High Performance Computing Framework for Tera-Scale Database Search of Mass Spectrometry Data

Database peptide search algorithms deduce peptides from mass spectrometry (MS) data. There has been substantial effort in improving their computational efficiency to achieve larger and more complex systems biology studies. However, modern serial and high-performance computing (HPC) algorithms exhibit sub-optimal performance mainly due to their ineffective parallel designs (low resource utilization), and high overhead costs. We present an HPC framework, called HiCOPS, for efficient acceleration of the database peptide search algorithms on distributed-memory supercomputers. HiCOPS provides, on average, more than 10-fold improvement in speed, and superior parallel performance over several existing HPC database search software. We also formulate a mathematical model for performance analysis and optimization, and report near-optimal results for several key metrics including strong-scale efficiency, hardware utilization, load-balance, inter-process communication and I/O overheads. The core parallel design, techniques, and optimizations presented in HiCOPS are search-algorithm independent and can be extended to efficiently accelerate the existing and future algorithms and software.