Presentation
Algorithmic Patterns from Computational Biology for Proxy Application Development and Co-Design
DescriptionHigh-performance computing hardware is co-developed with U.S. DOE codes, and proxy 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. MetaHipMer is implemented in C++, and offloads several routines to GPU. It has been used to assemble large (>50 Terabase) metagenomes on exascale-class machines (e.g., Summit). Our first proxy focuses on the expensive kmer analysis step. This and subsequent steps are memory-bound computations using CPU shared-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 design/testing.
Event Type
ACM Student Research Competition: Graduate Poster
ACM Student Research Competition: Undergraduate Poster
Doctoral Showcase
Posters
TimeTuesday, 19 November 202412pm - 5pm EST
LocationB302-B305
TP
XO/EX