Rosa M. Badia

Rosa M. Badia
Barcelona Supercomputing Center · Department of Computer Science

PhD

About

343
Publications
35,130
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
6,440
Citations
Introduction
Rosa M. Badia currently works at the Department of Computer Science, Barcelona Supercomputing Center. Rosa M. does research in Programming Models, Computer Architecture and Parallel Computing. She is contributing to several EU projects, such as TANGO, mf2C, CLASS, BioExcel, between others.

Publications

Publications (343)
Article
The evolution of High-Performance Computing (HPC) platforms enables the design and execution of progressively larger and more complex workflow applications in these systems. The complexity comes not only from the number of elements that compose the workflows but also from the type of computations they perform. While traditional HPC workflows target...
Preprint
Full-text available
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the pipelines on distributed systems increases the complexity of these developments. To address these issues, we prop...
Article
CFD users of supercomputers usually resort to rule-of-thumb methods to select the number of subdomains (partitions) when relying on MPI-based parallelization. One common approach is to set a minimum number of elements or cells per subdomain, under which the parallel efficiency of the code is “known” to fall below a subjective level, say 80%. The si...
Article
High-performance data analytics (HPDA) is a current trend in e-science research that aims to integrate traditional HPC with recent data analytic frameworks. Most of the work done in this field has focused on improving data analytic frameworks by implementing their engines on top of HPC technologies such as Message Passing Interface. However, there...
Article
Exascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups...
Preprint
Full-text available
The evolution of High-Performance Computing (HPC) platforms enables the design and execution of progressively larger and more complex workflow applications in these systems. The complexity comes not only from the number of elements that compose the workflows but also from the type of computations they perform. While traditional HPC workflows target...
Article
Full-text available
The evolution of High-Performance Computing (HPC) platforms enables the design and execution of progressively larger and more complex workflow applications in these systems. The complexity comes not only from the number of elements that compose the workflows but also from the type of computations they perform. While traditional HPC workflows target...
Article
Context. The improvements in the precision of the published data in Gaia EDR3 with respect to Gaia DR2, particularly for parallaxes and proper motions, offer the opportunity to increase the number of known open clusters in the Milky Way by detecting farther and fainter objects that have thus far gone unnoticed. Aims. Our aim is to continue to compl...
Preprint
Full-text available
With the advent of more powerful Quantum Computers, the need for larger Quantum Simulations has boosted. As the amount of resources grows exponentially with size of the target system Tensor Networks emerge as an optimal framework with which we represent Quantum States in tensor factorizations. As the extent of a tensor network increases, so does th...
Preprint
Full-text available
CFD users of supercomputers usually resort to rule-of-thumb methods to select the number of subdomains (partitions) when relying on MPI-based parallelization. One common approach is to set a minimum number of elements or cells per subdomain, under which the parallel efficiency of the code is "known" to fall below a subjective level, say 80%. The si...
Preprint
Full-text available
Storage systems have not kept the same technology improvement rate as computing systems. As applications produce more and more data, I/O becomes the limiting factor for increasing application performance. I/O congestion caused by concurrent access to storage devices is one of the main obstacles that cause I/O performance degradation and, consequent...
Preprint
Full-text available
The improvements in the precision of the published data in \textit{Gaia} EDR3 with respect to \textit{Gaia} DR2, particularly for parallaxes and proper motions, offer the opportunity to increase the number of known open clusters in the Milky Way by detecting farther and fainter objects that have so far go unnoticed. Our aim is to keep completing th...
Article
In this paper, we review the background and the state of the art of the Distributed Computing software stack. We aim to provide the readers with a comprehensive overview of this area by supplying a detailed big-picture of the latest technologies. First, we introduce the general background of Distributed Computing and propose a layered top–bottom cl...
Preprint
Full-text available
The landscape of workflow systems for scientific applications is notoriously convoluted with hundreds of seemingly equivalent workflow systems, many isolated research claims, and a steep learning curve. To address some of these challenges and lay the groundwork for transforming workflows research and development, the WorkflowsRI and ExaWorks projec...
Article
Full-text available
The necessity of dealing with uncertainties is growing in many different fields of science and engineering. Due to the constant development of computational capabilities, current solvers must satisfy both statistical accuracy and computational efficiency. The aim of this work is to introduce an asynchronous framework for Monte Carlo and Multilevel...
Chapter
Although smart devices markets are increasing their sales figures, their computing capabilities are not sufficient to provide good-enough-quality services. This paper proposes a solution to organize the devices within the Cloud-Edge Continuum in such a way that each one, as an autonomous individual –Agent–, processes events/data on its embedded com...
Preprint
Full-text available
Scientific workflows are a cornerstone of modern scientific computing, and they have underpinned some of the most significant discoveries of the last decade. Many of these workflows have high computational, storage, and/or communication demands, and thus must execute on a wide range of large-scale platforms, from large clouds to upcoming exascale H...
Article
Full-text available
Genome-wide association studies (GWAS) are not fully comprehensive, as current strategies typically test only the additive model, exclude the X chromosome, and use only one reference panel for genotype imputation. We implement an extensive GWAS strategy, GUIDANCE, which improves genotype imputation by using multiple reference panels and includes th...
Preprint
Machine learning has proved to be a useful tool for extracting knowledge from scientific data in numerous research fields, including astrophysics, genomics, and molecular dynamics. Often, data sets from these research areas need to be processed in distributed platforms due to their magnitude. This can be done using one of the various distributed ma...
Preprint
Full-text available
Deep Neural Network (DNN) frameworks use distributed training to enable faster time to convergence and alleviate memory capacity limitations when training large models and/or using high dimension inputs. With the steady increase in datasets and model sizes, model/hybrid parallelism is deemed to have an important role in the future of distributed tr...
Preprint
Full-text available
The usage of workflows has led to progress in many fields of science, where the need to process large amounts of data is coupled with difficulty in accessing and efficiently using High Performance Computing platforms. On the one hand, scientists are focused on their problem and concerned with how to process their data. On top of that, the applicati...
Preprint
Full-text available
Scientific workflows have been used almost universally across scientific domains, and have underpinned some of the most significant discoveries of the past several decades. Many of these workflows have high computational, storage, and/or communication demands, and thus must execute on a wide range of large-scale platforms, from large clouds to upco...
Article
Task-based programming models offer a flexible way to express the unstructured parallelism patterns of nowadays complex applications. This expressive capability is required to achieve maximum possible performance for applications that are executed in distributed execution platforms. In current task-based workflows, tasks are launched for execution...
Article
Storage systems have not kept the same technology improvement rate as computing systems. As applications produce more and more data, I/O becomes the limiting factor for increasing application performance. I/O congestion caused by concurrent access to storage devices is one of the main obstacles that cause I/O performance degradation and, consequent...
Article
In recent years, the areas of High-Performance Computing (HPC) and massive data processing (also know as Big Data) have been in a convergence course, since they tend to be deployed on similar hardware. HPC systems have historically performed well in regular, matrix-based computations; on the other hand, Big Data problems have often excelled in fine...
Preprint
Full-text available
Deep learning (DL) applications are increasingly being deployed on HPC systems, to leverage the massive parallelism and computing power of those systems for DL model training. While significant effort has been put to facilitate distributed training by DL frameworks, fault tolerance has been largely ignored. In this work, we evaluate checkpoint-rest...
Chapter
Current scientific workflows are large and complex. They normally perform thousands of simulations whose results combined with searching and data analytics algorithms, in order to infer new knowledge, generate a very large amount of data. To this end, workflows comprise many tasks and some of them may fail. Most of the work done about failure manag...
Article
The last improvements in programming languages and models have focused on simplicity and abstraction; leading Python to the top of the list of the programming languages. However, there is still room for improvement when preventing users from dealing directly with distributed and parallel computing issues. This paper proposes and evaluates AutoParal...
Preprint
This paper tries to reduce the effort of learning, deploying, and integrating several frameworks for the development of e-Science applications that combine simulations with High-Performance Data Analytics (HPDA). We propose a way to extend task-based management systems to support continuous input and output data to enable the combination of task-ba...
Article
In the past years, e-Science applications have evolved from large-scale simulations executed in a single cluster to more complex workflows where these simulations are combined with High-Performance Data Analytics (HPDA). To implement these workflows, developers are currently using different patterns; mainly task-based and dataflow. However, since t...
Preprint
Progress in science is deeply bound to the effective use of high-performance computing infrastructures and to the efficient extraction of knowledge from vast amounts of data. Such data comes from different sources that follow a cycle composed of pre-processing steps for data curation and preparation for subsequent computing steps, and later analysi...
Conference Paper
Fog computing brings cloud computing capabilities closer to the end-devices and users, while enabling location-dependent resource allocation, low latency services, and extending significantly the IoT services portfolio as well as market and business opportunities in the cloud and IoT sectors. With the number of devices growing exponentially globall...
Preprint
Full-text available
Genome-wide association studies (GWAS) are not fully comprehensive as current strategies typically test only the additive model, exclude the X chromosome, and use only one reference panel for genotype imputation. We implemented an extensive GWAS strategy, GUIDANCE, which improves genotype imputation by using multiple reference panels, includes the...
Conference Paper
The increasing complexity of modern and future computing systems makes it challenging to develop applications that aim for maximum performance. Hybrid parallel programming models offer new ways to exploit the capabilities of the underlying infrastructure. However, the performance gain is sometimes accompanied by increased programming complexity....
Article
Full-text available
Context. Open clusters are key targets for studies of Galaxy structure and evolution, and stellar physics. Since the Gaia data release 2 (DR2), the discovery of undetected clusters has shown that previous surveys were incomplete. Aims. Our aim is to exploit the Big Data capabilities of machine learning to detect new open clusters in Gaia DR2, and t...
Preprint
Full-text available
Open clusters are key targets for both Galaxy structure and evolution and stellar physics studies. Since \textit{Gaia} DR2 publication, the discovery of undetected clusters has proven that our samples were not complete. Our aim is to exploit the Big Data capabilities of machine learning to detect new open clusters in \textit{Gaia} DR2, and to compl...
Article
Full-text available
Abstract High-performance computing (HPC) and massive data processing (Big Data) are two trends that are beginning to converge. In that process, aspects of hardware architectures, systems support and programming paradigms are being revisited from both perspectives. This paper presents our experience on this path of convergence with the proposal of...
Conference Paper
Fog computing brings cloud computing capabilities closer to the end-devices and users, while enabling location-dependent resource allocation, low latency services, and extending significantly the IoT services portfolio as well as market and business opportunities in the cloud and IoT sectors. With the number of devices growing exponentially globall...
Article
Full-text available
Our society is generating an increasing amount of data at an unprecedented scale, variety, and speed. This also applies to numerous research areas, such as genomics, high energy physics, and astronomy, for which large-scale data processing has become crucial. However, there is still a gap between the traditional scientific computing ecosystem and b...
Presentation
The aim of this work is to build a highly efficient framework in order to run Monte Carlo algorithms, such as standard Monte Carlo (MC), Multi Level Monte Carlo (MLMC) or Continuation Multi Level Monte Carlo (CMLMC), in distributed environment. In the proposed models we work with adaptive mesh refinement, and we propose two different approaches: -...
Article
Full-text available
In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics...
Conference Paper
Full-text available
Machine Learning applications now span across multiple domains due to the increase in computational power of modern systems. There has been a recent surge in Machine Learning applications in High Performance Computing (HPC) in an attempt to speed up training. However, besides training, hyperparameters optimisation(HPO) is one of the most time consu...
Article
Workflow systems promise scientists an automated end-to-end path from hypothesis to discovery. However, expecting any single workflow system to deliver such a wide range of capabilities is impractical. A more practical solution is to compose the end-to-end workflow from more than one system. With this goal in mind, the integration of task-based and...
Article
Asymmetric multi-cores (AMCs) are a successful architectural solution for both mobile devices and supercomputers. By maintaining two types of cores (fast and slow) AMCs are able to provide high performance under the facility power budget. This paper performs the first extensive evaluation of how portable are the current HPC applications for such su...
Article
Distributed computing platforms are evolving to heterogeneous ecosystems with Clusters, Grids and Clouds introducing in its computing nodes, processors with different core architectures, accelerators (i.e. GPUs, FPGAs), as well as different memories and storage devices in order to achieve better performance with lower energy consumption. As a conse...
Article
Hardware in High Performance Computing environments in recent years have increasingly become more heterogeneous in order to improve computational performance. An additional aspect of such systems is the management of power and energy consumption. The increase in heterogeneity requires middleware and programming model abstractions to eliminate addit...
Preprint
Full-text available
Multiscale Genomics (MuG) Virtual Research Environment (MuGVRE) is a cloud-based computational infrastructure created to support the deployment of software tools addressing the various levels of analysis in 3D/4D genomics. Integrated tools tackle needs ranging from high computationally demanding applications (e.g. molecular dynamics simulations) to...
Poster
The following presents some initial results of integration of well-known algorithms developed to study Uncertainty Quantification (UQ) inside the KratosMultiphysics (Kratos) environment. The application of choice has been the resolution of the potential flow around an airfoil. The final aim is to perform Optimization Under Uncertainties (OUU) of th...
Article
Full-text available
Analysis of public transportation data in large cities is a challenging problem. Managing data ingestion, data storage, data quality enhancement, modelling and analysis requires intensive computing and a non-trivial amount of resources. In EUBra-BIGSEA (Europe–Brazil Collaboration of Big Data Scientific Research Through Cloud-Centric Applications)...
Chapter
The Transparent heterogeneous hardware Architecture deployment for eNergy Gain in Operation (TANGO) project’s goal is to characterise factors which affect power consumption in software development and operation for Heterogeneous Parallel Hardware (HPA) environments. Its main contribution is the combination of requirements engineering and design mod...
Article
Full-text available
The low computing power of mobile devices impedes the development of mobile applications with a heavy computing load. Mobile Cloud Computing (MCC) has emerged as the solution to this by connecting mobile devices with the “infinite” computing power of the Cloud. As mobile devices typically communicate over untrusted networks, it becomes necessary to...
Conference Paper
Task-based programming is becoming a tool of large interest for boosting High-Performance Computing (HPC) and Big Data applications. In particular, COMP Superscalar (COMPSs), is showing to be an effective task-based programming model for distributed computing of Big Data applications within HPC environments. Applications like NMMB-MONARCH, which is...
Conference Paper
Full-text available
The last improvements in programming languages, programming models, and frameworks have focused on abstracting the users from many programming issues. Among others, recent programming frameworks include simpler syntax , automatic memory management and garbage collection, which simplifies code re-usage through library packages, and easily configurab...
Preprint
Full-text available
The last improvements in programming languages, programming models, and frameworks have focused on abstracting the users from many programming issues. Among others, recent programming frameworks include simpler syntax, automatic memory management and garbage collection, which simplifies code re-usage through library packages, and easily configurabl...