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Early Career Lighting Talks - A Scalable Multi-Tiered Iterative Phasing Algorithm Using Partitioned Global Address Space (PGAS) Programming For 3D Structure Reconstruction of Biomolecules
Author/Presenter
Event Type
Workshop
Tags
Online Only
Career Development
Diversity Equity Inclusion (DEI)
Education and Training and Outreach
HPC Community Collaboration
Registration Categories
W
TimeSunday, 14 November 20213:30pm - 3:35pm CST
LocationOnline
DescriptionThe 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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