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Optimizations lead to significant speedups for NAMD on Frontera

One of the most well-known Charm++ applications, NAMD, made news last week when it was announced on HPCwire that AVX-512 optimizations on the Frontera supercomputer allowed the application to run up to 1.8x faster. NAMD is used by biophysicists for simulating and understanding functionality of large biomolecular systems, including viruses. It may be instrumental in several ongoing and planned studies involving SARS-COV-2. Charmworks is proud to have collaborated with Mellanox to develop and optimize a customized networking layer for Charm++, built on top of the UCX communication library to optimize communication performance on Frontera and other Infiniband machines. This effort enabled the multi-node performance of NAMD on Frontera as shown by the reported study, which scaled the STMV (Satellite Tobacco Mosaic Virus) benchmark on up to 512 nodes.

NAMD was developed and continues to be maintained by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign in collaboration with the Parallel Programming Laboratory at UIUC led by Prof. Kale, who is the founder of Charmworks.

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