Efficient High Performance Computing on Heterogeneous Platforms

Heterogeneous platforms are mixes of different processing units in a compute node (e.g., CPUs+GPUs, CPU+MICs) or a chip package (e.g., APUs). This type of platforms keeps gaining popularity in various computer systems ranging from supercomputers to mobile devices. In this context, improving their efficiency and usability has become increasingly...

Accelerating Protein Sequence Alignment with Different Parallel Hardware Platforms

Detecting similarities between (RNA, DNA, and protein) sequences is an important part of bioinformatics. Among the algorithms used to accomplish this, the Smith-Waterman algorithm is very popular. A sequential implementation of Smith-Waterman requires quadratic running time with respect to the length of the sequences. As the amount of data in...