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Supercomputing in Mexico WHERE HIGH PERFORMANCE COMPUTING FLIES ISUM 2014 Conference Proceedings Editorial Board Editor: Dr. Moisés Torres Martinez Primary Reviewers Dr. Alfredo J. Santillán Gonzalez (UNAM) Dr. Manuel Aguilar Cornejo (UAM-Iztapalapa) Dr. Andrei Tchernykh (CICESE) Dr. Mauricio Carrillo Tripp (CINVESTAV) Dr. Alfredo Cristóbal Salas (UV) Dr. Moisés Torres Martínez (UdeG) Dr. Jesús Cruz Guzmán (UNAM) Dr. Raúl Hazas Izquierdo (UNISON) Dr. Juan Carlos Chimal Enguía (IPN) Dr. René Luna García (IPN) Dr. Juan Manuel Ramírez Alcaraz (UCOLIMA) Dr. Salvador Castañeda (CICESE) Dr. Jaime Klapp Escribano (ININ) Secondary Reviewers Angel López Gómez José Lozano Rizk Edgardo Manuel Felipe Riverón José Luis Quiroz Fabián Frederic Masset Liliana Hernández Cervantes Jesús Alberto Verduzco Ramírez Miguel Angel Balderas Jorge Matadamas Hernández Oscar Eduardo Olivares Domínguez Supercomputing in Mexico Salvador Godoy Editorial Board Coordination Formatting Verónica Lizette Robles Dueñas Angie Fernández Olimón Teresa M. Rodriguez Jiménez Francisco Javier Díaz de León Magaña Ana Patricia de León Torres Pedro Gutiérrez García Cynthia Lynnette Lezama Canizales WHERE HIGH Daniela García Govea ISUM 2014 Conference proceedings are published by the PERFORMANCE , Volume 5, 1st edition, March 26, 2015. Authors are responsible for the contents of their papers. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording COMPUTING FLIES or otherwise, without prior permission of . Printed in Guadalajara, Jalisco México, March 26, 2015 in los Talleres Gráficos de Transición. Supercomputing in México WHERE HIGH PERFORMANCE COMPUTING FLIES Volume editor: Dr. Moisés Torres Martínez University of Guadalajara General Coordination of Information Technologies México 2015 ISBN: 978-607-742-205-1 Derechos Reservados © 2015 Universidad de Guadalajara Ave. Juárez No. 976, Piso 2 Col. Centro, C.P. 44100 Guadalajara, Jal., México Volume V: 1st Edition Obra Completa: 978-607-450-347-0 Printed and Edited in México SUPERCOMPUTING IN MÉXICO 2014 Contents Foreword Luis Alberto Gutierrez Díaz de León...................................................................................................10 Preface Moisés Torres Martínez.......................................................................................................................12 Acknowledgements......................................................................................................................... 14 Introduction A Perspective on the Self Sustainability Model of Supercomputer Centers and Review of Research Works in Supercomputing in Mexico....................................................................................................................................................16 Moisés Torres Martínez Applications HPC applied to Fluorescence Fluctuation Analsis: Contributing to Unravel Hidden Dynamical Processes............................................................................................24 Marcelo Ortega Martinez Sergio Enrique Nesmachnow Canovas Juan Francisco Angiolini Valeria Levi Esteban Eduardo Mocskos Application of an Adaptive Inversion Frequencies Algorithm for Router Bandwidth Improvement........................................................................................................................................38 Evgeniy Kravtsunov Timur Mustafin Andrei Tchernykh Valery Perekatov Alexander Drozdov Where High Performance Computing Flies Cloud Computing Cost Optimization of Virtual Machine Provisioning in Federated IaaS Clouds..........................................................................................................................48 Fermin Alberto Armenta Cano Andrei Tchnerykh Ramin Yahyapour Jaroslaw Nabrzyski Model of Video on Demand Service Provisioning on Multiple Third Party Cloud Storage Services.............................................................................................................58 Carlos Barba Jimenez Raúl Valente Ramirez Velarde Andrei Tchnerykh Grids and GPU´s An Optimization Method for Lennard-Jones Clusters using Conjugate Gradient and Molecular Simulations...............................................................................................73 José Luis Alonzo Velázquez Sergio Ivvan Valdéz Peña Salvador Botello Rionda GPU’s molecular dynamics simulation of a one million particles.............................................84 Pedro Damián Cruz Santiago Jesús Enrique Díaz Herrera Luis Miguel de la Cruz Salas Semi-automatic Historical Climate Data Recovering Using a Distributed Volunteer Grid Infrastructrure.............................................................................................................................100 Sergio Enrique Nesmachnow Canovas Miguel Orlando Da Silva Maciel Straightforward DSP Algorithm Suitable for GPU Computation............................................115 Raúl Gilberto Hazas Izquierdo José Luis Rodriguez Navarro Alan David Faz Gutierrez Raymundo Salazar Orozco SUPERCOMPUTING IN MÉXICO 2014 Performance Evaluation of Cellular Genetic Algorithms on GPU.......................................120 Migdaled López Juárez Ricardo Barrón Fernández Salvador Godoy Calderón Infrastructure A TCP/IP Replication with a Fault Tolerance Scheme for High Availability.................................................................................................................................132 Violeta Medina Rios Andrei Tchernikh Antonio Ramos Paz Parallel Computing Parallelization of filter BSS/WSS on GPGPU for classifying cancer subtypes with SVM..............................................................................................................146 Iliana Castro Liera, Jorge Enrique Luna Taylor, Jacob E. Merecías Pérez, Germán Meléndrez Carballo Application of Parallel Processing Based on Multithreading to the Optimal Trajectory Planning for Robot Manipulators............................................................154 Waldemar Pérez Bailón Antonio Ramos Paz Simulating a Hyperbolic-PDE Using a 2-Dimensional CA.....................................................164 Iliac Huerta Trujillo Juan Carlos Chimal Eguía Scheduling Analysis of Deterministic Timetabling Strategies for the Generation of University Timetables...................................................................................................................176 Marco Antonio Peña Luna Adán Hirales Carbajal Andrei Tchernykh Miguel Alberto Salinas Yañez Where High Performance Computing Flies Appendix I Conference Keynote Speakers...........................................................................................................193 Technology Speakers............................................................................................................................200 Abstracts................................................................................................................................................211 Author Index........................................................................................................................................255 SUPERCOMPUTING IN MÉXICO 2014 Foreword Supercomputers play an important role in computational science, and are used for a wide range of computationally intensive tasks in graphical visualizations, climate research, weather forecasting, molecular modeling, and physical simulations just to mention a few uses of the myriad of possibilities. We know that Supercomputing is a key enabler for most recent discoveries in science and technology, providing researchers computational power for analyzing really large datasets in a timely manner. It became crucial for the recent discovered Higgs boson particle in CERN. As well as, the recent climate change initiatives outlined by the US President Barack Obama that requires large-scale analysis of climate data. Now, supercomputers are considered the modern science labs. There are still many computational and technical challenges ahead that must be addressed and we need supercomputers to help researchers obtain faster results. Whether it is analyzing a mammogram to determine if a woman has cancer or not, the time needed to analyze the problem can mean the difference between life and death. For iterative processes you may find that your competitor, who is using a faster computer, comes up with a better answer or a better product faster than you do. These are only a few examples of the importance of supercomputers in our everyday lives. But, as we continue to produce large digital sets of data, these systems become more important in our society to be able to analyze these big data at faster speeds to obtain new knowledge. Thus, the knowledge obtain from these powerful computers is not useful unles it is shared with the scientific community. The 5th International Supercomputing Conference in México (ISUM) hosted in Ensenada, Baja California, México, is a space that allows researchers to share their work in the uses of supercomputing. It is also an open forum to exchange ideas, to discuss and provide feedback on the work of research and industry centers, for networking and consolidate collaborative networks of researchers, as well as industry and academia. Works presented in this book addresses research from the analyisis of deterministic timetabling strategies for the generation of university timetables, a tcp/ip replication