Alejandro Chacón
PhD. Student
     
High Performance Computing Applications for Science and Engineering,

Contact
Campus UAB, Edifici Q, 
08193 Bellaterra (Barcelona), 
Spain.



About myself

I am a PhD student in the Computer Architecture and Operating Systems department at the Autonomous University of Barcelona, advised by the professors Juan Carlos Moure and Antonio EspinosaMy research interests include computer architecture and parallel optimizations for heterogeneous HPC systems. Currently I am optimizing on GPU several bioinformatic algorithms, such as FM-Index and Myers, that are the building blocks for a wide number of bioinformatic applications. We are actively collaborating with the Algorithm Development Group from CNAG. I received an Phd Fellowship grant from UAB in 2011.


Publications

    Boosting the FM-index on the GPU: effective techniques to mitigate random memory accesses
    Alejandro Chacón, Santiago Marco-Sola, Antonio Espinosa, Paolo Ribeca, Juan Carlos Moure
    TCBB - Transactions on Computational Biology and Bioinformatics
    [doi] [pdf] [pptx] [cite]

    FM-index on GPU: a cooperative scheme to reduce memory footprint
    Alejandro Chacón, Santiago Marco-Sola, Antonio Espinosa, Paolo Ribeca, Juan Carlos Moure
    ISPA2014 - Symposium on Parallel & Distributed Processing with Applications 2014
    [doi] [pdf] [pptx] [cite]

    Thread-cooperative, bit-parallel computation of Levenshtein distance on GPU 
    Alejandro Chacón, Santiago Marco-Sola, Antonio Espinosa, Paolo Ribeca, Juan Carlos Moure
    ICS2014 – International Conference on Supercomputing 2014
    [doi] [pdf] [pptx] [cite]

    n-step FM-Index for faster pattern matching
    Alejandro Chacón, Juan Carlos Moure, Antonio Espinosa, Porfidio Hernández 
    ICCS2013 – International Conference on Computational Science 2013 
    [doi] [pdf] [pptx] [cite]

    Suffix-Array and FM-index analysis in Multi-ManyCore
    Alejandro Chacón, Pedro Erencia, Antonio Espinosa, Juan Carlos Moure, Porfidio Hernández
    JP2012 – Jornadas de Paralelismo 2012
    [pdf] [pptx] [cite]


Teaching

Fall of 2014
  Advanced Architectures          (Practical seminars)
Spring of 2014 
  Computer Architecture            (Theoretical problems)
Fall of 2013
  Advanced Architectures          (Practical seminars)
Fall of 2013
  Computer Architecture            (Theoretical problems)
  Computer Architecture 2         (Theoretical problems and Practical seminars)
Spring of 2012
  Computer Architecture 2         (Theoretical problems and Practical seminars)


Education

   Studies
  •  PhD in High Performance Computing (2012 - present)
  •  Master's Degree in High Performance Computing, Information Theory and Security  (1 year) 
    • Master Dissertation: Analysis of Suffix-Array and FM-Index in Multi-Manycore
  •  Bachelor Degree in Computer Engineering  (5 years)
    • Final Degree Project: Optimization of a bioinformatics application: sequence alignment executed in ManyCore Processors (GPUs)

    Related courses and seminars
  • Programming ARM based systems
  • Intel Xeon Phi and CUDA Programming
  • OpenACC and OmpSS Programming
  • Programming and Tuning Massively Parallel Systems summer school (PUMPS)
  • Heterogeneous Parallel Programming