TOPICS

My main research area is the acceleration of scientific computation through High Performance Computing, mainly using GPU computing. I am interested in applying and developing parallel solutions in several fields, such as the simulation of bioinspired computing models (Membrane Computing and Multi-Agent Systems), training and deployment of Machine Learning models (Deep Learning in image and video understanding), and image coding algorithms (JPEG2000 for DCP and IMF, and JPEGXS for lightweight and low latency compression).


So far I have been working on the acceleration of applications by leveraging GPUs with CUDA. At the RGNC (University of Seville), I have developed the first simulators for P systems on CUDA. At the Department of Moving Picture Technologies (Fraunhofer IIS), I contributed to the acceleration of JPEG2000 codecs with CUDA and to the standardization of JPEGXS for its parallelization on GPUs. Furthermore, I am working with Deep Learning and its potential applications to image and video understanding, automatic sign language translation and production, pose estimation and signal processing. I am also studying the parallelization of new Multi-agent Systems (e.g. for Crowd Simulation).


I am also interested in researching new design patterns for parallel scientific computations, in order to help adapting and implementing them to GPU architectures. Other topics I would like to study are also related to the fields of Data Science, High Energy Physics and Astrophysics. Although it is a diverse set of interests, I just love science and its applications.


In summary, my research topics today are:


  • GPU Computing (CUDA and standards such as OpenCL, Vulkan and SYCL)
  • Parallel Computing (High Performance Computing)
  • Deep Learning Applications (Image and Video Understanding)
  • Simulation and Modeling of Complex Systems (Population Dynamics, Multi-agent systems)
  • Bio-inspired Computing (Membrane Computing)
  • Acceleration of Image Coding (JPEG200, JPEGXS)

SOFTWARE

Founder of the PMCGPU project, and contributor to the P-Lingua project. Both of them are open-source copyrighted works, and published under GPLv3 license.

PMCGPU P-LINGUA

Collaborator in the development of NIN (previously Selenitas), a multi-agent system framework built with Lua programming language.


Contributor to the post-production workflow software easyDCPTM, by improving the CUDA JPEG2000 codec, including new functionalities like HDR compatibility, and providing technical to customers. Contributor to the Verification Model of the JPEG-XS standard from the early stage to almost the final one, by testing different modes of compression.

PROJECTS

National and regional

  • Máquinas bio-inspiradas sobre plataformas de altas prestaciones: Un enfoque multidisciplinar. Supported by Ministerio de Economía, Industria y Competitividad, TIN2017-89842-P. Duration of the project: from January 1, 2018 to September 30, 2021. Principal Investigators: Agustín Riscos Núñez, Mario de J. Pérez Jiménez.
  • De la Computación Celular a la Computación de alto rendimiento. Aplicación a la dinámica de poblaciones. Supported by: Ministerio de Economía y Competitividad. TIN2012-37434. Project duration: from January 1, 2013 to December 31, 2015. Principal Investigator: Mario de J. Pérez Jiménez.
  • Computación Celular: Aplicaciones a la Biología de Sistemas y Sintética. Supported by: Ministerio de Ciencia e Innovación. TIN2009-13192. Project duration: from January 1, 2010 to December 31, 2012. Principal Investigator: Mario de J. Pérez Jiménez.
  • Modelado y simulación computacional en Biología de Sistemas. Supported by: Junta de Andalucía, Proyecto de Excelencia con Investigador de Reconocida Valía. P08-TIC-04200. Project duration: from February 1, 2009 to January 31, 2013. Principal Investigators: Gheorghe Paun y Mario de J. Pérez Jiménez.
  • Red Temática en Computación Biomolecular y Biocelular. Supported by: Ministerio de Economía y Competitividad. TIN2011-15874-E. Project duration: from October 1, 2012 to September 30, 2013. Coordinator of the network and Principal Investigator: Mario de J. Pérez Jiménez.
  • Diseño y aplicación de un modelo PDP (Population Dynamics P Systems) para la estimación de la disponibilidad y distribución espacial de los recursos tróficos para aves carroñeras en Navarra. Supported by: Gestión Ambiental, Viveros y Repoblaciones de Navarra, S.A. (Proyecto NECROPIR - EFA 130/09. Unión Europea. Cooperación territorial España-Francia-Andorra). Project duration: from November 1, 2011 to June 30, 2012. Principal Investigators: Mª Angels Colomer Cugat y Mario de J. Pérez Jiménez.
  • Desarrollo de una aplicación interactiva para simular la gestión de un ecosistema formado por un río y un embalse gestionado por el hombre. Supported by: Endesa S.A. Project duration: from October 1, 2010 to November 30, 2011. Principal Investigators: Mª Angels Colomer Cugat y Mario de J. Pérez Jiménez.
  • Desarrollo, calibración y validación de un modelo de simulación del comportamiento de las poblaciones del mejillón cebra en embalses. Aplicación al embalse de Ribarroja. Supported by: Endesa S.A. Project duration: from January 1, 2009 to December 31, 2009. Principal Investigators: Mª Angels Colomer Cugat y Mario de J. Pérez Jiménez.
  • Red Temática en Computación Biomolecular y Biocelular. Supported by: Ministerio de Ciencia e Innovación. TIN2008-04487-E. Project duration: from December 1, 2008 to November 30, 2011. Coordinator of the network and Principal Investigator: Mario de J. Pérez Jiménez.
  • Análisis computacional y simulación de procesos biológicos en Computación
    Celular.
    Supported by: Ministerio de Educación y Ciencia. TIN - 2006 - 13425. Project duration: from October 1, 2006 to September 30, 2009.

International

  • Research on the unsupervised learning model of membrane computing and its learning mechanism. Supported by National Natural Science Foundation of China. Grant No. 61472328. Duration of the project: from January 1, 2015 to December 31, 2018. Principal Investigators: Jun Wang, Mario de J. Pérez Jiménez, Hong Peng, Agustín Riscos Núñez.
  • Cell-based Membrane Computing systems and their applications in Biology. Supported by: National Natural Science Foundation de China. Grant No. 61320106005. Project duration: from January 1, 2014 to December 31, 2018. Principal Investigators: Linqiang Pan, Gheorghe Paun and Mario J. Pérez-Jiménez.

Others

MEMBERSHIP


Committees


Research Groups and Institutes

  • Research Group on Natural Computing (RGNC) (Department of Computer Science and Artificial Intelligence, University of Seville): member since 2008. In this group I developed my doctoral dissertation on the parallel simulation of P systems on GPUs, and I am now developing new high-performance simulators for this bio-inspired models. The RGNC was funded by Prof. Mario J. Pérez-Jiménez, and is now headed by Prof. Agustín Riscos-Núñez.
  • Deepknowledge Research Group (University of Seville): member since 2020. I actively collaborate on the research and developments of Deep Learning-based solutions to complex systems. The R&D activities are related with ubiquitous computing, machine learning, deep learning and mobile development.
  • Unit of Excellence Smart Computer systems Research and Engineering (SCORE lab) (University of Seville): founder member, which contains 21 members. SCORE was first envisioned in 2017, funded during 2020, but formally constituted in November 2020.
  • Institute of Computer Engineering Research of the University of Seville (I3US): member since January 2021. I am also contributing to the configuration of the computing infrastructure of the I3US, including nodes for GPU computing.
  • Algorithms & Complexity Lab (ACLab) and Membrane Computing Research Group (University of the Philippines Diliman): external member since 2011, where I actively collaborate on the research and developments of GPU-based simulators for Spiking Neural P systems. The lab and the group are headed by Ph.D. Henry N. Adorna.
  • Digital Cinema Group (Moving Picture Department, Fraunhofer IIS, Erlangen, Germany): member from December 2014 to August 2017, where I developed a postdoc aimed at accelerating the encoding of pictures in the Digital Cinema world under the software easyDCP, and the standardization of lightweight image coding algorithms within JPEG XS (focus on GPU parallelization). The group is headed by Dr. Heiko Sparenberg.
  • Institute of Mathematics of the University of Seville (IMUS): member in training from April 2013 to December 2013, and collaborator member from December 2013 to December 2019.

DISSERTATION


Accelerating Membrane Systems Simulators using High Performance Computing with GPU

Grade: Apto cum laude por unanimidad y la acreditación de Doctorado Internacional
Date: 09/05/2013
Advisor: Mario J. Pérez-Jiménez
Co-advisor: Ignacio Pérez-Hurtado
Board: José María Sempere Luna (Universidad Politécnica de Valencia), Gheorghe Paun (member of the Academia Europaea -The Academy of Europe- and of the Institute of Mathematics of the Romanian Academia), Marian Gheorghe (University of Sheffield, UK), María Angels Colomer Cugat (Universidad de Lleida), Agustín Riscos-Núñez (Universidad de Sevilla)

  • PDF file of the dissertation (from the University of Seville library) Click here to download
  • PDF of the dissertation in Spanish (Long summary) Click here to download
  • URL at idUS (University of Seville)
  • URL at Teseo (Ministry of Education)

SEMINARS




These are some of the seminars I have delivered. Some of them have recordings.


DK

GPU days Universidad de Sevilla 2020. June 8-10, 2020. Included the workshop Fundamentals of Accelerated Computing with CUDA C/C++.


I3US

Organizer of CERN: Speedup Your Future, given by Daniel Campora (CERN fellow) and Adrian Oeftiger (PhD student at CERN) on Monday, May 12, 2014,

More seminars here.

OTHER STUFF


Administration

I am one of the main administrators of the High Performance and GPU Computing servers at the Research Group on Natural Computing. These servers have been funded by different R&D projects for more than 10 years.

These servers feature 2 GeForce RTX2080, a Tesla K40 (donated by NVIDIA), 3 Tesla C1060, a GeForce GTX 780 Ti, a GeForce GTX 550 Ti, and a GeForce 9400 GT. They run over CentOS Linux operating system. More information is available at the official webpage of the computing servers: http://www.gcn.us.es/gpucomputing
GPU server at RGNC

Prizes