The complete book is available at:

https://www.bsc.es/education/predoctoral-phd/doctoral-symposium/9thbsc- so-doctoral-symposium//

Editor: Carolina Olmo

Cover: Design based on artwork created by macrovector.com

Published by: Barcelona Supercomputing Center

Summary

  • Distributed tabulation of flamelet lookup tables 

    Abel, Nicholas; Borrell Pol, Ricard; Mira Martínez, Daniel (2022-05)
    Conference report
    Open Access
    One of the fundamental questions in combustion simulation is how to account for detailed chemistry effects, while controlling both the error of the chemical scheme and the computational cost. Combustion chemistry is ...
  • TACL: Interoperating asynchronous device APIs with task-based programming models 

    Alvarez, David; Sala Penadés, Kevin; Beltran, Vicenç (2022-05)
    Conference report
    Open Access
    Heterogeneous architectures have become commonplace in modern HPC systems. Eight of the world’s top ten supercomputers have accelerators, and the up-and-coming MareNostrum 5 will feature accelerated partitions. However, ...
  • Numerical simulations for the atomic beam probe 

    Aradi, Mátyás; Mantsinen, Mervi; Futatani, Shimpei (2022-05)
    Conference report
    Open Access
    Fusion plasmas are complex systems with several physical parameters which need continuous control and adjustment. Most plasma diagnostics have limitations of applications regarding the spatial, temporal resolution with ...
  • Focus! rating XAI methods and finding biases 

    Arias Duart, Anna; Parés, Ferran; Garcia-Gasulla, Dario (2022-05)
    Conference report
    Open Access
    Explainability has become a major topic of research in Artificial Intelligence (AI), aimed at increasing trust in models such as Deep Learning (DL) networks. However, trustworthy models cannot be achieved with explainable ...
  • Preparing plasma heating in ITER using integrated modelling 

    Bensadón, Tomás; Mantsinen, Mervi; Jonsson, Thomas (2022-05)
    Conference report
    Open Access
    Nuclear fusion takes place when two light nuclei combine to make a heavier nucleus, releasing energy in the process. Magnetic confinement fusion attempts to achieve fusion and use this energy by confining the fuel in ...
  • The development of high-order methods for finite elements to study turbulent reacting flow 

    Blanco Casares, Antonio; Mira Martínez, Daniel; Lehmkuhl Barba, Oriol (2022-05)
    Conference report
    Open Access
    Numerical methods for solving differential equations are the base of any computational simulation. The finite element method (FEM) has emerged as one of the most powerful numerical methods so far devised, mainly because of ...
  • Characterizing transcriptome variation in human populations at single-cell resolution 

    Chazarra-Gil, Ruben; Melé, Marta (2022-05)
    Conference report
    Open Access
    Phenotypic diversity in human populations is a direct consequence of genetic variation, which acts in conjunction with environmental and behavioral factors to produce phenotypic variation, from eye color and height to ...
  • Nuclear fusion reactor materials: modelling atomic-scale irradiation damage in metal 

    Chessey, Mary K.; Gutiérrez Moreno, J. Julio; García Romero, Marina; Settembri, Paolo; Kearney, Eoin; Mantsinen, Mervi (2022-05)
    Conference report
    Open Access
    Achieving nuclear fusion as an energy source on Earth is a practical goal that relies on continuing scientific and engineering innovation. Functional fusion reactors around the world today allow scientists and engineers ...
  • Comparison of five strategies for seasonal prediction of bioclimatic indicators in the olive sector 

    Chihchung, Chou; Marcos-Matamoros, Raül; González-Reviriego, Nube (2022-05)
    Conference report
    Open Access
    The forecast quality of five seasonal prediction strategies used to obtain tailored bioclimatic indicators in the olive sector has been assessed over the Iberian Peninsula (IP). In total, five indicators have been ...
  • Discovering the Ethereum2 P2P network 

    Cortes Goicoechea, Mikel; Bautista Gomez, Leonardo (2022-05)
    Conference report
    Open Access
    Achieving the equilibrium between scalability, sus­tainability, and security while keeping decentralization has pre­ vailed as the target solution for decentralized blockchain ap­ plications over the last few years. ...
  • Reaching a modular, domain-agnostic and containerized development in biomedical Natural Language Processing systems. 

    Corvi, Javier; Gelpi, Josep; Capella Gutiérrez, Salvador (2022-05)
    Conference report
    Open Access
    The last century saw an exponential increase in scientific publications in the biomedical domain. Despite the potential value of this knowledge; most of this data is only available as unstructured textual literature, which ...
  • Multi-model forecast quality assessment of CMIP6 decadal predictions 

    Delgado Torres, Carlos; Donat, Markus; Soret, Albert (2022-05)
    Conference report
    Open Access
    Decadal climate predictions are a new source of climate information for inter-annual to decadal time scales (filling the gap between seasonal predictions and climate projections), which is of increasing interest to users. ...
  • A platform for antibody design 

    Díaz Rovira, Anna Maria; Guallar, Victor (2022-05)
    Conference report
    Open Access
    Antibodies are specialized proteins produced by our adaptive immune system to identify and neutralize specific molecules (antigens) of foreign objects, such as pathogenic microorganisms or infected cells. Due to their ...
  • PredIG: a predictor of T-cell immunogenicity 

    Farriol-Duran, R.; Vazquez, M.; Porta, E.; Guallar, V. (2022-05)
    Conference report
    Open Access
    The identification of immunogenic epitopes (such as fragments of proteins, in particular peptides, that can trigger an immune response) is a fundamental need for immune-based therapies. A computational tool that could ...
  • Designing a cloud and HPC based M&S platform to Investigate the IVD diseases mechanisms 

    Ferri, Maria Paola; Codo, Laia; Gelpi, Josep Lluis (2022-05)
    Conference report
    Open Access
    The main objective of the PhD proposal consists of the creation of a platform for IVD Models & Simulations (M&S) tools and their integration into automated workflows, within the HORIZON MSCA Disc4All project. Based on the ...
  • Improving resource usage in large FPGA accelerators 

    Filgueras Izquierdo, Antonio; Alvarez, Carlos; Jiménez González, Daniel (2022-05)
    Conference report
    Open Access
    In modern FPGA devices, place and route has become a difficult task for the underlying FPGA implementation tools. This is caused by an increase of device size and complexity. As devices grow in size and number of resources, ...
  • Foreign and domestic contributions to surface ozone in Spain 

    Garatachea Solé, Roger; Jorba Casellas, Oriol; Pérez García-Pando, Carlos (2022-05)
    Conference report
    Open Access
    Tropospheric ozone (O3) exerts strong adverse impacts on human health, climate, vegetation, biodiversity, agricultural crop yields and thus food security. O3 is formed in the atmosphere through non-linear photochemical ...
  • CAMP first GPU solver: a solution to accelerate chemistry in atmospheric models 

    Guzman-Ruiz, Christian; Acosta Cobos, Mario César; Jorba, Oriol (2022-05)
    Conference report
    Open Access
    Atmospheric models are a representation of dynamical, physical, chemical, dynamical, and radiative processes in the atmosphere [1]. The load of these models is often spread across multiple processes in HPC environments. ...
  • Implementation of cellular transport models within a multiscale simulation software 

    Hayoun-Mya, Othmane; Ponce De Leon, Miguel; Montagud, Arnau; Valencia, Alfonso (2022-05)
    Conference report
    Open Access
    Agent-based models (ABM) have been increasingly employed to study dynamics of biological systems. However, these mostly lack transport mechanisms that interface between the agents and their microenvironment. We considered ...
  • Adaptive points to estimate the Lebesgue constant on the simplex 

    Jiménez Ramos, Albert; Gargallo Peiró, Abel; Roca, Xevi (2022-05)
    Conference report
    Open Access
    We present a novel adaptive sampling method to estimate the Lebesgue constant of nodal sets in n-dimensional simplices. The main application of this estimation is to assess the interpolation capabilities of a nodal ...
  • Respiratory tract microbiome modifications after lung transplantation and its impact in CLAD 

    Khannous-Lleiffe; Gabaldón, Toni (2022-05)
    Conference report
    Open Access
    Survival after lung transplantation is limited in large part due to the high incidence of chronic lung allograft dysfunction (CLAD). Infection is a recognized risk factor for the development of CLAD, and both acute infection ...
  • Numerical investigation of unsteady processes in combustion using flame transfer function 

    Koumides, Phivos Andreou; Mira Martínez, Daniel; Pérez-Sánchez, Eduardo J. (2022-05)
    Conference report
    Open Access
    Hydrogen has been recognized as a clean and sustainable energy carrier to help deliver significant emission reductions and is regarded as an accelerator in achieving a low carbon future. One of the main limitations of the ...
  • Ground-level ozone simulations improved by updating land cover databases 

    López, Franco; Di Tomaso, Enza; Jorba, Oriol (2022-05)
    Conference report
    Open Access
    Tropospheric ozone (O3) is one of the pollutants which raises great concern to the World Health Organization (WHO) because of the health effects associated with its exposure. It is formed in the atmosphere through non-linear ...
  • Low input promoter capture Hi-C method enables to decipher the molecular mechanisms underlying genetically complex diseases 

    López-Martí, Paula; Javierre, Biola M; Valencia, Alfonso (2022-05)
    Conference report
    Open Access
    Interactions between promoters and their regulatory elements (e.g., enhancers) are cell-type specific. Moreover, these promoter-enhancer contacts have been shown to be crucial for proper gene expression levels, and their ...
  • FAIRsoft - A practical implementation of FAIR principles for research software 

    Martín del Pico, Eva; Capella Gutiérrez, Salvador; Gelpi, Josep (2022-05)
    Conference report
    Open Access
    Computational tools are increasingly becoming constitutive parts of scientific research, from experimentation and data collection to the dissemination and storage of results. Unfortunately, however, research software is ...
  • Task scheduling sensitivity to L1 cache settings on an area-constrained 32-core RISC-V processor 

    Morais, Lucas; Jiménez-González, Daniel; Álvarez, Carlos (2022-05)
    Conference report
    Open Access
    High-performance applications are highly sensitive to memory performance characteristics. While programs with comparatively low memory-to-computation ratio are less likely to be hampered by limited memory bandwidth, most ...
  • Rational enzyme engineering of different active sites on a xylanase 

    Muñoz, Rubén; Guallar, Victor (2022-05)
    Conference report
    Open Access
    In the current times, many processes in industry are switching from using chemical compounds, requiring extreme conditions, to enzymatic technology, which is a more sustainable and greener alternative [1]. In the paper ...
  • Characterisation of ozone levels and associated NMVOC emissions in Spain: 

    Oliveira, Kevin; Guevara Vilardell, Marc (2022-05)
    Conference report
    Open Access
    In Europe, for the last decades, multiple efforts have been made to regulate and reduce air pollution. Despite the overall reduction trends in emissions, air quality remains poor in many areas, where 99% of the urban ...
  • b8c: an FPGA-friendly sparse matrix representation suitable for the SpMV kernel 

    Oliver, José; Ayguadé Parra, Eduard; Martorell Bofill, Xavier; Álvarez, Carlos (2022-05)
    Conference report
    Open Access
    Sparse Matrix-Vector multiplication (SpMV), computing y = Ax where y and x are dense vectors and A is a sparse matrix, is a key kernel in many HPC applications. SpMV exhibits a kind of memory access that is extremely hard ...
  • Organic particle export, remineralization and advection in the North Atlantic mesopelagic layer 

    Orihuela-García, M. Andrea; Gali Tapias, Martí; Ruprich-Robert, Yohan (2022-05)
    Conference report
    Open Access
    The mesopelagic layer of the oceans extends between ~200 and 1000 m depth and plays a fundamental role in global biogeochemical cycles and climate. In addition, it hosts a massive biomass of zooplankton and small fish, ...
  • QUARQ: QUick approximate and relaxed querying 

    Ortiz Santiago, Víctor Alejandro; Marinescu, Maria Cristina; Sancho Samsó, María Ribera (2022-05)
    Conference report
    Open Access
    Executing queries over Linked Open Data (LOD) is a complex task. The total number of sources triggered by a single query cannot be known in advance, nor the reasoning complexity applied to each source. In order to avoid ...
  • HBM, present and future of HPC based on FPGAs 

    Perdomo Hourné, Elias A.; Cervero, Teresa; Martorell Bofill, Xavier (2022-05)
    Conference report
    Open Access
    In the past decades, advances in the speed of commodity CPUs have far out-paced advances in memory latency. Mainmemory access is therefore increasingly a performance bottleneck for many computer applications, including HPC ...
  • Development of corrections for the absolute free binding energy prediction 

    Puch-Giner, Ignasi; Municoy Terol, Martí; Guallar, Victor (2022-05)
    Conference report
    Open Access
    The early stages of drug design rely on hit discovery programs, where initial possible inhibitors’ binding affinities are assessed when bound to their biological target. It is an expensive and time-consuming process, ...
  • Experimental analysis on the NXP’s T2080 cache coherence: a step towards MPSoCs in critical systems 

    Pujol, Roger; Hassan, Mohamed; Cazorla Almeida, Francisco Javier (2022-05)
    Conference report
    Open Access
    The adoption of complex MPSoCs in critical real-time embedded systems [1], [2] mandates a detailed analysis of their architecture to facilitate certification [3]. This analysis is hindered by the lack of a thorough ...
  • Transcriptome analysis of differential gene expression in disease 

    Ramirez, Jose Miguel; García-Pérez, Raquel; Melé, Marta (2022-05)
    Conference report
    Open Access
    Many diseases strongly impact the human transcriptome at the gene expression level [1]. However, previous work has focused on accessible tissues [2], and has not incorporated the effect of demographic traits, known risk ...
  • CSDownscale: an R package for statistical downscaling 

    Ramón, Jaume; Lledó, Llorenç; Palma, Lluís; Delgado-Torres, Carlos; Marcos, Raül (2022-05)
    Conference report
    Open Access
    Downscaling is any procedure to infer highresolution information from low-resolution variables. Many of these techniques have been defined and applied to climate predictions, which suffer from important biases due to the ...
  • Non-reacting large eddy simulation of a low swirl burner 

    Rodrigues, Fredherico; Garíıa-Oliver, José Maria; Mira Martínez, Daniel (2022-05)
    Conference report
    Open Access
    Reduction of the emission of pollutants is one of the main concerns in the study of combustion today. Thermal NOx for example, is generated when high temperatures are achieved in the combustion process. The use of Lean ...
  • Space shuttle: a test vehicle for the reliability of the SkyWater 130nm PDK using OpenLane and the Google/E-fabless shuttle run for future space systems 

    Rodríguez Ferrández, Iván; Jover-Alvarez, Alvaro; Kosmidis, Leonidas; Steenari, David (2022-05)
    Conference report
    Open Access
    The ASIC industry is experiencing a massive change in the recent years with more and more small and medium business entering the custom ASIC development. This trend is fueled by the recent open hardware movement and relevant ...
  • RosneT: a block tensor algebra library for out-of-core quantum computing simulation 

    Sanchez-Ramirez, Sergio; Conejero, Javier; Garcia-Saez, Artur (2022-05)
    Conference report
    Open Access
    With recent Quantum Devices showing increasing capabilities to perform controlled operations, further development on Quantum Algorithms may benefit from Quantum Simulations on classical hardware. Among important applications ...
  • JLOH: extracting loss of heterozygosity blocks from short-read sequencing data 

    Schiavinato, Matteo; del Olmo, Valentina; Gabaldón, Toni (2022-05)
    Conference report
    Open Access
    Loss of heterozygosity (LOH) happens when a heterozygous genome loses one of the two alleles at a locus. This may have an evolutionary advantage in highly unstable genomes such as those of hybrids (Smukowski Heil et al., ...
  • Exploring the recent evolution of yeast pathogens using the CandidaMine database 

    Schikora-Tamarit, Miquel Àngel; Gabaldón#, Toni (2022-05)
    Conference report
    Open Access
    Advances in medicine (such as chemotherapy or transplants) have extended the life expectancy of patients at the cost of impairing their immune system. This has generated an increasing population of patients highly susceptible ...
  • Investigating memory prefetcher performance over parallel applications: from real to simulated 

    Girelli, Valéria S.; Moreira, Francis B.; Serpa, Matheus S.; Santos, Danilo C.; Navaux, Philippe O. A. (2022-05)
    Conference report
    Open Access
    In recent years, there have been significant advances in the performance of processors, exemplified by the reduction of transistor size and the increase in the number of cores in a processor. Conversely, the memory subsystem ...
  • Hyperparameter optimization using agents for large scale machine learning 

    Vergés Boncompte, Pere; Vlassov, Vladimir; Badia, Rosa M. (2022-05)
    Conference report
    Open Access
    Machine learning (ML) has become an essential tool for humans to get rational predictions in different aspects of their lives. Hyperparameter algorithms are a tool for creating better ML models. The hyperparameter algorithms ...