Antoine Dujardin
SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA

Elliott Slaugther
SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA

Jeffrey Donatelli
Department of Applied Mathematics, Lawrence Berkeley National Laboratory, Berkeley, CA USA 94720-8142
Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA USA 94720-8142

Peter Zwart
Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA 94720-8142
Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley, CA USA 94720-8142

Amedeo Perazzo
SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA

Chun Hong Yoon
SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA

Video: https://youtu.be/IYADjGOiJhA

Abstract

The Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory is an X-ray Free Electron Laser (X-FEL) facility enabling scientists to take snapshots of single macromolecules to study their structure and dynamics. A major LCLS upgrade, LCLS-II, will bring the repetition rate of the X-ray source from 120 to 1 million pulses per second and exascale High Performance Computing (HPC) capabilities will be required for the data analysis to keep up with the future data taking rates.

We present here a Python application for Fluctuation X-ray Scattering (FXS), an emerging technique for analyzing biomolecular structure from the angular correlations of FEL diffraction snapshots with one or more particles in the beam. This FXS application for experimental data analysis is being developed to run on supercomputers in near real-time while an experiment is taking place.

We discuss how we accelerated the most compute intensive parts of the application and how we used Pygion, a Python interface for the Legion task-based programming model, to parallelize and scale the application.

Keywords

fluctuation x-ray scattering, free electron laser, real-time analysis, coherent diffractive imaging

DOI

10.25080/Majora-342d178e-003

Bibtex entry

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Copyright © 2020 Antoine Dujardin et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.