Rafael Mayo-Garcia

• PhD
• Senior Researcher at Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas

The fast growth worldwide of linkable scientific datasets supposes significant challenges in their management and reuse. Large experiments, such as the Latin American Giant Observatory, generate volumes of data that can benefit other kinds of studies. In this sense, there is a modular ecosystem of external radiation tools that should harvest and su...

There has been great interest in the Singular Value Decomposition (SVD) algorithm over the last years because of its wide applicability in multiple fields of science and engineering, both standalone and as part of other computing methods. The advent of the exascale era with massively parallel computers brings incredible possibilities to deal with v...

Every computation presents a small chance that an unexpected phenomenon ruins or modifies its output. Computers are prone to errors that, although may be very unlikely, are hard, expensive or simply impossible to avoid. In the exascale, with thousands of processors involved in a single computation, those errors are especially harmful because they c...

The Latin American Giant Observatory (LAGO) is a ground-based extended cosmic rays observatory designed to study transient astrophysical events, the role of the atmosphere on the formation of secondary particles, and space-weather-related phenomena. With the use of a network of Water Cherenkov Detectors (WCDs), LAGO measures the secondary particle...

Information and Communication Technologies and Internet networks are present in all aspects of social reality and are essential elements in research, development and innovation centers (R&D&I). Cyber-security is crucial for the progress of the research activities developed in these centers, especially given the exponential growth of cyber-attacks a...

The goal is to do a text mining analysis of all scientific publications and find out what journal and what aspects are studying about the conspiracy theories of Covid-19. For this purpose, all publications available in the National Center for Biotechnology Information (NCBI) database were consulted as they were peer-reviewed papers. Of all these pa...

Atmospheric radiation produced during the interaction of cosmic rays with the atmosphere could be considerably high at typical flight altitudes and constitutes a risk factor for people and avionics onboard the plane. In this work, we present ACORDE, a Monte Carlo-based method to estimate the dose during a commercial flight by using state-of-the-art...

The present investigation summarizes the numerical prediction and DMD analysis of the flow in the vicinity of a Gurney flap set on an airfoil NACA0015 at Re = 10,300 tested in a water tunnel with time-resolved Particle Image Velocimetry. A series of two-dimensional U-RANS simulations has been accomplished using an incom­ pressible, time-accurate so...

The age of exascale computing has arrived and the risks associated with neutron and other atmospheric radiation are becoming more critical as the computing power increases, hence, the expected Mean Time Between Failures will be reduced because of this radiation. In this work, a new and detailed calculation of the neutron flux for energies above 50...

The age of exascale computing has arrived, and the risks associated with neutron and other atmospheric radiation are becoming more critical as the computing power increases; hence, the expected mean time between failures will be reduced because of this radiation. In this work, a new and detailed calculation of the neutron flux for energies above 50...

This work proposes a modification of a compartmental-type model based on the Susceptible-Exposed-Infected-Recovered (SEIR) scheme to describe the dynamics of contagion by Covid-19 in any part of the world, including also the numerical and analytical calculation of the mantissa and the resolution of a partial differential equation system. As an exam...

LAGO, the Latin American Giant Observatory, is an extended cosmic ray observatory, consisting of a wide network of water Cherenkov detectors located in 10 countries. With different altitudes and geomagnetic rigidity cutoffs, their geographic distribution, combined with the new electronics for control, atmospheric sensing and data acquisition, allow...

The goal of this paper is to show that it is possible to obtainan analytical solution of the life cycle of SARS-CoV-2 based on a deterministic model. To do this, this work solved a system of twelve differential equations where we obtained two points of equilibrium. The first critical point corresponds to the initial conditions regarding the virus e...

The resilience behavior of three GMRES prototyped implementations (with Incomplete LU, Flexible and randomized-SVD—based preconditioners) has been analyzed with a soft errors injection approach. A low-level fault injector is inserted into the GMRES solvers, which randomly select locations in the program to inject the fault across multiple execution...

We present a study of the performance of the Weather Research and Forecasting [WRF] code under several hardware configurations in an HPC environment. The WRF code is a standard code for weather prediction, used in several fields of science and industry. The metrics used in this case are the execution time of the run and the energy consumption of th...

The microscopic mechanisms of transport and recombination mechanisms in silicon heterojunction solar cells are still poorly understood. The purpose of the present work is to understand the transport mechanisms underlying photovoltaic devices based on silicon heterojunction technology by simulating at atomistic resolution amorphous-crystalline heter...

The Latin American Giant Observatory (LAGO) is a distributed cosmic ray observatory at a regional scale in Latin America, by deploying a large network of Water Cherenkov detectors (WCD) and other astroparticle detectors in a wide range of latitudes from Antarctica to M\'exico, and altitudes from sea level to more than 5500 m a.s.l. Detectors teleme...

The principles of Findability, Accessibility, Interoperability, and Reusability (FAIR) have been put forward to guide optimal sharing of data. The potential for industrial and social innovation is vast. Domain-specific metadata standards are crucial in this context, but are widely missing in the energy sector. This report provides a collaborative r...

The control and mitigation of magnetohydrodynamic (MHD) oscillation modes is an issue in fusion science because these modes can contribute to the outward particle/energy flux and can drive the device away from ignition conditions. It is of general interest to extract the mode information from large experimental databases in a fast and reliable way....

Abstract Solar activity was intense in September 2017 and its effects were observed in different detectors placed at the Earth's surface. Three halo Coronal Mass Ejections (CME) hit the planet and caused magnetic storms. The effects of the CMEs on the flux of galactic cosmic rays at ground level were observed by the Tanca detector, which is one of...

A dynamic version of Cloudbook is presented in this work, a new tool for automatically and unattendedly parallelizing codes which also lately distributes the tasks dynamically. Cloudbook is designed for Python codes and, above all, makes the parallelization in a way in which the number and main characteristics of the available infrastructure is tak...

In the silicon heterojunction solar cells, intrinsic hydrogenated amorphous silicon a-Si:H is used to passivate the crystal silicon c-Si surface to suppress the electrical losses at interfaces and to keep ultralow contact resistivity for the selective transport of one type of carrier only. We use ReaxFF (Reactive Force Field) molecular dynamics to...

The control and mitigation of MHD oscillations modes is an open problem in fusion science because they can contribute to the outward particle/energy flux and can drive the device away from ignition conditions. It is then of general interest to extract the mode information from large experimental databases in a fast and reliable way. We present a so...

The work analyzes the dynamics of transmission of infections by the new coronavirus in twelve European countries, including France, Germany, Italy, Spain, UK, Austria, Croatia, Denmark, Greece, Romania, Czech Republic, and Portugal, whose data from contagion were obtained by Johns Hopkins University until September 24, 2020. The study confirmed tha...

This work summarizes the results of a set of executions completed on three fat-tree network supercomputers: Stampede at TACC (USA), Helios at IFERC (Japan) and Eagle at PSNC (Poland). Three MPI-based, communication-intensive scientific applications compiled for CPUs have been executed under weak-scaling tests: the molecular dynamics solver LAMMPS;...

Since its establishment in 1951, CIEMAT has been continuously boosting the use of computation as a research method, deploying innovative computing facilities. Hence, Vectorial, MPP, NUMA, and distributed architectures have been managed at CIEMAT, resultingin an extensive expertise on HPC maintainability as well as on the computational needs of the...

In this work the Numerical Aerodynamic Simulation (NAS) benchmarks have been executed in a systematic way on two clusters of rather different architectures and CPUs, to identify dependencies between MPI tasks mapping and the speedup or resource occupation. To this respect, series of experiments with the NAS kernels have been designed to take into a...

The data of this research describes the logged usage of the Euler cluster located at CIEMAT (Centre for Energy, Environment, and Technology Research), spanning the period between November 2008 and March 2018. The Euler database is open access in Parallel Workload Archive format, available from the PWA repository [1] and Mendeley Data [2], allowing...

Until now, jobs running on HPC clusters were tied to the node where their execution started. We have removed that limitation by integrating a user-level checkpoint/restart library into a resource manager, fully transparent to both the user and running application. This opens the door to a whole new set of tools and scheduling possibilities based on...

The LAGO (Latin American Giant Observatory) observatory is an experiment that spans over Latin America in a wide range of latitudes that gives different rigidity cut offs for the enter of cosmic rays in the atmosphere. The motivation of the Observatory is to study atmospheric radiation and space weather through the measurement of the secondary emis...

This work revises current assumptions adopted in the checkpointing modelling and evaluates their impact on the attained prediction of the optimal coordinated single-level checkpoint period. An accurate a priori assessment of the optimal checkpoint period for a given computing facility is necessary as it drives the incurred overhead due to frequent...

This investigation summarizes a set of executions completed on the supercomputers Stampede at TACC (USA), Helios at IFERC (Japan), and Eagle at PSNC (Poland), with the molecular dynamics solver LAMMPS, compiled for CPUs. A communication-intensive benchmark based on long-distance interactions tackled by the Fast Fourier Transform operator has been s...

Although computing research and facilities in Latin America have been developing steadily, a remarkable gap nevertheless remains in the availability of resources and specialized human resources compared to other regions. RICAP (Red Iberoamericana de Computación de Altas Prestaciones, or Ibero-American Network for High-Performance Computing) aims to...

Exploiting resources belonging to multiple cloud providers in an efficient way is still an open issue for distributed computing. Scheduling algorithms based on heuristic, probabilistic, queue theory, or complex soft computing methods are suitable to tackle the heterogeneity and dynamism present in cloud federations. Nevertheless, the available brok...

High Performance Computing (HPC) resources have become the key actor for achieving more ambitious challenges in many disciplines. In this step beyond, an explosion on the available parallelism and the use of special purpose processors are crucial. With such a goal, the HPC4E project applies new exascale HPC techniques to energy industry simulations...

A timely immunization can be effective against certain diseases and can save thousands of lives. However, for some diseases it has been difficult, so far, to develop an efficient vaccine. Malaria, a tropical disease caused by a parasite of the genus Plasmodium, is one example. Bioinformatics has opened the way to new lines of experimental investiga...

A timely immunization can be effective against certain diseases and can save thousands of lives. However, for some diseases it has been difficult, so far, to develop an efficient vaccine. Malaria, a tropical disease caused by a parasite of the genus Plasmodium, is one example. Bioinformatics has opened the way to new lines of experimental investiga...

Neoclassical transport properties are studied in the TJ-II stellarator, taking effective ripple and plateau factor as the figures of merit. Using the DKES code run by grid computing techniques, these two quantities have been estimated as functions of rotational transform and plasma volume. The effective helical ripple increases with plasma volume a...

The appliance of new exascale HPC techniques to energy industry simulations is absolutely needed nowadays. In this sense, the common procedure is to customize these techniques to the specific energy sector they are of interest in order to go beyond the state-of-the-art in the required HPC exascale simulations. With this aim, the HPC4E project is de...

In this work the strategy of the Latin American Giant Observatory (LAGO) to build a Latin American collaboration is presented. Installing Cosmic Rays detectors settled all around the Continent, from Mexico to the Antarctica, this collaboration is forming a community that embraces both high energy physicist and computer scientists. This is so becaus...

In this work the strategy of the Latin American Giant Observatory (LAGO) to build a Latin American collaboration is presented. Installing Cosmic Rays detectors settled all around the Continent, from Mexico to the Antarctica, this collaboration is forming a community that embraces both high energy physicist and computer scientists. This is so becaus...

Measurements of 161 oscillator strengths arising from highly excited levels of Mo II are presented, 148 of which are obtained for the first time. These results extend the previous ones already published on lower excited levels of Mo II. A laser-induced plasma generated from a fused glass sample prepared from molybdenum oxide with a Mo atomic concen...

The Latin American Giant Observatory (LAGO) is an extended cosmic ray observatory composed by a network of water-Cherenkov detectors spanning over different sites located at significantly different altitudes (from sea level up to more than $5000$\,m a.s.l.) and latitudes across Latin America, covering a huge range of geomagnetic rigidity cut-offs a...

In the pool of cloud providers that are currently available there is a lack of standardised APIs and brokering tools to effectively distribute high throughput calculations among them. Moreover, the current middleware tools are not able to straightforwardly provision the ephemeral and specific environments that certain codes and simulations require....

Nowadays, computing calculations are becoming more and more demanding due to the huge pool of resources available. This demand must be satisfied in terms of computational efficiency and resilience, which is compromised in distributed and heterogeneous platforms. Not only this, data obtained are often either reused by other researchers or recalculat...

In this article, 112 oscillator strengths from Mo II have been measured, 79 of which for the first time. The radiative parameters have been obtained by laser-induced breakdown spectroscopy (LIBS). The plasma is produced from a fused glass sample prepared from molybdenum oxide with a Mo atomic concentration of 0.1%. The plasma evolved in air at atmo...

This paper presents a system of differential equations that describes the spreading of a rumor when it is propagated by different subgroups of spreaders. The system that is developed is a generalization of the model proposed by Daley and Kendall. Finally, the system is applied to the exchange rate of the parallel dollar in Venezuela, where the sour...

Cloud Computing promises to be more flexible, usable, available and simple than Grid, covering also much more computational needs than the ones required to carry out distributed calculations. However, the diversity of cloud providers, the lack of standardised APIs and brokering tools prevent the massive portability of legacy applications to cloud e...

In this work, the authors present a set of tools to overcome the problem of creating and executing distributed applications on dynamic environments in a resilient way, also ensuring the reproducibility of the performed experiments. The objective is to provide a portable, unattended and fault-tolerant set of tools, encapsulating the infrastructure-d...

CHAIN-REDS, an EU co-funded project, focuses on promoting and supporting technological and scientific collaboration across different e-Infrastructures established and operated in various continents. The project implemented a Regional Operations Centre (ROC) model for enabling Grid computing interoperation across continents, and an operational ROC h...

Solving certain calculations in time is crucial for some industrial, medical or research areas. However, problems with high computational requirements are specially constrained to the dependability of the computational resources. Distributed Computing Infrastructures have consolidated as the platform that can solve the issue in last decade. Grid an...

Current systems based on pilot jobs are not exploiting all the scheduling advantages that the technique offers, or they lack compatibility or adaptability. To overcome the limitations or drawbacks in existing approaches, this study presents a different general-purpose pilot system, GWpilot. This system provides individual users or institutions with...

CHAIN-REDS (Coordination and Harmonisation of Advanced e-infrastructure for Research and Education Data Sharing) is EU project focused on promoting and supporting technological and scientific collaboration across different communities established in various continents. Nowadays, one of the most challenging scenarios scientist and scientific communi...

Grid computing environments are distributed systems composed by heterogeneous and geographically distributed resources. This type of systems mainly emerged to satisfy the increasing computing power demand within the scientific community. Despite the advantages of such paradigm, there are still several challenges related to the discovery, monitoring...

CHAIN-REDS started on December 2012 focused on promoting and supporting technological and scientific collaboration across different communities established in various continents. One of the main issues is the access to the offered computational services, which can be administrative services associated to Universities and Academic Networks, Data Rep...

There are many applications in every scientific and engineering fields that have high computational requirements. They have to be adapted to either high-performance computing or high-throughput computing platforms, depending on their characteristics. For the latter case, the high volume of resources available in grid infrastructures should allow fo...

In the present work, we have studied experimentally the Stark widths from several lines of Ni II, some of them not measured before. For doing this, the Laser Induced Breakdown Spectroscopy technique (LIBS) has been used on an Alluminium-Nickel alloy with a lower content of Nickel in a controlled atmosphere. The final results are compared with the o...

Cancer is a disease involving many genes, consequently it has been difficult to design anticancer drugs that are efficacious over a broad range of cancers. The robustness of cellular responses to gene knockout and the need to reduce undesirable side effects also contribute to the problem of effective anti-cancer drug design. To promote the successf...

Experimental transition probabilities for 37 spectral lines of Re II (15 measured for the first time) have been obtained from a plasma produced by ablation of a Zn–Re alloy with a Nd:YAG laser. The plasma evolved in air at atmospheric pressure, and measurements were performed for the following plasma parameters: an electron density of (1.27 ± 0.19)...

The numerical simulation of the dynamics of fast ions coming from neutral beam injection (NBI) heating is an important task in fusion devices, since these particles are used as sources to heat and fuel the plasma and their uncontrolled losses can damage the walls of the reactor. This paper shows a new application that simulates these dynamics on th...

The objective of this work is to improve the performance of Monte Carlo codes on Grid production infrastructures. To do so, the codes and the grid sites are characterized with simple parameters to model their behaviors. Then, a new performance model for grid infrastructures is proposed, and an algorithm that employs this information is described. T...

This work presents anew computational analysis using post-genomic data in order to design a new vaccine candidate against Plasmodium falciparum, a parasite responsible for malaria. It is based on a poly(amidoamine) (PAMAM) eight-branched dendrimeric structure integrating B cell epitopes. To do so, all available experimental epitopes were identified...

This paper has a dual purpose. First, to determine the stable regions of the capsid human papillomavirus type HPV16 L1 from a molecular dynamics simulation up to 4 ns. This study introduces the concept of standard normalized deviation to confirm that the dynamics converge to a stationary value. We found that the region of greatest mobility is the a...

The CHAIN project has been working on coordinating and leveraging the efforts made over the past years to extend the European e-Infrastructure (and particularly the Grid) operational and organisational principles to a number of Regions over the world. In this sense, the project is currently working on elaborating a strategy and defining instruments...

Nb films have been fabricated on top of array of Ni nanodots. The array of periodic pinning potentials modifies the vortex lattice for specific values of the external applied magnetic field. By means of an implemented code developed from scratch, computer simulations based only on the vortex–vortex and the vortex–nanodot interactions provide the to...

The neoclassical transport is a lower limit of the whole transport in plasmas confined in fusion devices, either stellarators or tokamaks. Even more, the determination of a vast database compiling monoenergetic and transport coefficients is very useful for coupling different codes, which can use those values as input data. The DKEsG application is...

The oscillator strengths of 30 lines of ReI (26 of them have been measured for the first time) have been measured in a plasma produced by ablation of a Zn–Re alloy with a Nd:YAG laser. The radiative parameters were obtained with the target placed in molecular argon at 8 Torr, which provides appropriate measurement conditions. Branching fractions co...

PhyloGrid is an application developed in the framework of the EELA-2 project devoted to the calculation of Phylogenies by means of the MrBayes software, that is, Bayesian statistics. To the moment, it has been used to perform studies on the Human Immunodeficiency Virus (HIV), the Human Papillomavirus (HPV), and the DENgue Virus (DENV). PhyloGrid ai...

ISDEP (Integrator of Stochastic Differential Equations for Plasmas) is a Monte Carlo code that solves the plasma dynamics in a fusion device and perfectly scales on distributed computing platforms. Montera is a recent framework developed for achieving Grid efficient executions of Monte Carlo applications, as ISDEP is. In this work, the improvement...

PhyloGrid is an application developed in the framework of the EELA-2 project devoted to the calculation of Phylogenies by means of the MrBayes software, that is, Bayesian statistics. To the moment, it has been used to perform studies on the Human Immunodeficiency Virus (HIV), the Human Papillomavirus (HPV), and the DENgue Virus (DENV). PhyloGrid ai...

The CHAIN project aims to further coordinate and leverage the experience of several e- Infrastructure projects and initiatives addressing various regions of the world and specifically those emerging in Asia and Africa, but also Latin America and the Mediterranean. CHAIN focuses on the harmonised and optimised interaction model for e-Infrastructure...

In this work we present the development of a workflow based on Taverna which is going to be implemented for calculations in Phylogeny by means of the MrBayes tool. It has a friendly interface developed with the Gridsphere framework. The user is able to define the parameters for doing the Bayesian calculation, determine the model of evolution, check...

El presente trabajo destaca las ventajas de implementar una computación distribuida para el uso intensivo en cómputo científico dedicado a la identificación de posibles medicamentos que pueden ser aplicados para la resolución de problemas en salud pública. Palabras clave Computación Grid, informática, EELA (E-infraestructura compartida entre Europa...

Neoclassical (NC) transport calculations are necessary for the complete simulation cycle of the behavior of plasmas inside both tokamaks and stellarators, which are more complex to be performed on the latest. In addition, due to the fact that the NC transport is mainly determined by the magnetic properties of the device (mathematically designed by...

The study of core turbulence represents a key line of research in fusion plasmas. By adding collisions and electromagnetic induction to the parallel dynamics of the standard six-moment toroidal model, it is possible to study the gyrofluid electromagnetic phenomena in the context of edge turbulence with the GEM code. Currently, the code describes th...

FAFNER2, which is a 3-D code adapted to the TJ-II helical axis stellarator from the original one developed by Lister at Max Planck IPP, simulates by Monte Carlo methods the neutral beam injection technology (a key heating method for most of the fusion experiments worldwide). To date, FAFNER2 has been usually run at CIEMAT by means of a batch mode o...

The goal of the work is to implement molecular phylogenetic calculations using the Grid paradigm by means of the MrBayes software using Directed Acyclic Graphs (DAG) jobs. In this method, a set of jobs depends on the input or the output of other jobs. Once the runs have been successfully done, all the results can be collected by a specific Perl scr...

FAFNER2 is a 3D code that simulates by Monte Carlo methods the Neutral Beam Injection (NBI) technology. The original version was implemented for shared memory computers with MIPS proccesors, so an update to be executed by means of MPI on standard Linux clusters has been carried out as well as a new version to be run on Grid. To do the latest, a ser...

The EELA (E-Infrastructure shared between Europe and Latin America) and EELA-2 (E-science grid facility for Europe and Latin America) projects, co-funded by the European Commission under FP6 and FP7, respectively, have been successful in building a high capacity, production-quality, scalable Grid Facility for a wide spectrum of applications (e.g. E...

Calculating neoclassical (NC) transport is a fundamental part of the complete simulation cycle of the behavior of plasmas inside all tokamaks and stellerators. Also, due to NC transport is mainly determined by the magnetic properties of the device, its study is mandatory to ensure the efficiency of a certain coil configuration before it is implemen...