The International Conference for High Performance Computing, Networking, Storage, and Analysis
The International Conference for High Performance Computing, Networking, Storage, and Analysis
Workshop:PAW-ATM 2021: The 4th Annual Parallel Applications Workshop, Alternatives To MPI+X
Authors: Hsing-Yin Chang, Elliott Slaughter, and Seema Mirchandaney (SLAC National Accelerator Laboratory); Jeffrey Donatelli (Lawrence Berkeley National Laboratory); and Chun Hong Yoon (SLAC National Accelerator Laboratory)
Abstract: The Linac Coherent Light Source is an X-ray free electron laser 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 computing capabilities will be required to process the corresponding data rates. We present SpiniFEL, an application for structure determination of proteins from single-particle imaging experiments, an emerging technique which breaks free from the need for crystallization and allows for imaging single molecule at ambient conditions. SpiniFEL is being developed to run on supercomputers to perform near real-time data analysis and guide data collection strategy. We describe how we reformulated the mathematical framework for parallelizable implementation and accelerated 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 its equivalent MPI+GPU implementation.