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DTSTAMP:20250626T233531Z
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UID:submissions.supercomputing.org_SC24_sess534_post162@linklings.com
SUMMARY:Algorithmic Patterns from Computational Biology for Proxy Applicat
 ion Development and Co-Design
DESCRIPTION:Logan Williams and Gavin Conant (North Carolina State Universi
 ty) and Jan Ciesko and Amy Powell (Sandia National Laboratories)\n\nHigh-p
 erformance computing hardware is co-developed with U.S. DOE codes, and pro
 xy applications (apps) based on these codes are critical technologies for 
 iterative innovation. Numerical modeling/simulation proxies have been the 
 most impactful in co-design. To broaden the types of computation available
  for co-design, we are developing proxy apps based on MetaHipMer (mhm2), a
  DOE-developed, scalable, \textit{de novo} metagenome assembler. MetaHipMe
 r is implemented in C++, and offloads several routines to GPU. It has been
  used to assemble large (>50 Terabase) metagenomes on exascale-class machi
 nes (e.g., Summit). Our first proxy focuses on the expensive kmer analysis
  step. This and subsequent steps are memory-bound computations using CPU s
 hared-memory distributed data structures (e.g., distributed hash tables). 
 These data structures are often larger than inputs, and operations on them
  account for most of runtime. Our proxies will be implemented in Kokkos, a
  C++ performance portability programming model for emerging architecture d
 esign/testing.\n\nRegistration Category: Tech Program Reg Pass, Exhibits R
 eg Pass\n\nSession Chairs: Ayesha Afzal (Friedrich-Alexander University, E
 rlangen-Nuremberg; Erlangen National High Performance Computing Center); S
 ally Ellingson (University of Kentucky); and Alan Sussman (University of M
 aryland)\n\n
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