
Scaling and Acceleration of Three-dimensional Structure Determination for Single-Particle Imaging Experiments with SpiniFEL
摘要：
直线加速器相干光源（LCLS）是一种X射线自由电子激光（XFEL）设备，可用于研究单个大分子的结构和动力学。一项重大升级将使X射线源的重复率从每秒120个脉冲提高到100万个脉冲。处理相应的数据速率将需要Exascale高性能计算（HPC）能力。我们提出了SpiniFEL，用于单粒子成像（SPI）实验的蛋白质结构测定的应用程序。SPI是一种新兴的技术，通过超越辐射损伤来对单个蛋白质和其他大分子复合物进行成像，它摆脱了结晶的需要（这对某些蛋白质来说是困难的），并允许在接近环境条件下对分子动力学进行成像。SpiniFEL正在开发中，可以在实验进行时在超级计算机上近乎实时地运行，因此有关数据的反馈可以指导数据收集策略。我们在这里描述我们如何重新制定的数学框架，并行实现和加速应用程序的计算密集型部分。我们还描述了Pygion的使用，这是一个用于Legion基于任务的编程模型的Python接口，并与我们现有的MPI + GPU实现进行比较。
英文摘要：
The Linac Coherent Light Source (LCLS) is an X- ray free electron laser (XFEL) facility enabling the study of the structure and dynamics of single macromolecules. A major upgrade will bring the repetition rate of the X-ray source from 120 to 1 million pulses per second. Exascale high performance computing (HPC) capabilities will be required to process the corresponding data rates. We present SpiniFEL, an application used for structure determination of proteins from single-particle imaging (SPI) experiments. An emerging technique for imaging individual proteins and other large molecular complexes by outrunning radiation damage, SPI breaks free from the need for crystallization (which is difficult for some proteins) and allows for imaging molecular dynamics at near ambient conditions. SpiniFEL is being developed to run on supercomputers in near real-time while an experiment is taking place, so that the feedback about the data can guide the data collection strategy. We describe here how we reformulated the mathematical framework for parallelizable implementation and accelerated the most compute intensive parts of the application. We also describe the use of Pygion, a Python interface for the Legion task-based programming model and compare to our existing MPI+GPU implementation.
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