Rapid advances in high-throughput sequencers have made it possible to obtain large
amounts of whole genome data quickly and inexpensively. As the amount of data increases …

BLAST is a widely used software toolkit for genomic sequence search. mpiBLAST is a freely
available, opensource parallelization of BLAST that uses database segmentation to allow …

The growing speed gap between CPU and memory makes I/O the main bottleneck of many
industrial applications. Some applications need to perform I/O operations for very large …

Modern-era high performance computing (HPC) systems are providing multiple levels of
memory and storage layers to bridge the performance gap between fast memory and slow …

Data-intensive scientific workflows are composed of many tasks that exhibit data
precedence constraints leading to communication schemes expressed by means of …

As processors become more powerful and clusters larger, users will exploit this increased
power to progressively run larger and larger problems. Today's datasets in biology, physics …

As processors become more powerful and clusters larger, users will exploit this increased
power to progressively run larger and larger problems. Today's datasets in biology, physics …

Abstract Input/Output (I/O) operations can represent a significant proportion of the run-time of
parallel scientific computing applications. Although there have been several advances in file …

We propose an approach for faster file reading of multiple sequence alignment input through
the use of MPI-I/O over a subset of MPI cores. The idea is to allow a subset of MPI cores that …

Since the development of next generation sequencing technologies, genome assembly has
become one of the most computational and I/O intensive analyses done on the genomic …