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DTSTAMP:20250822T115804Z
LOCATION:Room 6.0D13
DTSTART;TZID=Europe/Stockholm:20250616T143000
DTEND;TZID=Europe/Stockholm:20250616T150000
UID:submissions.pasc-conference.org_PASC25_sess136_msa193@linklings.com
SUMMARY:Computational Biology Patterns as a Co-Design Resource and Propose
 d Technology Roadmap for Modernizing Workhorse Biomedical Codes
DESCRIPTION:Amy Powell (Sandia National Laboratories, University of New Me
 xico); Logan Williams (North Carolina State University); Jan Ciesko (Sandi
 a National Laboratories); and Gavin C. Conan (North Carolina State Univers
 ity)\n\nApplication proxies in high-performance computing play an importan
 t role for software/hardware co-design.  To broaden the types of computati
 on available for co-design, we are developing a suite of proxy apps based 
 on MetaHipMer2 (mhm2), a DOE-developed, scalable, de novo metagenome assem
 bler.  MetaHipMer2 is implemented in C++, and offloads several routines to
  GPU (K-mer Analysis, Alignment, Local Assembly).  It has been used to ass
 emble large (> 50 Terabase), complex metagenomes on exascale-class machine
 s (e.g., Summit).  Our first proxy, "mhm2-kmer-analysis," focuses on the e
 xpensive K-mer Analysis step, which we have implemented in the Kokkos perf
 ormance portability framework.  In this this talk, we give an overview of 
 mhm2, its execution phases, and their correlation to common “big data” com
 putational patterns.  Further, we make the case for modernization of codes
  via vendor-independent portability frameworks, such as Kokkos, and discus
 s our porting experience, including vignettes on expressing common CUDA id
 ioms in Kokkos. Finally, we give an outlook on future software and hardwar
 e trends that will likely impact computational biology. Sandia National La
 boratories is managed and operated by NTESS under DOE NNSA contract DE-NA0
 003525.\n\nDomain: Engineering, Life Sciences\n\nSession Chairs: Bertil Sc
 hmidt (Johannes Gutenberg University Mainz), Gagandeep Singh (AMD), and Sr
 iranjani Sitaraman (AMD)\n\n
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