Minisymposium Presentation

Application proxies in high-performance computing play an important role for software/hardware co-design. To broaden the types of computation available for co-design, we are developing a suite of proxy apps based on MetaHipMer2 (mhm2), a DOE-developed, scalable, de novo metagenome assembler. MetaHipMer2 is implemented in C++, and offloads several routines to GPU (K-mer Analysis, Alignment, Local Assembly). It has been used to assemble large (> 50 Terabase), complex metagenomes on exascale-class machines (e.g., Summit). Our first proxy, "mhm2-kmer-analysis," focuses on the expensive K-mer Analysis step, which we have implemented in the Kokkos performance portability framework. In this this talk, we give an overview of mhm2, its execution phases, and their correlation to common “big data” computational patterns. Further, we make the case for modernization of codes via vendor-independent portability frameworks, such as Kokkos, and discuss our porting experience, including vignettes on expressing common CUDA idioms in Kokkos. Finally, we give an outlook on future software and hardware trends that will likely impact computational biology. Sandia National Laboratories is managed and operated by NTESS under DOE NNSA contract DE-NA0003525.