Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

The HiSCORE concept for gamma-ray and cosmic-ray astrophysics beyond 10\,TeV

Air-shower measurements in the primary energy range beyond 10 TeV can be used to address important questions of astroparticle and particle physics. The most prominent among these questions are the search for the origin of charged Galactic cosmic rays and the so-far little understood transition from Galactic to extra-galactic cosmic rays. A very promising avenue towards answering these fundamental questions is the construction of an air-shower detector with sufficient sensitivity for gamma-rays to identify the accelerators and large exposure to achieve accurate spectroscopy of local cosmic rays. With the new ground-based large-area (up to 100 square-km) wide-angle (Omega ~ 0.6-0.85 sr) air-shower detector concept HiSCORE (Hundred*i Square-km Cosmic ORigin Explorer), we aim at exploring the cosmic ray and gamma-ray sky (accelerator-sky) in the energy range from few 10s of TeV to 1 EeV using the non-imaging air-Cherenkov detection technique. The full detector simulation is presented here. The resulting sensitivity of a HiSCORE-type detector to gamma-rays will extend the energy range so far accessed by other experiments beyond energies of 50 - 100 TeV, thereby opening up the ultra high energy gamma-ray (UHE gamma-rays, E > 10 TeV) observation window.Comment: 31 pages, 15 figures, accepted by Astroparticle Physics, DOI information: 10.1016/j.astropartphys.2014.03.00

An investigation of the performance portability of OpenCL

This paper reports on the development of an MPI/OpenCL implementation of LU, an application-level benchmark from the NAS Parallel Benchmark Suite. An account of the design decisions addressed during the development of this code is presented, demonstrating the importance of memory arrangement and work-item/work-group distribution strategies when applications are deployed on different device types. The resulting platform-agnostic, single source application is benchmarked on a number of different architectures, and is shown to be 1.3–1.5× slower than native FORTRAN 77 or CUDA implementations on a single node and 1.3–3.1× slower on multiple nodes. We also explore the potential performance gains of OpenCL’s device fissioning capability, demonstrating up to a 3× speed-up over our original OpenCL implementation

Beyond Binary Search: Parallel In-Place Construction of Implicit Search Tree Layouts.

M.S. Thesis. University of Hawaiʻi at Mānoa 2018