High Performance Histograms on SIMT and SIMD Architectures

Using the histogram procedure, this work studies performance determining factors in computing in parallel on SIMD and SIMT devices. Modern graphics pro-cessing units (GPUs) support SIMT, multiple threads running the same instruction, whereas central processing units (CPUs) use SIMD, in which one instruction op-erates on multiple operands. As...

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...