Team Including Fellow and Alumnus Wins HPC Prize for COVID-19 Research


An alumnus and a current recipient of the Department of Energy Computational Science Graduate Fellowship (DOE CSGF) are on a team that won a top prize at the Supercomputing 2020 (SC20) conference for its high-performance computing (HPC) research designed to address the COVID-19 pandemic. Another program alumnus placed second in the SC20 student research competition.

James Phillips, a fellow from 1995 to 1999, and fellow Anda Trifan, both of the University of Illinois at Urbana-Champaign (UIUC), are part of the team that won an Association for Computing Machinery Gordon Bell Special Prize for HPC-based COVID-19 research. The award is a new version, for 2020, of the annual Gordon Bell Prize for outstanding achievement in HPC. Both awards were presented Nov. 19 at the closing session of SC20, held virtually this year.

SARS-CoV-2 envelope

Phillips, a senior research programmer at the UIUC-based National Center for Supercomputing Applications, and Trifan are part of a multi-institutional team that developed an artificial intelligence-driven workflow to investigate the workings of the virus spike protein, the main means by which it infects cells. Using the Summit supercomputer at DOE’s Oak Ridge Leadership Computing Facility, the team uncovered aspects of the molecule and its interactions with a protein that lets it enter human cells. The research included a complete model of SARS-CoV-2 containing 305 million atoms. The team used computers at DOE’s Argonne Leadership Computing Facility, the Texas Advanced Computing Center and the San Diego Supercomputer Center to prepare its code to run on Summit.

Trifan, a theoretical and computational biophysics doctoral candidate, started the research earlier this year while on a practicum at Argonne National Laboratory. She’s now a lab intern. Trifan and the team recently received two Impact Argonne Awards from lab leadership for accomplishments related to their COVD-19 HPC project, adding to one they received earlier in the year.

Two DOE CSGF alumni were part of another team vying for the special prize. Another alumnus was on a team that was a finalist for the annual Gordon Bell Prize.

Alumnus Richard Barnes (2015-2019) of the University of California, Berkeley, won second prize in the ACM Student Research competition for his presentation, “Communication-Avoiding Large Graph Algorithms for Flow Modeling.” In the project, Barnes developed a way to accelerate HPC hydrology models that help depict how landscapes evolved.

Image caption: A snapshot of a visualization of the SARS-CoV-2 viral envelope comprising 305 million atoms. Credit: Rommie Amaro, University of California San Diego; Arvind Ramanathan, Argonne National Laboratory.