CS Students at CCSCNE 2022
Sojin Lim, Katie Knox, and Alice Huang presented their research work (with Tillie Ferguson, not pictured) on "Parallelizing the RNA Secondary Structure Dynamic Programming Problem" at the Conference of the Consortium for Computing in Colleges Northeast Region, in Pleasantville, NY, March, 2022.
Alice, Katie, Sojin, and Tillie's work investigates solutions for parallelizing dynamic programming algorithms that can be used to solve the RNA Secondary Structure problem. These algorithms have irregular computation and communication patterns, which pose difficulties in efficiently parallelizing these types of algorithms. The group developed two variations of parallel solutions: one in CUDA that is designed to run on GPUs; and the other in MPI that is designed to run on parallel cluster computers. Their approaches produced promising results, improving performance over sequential solutions by a factor of up to 13. The group's work started as a course project in Professor Newhall's Fall 2021 Parallel and Distributed Computing class.