4th BSC Severo Ochoa Doctoral Symposium, 2nd, 3rd and 4th, May 2017
The complete book is available at:
Editors: Nia Alexandrov, María José García Miraz
Cover: Design based on artwork created by macrovector.com
Published by: Barcelona Supercomputing Center
Suported by: The “Severo Ochoa Centres of Excellence” programme
Summary
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Acknowledgments
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Editorial comment
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Welcome address
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Keynote speaker
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Tutorial
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BSC International Doctoral Symposium agenda
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Relevant aspects of the seismic hazard in Colima, Mexico
(2017-05-04)
Conference report
Open AccessPerform probabilistic assessment of seismic hazard (PSHA) is a fundamental activity that offer valuable information to the seismic risk management of cities. In the present work some relevant aspects about a recent analysis ... -
Performance impact of a slower main memory: a case study of STT-MRAM in HPC
(2017-05-04)
Conference report
Open AccessMemory systems are major contributors to the deployment and operational costs of large-scale HPC clusters [1][2][3], as well as one of the most important design parameters that significantly affect system performance. In ... -
A new reliability-based data-driven approach to simulation-based models
(2017-05-04)
Conference report
Open AccessData Science has burst into simulation-based en-gineering sciences with an impressive impulse. However, data are never uncertainty-free and a suitable approach is needed to face data measurement errors and their intrinsic ... -
Testing simple models for street wind conditions in Barcelona
(2017-05-04)
Conference report
Open AccessStreet wind speed and direction drive models to estimate air quality levels at street scale. In this study, simple models are combined with a mesoscale meteorological model to provide wind conditions at street level. Then, ... -
Python for HPC geophysical electromagnetic applications: experiences and perspectives
(2017-05-04)
Conference report
Open AccessNowadays, the electromagnetic modelling are a fun-damental tool in geophysics due to their wide field of application: hydrocarbon and mineral exploration, reservoir monitoring, CO storage characterization, geothermal ... -
Aggregating and managing memory capacity across computing nodes in cloud environments
(2017-05-04)
Conference report
Open AccessManaging memory capacity in cloud environments is a challenging issue, mainly due to the temporal variability in virtual machine (VM) memory demand. The Virtual Machine Manager or the hypervisor allocates a portion of the ... -
Discovering ship navigation patterns towards environmental impact modeling
(2017-05-04)
Conference report
Open AccessIn this work a data pipe-line to manage and extract patterns from time-series is described. The patterns found with a combination of Conditional Restricted Boltzmann Machine (CRBM) and k-Means algorithms are then validated ... -
Production planning and scheduling optimization model: a case of study for a glass container company
(2017-05-04)
Conference report
Open AccessBased on a case study, this paper deals with the production planning and scheduling problem of the glass con-tainer industry. This is a facility production system that has a set of furnaces where the glass is produced in ... -
Web-based tool for the annotation of pathological variants on proteins: PMut 2017 update
(2017-05-04)
Conference report
Open AccessAssessing the impact of amino acid mutations in human health is an important challenge in biomedical research. As sequencing technologies are more available, and more individual genomes become accessible, the number of ... -
Programming models for mobile environments
(2017-05-04)
Conference report
Open AccessIn this article, we present COMPSs-Mobile: a framework that aims to ease the development of MCC applications by freeing the developer of all these concerns. At packaging time applications, written following its own programming ... -
Machine learning performance prediction model for heterogeneous systems
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Energy optimizing methodologies on heterogeneous data centers
(2017-05-04)
Conference report
Open AccessIn 2013, U.S. data centers accounted for 2.2% of the country’s total electricity consumption, a figure that is projected to increase rapidly over the next decade. Many important work-loads are interactive, and they demand ... -
Data-driven crowd simulation
(2017-05-04)
Conference report
Open AccessOur objective is to simulate entire cities with the most realistic possible scenario. This kind of systems require a lot of processing power, therefore we use hybrid computer clusters with graphics cards (GPUs). GPUs allow ... -
pyDockDNA: a new approach for protein-DNA docking
(2017-05-04)
Conference report
Open AccessHere we present pyDockDNA, which is based on the pyDock program, with a new module for reading and parsing DNA molecules. The protocol is composed of two major steps: sampling and scoring. The first sampling step consists ... -
Protein modelling for enzyme engineering
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Exploring the use of mixed precision in NEMO
(2017-05-04)
Conference report
Open AccessIt has been a widely extended practice in scientific computing to use 64-bit to represent data without even considering which level of precision is really needed. In many applications, 32-bit should provide enough accuracy, ... -
ORCHESTRA: an asyncrhonous non-blocking distributed GVT algorithm
(2017-05-04)
Conference report
Open AccessTaking advantage of high computing capabilities of modern distributed architectures is fundamental to run large-scale simulation models based on the Parallel Discrete Event Simulation (PDES) paradigm. In particular, by ... -
Level of detail for complex urban scenes with varied animated crowds, using XML
(2017-05-04)
Conference report
Open AccessWe present a system capable of handling several thousands of varied animated characters within a crowd. These characters are designed to have geometric, color animation and behaviour variety, nevertheless when a crowd ... -
Uncertainty in near-surface wind speed trends at seasonal time scales
(2017-05-04)
Conference report
Open AccessObservational studies have identified wind speed trends in the last decades [1,2] attributed to several factors such as changes in the land use, aerosol emissions or atmospheric circulation. However, in spite of the potential ... -
Effect of terrain relief on dust transport over complex terrains in West Asia
(2017-05-04)
Conference report
Open AccessThis work investigates the impact of orography on dust transport using the multi-scale NMMB/BSC-Dust model. For this purpose, two model simulations at horizontal resolutions of 0.03º x 0.03º (Low-resolution; LR) and 0.3º ... -
Performance analysis on the Intel Knights Landing architecture
(2017-05-04)
Conference report
Open AccessOne of the emerging architectures in HPC systems is Intel’s Knights Landing (KNL) many core chip, which will also be part of BSC’s next HPC installation MareNostrum 4. KNL is the code name of the second generation of Intel ... -
SMuFin2: generating and implementing new and more efficient search engines integrated in particular hardware architectures
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GUIDANCE: an integrated framework for large-scale genome and phenome-wide association studies on parallel computing platforms
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Functional implications of the structural genomic rearrangements in cancer
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Classification of retrotransposition during somatic variant calling in cancer genomes
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Advanced vector architectures for future applications
(2017-05-04)
Conference report
Open AccessAlthough there has been a lot of progress in the domain of automatic knowledge discovery (e.g., deep learning), we believe humans play a central role in the data analysis task. Therefore, we propose to build a visual stream ... -
A case for code-representative microbenchmarks
(2017-05-04)
Conference report
Open AccessMicrobenchmarks are fundamental in the design of a microarchitecture. They allow rapid evaluation of the system, while incurring little exploration overhead. One key design aspect is the thermal design point (TDP), the ... -
Esterases computational study
(2017-05-04)
Conference report
Open AccessIn our project, we are focusing on two different esterases called LAE6 and LAE5. LAE6 is very promiscuous since it presents activity towards a wide range of different substrates, whereas LAE5 presents activity towards few ... -
Prediction of binding energies upon mutation in 3D-structure-known complexes through PyDock scoring functions
(2017-05-04)
Conference report
Open AccessThe main objective of this work is to build a simple but robust predictor of binding energy changes upon mutation, once structural information is provided. Three different tools are being employed: First, given the wild ... -
Deep and cognitive learning applied to Precision Medicine: the initial experiments linking (epi)genome to phenotypes-disease characteristics
(2017-05-04)
Conference report
Open AccessPresent-day era of Big Data provides the unique opportunity to develop innovative approaches for data analysis to find new insights into specialized fields of biomedical research such as Precision Medicine [1]. Precision ... -
Exploring the relationship between gene expression and topological properties of Arabidopsis thaliana interactome network.
(2017-05-04)
Conference report
Open AccessThe aim of this study is to integrate and link up transcriptomic data with biological networks approaches. The main objective was to determinate the correlation of transcriptomic profiles with PPI topology, seeking to ... -
Composite materials calculation using HPC-based multiscale technique
(2017-05-04)
Conference report
Open AccessCalculating the behavior of large composite material structures still demanding large computational effort. The solu-tion proposed to tackle the problem is to combine multi-scale homogenization methods with the high ... -
Saiph, a domain specific language for computational fluid dynamics simulations
(2017-05-04)
Open AccessNowadays, High-Performance Computing (HPC) is assuming an increasingly central role in scientific research while computer architectures are becoming more and more hetero-geneous and using different parallel programming ... -
Excited state gradients within a polarizable QM/MM formulation
(2017-05-04)
Conference report
Open AccessMultiscale approaches that partition the system into an active site (where the electronic process under study occurs) and a remaining region, the environment, have proven to be good strategies for the computation of ... -
Impact of aerosol microphysical properties on mass scattering cross sections
(2017-05-04)
Conference report
Open AccessWe assessed the sensitivity of simulated mass scattering cross sections (αλsca [m2/g]) of three aerosol perturbed particle microphysical properties and derived constraintspecies to on these microphysical properties, suitable ... -
Stabilization of microturbulence by fast ions n ASDEX upgrade
(2017-05-04)
Conference report
Open AccessThe goal of the present work is to study the impact of fast ions, generated by ICRH, on microturbulence. Our methodology is similar to that in [2] and is based on extensive simulations of discharges carried out on the ASDEX ... -
Vortex Induced Vibration (VIV) of circular cylinders at high Reynolds numbers
(2017-05-04)
Conference report
Open AccessIn this contribution, preliminary results on the study of the VIV at high Reynolds numbers are presented. First, a validation of the code and the turbulent LES WALE formulation in conjunction with a low-dissipative ... -
Application of reduced order modelling in geophysics
(2017-05-04)
Conference report
Open AccessThe main objective of this work is to effectively design an apriori Reduce Order Method solver to solve parametric high dimensional geophysical problems in a cost effective and fast manner. -
Simulations of Alfvénic modes in TJ-II Stellarator
(2017-05-04)
Conference report
Open AccessAlfvénic modes are one of the subclass of instabilities prevalent in burning plasmas due to interaction of energetic particles with background plasma. In this paper we investigate the properties of these modes with 3D ... -
Leveraging FPGAs to accelerate the query processing of SQL-based databases
(2017-05-04)
Conference report
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Time-predictable parallel programming models
(2017-05-04)
Conference report
Open AccessEmbedded Computing (EC) systems are increas-ingly concerned with providing higher performance in real-time while HPC applications require huge amounts of information to be processed within a bounded amount of time. Addressing ... -
On the suitability of time-randomized processors for secure and reliable high-performance computing
(2017-05-04)
Conference report
Open AccessTime-randomized processor (TRP) architectures have been shown as one of the most promising approaches to deal with the overwhelming complexity of the timing analysis of high complex processor architectures for safety-related ... -
Main memory in HPC: do we need more or could we live with less?
(2017-05-04)
Conference report
Open AccessThis study analyzes the memory capacity requirements of important HPC benchmarks and applications. We find that the High Performance Conjugate Gradients benchmark could be an important success story for 3D-stacked memories ...
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