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DTSTART;TZID=America/Chicago:20211115T103000
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UID:submissions.supercomputing.org_SC21_sess350_ws_ia102@linklings.com
SUMMARY:Mapping Irregular Computations for Molecular Docking to the SX-Aur
 ora TSUBASA Vector Engine
DESCRIPTION:Workshop\n\nMapping Irregular Computations for Molecular Docki
 ng to the SX-Aurora TSUBASA Vector Engine\n\nSolis Vasquez, Focht, Koch\n\
 nMolecular docking is a key method in computer-aided drug design, where th
 e rapid identification of drug candidates is crucial for combating disease
 s. AutoDock is a widely-used molecular docking program, having an irregula
 r structure characterized by a divergent control flow and compute-intensiv
 e calculations. This work investigates porting AutoDock to the SX-Aurora T
 SUBASA vector engine and evaluates the achievable performance on a number 
 of real-world input compounds. In particular, we discuss the platform-spec
 ific coding styles required to handle the high degree of irregularity in b
 oth local-search methods employed by AutoDock. These Solis-Wets and ADADEL
 TA methods take up a large part of the total computation time. Based on ou
 r experiments, we achieved runtimes on the SX-Aurora TSUBASA VE20B that ar
 e on average 3× faster than on modern dual-socket 64-core CPU nodes. Our s
 olution is competitive with V100 GPUs, even though these already use newer
  chip fabrication technology (12nm vs. 16nm on the VE20B).\n\nTag: Algorit
 hms, Architectures, Big Data, Data Analytics, Memory Systems, Numerical Al
 gorithms\n\nRegistration Category: Workshop Reg Pass
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