Optimizing domain decomposition in an ocean model: the case of NEMO

Earth System Models are critical tools for the study of our climate and its future trends. These models are in constant evolution and their growing complexity entails an incrementing demand of the resources they require. Since the cost of using these state-of-the-art models is huge, looking closely at the factors that are able to impact their computational performance is mandatory. In the case of the state-of-the-art ocean model NEMO (Nucleus for European Modelling of the Ocean), used in many projects around the world, not enough attention has been given to the domain decomposition. In this work we show the impact that the selection of a particular domain decomposition can have on computational performance and how the proposed methodology substantially improves it.The research leading to these results has received funding from the EU H2020 Framework Programme under grant agreement no 675191 and by the Ministerio de Economa y Competitividad (MINECO) under grant TIN201453234C21RPeer ReviewedPostprint (published version

Qualitative Study on the Interaction of Artificial Intelligence with the Development of Crucial Human Capital Skills

En los últimos diez años, los avances tecnológicos han sido enormes, cambiando radicalmente la forma de trabajo y las habilidades cruciales requeridas dentro de las organizaciones. Anteriormente solo expertos seleccionados anticipaban el potencial de herramientas emergentes como la inteligencia artificial (IA). El objetivo de esta investigación consiste en explicar los factores que inciden en la interacción de la IA con los trabajadores actuales, con ello fomentar un debate sobre las medidas necesarias para garantizar una transición adecuada en su área de trabajo ante los próximos avances, considerando principios éticos y de responsabilidad, y evaluando las habilidades que serán esenciales en un entorno cada vez más influenciado por la IA. Se utilizó el software de análisis cualitativo Atlas.Ti seleccionando libros y publicaciones científicas en buscadores digitales, relacionadas con las variables de estudio combinando palabras clave (Inteligencia Artificial, Capital Humano, Habilidades, Profesiones) filtrando las investigaciones publicadas desde 2017 a 2022 y se seleccionaron aquellas que cumplieran con los criterios de búsqueda, se utilizó la técnica de saturación para considerar el límite de documentos. Los resultados arrojan que se hace imperativo prepararse para adaptarse a los cambios que potenciarán las capacidades humanas de manera sin precedente, estas habilidades no se limitan a unos cuantos expertos, cualquier trabajador o profesionista es capaz de adquirirlas dentro de su formación académica o en el campo laboral.Over the last ten years, technological advances have been enormous, radically changing the way we work and the crucial skills required within organizations. Previously only selected experts anticipated the potential of emerging tools such as artificial intelligence (AI). The objective of this research is to explain the factors that affect the interaction of AI with current workers, thereby promoting a debate on the necessary measures to guarantee an adequate transition in their work area in the face of upcoming advances, considering ethical principles. and responsibility, and evaluating the skills that will be essential in an environment increasingly influenced by AI. The qualitative analysis software Atlas.Ti was used to select books and scientific publications in digital search engines, related to the study variables by combining keywords (Artificial Intelligence, Human Capital, Skills, Professions) filtering the research published from 2017 to 2022 and selected those that met the search criteria, the saturation technique was used to consider the document limit. The results show that it is imperative to prepare to adapt to the changes that will enhance human capabilities in an unprecedented way. These skills are not limited to a few experts; any worker or professional is capable of acquiring them within their academic training or in the field. labor

How to use mixed precision in ocean models : Exploring a potential reduction of numerical precision in NEMO 4.0 and ROMS 3.6

ceived funding from the EU ESiWACE H2020 Framework Programme under grant agreement no. 823988, from the Severo Ochoa (SEV-2011-00067) program of the Spanish Government and from the Ministerio de Economia y Competitividad under contract TIN2017-84553-C2-1-R.Mixed-precision approaches can provide substantial speed-ups for both computing- and memory-bound codes with little effort. Most scientific codes have overengineered the numerical precision, leading to a situation in which models are using more resources than required without knowing where they are required and where they are not. Consequently, it is possible to improve computational performance by establishing a more appropriate choice of precision. The only input that is needed is a method to determine which real variables can be represented with fewer bits without affecting the accuracy of the results. This paper presents a novel method that enables modern and legacy codes to benefit from a reduction of the precision of certain variables without sacrificing accuracy. It consists of a simple idea: we reduce the precision of a group of variables and measure how it affects the outputs. Then we can evaluate the level of precision that they truly need. Modifying and recompiling the code for each case that has to be evaluated would require a prohibitive amount of effort. Instead, the method presented in this paper relies on the use of a tool called a reduced-precision emulator (RPE) that can significantly streamline the process. Using the RPE and a list of parameters containing the precisions that will be used for each real variable in the code, it is possible within a single binary to emulate the effect on the outputs of a specific choice of precision. When we are able to emulate the effects of reduced precision, we can proceed with the design of the tests that will give us knowledge of the sensitivity of the model variables regarding their numerical precision. The number of possible combinations is prohibitively large and therefore impossible to explore. The alternative of performing a screening of the variables individually can provide certain insight about the required precision of variables, but, on the other hand, other complex interactions that involve several variables may remain hidden. Instead, we use a divide-and-conquer algorithm that identifies the parts that require high precision and establishes a set of variables that can handle reduced precision. This method has been tested using two state-of-the-art ocean models, the Nucleus for European Modelling of the Ocean (NEMO) and the Regional Ocean Modeling System (ROMS), with very promising results. Obtaining this information is crucial to build an actual mixed-precision version of the code in the next phase that will bring the promised performance benefits

The influence of Ni2+ and other ions on the trigonal structure of DNA

We present a new structure of a DNA dodecamer obtained in the presence of Ni2+ ions. The DNA forms Ni-guanine cross-links between neighboring molecules. Our results show that an adequate dosage of Ni2+ may help to form well-defined DNA nanostructures. We also compare our structure with other dodecamers which present unique features and also crystallize in trigonal unit cells, strongly influenced by the counterions associated with DNA. In all cases, the DNA duplexes form parallel pseudo-helical columns in the crystal, similar to DNA-protamine and native DNA fibers.Peer ReviewedPostprint (author's final draft

In and out of the minor groove: Interaction of an AT-rich DNA with the drug CD27

The DNA of several pathogens is very rich in AT base pairs. Typical examples include the malaria parasite Plasmodium falciparum and the causative agents of trichomoniasis and trypanosomiases. This fact has prompted studies of drugs which interact with the minor groove of DNA, some of which are used in medical practice. Previous studies have been performed almost exclusively with the AATT sequence. New features should be uncovered through the study of different DNA sequences. In this paper, the crystal structure of the complex of the DNA duplex d(AAAATTTT)2 with the dicationic drug 4,4'-bis(imidazolinylamino) diphenylamine (CD27) is presented. The drug binds to the minor groove of DNA as expected, but it shows two new features that have not previously been described: (i) the drugs protrude from the DNA and interact with neighbouring molecules, so that they may act as cross-linking agents, and (ii) the drugs completely cover the whole minor groove of DNA and displace bound water. Thus, they may prevent the access to DNA of proteins such as AT-hook proteins. These features are also expected for other minor-groove binding drugs when associated with all-AT DNA. These findings allow a better understanding of this family of compounds and will help in the development of new, more effective drugs. New data on the biological interaction of CD27 with the causative agent of trichomoniasis, Trichomonas vaginalis, are also reported.Postprint (published version

Non-Hodgkin lymphomas of oral cavity

Non-Hodgkin lymphomas (NHL) often show up in an extranodal pattern, especially in the head and neck. Intraoral locations are much less frequent, particularly when they are single. This, in turn, can lead to a prolonged diagnosis and even to inadequate treatment. Different patients with initial extranodal location of NHL which were not previously diagnosed and in which it was manifested only intraoraly are presented in this paper. These cases are presented together with the additional examinations used for the early diagnosis and with the corresponding clinical pictures, as well as with the overview of other cases from the available literature

Patología ocular y problemas refractivos por causa de la ceniza

La investigación trata de las patologías oculares y los problemas refractivos que produce la ceniza volcánica al estar expuesto directa o indirectamente a las personas que habitan en los alrededores del volcán Tungurahua. Lo cual es de suma importancia debido a la gravedad que presenta una serie de sintomatologías a nivel ocular y al sistema respiratorio a causa de los componentes químicos que emanan del volcán al no usar una debida protección cuando se producen estas emanaciones de ceniza y gases tóxicos. El objetivo de la investigación es que los habitantes del sector de la serranía y la población en general tomen conciencia de la peligrosidad de estas substancias y busquen informarse más acerca de las composiciones de los elementos químicos que perjudican la salud tanto visual como general, la investigación utilizara los métodos deductivos, inductivos y descriptivos usando datos retrospectivos y prospectivo además de varias fuentes de consulta bibliográfica y entrevistas a profesionales de la salud visual, dentro de la técnica de investigación se utilizara pruebas objetivas y subjetivas, además como instrumento se utilizara una guía de cuestionario con la respectiva historia clínica de los pacientes los mismos que evidenciaran en base a la sintomatología por la falta de protección a nivel ocular y respiratorio molestias como ardor, lagrimeo, picazón, escozor y enrojecimiento de los ojos dando como resultado la alteración del sistema visual, respiratorio, e incluso irritación cutánea. Se concluye que la falta de conocimientos de los respectivos componentes de los elementos químicos y gases, hace que los habitantes de las zonas aledañas y sus alrededores presenten síntomas constantes en el órgano visual

Evaluation of the potential of Mycobacterium smegmatis as vaccine Candidate against tuberculosis by in silico and in vivo studies

In this study, we scanned multiple published databases of gene expression in vivo of M. tuberculosis at different phases of infection in animals and humans, to select 38 proteins that are highly expressed in the active, latent and reactivation phases. The selected proteins were predicted for T and B epitopes. For each proteins, the regions containing T and B epitopes were selected at the same time to look for identical epitopes on M. smegmatis based on sequence alignments. Preliminary studies of humoral immunogenicity and cross-reactivity with M. tuberculosis in mice using two M. smegmatis-derived experimental vaccines were carried out, demonstrating the immunogenicity of M. smegmatis proteoliposomes and the recognition of M. tuberculosis proteins by the sera of animals immunized with this vaccine candidate. The conjunction of in silico and in vivo studies suggested the potential for future evaluation of M. smegmatis as vaccine candidate against tuberculosis using different strategie

Structure vs. properties chirality, optics and shapes in amphiphilic porphyrin J-aggregates

The structure of the meso-tetrakis(4-sulfonatophenyl)porphyrin (TPPS4) J-aggregates could be determined by X-ray and electron diffraction methods. A sheet-like architecture reveals the relationship between structure and chirality, optics and shapes of the J-aggregate of the meso 4-sulfonatophenyl- and phenyl- substituted porphyrins. The structure of the J-aggregates of H4TPPS4 belongs to the chiral space group P21 and includes four porphyrin molecules in its unit cell. The intermolecular stabilization of the zwitterionic units by hydrogen bonding and electrostatic interactions between the positively charged central NH groups and the periphery anionic sulfonato groups results in a structure of porphyrins sheets along the [ ] plane direction. The structure of the sheet on the [ ] plane is already chiral and its molecular architecture explains the simultaneous presence of H- and J-aggregate bands in their absorption spectra. This structure also accounts for the high similarity observed between the absorption spectra of different mesophorms of the same substance and even between different members of the series of meso-4-sulfonatophenyl-and-aryl substituted diprotonated porphyrins. The possibility, or not, of the sheet-like structure on [ ] to interact with other layers, either through ionic or hydrophobic interactions, depends on the substitution pattern at the meso-positions of the porphyrin ring. Thus, the different morphologies of the particles [mono- bi- and multilayered] of this series of J-aggregates are explained taking into account the role that the fourth meso-subtituent plays in the interlayer stabilization. The results suggest that supramolecular helicity, previously detected in several J-aggregates, is not the explanation of their chirality but would be the expression of the intrinsic chirality of the packing between building blocks

Using EC-Earth for climate prediction research

Climate prediction at the subseasonal to interannual time range is now performed routinely and operationally by an increasing number of institutions. The feasibility of climate prediction largely depends on the existence of slow and predictable variations in the ocean surface temperature, sea ice, soil moisture and snow cover, and on our ability to model the atmosphere’s interactions with those variables. Climate prediction is typically performed with statistical-empirical or process-based models. The two methods are complementary. Although forecasting systems using global climate models (GCMs) have made substantial progress in the last few decades (Doblas-Reyes et al., 2013), systematic errors and misrepresentations of key processes still limit the value of dynamical prediction in certain areas of the globe. At the same time, model initialisation, ensemble generation, understanding the processes at the origin of predictability, forecasting extremes, bias adjustment and model evaluation are all challenging aspects of the climate prediction problem. Addressing them requires both a large base of researchers with expertise in physics, mathematics, statistics, high-performance computing and data analysis interested in climate prediction issues and a tool for them to work with. This article illustrates how one of these tools, the EC-Earth climate model (Box A), has been used to train scientists in climate prediction and to address scientific challenges in this field. The use of model components from ECMWF’s Integrated Forecasting System (IFS) in EC-Earth means that some of the results obtained with EC-Earth can feed back into ECMWF’s activities. EC-Earth has been run extensively on ECMWF’s high-performance computing facility (HPCF), among a range of HPCFs across Europe and North America. The availability of ECMWF’s HPCF to EC-Earth partners, including the use of the successful ECMWF Special Project programme, means that a substantial amount of EC-Earth’s collaborative work, both within the consortium and with ECMWF, takes place on this platform.Postprint (published version