DALIGNER Performance Evaluation on Intel Xeon Phi Architecture

Abstract

In bioinformatics, DNA sequence assembly refers to the reconstruction of an original DNA sequence by the alignment and merging of fragments that can be obtained from several sequencing methods. The main sequencing methods process thousands or even millions of these fragments, which can be short (hundreds of base pairs) or long (thousands of base pairs) read sequences. This is a highly computational task, which usually requires the use of parallel programs and algorithms, so that it can be performed with desirable accuracy and within suitable time limits. In this paper, we evaluate the performance of DALIGNER long read sequences aligner in a system using the Intel Xeon Phi 7210 processor. We are looking for scalable architectures that could provide a higher throughput that can be applied to future sequencing technologies.

Performance Evaluation of Massively Parallel Systems Using SPEC OMP Suite

“…Several studies concentrated on one specific application [33][34][35], while others focused on smaller compute kernels as well as NAS parallel benchmarks [32,36,37]. recent performance studies of HPC architectures, more specifically Blue Genes and Xeon Phi, concentrated on specific compute-intensive applications, such as drug discovery [26], lattice QCD [27], molecular dynamics [28], DNA sequence aligner [38], pseudospectral ultrasound simulations [39], and Alpha magnetic spectrometer [40].…”