Book of Abstracts 3rd BSC International Doctoral Symposium Editors Nia Alexandrov María José García Miraz Graphic and Cover Design: Cristian Opi Muro Laura Bermúdez Guerrero This is an open access book registered at UPC Commons (http://upcommons.upc.edu) under a Creative Commons license to protect its contents and increase its visibility. This book is available at http://www.bsc.es/doctoral-symposium-2016 published by: Barcelona Supercomputing Center supported by: The “Severo Ochoa Centres of Excellence" programme 3rd Edition, September 2016 Introduction ACKNOWLEDGEMENTS The BSC Education & Training team gratefully acknowledges all the PhD candidates, Postdoc researchers, experts and especially the Keynote Speaker Francisco J. Doblas-Reyes and the tutorial lecturers Vassil Alexandrov and Javier Espinosa, for contributing to this Book of Abstracts and participating in the 3rd BSC International Doctoral Symposium 2016. We also wish to expressly thank the volunteers that supported the organisation of the event: Carles Riera and Felipe Nathan De Oliveira. BSC Education & Training team [email protected] 5 Introduction 6 Introduction CONTENTS EDITORIAL COMMENT ................................................................................................ 11 WELCOME ADDRESS .................................................................................................. 13 PROGRAM .................................................................................................................... 15 KEYNOTE SPEAKER .................................................................................................... 19 TUTORIALS .................................................................................................................. 20 TALK PRESENTERS .................................................................................................... 23 POSTER PRESENTERS ............................................................................................... 34 EXTENDED ................................................................................................................... 43 ABSTRACTS ................................................................................................................. 43 Development of a wind energy climate service based on seasonal climate prediction ..................... 44 Assessment of Meteorological Models for Air Pollution Transport: Analysis between Mexico and Puebla Metropolitan Areas ............................................................................................................... 47 Enhanced Monte Carlo Methods for Sparse Approximate Matrix Inversion ................................... 50 Dynamic Load Balancing for hybrid applications ............................................................................ 52 Effects of detailed ventricular anatomy on the blood flow ............................................................... 54 Probabilistic seismic risk assessment using CRISIS2015 & USERISK2015. Application to buildings of Barcelona, Spain. .......................................................................................................... 56 DimLightSim: Optical/Electrical Network Simulator for HPC Applications ....................................... 59 Integrated approach to assignment, scheduling and routing problems .......................................... 63 Innovative Algorithm for Particles Transport in a Fluid .................................................................... 66 Validating the Reliability of WCET Estimates with MBPTA ............................................................... 69 Efficient and versatile data analytics for deep networks ................................................................. 72 Numbering along advection for Gauss-Seidel and Bidiagonal preconditioners ............................... 74 7 Introduction Exploring the protonation properties of photosynthetic phycobiliprotein pigments from molecular modeling and spectral line shapes .................................................................................................... 76 Clustering the Roman Empire: the use of multivariable analysis to understand cultural dynamics 78 Assessing drug-protein binding by simulation of stereoselective energy transfer dynamics: electronic interactions between tryptophan and flurbiprofen ............................................................ 80 Extrapolations of the fusion performance in JET ............................................................................. 83 Regional Arctic sea ice predictability and prediction on seasonal to interannual timescales ........... 86 Genomic Instability Promoted by Expression of Human Transposase-Derived Gene ..................... 88 Docking through Democracy Re-ranking protein-protein decoys with a voting system .................. 89 Block-Based Execution on an Integrated Vector-Scalar In-Order Core ............................................ 90 Photoprotection and triplet energy transfer in higher plants: the role of electronic and nuclear fluctuations ........................................................................................................................................ 92 Modelling the Co-evolution of Trade and Culture ............................................................................ 95 Simulating Gravitational Collapse with Arbitrary-Precision Arithmetic ........................................... 97 Crowd Simulation and Visualization ................................................................................................. 99 Reproducing crowd turbulence with Verlet integration and agent modeling ................................. 102 Generation of a simulation scenario from medical data: Carto and MRI ........................................ 105 How Can We improve Energy Efficiency through User-directed Vectorization and Task-based Parallelization? ................................................................................................................................ 107 Using Graph Partitioning to Accelerate Task-Based Parallel Applications .................................... 110 Improving Scalability of Task-Based Programs ............................................................................. 113 Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses . 115 Enrichment of Virtual Screening results using induced-fit techniques ........................................... 122 On the way to real time protein-ligand sampling ............................................................................ 125 PMut2: a web-based tool for predicting pathological mutations on proteins ................................. 128 Per-Task Energy Metering and Accounting in the Multicore era ................................................... 131 Task Dependences Management Hardware Acceleration for Task-based Dataflow Programming models ............................................................................................................................................. 134 The OmpSs Reductions Model and how to deal with Scatter-Updates .......................................... 137 Runtime Estimation of Performance–Power in CMPs under QoS constraints ............................... 140 Conformational landscape of small ligands: A Multilevel strategy to determine the conformational penalty of bioactive ligands ............................................................................................................ 143 Characteritzation of Protein-Protein Interfaces and Identification of Transient Cavities for its Modulation. ..................................................................................................................................... 146 8 Introduction Improvement of Protein-Ligand Binding Affinity Prediction using Machine Learning Techniques ........................................................................................................................................................ 149 Towards accurate solvation free energies of large biological systems ........................................... 152 POSTERS ................................................................................................................... 154 9 Introduction 10 Introduction EDITORIAL COMMENT We are proud to present the Book of Abstracts for the 3rd BSC International Doctoral Symposium. During more than ten years, the Barcelona Supercomputing Center has been receiving undergraduate, master and PhD students, and providing them training and skills to develop a successful career. Many of those students are now researchers and experts at BSC and in other international research institutions. In fact, the number of students has never decreased. On the contrary, their number and research areas have grown and we noticed that these highly qualified students, especially the PhD candidates, needed a forum to present their findings and fruitfully exchange ideas. As a result, in 2014, the first BSC Doctoral Symposium was born. Last year, a total of 34 presentations were given, 32 posters were exhibited, a two days training on an Introduction to Scientific Writing was conducted; and we reached more than 90 attendees. Furthermore, we opened the participation to students all over the world and have succeeded enrolling students from different countries In this third edition of the BSC Doctoral Symposium we have planned a keynote speaker’ talk, and two extensive training