Modifying HMMER3 to Run Efficiently on the Cori Supercomputer using OpenMP Tasking

HMMER3 is biological sequence search suite used in significant volume on systems hosted at the National Energy Research Scientific Computing Center. This heavy usage has revealed ways that HMMER3 underutilizes the resources available in an HPC environment such as the Manycore architecture Knights Landing processors available in the Cori supercomputer. After rigorous performance analysis it was determined that the thread architecture of HMMER3 is the most promising optimization target to increase throughput and efficiency. A refactoring effort introduced an OpenMP task based threading design, the ability to respond to imbalanced computation with work stealing, and input buffering to eliminate a large amount of redundant parsing. These efforts have been implemented and in production on Cori for over a year. In that time they have simplified the best practice for use of HMMER3 in workflows and conserved hundreds of thousands of CPU hours.