Listar Grupo de Arquitectura de Computadores (GAC) por título
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Java in the High Performance Computing arena: Research, practice and experience
(Elsevier BV, 2013-05-01)[Abstract] The rising interest in Java for High Performance Computing (HPC) is based on the appealing features of this language for programming multi-core cluster architectures, particularly the built-in networking and ... -
Jmodeltest.org: selection of nucleotide substitution models on the cloud
(Oxford University Press, 2014)[Abstract] The selection of models of nucleotide substitution is one of the major steps of modern phylogenetic analysis. Different tools exist to accomplish this task, among which jModelTest 2 (jMT2) is one of the most ... -
Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model
(Sage Publications Ltd., 2015)[Abstract] Detecting epistasis, such as 2-SNP interactions, in genome-wide association studies (GWAS) is an important but time consuming operation. Consequently, GPUs have already been used to accelerate these studies, ... -
Local Rollback for Resilient Mpi Applications With Application-Level Checkpointing and Message Logging
(Elsevier BV * North-Holland, 2019-02)[Abstract] The resilience approach generally used in high-performance computing (HPC) relies on coordinated checkpoint/restart, a global rollback of all the processes that are running the application. However, in many ... -
Locality-Aware Automatic Parallelization for GPGPU with OpenHMPP Directives
(Springer New York LLC, 2016-06)[Abstract] The use of GPUs for general purpose computation has increased dramatically in the past years due to the rising demands of computing power and their tremendous computing capacity at low cost. Hence, new programming ... -
Low‐latency Java communication devices on RDMA‐enabled networks
(John Wiley & Sons Ltd., 2015)[Abstract] Providing high‐performance inter‐node communication is a key capability for running high performance computing applications efficiently on parallel architectures. In fact, current systems deployments are aggregating ... -
MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud
(Oxford University Press, 2017)[Abstract] This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted ... -
Mobile Robot Positioning with 433-MHz Wireless Motes with Varying Transmission Powers and a Particle Filter
(Multidisciplinary Digital Publishing Institute, 2015)In wireless positioning systems, the transmitter’s power is usually fixed. In this paper, we explore the use of varying transmission powers to increase the performance of a wireless localization system. To this extent, we ... -
ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models
(Oxford University Press, 2019-08-21)[Abstract] ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two ... -
MPI and UPC broadcast, scatter and gather algorithms in Xeon Phi
(John Wiley & Sons Ltd., 2016-05-06)[Abstract] Accelerators have revolutionised the high performance computing (HPC) community. Despite their advantages, their very specific programming models and limited communication capabilities have kept them in a ... -
MPI-dot2dot: A Parallel Tool to Find DNA Tandem Repeats on Multicore Clusters
(Springer, 2022)[Abstract] Tandem Repeats (TRs) are segments that occur several times in a DNA sequence, and each copy is adjacent to other. In the last few years, TRs have gained significant attention as they are thought to be related ... -
MREv: An Automatic MapReduce Evaluation Tool for Big Data Workloads
(Elsevier, 2015)[Abstract]: The popularity of Big Data computing models like MapReduce has caused the emergence of many frameworks oriented to High Performance Computing (HPC) systems. The suitability of each one to a particular use case ... -
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems
(Oxford University Press, 2016)[Abstracts] MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input ... -
Multimethod Optimization for Reverse Engineering of Complex Biological Networks
(Association for Computing Machinery, 2018-09)[Abstract] Optimization problems appears in different areas of science and engineering. This paper considers the general problem of reverse engineering in computational biology by means of mixed-integer nonlinear dynamic ... -
Multimethod optimization in the cloud: A case‐study in systems biology modelling
(Wiley, 2018-06-25)[Abstract] Optimization problems appear in many different applications in science and engineering. A large number of different algorithms have been proposed for solving them; however, there is no unique general optimization ... -
Multithreaded and Spark parallelization of feature selection filters
(2016)[Abstract]: Vast amounts of data are generated every day, constituting a volume that is challenging to analyze. Techniques such as feature selection are advisable when tackling large datasets. Among the tools that provide ... -
Non-blocking Java Communications Support on Clusters
(Springer, 2006)[Abstract] This paper presents communication strategies for supporting efficient non-blocking Java communication on clusters. The communication performance is critical for the overall cluster performance. It is possible ... -
Non-IID data and Continual Learning processes in Federated Learning: A long road ahead
(Elsevier, 2022)[Abstract] Federated Learning is a novel framework that allows multiple devices or institutions to train a machine learning model collaboratively while preserving their data private. This decentralized approach is prone ... -
Nonblocking collectives for scalable Java communications
(John Wiley & Sons Ltd., 2015-04-22)[Abstract] This paper presents a Java implementation of the recently published MPI 3.0 nonblocking message passing collectives in order to analyze and assess the feasibility of taking advantage of these operations in shared ... -
Novel parallelization of simulated annealing and Hooke & Jeeves search algorithms for multicore systems with application to complex fisheries stock assessment models
(Elsevier Ltd, 2016-11)[Abstract] Estimating parameters of a statistical fisheries assessment model typically involves a comparison of disparate datasets to a forward simulation model through a likelihood function. In all but trivial cases the ...
