8th BSC Doctoral Symposium, 11th-13th May 2021
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
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Cost-aware prediction of uncorrected DRAM errors in the field
(2021-05)
Conference report
Open AccessOne 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
(2021-05)
Conference report
Open AccessDecadal 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
(2021-05)
Conference report
Open AccessAn 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
(2021-05)
Conference report
Open AccessWhile 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
(2021-05)
Conference report
Open AccessQuantum 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
(2021-05)
Conference report
Open AccessSparse 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
(2021-05)
Conference report
Open AccessA 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
(2021-05)
Conference report
Open AccessThe 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
(2021-05)
Conference report
Open AccessAtmospheric 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
(2021-05)
Conference report
Open AccessNowadays, 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
(2021-05)
Conference report
Open AccessWe 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
(2021-05)
Conference report
Open AccessOur 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
(2021-05)
Conference report
Open AccessScientific 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
(2021-05)
Conference report
Open AccessAir 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
(2021-05)
Conference report
Open AccessDesigning 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
(2021-05)
Conference report
Open AccessAtmospheric 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
(2021-05)
Conference report
Open AccessBiomedical 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
(2021-05)
Conference report
Open AccessCholangiocarcinoma (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
(2021-05)
Conference report
Open AccessSparsematrix 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
(2021-05)
Conference report
Open AccessThe 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
(2021-05)
Conference report
Open AccessThe 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
(2021-05)
Conference report
Open AccessThe 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
(2021-05)
Conference report
Open AccessAs 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
(2021-05)
Conference report
Open AccessStructural 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
(2021-05)
Conference report
Open AccessEpidemiological 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
(2021-05)
Conference report
Open AccessFrequent 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
(2021-05)
Conference report
Open AccessAs 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
(2021-05)
Conference report
Open AccessMineral 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
(2021-05)
Conference report
Open AccessThe 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
(2021-05)
Conference report
Open AccessChronic 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
(2021-05)
Conference report
Open AccessPoverty 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
(2021-05)
Conference report
Open AccessWhen 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
(2021-05)
Conference report
Open AccessMineral 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 ...