ScalaParBiBit: Scaling the Binary Biclustering in Distributed-Memory Systems

[Abstract] Biclustering is a data mining technique that allows us to find groups of rows and columns that are highly correlated in a 2D dataset. Although there exist several software applications to perform biclustering, most of them suffer from a high computational complexity which prevents their use in large datasets. In this work we present ScalaParBiBit, a parallel tool to find biclusters on binary data, quite common in many research fields such as text mining, marketing or bioinformatics. ScalaParBiBit takes advantage of the special characteristics of these binary datasets, as well as of an efficient parallel implementation and algorithm, to accelerate the biclustering procedure in distributed-memory systems. The experimental evaluation proves that our tool is significantly faster and more scalable that the state-of-the-art tool ParBiBit in a cluster with 32 nodes and 768 cores. Our tool together with its reference manual are freely available at https://github.com/fraguela/ScalaParBiBit.This research was supported by the Ministry of Science and Innovation of Spain (TIN2016-75845-P and PID2019-104184RB-I00, AEI/FEDER/EU, 10.13039/ 501100011033), and by the Xunta de Galicia co-founded by the European Regional Development Fund (ERDF) under the Consolidation Programme of Competitive Reference Groups (ED431C 2017/04). We acknowledge also the support from the Centro Singular de Investigación de Galicia “CITIC”, funded by Xunta de Galicia and the European Union (European Regional Development Fund- Galicia 2014-2020 Program), by grant ED431G 2019/01. We also acknowledge the Centro de Supercomputación de Galicia (CESGA) for the usage of their resourcesXunta de Galicia; ED431C 2017/04Xunta de Galicia; ED431G 2019/0

Automatic mapping of parallel applications on multicore architectures using the Servet benchmark suite

This is a post-peer-review, pre-copyedit version of an article published in Computers & Electrical Engineering. The final authenticated version is available online at: https://doi.org/10.1016/j.compeleceng.2011.12.007[Abstract] Servet is a suite of benchmarks focused on detecting a set of parameters with high influence on the overall performance of multicore systems. These parameters can be used for autotuning codes to increase their performance on multicore clusters. Although Servet has been proved to detect accurately cache hierarchies, bandwidths and bottlenecks in memory accesses, as well as the communication overhead among cores, up to now the impact of the use of this information on application performance optimization has not been assessed. This paper presents a novel algorithm that automatically uses Servet for mapping parallel applications on multicore systems and analyzes its impact on three testbeds using three different parallel programming models: message-passing, shared memory and partitioned global address space (PGAS). Our results show that a suitable mapping policy based on the data provided by this tool can significantly improve the performance of parallel applications without source code modification.Ministerio de Ciencia e Innovación; TIN2010-16735Ministerio de Educación; FPU; AP2008-01578Xunta de Galicia; INCITE08PXIB105161P

Servet: A Benchmark Suite for Autotuning on Multicore Clusters

This is a post-peer-review, pre-copyedit version of an article published in 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS). Proceedings. The final authenticated version is available online at: http://dx.doi.org/10.1109/IPDPS.2010.5470358.[Abstract] MapReduce is a powerful tool for processing large data sets used by many applications running in distributed environments. However, despite the increasing number of computationally intensive problems that require low-latency communications, the adoption of MapReduce in High Performance Computing (HPC) is still emerging. Here languages based on the Partitioned Global Address Space (PGAS) programming model have shown to be a good choice for implementing parallel applications, in order to take advantage of the increasing number of cores per node and the programmability benefits achieved by their global memory view, such as the transparent access to remote data. This paper presents the first PGAS-based MapReduce implementation that uses the Unified Parallel C (UPC) language, which (1) obtains programmability benefits in parallel programming, (2) offers advanced configuration options to define a customized load distribution for different codes, and (3) overcomes performance penalties and bottlenecks that have traditionally prevented the deployment of MapReduce applications in HPC. The performance evaluation of representative applications on shared and distributed memory environments assesses the scalability of the presented MapReduce framework, confirming its suitability.Xunta de Galicia; INCITE08PXIB105161PRMinisterio de Ciencia e Innovación; TIN2007-67537-C03-02Ministerio de Educación; FPU; AP2008-0157

On the validity of the 630 nm Fe I nm lines for the magnetometry of the internetwork quiet Sun

The purpose of this work is to analyze the reliability of the magnetic field strengths inferred from the 630 nm pair of Fe I lines at internetwork quiet Sun regions. Some numerical experiments have been performed that demonstrate the inability of these lines to recover the magnetic field strength in such low flux solar regions. It is shown how different model atmospheres, with magnetic field strengths ranging from few hundred Gauss to kiloGauss, give rise to Stokes profiles that can not be distinguished. The reasons for this degeneracy are discussed.Comment: Accepted for publication in A&

SHARDS: Constraints on the dust attenuation law of star-forming galaxies at z~2

We make use of SHARDS, an ultra-deep (<26.5AB) galaxy survey that provides optical photo-spectra at resolution R~50, via medium band filters (FWHM~150A). This dataset is combined with ancillary optical and NIR fluxes to constrain the dust attenuation law in the rest-frame NUV region of star-forming galaxies within the redshift window 1.5<z<3. We focus on the NUV bump strength (B) and the total-to-selective extinction ratio (Rv), targeting a sample of 1,753 galaxies. By comparing the data with a set of population synthesis models coupled to a parametric dust attenuation law, we constrain Rv and B, as well as the colour excess, E(B-V). We find a correlation between Rv and B, that can be interpreted either as a result of the grain size distribution, or a variation of the dust geometry among galaxies. According to the former, small dust grains are associated with a stronger NUV bump. The latter would lead to a range of clumpiness in the distribution of dust within the interstellar medium of star-forming galaxies. The observed wide range of NUV bump strengths can lead to a systematic in the interpretation of the UV slope ($\beta$) typically used to characterize the dust content. In this study we quantify these variations, concluding that the effects are $\Delta\beta$~0.4.Comment: 13 pages, 11+2 figures, 3 tables. MNRAS, in pres

Resonant states in an attractive one dimensional cusp potential

We solve the two-component Dirac equation in the presence of a spatially one dimensional symmetric attractive cusp potential. The components of the spinor solution are expressed in terms of Whittaker functions. We compute the bound states solutions and show that, as the potential amplitude increases, the lowest energy state sinks into the Dirac sea becoming a resonance. We characterize and compute the lifetime of the resonant state with the help of the phase shift and the Breit-Wigner relation. We discuss the limit when the cusp potential reduces to a delta point interaction.Comment: 11 pages. To appear in Physica Script

Analysis and control of the intermediate memory states of RRAM devices by means of admittance parameters

Producción CientíficaA thorough study of the admittance of TiN/Ti/HfO2/W bipolar resistive memories [resistance random access memory (RRAM)] was carried out under different bias conditions and in a wide range of ac signal frequencies. We demonstrate that a continuum of intermediate states can be obtained by applying appropriate dc bias waveforms. Cumulative writing and erasing admittance cycles were performed by applying triangular voltage waveform of increasing amplitude. The influence of the initial conditions on the variation of the real (conductance) and imaginary (susceptance) components of the admittance is described. An accurate control of the memory state is achieved both in terms of the conductance and the susceptance by means of an adequate selection of the voltage values previously applied. A method to obtain three-dimensional voltage-conductance-susceptance state-plots is described in detail. Memory maps of admittance parameters as a function of the programming voltage are made by sensing the memory state at 0 V, without static power consumption. The multilevel nature of RRAM devices and their suitability for neuromorphic computation are demonstrated.Ministerio de Economía, Industria y Competitividad - Fondo Europeo de Desarrollo Regional (grants TEC2014-52152-C3-3-R and TEC2014- 52152-C3-1-R

Reading Strategies for Children with Developmental Language Disorder

Developmental language disorder (DLD) is considered a neurodevelopmental disorder that compromises language comprehension and/or expression and constitutes a risk factor for learning to read. The aim of the present study was to analyse the reading strategies used by students with DLD to read sentences. There is evidence in the literature that, when linguistic resources are insufficient, the keyword strategy (identifying some of the words in the sentence with their own semantic content, with barely no processing of the function words) is used to read sentences. A total of 31 primary and secondary school students diagnosed with DLD were evaluated using the PEALE battery. The results reveal that students with DLD present heterogeneous profiles that are below the established reading level for their age. In addition, children with DLD and better reading skills use the keyword strategy to read sentences. In conclusion, clinical and educational implications for reading intervention in individuals with DLD are discussed

Prevalencia de hipotensión ortostática en ancianos hipertensos tratados en atención primaria

ObjetivoConocer la prevalencia de hipotensión ortostática (HO) y los factores asociados en ancianos hipertensos tratados en atención primaria (AP).DiseñoEstudio descriptivo, transversal.EmplazamientoCentro de Salud La Marina (centro urbano en Santander).PacientesUna muestra aleatoria de 295 pacientes de 65 o más años atendidos regularmente por presentar hipertensión arterial (HTA).Mediciones y resultados principalesSe han obtenido cifras de presión arterial (PA) en sedestación y en bipedestación. La definición de HO utilizada ha sido: disminución de 20 mmHg o más en la PA sistólica (PAS) o de 10 mmHg o más en la PA diastólica (PAD), tras 1 o 5 minutos de bipedestación. También se han recogido datos sobre enfermedades asociadas, síntomas en bipedestación, medicación utilizada, hábitos de los pacientes y resultados de otras exploraciones clínicas. La prevalencia global encontrada de HO fue del 14,6%. La prevalencia de HO sistólica tras un minuto (HO-S1) y tras 5 minutos (HO-S5) de bipedestación ha sido del 5,8% en ambas, y la de HO diastólica del 5,1% tras un minuto (HO-D1) y del 4,1% tras 5 minutos (HO-D5) de bipedestación. En el análisis de regresión logística se encontró una asociación entre la existencia de HO global y la mayor elevación de la PA sistólica inicial, la presencia de síntomas de intolerancia ortostática (aunque sólo un 25,6% de los pacientes con HO presentaba síntomas) y el hábito tabáquico. Asimismo, se encontró una asociación con el uso de bloqueadores beta y antagonistas del calcio (diferentes de las dihidropiridinas) y la existencia de HO al minuto de bipedestación, y entre el consumo de tabaco y la HO a los 5 minutos de bipedestación.ConclusionesLa prevalencia detectada es alta y justifica la búsqueda sistemática de HO en los pacientes ancianos que son tratados de HTA en AP. La existencia de síntomas con el ortostatismo se relaciona con una mayor prevalencia de HO, pero sólo los presentó uno de cada 4 pacientes con HO. El consumo de tabaco podría estar relacionado con la presencia de HO, así como el uso de bloqueadores beta y antagonistas del calcio (diferentes de las dihidropiridinas).ObjectiveTo find the prevalence of orthostatic hypotension (OH) and associated factors in elderly hypertensive patients in a primary care setting.DesignDescriptive cross-sectional study.SettingLa Marina Health Centre (an urban centre in Santander).PatientsA random sample of 295 patients aged 65 years or older regularly assisted from hypertension.Measurements and main resultsMeasurements of sitting and standing blood pressure were obtained. Orthostatic hypotension was defined as 20 mmHg or greater decrease in systolic or 10 mmHg or greater decrease in diastolic blood pressure after 1-minute or 5-minute standing. Associated diseases, symptoms upon standing, medication use, habits and other clinical assessments were also recorded. The prevalence of OH was 14.6%. The prevalence of systolic OH after 1-minute (OH-S1) and after 5-minute (OH-S5) standing was 5.8% in both, and the diastolic OH was 5.1% after 1-minute (OH-D1) and 4.1% after 5-minute (OH-D5) standing. By logistic regression analysis, association between higher level of systolic blood pressure and global OH was found, also with the presence of orthostatic intolerance symptoms (although only 25.6% of the patients with OH showed symptoms) and smoking. Beta-blockers and calcium channel blockers (different from dihydropyridines) use was associated with OH after 1-minute standing and smoking with OH after 5-minute standing.ConclusionsThe detected prevalence is high and justifies the case finding of OH in elderly hypertensive patients in primary care. The symptoms of orthostatic intolerance are correlated with OH, but only 1 out of 4 patients showed symptoms. Smoking could be related with OH, so beta-blockers and calcium channel blockers (different from dihydropyridines) use