Accelerated Event-by-Event Neutrino Oscillation Reweighting with Matter Effects on a GPU

Oscillation probability calculations are becoming increasingly CPU intensive in modern neutrino oscillation analyses. The independency of reweighting individual events in a Monte Carlo sample lends itself to parallel implementation on a Graphics Processing Unit. The library "Prob3++" was ported to the GPU using the CUDA C API, allowing for large scale parallelized calculations of neutrino oscillation probabilities through matter of constant density, decreasing the execution time by a factor of 75, when compared to performance on a single CPU.Comment: Final Update: Post submission update Updated version: quantified the difference in event rates for binned and event-by-event reweighting with a typical binning scheme. Improved formatting of reference

Accelerated large-scale multiple sequence alignment

<p>Abstract</p> <p>Background</p> <p>Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations according to Amdahl's Law. This work is the first known to accelerate the third stage of progressive alignment on reconfigurable hardware.</p> <p>Results</p> <p>We reduce subgroups of aligned sequences into discrete profiles before they are pairwise aligned on the accelerator. Using an FPGA accelerator, an overall speedup of up to 150 has been demonstrated on a large data set when compared to a 2.4 GHz Core2 processor.</p> <p>Conclusions</p> <p>Our parallel algorithm and architecture accelerates large-scale MSA with reconfigurable computing and allows researchers to solve the larger problems that confront biologists today. Program source is available from <url>http://dna.cs.byu.edu/msa/</url>.</p

Distributed Block Coordinate Descent for Minimizing Partially Separable Functions

In this work we propose a distributed randomized block coordinate descent method for minimizing a convex function with a huge number of variables/coordinates. We analyze its complexity under the assumption that the smooth part of the objective function is partially block separable, and show that the degree of separability directly influences the complexity. This extends the results in [Richtarik, Takac: Parallel coordinate descent methods for big data optimization] to a distributed environment. We first show that partially block separable functions admit an expected separable overapproximation (ESO) with respect to a distributed sampling, compute the ESO parameters, and then specialize complexity results from recent literature that hold under the generic ESO assumption. We describe several approaches to distribution and synchronization of the computation across a cluster of multi-core computers and provide promising computational results.Comment: in Recent Developments in Numerical Analysis and Optimization, 201