Online

The complete book is available at:

https://www.bsc.es/education/predoctoral-phd/doctoral-symposium/8thbsc- so-doctoral-symposium//

Editor: Carolina Olmo, Michelle Pinto

Cover: Design based on artwork created by macrovector.com

Published by: Barcelona Supercomputing Center

Summary

  • Cost-aware prediction of uncorrected DRAM errors in the field 

    Boixaderas, Isaac; Carpenter, Paul; Radojkovic, Petar; Ayguadé Parra, Eduard (2021-05)
    Conference report
    Open Access
    One of the main causes of hardware failure in large-scale clusters is an uncorrected error in main memory [1]–[4]. Node failures are especially problematic in high-performance computing (HPC), where a single tightly-coupled ...
  • High-resolution decadal prediction - impacts on the predictability of the Pacific variability 

    Carréric, Aude; Ortega, Pablo (2021-05)
    Conference report
    Open Access
    Decadal prediction is a relatively recent field of research, attracting growing interest beyond the scientific community due to its strong potential to provide key information for decision making in economic sectors ...
  • Algebraic linelet preconditioner for the solution of the Poisson equation on boundary layer flows 

    de Olazábal, Ramiro; Lehmkuhl Barba, Oriol; Borrell Pol, Ricard (2021-05)
    Conference report
    Open Access
    An algebraic linelet preconditioner is presented, which works in parallel regardless of the mesh’s geometry and without imposing constraints on the domain partition. It is designed to deal with highly anisotropic meshes. ...
  • Optimizing execution on large-scale infrastructures by integrating task-based workflows and MPI 

    Elshazly, Hatem Mohamed Abdelfattah Eid; Lordan, Francesc; Ejarque, Jorge; Badia Sala, Rosa Maria (2021-05)
    Conference report
    Open Access
    While MPI [1] + X (where X is another parallel programming model) has been proposed and used by the community, we propose a hybrid programming model that combines taskbased model + MPI. Task-based workflows offer the ...
  • Quantum singular value decomposer 

    Bravo-Prieto, Carlos; García-Martín, Diego; Latorre, José Ignacio (2021-05)
    Conference report
    Open Access
    Quantum computing is emerging as a new computational paradigm that promises substantial speed-ups (exponential in some cases [1]) for a variety of problems, with a potentiallylarge impact on science, knowledge and ...
  • Optimizing the SpMV kernel on long-vector accelerators 

    Gómez Crespo, Constantino; Mantovani, Filippo; Focht, Erich; Casas, Marc (2021-05)
    Conference report
    Open Access
    Sparse Matrix-Vector multiplication (SpMV) is an essential kernel for parallel numerical applications. SpMV displays sparse and irregular data accesses, which complicate its vectorization. Such difficulties make SpMV ...
  • Super-resolution for downscaling climate data 

    Gómez-Gonzalez, Carlos; Serradell Maronda, Kim (2021-05)
    Conference report
    Open Access
    A common task in Earth Sciences is to infer climate information at local and regional scales from global climate models. An alternative to running expensive numerical models at high resolution is to use statistical downscaling ...
  • Determining the structure of small molecules via their pseudo-electrons and atoms 3D models using FPGA 

    González, César; Balocco, Simone; Pons, Ramon (2021-05)
    Conference report
    Open Access
    The particle-pair or particle-particle distance problem (ppdistance) appears in several scientific fields. The pp-distance calculation is a computationally demanding task involved, for instance, in the calculation of ...
  • Exploiting parallelism for CPU and GPU linear solvers on chemistry for atmospheric models 

    Guzman-Ruiz, Christian; Acosta, Mario; Jorba Casellas, Oriol (2021-05)
    Conference report
    Open Access
    Atmospheric models are a representation of dynamical, physical, chemical, dynamical, and radiative processes in the atmosphere [1]. Most of the algorithms used in these models have been developed decades ago. With the ...
  • StartR: a tool for large multi-dimensional data processing 

    Pérez-Zanón, Núria; Ho, An-Chi; Manubens, Nicolau; Benincasa, Francesco; Bretonnière, Pierre-Antoine (2021-05)
    Conference report
    Open Access
    Nowadays, the huge amount of data produced in various scientific domains has made data analysis challenging. In the climate science domain, with the constant increase of resolution in all possible dimensions of model ...
  • Curved geometry modeling: interpolation of subdivision features 

    Jiménez Ramos, Albert; Gargallo Peiró, Abel; Roca Navarro, Francisco Javier (2021-05)
    Conference report
    Open Access
    We present a nodal interpolation method to approximate a subdivision model. The main application is to model and represent curved geometry without gaps and preserving the required simulation intent. Accordingly, the ...
  • Mining the essential motions of pyruvate kinase 

    Jordà, Luis; Gelpi, Josep (2021-05)
    Conference report
    Open Access
    Our current study revolves around the dynamic characterization of the human erythrocyte pyruvate kinase (PKR). The deficiency of this protein is a common cause of nonspherocytic hemolytic anemia, a rare, autosomal ...
  • An architecture for automatic ML/AI workflow management and supervision 

    Liu, Peini; Guitart Fernández, Jordi (2021-05)
    Conference report
    Open Access
    Scientific computation problems have been faced with the need to analyze increasing amounts of data as part of their application workflows, and the science-based model is being combined with big data and machine learning ...
  • Bias-adjustment method for street-scale air quality models 

    Armengol, J.M.; Criado, A.; Benavides, Jaime; Jorba Casellas, Oriol; Guevara, Marc; Soret, Albert (2021-05)
    Conference report
    Open Access
    Air quality (AQ) is a growing concern, especially in urban areas where high-density populated regions are exposed to frequent exceedances of regulated pollutants. To take action in reducing citizen exposure to pollution, ...
  • Predicate-based filtering for multi-GPU utilization in directive-based programming 

    Matsumura, Kazuaki; García De Gonzalo, Simón; Peña, Antonio (2021-05)
    Conference report
    Open Access
    Designing and building supercomputers is a complex task in the field of high-performance computing (HPC). The hardware, middleware and algorithms need to effectively collaborate to achieve ideal results for massive and ...
  • Constraining the chemical composition of particulate matter in an atmospheric chemistry model 

    Navarro-Barboza, Hector; Pandolfi, Marco; Jorba Casellas, Oriol (2021-05)
    Conference report
    Open Access
    Atmospheric aerosols have a significant impact on the climate system [1]. Depending on their chemical composition, aerosols cool the atmosphere directly by scattering solar radiation and indirectly through aerosol–cloud ...
  • The multilayer community structure of medulloblastoma 

    Nuñez Carpintero, Iker; Cirillo, Davide; Valencia, Alfonso (2021-05)
    Conference report
    Open Access
    Biomedical multilayer networks offer a wide range of possibilities for the interpretation of the molecular basis of diseases; a particularly challenging task in the case of rare diseases, where the number of cases is ...
  • Epigenetic characterization of cholangiocarcinomas 

    Oliveros, Winona; Peiró, Sandra; Melé, Marta (2021-05)
    Conference report
    Open Access
    Cholangiocarcinoma (CCA) is a rare type of cancer and accounts for 10-20% of primary liver diagnosed cancers, being the second most common hepatobiliary malignancy.The only prospect of a long-term cure for these malignancies ...
  • VIA: a smart scratchpad for vector units with application to sparse matrix computations 

    Pavón Rivera, Julián; Unsal, Osman Sabri; Cristal Kestelman, Adrián (2021-05)
    Conference report
    Open Access
    Sparsematrix operations are critical kernels inmultiple application domains such as High Performance Computing, artificial intelligence and big data. Vector processing is widely used to improve performance on mathematical ...
  • Climate forecast analysis tools framework 

    Pérez-Zanón, Núria; Ho, An-Chi; Benincasa, Francesco; Bretonnière, Pierre-Antoine; Caron, Louis-Philippe; Chou, Chihchung; Delgado-Torres, Carlos; Lledó, Llorenç; Manubens, Nicolau; Palma, Lluís (2021-05)
    Conference report
    Open Access
    The climate forecast analysis tools provide functions implementing the steps required for the analysis of sub-seasonal, seasonal and decadal forecast and operational climate services, allowing researchers to manipulate ...
  • Tunaoil: a tuning algorithm strategy for reservoir simulation workloads 

    Portella, Felipe; Berral García, Josep Lluís (2021-05)
    Conference report
    Open Access
    The state-of-the-art techniques to tune the numerical parameters of reservoir simulators are based on running numerous simulations, specific for that purpose, to find good candidates. As the simulations for real petroleum ...
  • A machine learning based wall model for LES of turbulent flows 

    Radhakrishnan, Sarath; Lehmkuhl Barba, Oriol (2021-05)
    Conference report
    Open Access
    The trubulent flow of fluids is still an enigma for mathematicians and engineers alike. The partial differential equation that reperesents the flow of fluids does not have an analytical solution for turbulent regimes. ...
  • Unveiling the transcriptional and cellular landscape of age across human tissues 

    Ripoll-Cladellas, Aida; G.P. van der Wijst, Monique; Melé, Marta (2021-05)
    Conference report
    Open Access
    As the aging population grows progressively around the globe, the need to research and develop strategies to healthy aging is ever more critical and takes on new urgency1. Primary hallmarks of aging include cell autonomous ...
  • PerSVade: personalized structural variation detection in your species of interest 

    Schikora-Tamarit, Miquel Àngel; Gabaldón, Toni (2021-05)
    Conference report
    Open Access
    Structural variants (SV) such as translocations, inversions, deletions, and other genomic rearrangements can contribute significantly to genetic and phenotypic variability across many species. The role of SV has been ...
  • From comorbidities to gene expression fingerprints and back 

    Urda-García, Beatriz; Valencia, Alfonso (2021-05)
    Conference report
    Open Access
    Epidemiological evidence shows that some diseases tend to co-occur more than expected by chance and that patientspecific trends are observed. However, the molecular processes underlying these phenomena remain unclear. Here ...
  • Pushing the envelope on free TLB prefetching 

    Vavouliotis, Georgios; Álvarez Martí, Lluc; Casas, Marc (2021-05)
    Conference report
    Open Access
    Frequent Translation Lookaside Buffer (TLB) misses pose significant performance and energy overheads due to page walks required for fetching the translations. The address translation performance bottleneck is further ...
  • Tsunami inundation forecast in central Chile using stochastic earthquake scenarios 

    Zamora, Natalia; Gubler, Alejandra; Catalán, Patricio A.; Carvajal, Matías (2021-05)
    Conference report
    Open Access
    As demonstrated by recent mega-tsunamis, tsunami coastal inundation could vary substantially as a result of the source characteristics and the local geomorphologic-related- effects. Here, numerical simulations are used ...
  • Sensitivity of soluble iron deposition to soil mineralogy uncertainty 

    Bergas-Massó, Elisa; Gonçalves Ageitos, María; Pérez García-Pando, Carlos (2021-05)
    Conference report
    Open Access
    Mineral dust emitted from arid and semi-arid areas has several effects on the Earth system (e.g., perturbation of the radiative budget, interaction with cloud processes, implications on ocean and land biogeochemical ...
  • Analysis of hybrid genomes in the candida parapsilosis clade 

    del Olmo Toledo, V.; Gabaldón, T. (2021-05)
    Conference report
    Open Access
    The term inter-species hybridisation refers to the crossing of two divergent organisms, leading to a situation where the two parental genomes coexist in the same nuclear compartment. In higher eukaryotes, this scenario ...
  • Multiplex network uncovers chronic obstructive pulmonary disease endotypes 

    Olvera, Núria; Faner, Rosa; Valencia, Alfonso (2021-05)
    Conference report
    Open Access
    Chronic Obstructive Pulmonary Disease (COPD) was the fourth leading cause of death in the world in 2019, and its burden is projected to increase in coming decades in relation to the aging of the population [1]. COPD is ...
  • Lindaview: an OBDA-based tool for self-sufficiency assessment 

    Ortiz Santiago, Víctor Alejandro; Estañol Lamarca, Montserrat; Marinescu, Maria Cristina; Sancho Samsó, María Ribera; Teniente López, Ernest (2021-05)
    Conference report
    Open Access
    Poverty and social exclusion are a reality in every society. They are complex problems that require updated information and access to scattered data sources to make a proper assessment of a person’s situation. To help ...
  • Adaptive optics control with reinforcement learning: first steps 

    Pou Mulet, Bartomeu; Quiñones, Eduardo; Martín Muñoz, Mario (2021-05)
    Conference report
    Open Access
    When planar wavefronts from distant stars traverse the atmosphere, they become distorted due to the atmosphere’s inhomogeneous temperature distribution. Adaptive Optics (AO) is the field in charge of correcting those ...
  • Modeling nitric acid uptake by mineral dust 

    Soussé Villa, Rubén; Jorba Casellas, Oriol; Pérez García-Pando, Carlos (2021-05)
    Conference report
    Open Access
    Mineral dust is amongst the largest contributors to the global aerosol mass load and dominates climate effects over large areas of the Earth. Dust undergoes heterogeneous chemical reactions during transport that increase ...