• openAccess   A framework for genomic sequencing on clusters of multicore and manycore processors 

      Martínez Pérez, Héctor; Barrachina Mir, Sergio; Castillo Catalán, María Isabel; Tárraga, Joaquín; Medina, Ignacio; Dopazo, Joaquín; Quintana-Orti, Enrique S. Sage (2016-06)
      The advances in genomic sequencing during the past few years have motivated the development of fast and reliable software for DNA/RNA sequencing on current high performance architectures. Most of these efforts target ...
    • openAccess   Dynamic reconfiguration of noniterative scientific applications A case study with HPG aligner 

      Iserte, Sergio; Martínez Pérez, Héctor; Barrachina Mir, Sergio; Castillo Catalán, María Isabel; Mayo, Rafael; Peña Monferrer, Antonio J. Springer (2018-09)
      Several studies have proved the benefits of job malleability, that is, the capacity of an application to adapt its parallelism to a dynamically changing number of allocated processors. The most remarkable advantages of ...
    • closedAccess   Exploiting the capabilities of modern GPUs for dense matrix computations 

      Barrachina Mir, Sergio; Castillo Catalán, María Isabel; Igual, Francisco D.; Mayo, Rafael; Quintana-Orti, Enrique S.; Quintana-Ortí, Gregorio John Wiley & Sons (2009)
      We present several algorithms to compute the solution of a linear system of equations on a graphics processor (GPU), as well as general techniques to improve their performance, such as padding and hybrid GPU-CPU computation. ...
    • openAccess   FaST-LMM for Two-Way Epistasis Tests on High-Performance Clusters 

      Martínez Pérez, Héctor; Barrachina Mir, Sergio; Castillo Catalán, María Isabel; Quintana-Orti, Enrique S.; Rambla, Jordi; Farré, Xavier; Navarro, Arcadi Mary Ann Liebert (2018-08)
      We introduce a version of the epistasis test in FaST-LMM for clusters of multithreaded processors. This new software maintains the sensitivity of the original FaST-LMM while delivering acceleration that is close to linear ...
    • openAccess   Highly sensitive and ultrafast read mapping for RNA-seq analysis 

      Barrachina Mir, Sergio; Castillo Catalán, María Isabel; Martínez Pérez, Héctor; Medina, Ignacio; Tárraga, Joaquín; Quintana-Orti, Enrique S.; Dopazo, Joaquín; Salavert Torres, José; Blanquer Espert, Ignacio; Paschall, J.; Hernández-García, V. Oxford University Press (2016)
      As sequencing technologies progress, the amount of data produced grows exponentially, shifting the bottleneck of discovery towards the data analysis phase. In particular, currently available mapping solutions for RNA-seq ...
    • openAccess   Introduction to Programming Using Mobile Phones and MIT App Inventor 

      Barrachina Mir, Sergio; Fabregat Llueca, German Institute of Electrical and Electronics Engineers (2020-07-09)
      At the beginning of each year, we ask our new undergraduate students in Computer Engineering if they have ever developed a computer program. Surprisingly, the most frequent answer is no. The few students who have ...
    • openAccess   PyDTNN: A user-friendly and extensible framework for distributed deep learning 

      Barrachina Mir, Sergio; Castelló, Adrián; Catalán Carbó, Mar; Dolz, Manuel F.; Mestre Miravet, Jose Ignacio Springer (2021-02-22)
      We introduce a framework for training deep neural networks on clusters of computers with the following appealing properties: (1) It is developed in Python, exposing an amiable interface that provides an accessible entry ...
    • openAccess   Statistical Approaches to Computer-Assisted Translation 

      Barrachina Mir, Sergio; Bender, Oliver; Casacuberta, Francisco; Civera, Jorge; Cubel, Elsa; Khadivi, Shahram; Lagarda, Antonio; Ney, Hermann; Tomás, Jesús; Vidal, Enrique; Vilar Torres, Juan Miguel Massachusetts Institute of Technology Press (MIT) (2009)
      Current machine translation (MT) systems are still not perfect. In practice, the output from these systems needs to be edited to correct errors. A way of increasing the productivity of the whole translation process (MT ...
    • closedAccess   Toward the parallelization of GSL 

      Aliaga Estellés, José Ignacio; Almeida, Francisco; Badía, José; Barrachina Mir, Sergio; Blanco, Vicente; Castillo Catalán, María Isabel; Mayo, Rafael; Quintana-Orti, Enrique S.; Quintana-Ortí, Gregorio; Remón Gómez, Alfredo; Rodríguez, Casiano; De Sande, Francisco; Santos, Adrián Springer-Verlag (2009)
      In this paper, we present our joint efforts to design and develop parallel implementations of the GNU Scientific Library for a wide variety of parallel platforms. The multilevel software architecture proposed provides ...
    • openAccess   Using machine learning to model the training scalability of convolutional neural networks on clusters of GPUs 

      Barrachina Mir, Sergio; Castelló, Adrián; Catalán Carbó, Mar; Dolz, Manuel F.; Mestre Miravet, Jose Ignacio Springer (2021-08-30)
      In this work, we build a general piece-wise model to analyze data-parallel (DP) training costs of convolutional neural networks (CNNs) on clusters of GPUs. This general model is based on i) multi-layer perceptrons (MLPs) ...
    • openAccess   Utilizando ARMSim y QtARMSim para la docencia de Arquitectura de Computadores 

      Barrachina Mir, Sergio; Fabregat Llueca, German; Fernández Fernández, Juan Carlos; León Navarro, Germán Universitat Jaume I (2015)
      Muchos de los objetivos formativos de las asignaturas de introducción a la Arquitectura de Computadores se centran en aquellos aspectos que conforman la visión que un programador en lenguaje ensamblador tiene de un ...