Tomás F. Pena

BigBWA: approaching the Burrows–Wheeler aligner to Big Data technologies

UNLABELLED BigBWA is a new tool that uses the Big Data technology Hadoop to boost the performance of the Burrows-Wheeler aligner (BWA). Important reductions in the execution times were observed when using this tool. In addition, BigBWA is fault tolerant and it does not require any modification of the original BWA source code. AVAILABILITY AND IMPLEMENTATION BigBWA is available at the project GitHub repository: https://github.com/citiususc/BigBWA.

SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data.

Next-generation sequencing (NGS) technologies have led to a huge amount of genomic data that need to be analyzed and interpreted. This fact has a huge impact on the DNA sequence alignment process, which nowadays requires the mapping of billions of small DNA sequences onto a reference genome. In this way, sequence alignment remains the most time-consuming stage in the sequence analysis workflow. To deal with this issue, state of the art aligners take advantage of parallelization strategies. However, the existent solutions show limited scalability and have a complex implementation. In this work we introduce SparkBWA, a new tool that exploits the capabilities of a big data technology as Spark to boost the performance of one of the most widely adopted aligner, the Burrows-Wheeler Aligner (BWA). The design of SparkBWA uses two independent software layers in such a way that no modifications to the original BWA source code are required, which assures its compatibility with any BWA version (future or legacy). SparkBWA is evaluated in different scenarios showing noticeable results in terms of performance and scalability. A comparison to other parallel BWA-based aligners validates the benefits of our approach. Finally, an intuitive and flexible API is provided to NGS professionals in order to facilitate the acceptance and adoption of the new tool. The source code of the software described in this paper is publicly available at https://github.com/citiususc/SparkBWA, with a GPL3 license.

Parallel iterative solvers involving fast wavelet transforms for the solution of BEM systems

This paper describes the parallelization of a strategy to speed up the convergence of iterative methods applied to boundary element method (BEM) systems arising from problems with non-smooth boundaries and mixed boundary conditions. The aim of the work is the application of fast wavelet transforms as a black box transformation in existing boundary element codes. A new strategy was proposed, applying wavelet transforms on the interval, so it could be used in case of non-smooth coefficient matrices. Here, we describe the parallel iterative scheme and we present some of the results we have obtained.

Parallel Computation of Wavelet Transforms Using the Lifting Scheme

The lifting scheme [14] is a method for construction of biorthogonal wavelets and fast computation of the corresponding wavelet transforms. This paper describes a message–passing parallel implementation in which high efficiency is achieved by a modified data–swapping approach allowing communications to overlap computations. The method illustrated by application to Haar and Daubechies (D4) wavelets. Timing and speed–up results for the Cray T3E and the Fujitsu AP3000 are presented.

Dual BEM for crack growth analysis on distributed-memory multiprocessors

Abstract The Dual Boundary Element Method (DBEM) has been presented as an effective numerical technique for the analysis of linear elastic crack problems [Portela A, Aliabadi MH. The dual boundary element method: effective implementation for crack problems. Int J Num Meth Engng 1992;33:1269–1287]. Analysis of large structural integrity problems may need the use of large computational resources, both in terms of CPU time and memory requirements. This paper reports a message-passing implementation of the DBEM formulation dealing with the analysis of crack growth in structures. We have analyzed the construction of the system and its resolution. Different data distribution techniques have been studied with several problems. Results in terms of scalability and load balance for these two stages are presented in this paper.

Accurate analytical performance model of communications in MPI applications

This paper presents a new LogP-based model, called LoOgGP, which allows an accurate characterization of MPI applications based on microbenchmark measurements. This new model is an extension of LogP for long messages in which both overhead and gap parameters perform a linear dependency with message size. The LoOgGP model has been fully integrated into a modelling framework to obtain statistical models of parallel applications, providing the analyst with an easy and automatic tool for LoOgGP parameter set assessment to characterize communications. The use of LoOgGP model to obtain a statistical performance model of an image deconvolution application is illustrated as a case of study.

AVISPA : visualizing the performance prediction of parallel iterative solvers

The selection of the best method and preconditioner for solving a sparse linear system is as determinant as the efficient parallelization of the selected method. We propose a tool for helping to solve both problems on distributed memory multiprocessors using iterative methods. Based on a previously developed library of HPF and message-passing interface (MPI) codes, a performance prediction is developed and a visualization tool (AVISP A) is proposed. The tool combines theoretical features of the methods and preconditioners with practical considerations and predictions about aspects of the execution performance (computational cost, communications overhead, etc.). It offers detailed information about all the topics that can be useful for selecting the most suitable method and preconditioner. Another capability is to offer information on different parallel implementations of the code (HPF and MPI) varying the number of available processors.

PARALLEL INCOMPLETE LU FACTORIZATION AS A PRECONDITIONER FOR KRYLOV SUBSPACE METHODS

In this paper we describe a new method for the ILU(0) factorization of sparse systems in distributed memory multiprocessor architectures. This method uses a symbolic reordering technique, so the final system can be grouped in blocks where the rows are independent and the factorization of these entries can be carried out in parallel. The parallel ILU(0) factorization has been tested on the Cray T3E multicomputer using the MPI communication library. The performance was analysed using matrices from the Harwell–Boeing collection.

Numerical analysis of abrupt heterojunction bipolar transistors

This paper presents a physical–mathematical model for abrupt heterojunction transistors and its solution using numerical methods with application to InP/InGaAs HBTs. The physical model is based on the combination of the drift–diffusion transport model in the bulk with thermionic emission and tunnelling transmission through the emitter–base interface. Fermi–Dirac statistics and bandgap narrowing distribution between the valence and conduction bands are considered in the model. A compact formulation is used that makes it easy to take into account other effects such as the non-parabolic nature of the bands or the presence of various subbands in the conduction process. The simulator has been implemented for distributed memory multicomputers, making use of the MPI message-passing standard library. In order to accelerate the solution process of the linear system, iterative methods with parallel incomplete factorization-based preconditioners have been used.

Finite element simulation of semiconductor devices on multiprocessor computers

In this work we describe a methodology for solving the basic set of state stationary semiconductor device equations. We present a new iterative method for the solution using finite elements of the non linear Poisson equation and use a Conjugate Gradient type method for solving the non symmetric continuity equations. The parallelization of this approach and its projection onto a multiprocessor system with a hypercube topology are carried out. We study the distribution of an irregular mesh of triangular elements over a hypercube and the later parallelization of the resolution method.