Finite difference methods fengshui: alignment through a mathematics of arrays

Numerous scientific-computational domains make use of array data. The core computing of the numerical methods and the algorithms involved is related to multi-dimensional array manipulation. Memory layout and the access patterns of that data are crucial to the optimal performance of the array-based computations. As we move towards exascale computing, writing portable code for efficient data parallel computations is increasingly requiring an abstract productive working environment. To that end, we present the design of a framework for optimizing scientific array-based computations, building a case study for a Partial Differential Equations solver. By embedding the Mathematics of Arrays formalism in the Magnolia programming language, we assemble a software stack capable of abstracting the continuous high-level application layer from the discrete formulation of the collective array-based numerical methods and algorithms and the final detailed low-level code. The case study lays the groundwork for achieving optimized memory layout and efficient computations while preserving a stable abstraction layer independent of underlying algorithms and changes in the architecture.Peer ReviewedPostprint (author's final draft

Extending Saiph to simulate fluid mechanics and chemistry problems

Saiph is a domain specific language for solving partial differential equations in high performance computing systems, developed at the Barcelona Computing Center. The aim of this project is to extend this language to support fluid mechanics and chemistry problems

Saiph, a domain specific language for computational fluid dynamics simulations

Nowadays, High-Performance Computing (HPC) is assuming an increasingly central role in scientific research while computer architectures are becoming more and more hetero-geneous and using different parallel programming models and techniques. Under this scenario, the only way to successfully exploit an HPC system requires that computer and domain scientists work closely towards producing applications to solve domain problems, ensuring productivity and performance at the same time. Facing such purpose, Saiph is a Domain Specific Language designed to ease the task of solving couple and uncouple Partial Differential Equations (PDE’s), with a primary focusing on Computational Fluid Dynamics (CFD) applications. Saiph allows to model complex physical phenomena featured by PDE’s, easing the use of numerical methods and optimizations on different computer architectures to the users

Macroautophagic process was differentially modulated by long-term moderate exercise in rat brain and peripheral tissues

The autophagic process is a lysosomal degradation pathway, which is activated during stress conditions, such as starvation or exercise. Regular exercise has beneficial effects on human health, including neuroprotection. However, the cellular mechanisms underlying these effects are incompletely understood. Endurance and a single bout of exercise induce autophagy not only in brain but also in peripheral tissues. However, little is known whether autophagy could be modulated in brain and peripheral tissues by long-term moderate exercise. Here, we examined the effects on macroautophagy process of long-term moderate treadmill training (36 weeks) in adult rats both in brain (hippocampus and cerebral cortex) and peripheral tissues (skeletal muscle, liver and heart). We assessed mTOR activation and the autophagic proteins Beclin 1, p62, LC3B (LC3B-II/LC3B-I ratio) and the lysosomal protein LAMP1, as well as the ubiquitinated proteins. Our results showed in the cortex of exercised rats an inactivation of mTOR, greater autophagy flux (increased LC3-II/LC3-I ratio and reduced p62) besides increased LAMP1. Related with these effects a reduction in the ubiquitinated proteins was observed. No significant changes in the autophagic pathway were found either in hippocampus or in skeletal and cardiac muscle by exercise. Only in the liver of exercised rats mTOR phosphorylation and p62 levels increased, which could be related with beneficial metabolic effects in this organ induced by exercise. Thus, our findings suggest that long-term moderate exercise induces autophagy specifically in the corte

Magneto-Acoustic Waves in antiferromagnetic CuMnAs excited by Surface Acoustic Waves

Magnetoelastic effects in antiferromagnetic CuMnAs are investigated by applying dynamic strain in the 0.01% range through surface acoustic waves in the GaAs substrate. The magnetic state of the CuMnAs/GaAs is characterized by a multitude of submicron-sized domains which we image by x-ray magnetic linear dichroism combined with photoemission electron microscopy. Within the explored strain range, CuMnAs shows magnetoelastic effects in the form of N\'eel vector waves with micrometer wavelength, which corresponds to an averaged overall spin-axis rotation up to 2.4 deg driven by the time-dependent strain from the surface acoustic wave. Measurements at different temperatures indicate a reduction of the wave amplitude when lowering the temperature. However, no domain wall motion has been detected on the nanosecond timescal

Longitudinal association between hippocampus atrophy and episodic-memory decline in non-demented APOE ε4 carriers.

Introduction: The apolipoprotein E (APOE) ε4 allele is the main genetic risk factor for Alzheimer's disease (AD), accelerated cognitive aging, and hippocampal atrophy, but its influence on the association between hippocampus atrophy and episodic-memory decline in non-demented individuals remains unclear. Methods: We analyzed longitudinal (two to six observations) magnetic resonance imaging (MRI)-derived hippocampal volumes and episodic memory from 748 individuals (55 to 90 years at baseline, 50% female) from the European Lifebrain consortium. Results: The change-change association for hippocampal volume and memory was significant only in ε4 carriers (N = 173, r = 0.21, P = .007; non-carriers: N = 467, r = 0.073, P = .117). The linear relationship was significantly steeper for the carriers [t(629) = 2.4, P = .013]. A similar trend toward a stronger change-change relation for carriers was seen in a subsample with more than two assessments. Discussion: These findings provide evidence for a difference in hippocampus-memory association between ε4 carriers and non-carriers, thus highlighting how genetic factors modulate the translation of the AD-related pathophysiological cascade into cognitive deficits

Implantació i Millora de l'European Project Semester (EPS) a l'EPSEVG

L'EPSEVG de la UPC va implantar l’European Project Semester (EPS) un programa formatiu innovador que respon a les demandes plantejades per la societat i l’Espai Europeu d’Ensenyament Superior (EEES) durant el curs 2007‐2008. L’EPS permet cobrir la demanda d’estudiants estrangers que volen venir a estudiar a l’escola, demanda, que, a nivell de grau en enginyeria no esta coberta en cap universitat catalana.L’EPS també és una oportunitat per augmentar el compromís de l’EPSEVG vers la sostenibilitat. El programa s’ha ambientalitzat d’acord amb les directrius del Pla UPC Sostenible 2015 essent la sostenibilitat un dels eixos transversals que li dona contingut i que identifica a tots els projectes desenvolupats. A més de la sostenibilitat, el programa inclou altres matèries transversals (com ara, la innovació, la gestió de projectes, l’accessibilitat...). L’EPS utilitza el model d’aprenentatge basat en projectes (Project Based Learning), i hi introdueix dos components nous: la docència en anglès i la interculturalitat dins de l’aula. Les noves tecnologies s’utilitzen tant per dinamitzar el treball dels grups com per facilitar el seu aprenentatge, doncs l’EPS inclou tallers i seminaris en la modalitat semipresencial.Peer Reviewe

Extending Saiph to simulate fluid mechanics and chemistry problems

Saiph is a domain specific language for solving partial differential equations in high performance computing systems, developed at the Barcelona Computing Center. The aim of this project is to extend this language to support fluid mechanics and chemistry problems

Examen Final

Resolve

Combining one-sided communications with task-based programming models

Hybrid programming combining task-based and message-passing models is an increasingly popular technique to exploit multi-core clusters. The Task-Aware MPI (TAMPI) library integrates both models enabling the safe overlap of computation and communication tasks using two-sided MPI communications. Two-sided primitives combine data transfers with implicit synchronizations, but one-sided models usually offer more efficient data transfers decoupling synchronizations. MPI offers four distinct one-sided synchronization modes, while GASPI is a PGAS API providing one-sided operations with remote notifications for fine inter-process synchronizations.In this paper, we study the challenges of integrating MPI and GASPI one-sided operations with the OpenMP and OmpSs-2 tasking models. We propose and implement several extensions to the GASPI and OmpSs-2 programming models, which are leveraged by a new library called Task-Aware GASPI (TAGASPI). The TAGASPI library allows the efficient and safe use of one-sided operations with remote notifications inside tasks. Both TAGASPI and TAMPI transparently manage communications issued by tasks and allow these to overlap with computation tasks naturally, following a data-flow model. These libraries are complementary and can be mixed in the same application.Our experience porting several mini-apps to this hybrid model shows that TAGASPI helps leverage one-sided communications with similar complexity to pure and hybrid two-sided MPI approaches. We show that our hybrid one-sided approach outperforms the pure MPI strategies, but it also surpasses the TAMPI’s performance when stressing communication phases, e.g., increasing the communication parallelism and reducing the communication tasks’ sizes.This work has been supported by the European Union H2020 Programme through the LoSync PRACE6IP project (agreement No. INFRAEDI-823767); the Spanish Ministry of Economy through the Severo Ochoa Center of Excellence Program (SEV-2015-0493); the Spanish Ministry of Science and Innovation (PID2019-107255GB); and the Generalitat de Catalunya (2017-SGR-1414).Peer ReviewedPostprint (author's final draft