Two projects that relied on Charm++ have been named finalists for the Gordon Bell Special Prize for High Performance Computing-Based COVID-19. In its second year, the special prize recognizes outstanding research achievement toward the understanding of the COVID-19 pandemic. Both projects use NAMD, which is one of the earliest Charm++ applications.
The first project, led by the University of California San Diego’s Rommie Amaro and a multi-institution team, sought to provide atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Current experimental methods are limited in their ability to study aerosols at the atomic/molecular level, and the work extends the capabilities of multi-scale computational microscopy to address those limits. A full list of team members is available here.
The second, authored by a multi-institutional team including researchers from Argonne National Laboratory and the University of Illinois Urbana-Champaign, considered the COVID-19 replication transcription complex, which is responsible for replicating and transcribing the viral mRNA. Conventional tools do not capture important dynamics of this molecular machine. This study provided an innovative workflow using a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between finite element analysis continuum simulations and all-atom molecular dynamics simulations. A full list of team members is available here.
“COVID-19 has been massively disruptive on a global scale,” said Charmworks CEO Sanjay Kale. “We are proud that Charm++ has had a significant role in understanding the virus, its spread, and prospective treatments, and we’re very impressed by the ways our colleagues have used the tools to combat the pandemic. Congratulations also to the Charm++ and NAMD teams at UIUC and Charmworks for their direct and indirect contributions. ”
About Charm++
Charm++ is a C++ based parallel programming system based on an introspective adaptive runtime system, with many features suitable for addressing upcoming extreme scale as well as mid-scale challenges, and with multiple highly scalable parallel applications such as NAMD, ChaNGa, and OpenAtom. It is developed by the Parallel Programming Laboratory at the University of Illinois Urbana-Champaign.
About Charmworks
Charmworks provides scalable solutions that improve productivity in parallel programming. A commercial version of Charm++, the company’s primary product and core technology, is an adaptive runtime and supporting tools that allows developers to easily incorporate automatic load balancing, fault tolerance, and energy saving features into their codes. Charmworks also offers a suite of software built on top of Charm++, including an MPI implementation called CharmMPI and a discrete event simulator called CharmDES.