Parallel SFC-based mesh partitioning and load balancing

Modern supercomputers allow the simulation of complex phenomena with increased accuracy. Eventually, this requires finer geometric discretizations with larger numbers of mesh elements. In this context, and extrapolating to the Exascale paradigm, meshing operations such as generation, adaptation or partition, become a critical bottleneck within the simulation workflow. In this paper, we focus on mesh partitioning. In particular, we present some improvements carried out on an in-house parallel mesh partitioner based on the Hilbert Space-Filling Curve. Additionally, taking advantage of its performance, we present the application of the SFC-based partitioning for dynamic load balancing. This method is based on the direct monitoring of the imbalance at runtime and the subsequent re-partitioning of the mesh. The target weights for the optimized partitions are evaluated using a least-squares approximation considering all measurements from previous iterations. In this way, the final partition corresponds to the average performance of the computing devices engaged.Comment: 10 pages, 9 figures. arXiv admin note: text overlap with arXiv:2005.0589

Characterization of anionic reverse micelles formulated on biobased solvents as replacing conventional nonpolar organic solvents

Two reverse micelles (RMs) employing 1,4-bis-2-ethylhexylsulfosuccinate (AOT) and two biobased solvents, p-cymene (p-cym) or limonene (lim), have been formulated with the aim to obtain systems more environmentally friendly. Both RMs were studied by using different techniques such as dynamic light scattering (DLS) and 1H NMR. Additionally, spectroscopy techniques were used to obtain information such as critical micellar concentration and aggregation number of the system investigated. Our results show that both biobased solvents can be used to generate AOT RMs. Interestingly, even the maximum amount of water dispersed are similar for both RMs, and the sizes of the systems are not identical, being that the RMs are formulated in lim larger than in p-cym. Both the biobased solvent and RMs show interaction of the entrapped water and the interface; however, this interaction is different depending on the solvent employed to prepare the RMs. Thus, the interaction water-surfactant at the interface is weaker in p-cym/AOT than in lim/AOT RMs. We think that the different penetration of the external solvent to the interfacial region is the main reason for the facts observed. In this sense, the polarity of these biobased solvents could explain why the penetration of both biobased solvents is different, making the p-cym/AOT RMs less interactive and, therefore, with smaller droplets sizes values. In summary, the different capacities of these biobased solvents to penetrate into the AOT interface allow us to obtain a new interface with peculiar characteristics and therefore with diverse applications.Fil: Oyarzun, Mauricio. Pontificia Universidad Católica de Chile; ChileFil: Oliva, Guillermo. Pontificia Universidad Católica de Chile; ChileFil: Falcone, Ruben Dario. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Departamento de Química; Argentina. Universidad Nacional de Río Cuarto. Instituto para el Desarrollo Agroindustrial y de la Salud. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto para el Desarrollo Agroindustrial y de la Salud; ArgentinaFil: Pavez, Paulina. Pontificia Universidad Católica de Chile; Chil

RHEA: an open-source Reproducible Hybrid-architecture flow solver Engineered for Academia

The study of complex multiscale flows (Groen et al., 2014), like for example the motion of small-scale turbulent eddies over large aerodynamic structures (Jofre & Doostan, 2022), microconfined high-pressure supercritical fluids for enhanced energy transfer (Bernades & Jofre, 2022), or hydrodynamic focusing of microorganisms in wall-bounded flows (Palacios et al., 2022), greatly benefits from the combination of interconnected theoretical, computational and experimental approaches. This manifold methodology provides a robust framework tocorroborate the phenomena observed, validate the modeling assumptions utilized, and facilitatesthe exploration of wider parameter spaces and extraction of more sophisticated insights. These analyses are typically encompassed within the field of Predictive Science & Engineering (Njam, 2009), which has attracted attention in the Fluid Mechanics community and is expected to exponentially grow as computational studies transition from (mostly) physics simulations to active vectors for scientific discovery and technological innovation with the advent of Exascale computing (Alowayyed et al., 2017). In this regard, the computational flow solver presented aims at bridging the gap between studying complex multiscale flow problems and utilizing present and future state-of-the-art supercomputing systems in academic environments.The solver presented is named RHEA, which stands for open-source Reproducible Hybrid-architecture flow solver Engineered for Academia, and is available as an open-source Git repository at https://gitlab.com/ProjectRHEA/flowsolverrheaPeer ReviewedPostprint (author's final draft

Portable implementation model for CFD simulations. Application to hybrid CPU/GPU supercomputers

Nowadays, high performance computing (HPC) systems experience a disruptive moment with a variety of novel architectures and frameworks, without any clarity of which one is going to prevail. In this context, the portability of codes across different architectures is of major importance. This paper presents a portable implementation model based on an algebraic operational approach for direct numerical simulation (DNS) and large eddy simulation (LES) of incompressible turbulent flows using unstructured hybrid meshes. The strategy proposed consists in representing the whole time-integration algorithm using only three basic algebraic operations: sparse matrix–vector product, a linear combination of vectors and dot product. The main idea is based on decomposing the nonlinear operators into a concatenation of two SpMV operations. This provides high modularity and portability. An exhaustive analysis of the proposed implementation for hybrid CPU/GPU supercomputers has been conducted with tests using up to 128 GPUs. The main objective consists in understanding the challenges of implementing CFD codes on new architectures.Peer ReviewedPostprint (author's final draft

Efficient CFD code implementation for the ARM-based Mont-Blanc architecture

Since 2011, the European project Mont-Blanc has been focused on enabling ARM-based technology for HPC, developing both hardware platforms and system software. The latest Mont-Blanc prototypes use system-on-chip (SoC) devices that combine a CPU and a GPU sharing a common main memory. Specific developments of parallel computing software and well-suited implementation approaches are of crucial importance for such a heterogeneous architecture in order to efficiently exploit its potential. This paper is devoted to the optimizations carried out in the TermoFluids CFD code to efficiently run it on the Mont-Blanc system. The underlying numerical method is based on an unstructured finite-volume discretization of the Navier–Stokes equations for the numerical simulation of incompressible turbulent flows. It is implemented using a portable and modular operational approach based on a minimal set of linear algebra operations. An architecture-specific heterogeneous multilevel MPI+OpenMP+OpenCL implementation of such kernels is proposed. It includes optimizations of the storage formats, dynamic load balancing between the CPU and GPU devices and hiding of communication overheads by overlapping computations and data transfers. A detailed performance study shows time reductions of up to on the kernels’ execution with the new heterogeneous implementation, its scalability on up to 128 Mont-Blanc nodes and the energy savings (around ) achieved with the Mont-Blanc system versus the high-end hybrid supercomputer MinoTauro.The research leading to these results has received funding from the European Community’s Seventh Framework Programme [FP7/2007–2013] and Horizon 2020 under the Mont-Blanc Project (www.montblanc-project.eu), grant agreement n 288777, 610402 and 671697. The work has been financially supported by the Ministerio de Ciencia e Innovación, Spain (ENE- 2014-60577-R), the Russian Science Foundation, project 15-11-30039, CONICYT Becas Chile Doctorado 2012, the Juan de la Cierva posdoctoral grant (IJCI-2014-21034), and the Initial Training Network SEDITRANS (GA number: 607394), implemented within the 7th Framework Programme of the European Commission under call FP7-PEOPLE- 2013-ITN. Our calculations have been performed on the resources of the Barcelona Supercomputing Center. The authors thankfully acknowledge these institutions.Peer ReviewedPostprint (published version

Optimising the Termofluids CFD code for petascale simulations

This paper presents some recent efforts carried out on the expansion of the scalability of TermoFluids multi-physics Computational Fluid Dynamics (CFD) code, aiming to achieve petascale capacity for a single simulation. We describe different aspects that we have improved in our code in order to efficiently run it on 131,072 CPU-cores. This work has been developed using the BlueGene/Q Mira supercomputer of the Argonne Leadership Computing Facility, where we have obtained feedback at the targeted scale. In summary, this is a practical paper showing our experience at reaching the petascale paradigm for a single simulation with TermoFluids.Peer ReviewedPostprint (author's final draft

A Magellan M2FS Spectroscopic Survey of Galaxies at 5.5<z<6.8: Program Overview and a Sample of the Brightest Lyman-alpha Emitters

We present a spectroscopic survey of high-redshift, luminous galaxies over four square degrees on the sky, aiming to build a large and homogeneous sample of Ly$\alpha$ emitters (LAEs) at $z\approx5.7$ and 6.5, and Lyman-break galaxies (LBGs) at $5.5<z<6.8$. The fields that we choose to observe are well-studied, such as SXDS and COSMOS. They have deep optical imaging data in a series of broad and narrow bands, allowing efficient selection of galaxy candidates. Spectroscopic observations are being carried out using the multi-object spectrograph M2FS on the Magellan Clay telescope. M2FS is efficient to identify high-redshift galaxies, owing to its 256 optical fibers deployed over a circular field-of-view 30 arcmin in diameter. We have observed $\sim2.5$ square degrees. When the program is completed, we expect to identify more than 400 bright LAEs at $z\approx5.7$ and 6.5, and a substantial number of LBGs at $z\ge6$. This unique sample will be used to study a variety of galaxy properties and to search for large protoclusters. Furthermore, the statistical properties of these galaxies will be used to probe cosmic reionization. We describe the motivation, program design, target selection, and M2FS observations. We also outline our science goals, and present a sample of the brightest LAEs at $z\approx5.7$ and 6.5. This sample contains 32 LAEs with Ly$\alpha$ luminosities higher than 10$^{43}$ erg s$^{-1}$. A few of them reach $\ge3\times10^{43}$ erg s$^{-1}$, comparable to the two most luminous LAEs known at $z\ge6$, `CR7' and `COLA1'. These LAEs provide ideal targets to study extreme galaxies in the distant universe.Comment: 18 pages, 11 figures, Accepted for publication in The Astrophysical Journa

Composição proximal e perfil de ácidos graxos de Hemigrapsus crenulatus (H. Milne Edwards, 1837) como um dos principais alimentos da “blenny patagônica” Eleginops maclovinus (Cuvier, 1830)

The Patagonian blenny (Eleginops maclovinus) is species endemic to South America with physiological characteristics that would facilitate its incorporation into Chilean aquaculture. However, there is currently no specific artificial food that can be used to raise E. maclovinus. In light of this problem, this study describes the proximal composition and fatty acid profile of the crab Hemigrapsus crenulatus, one of the main foods of E. maclovinus. The purpose of the study is to serve as basic information for the development of a specific artificial diet for juveniles of this fish species. The proximal analysis of the complete body of H. crenulatus indicates that it is mainly composed of ash (35.9%), proteins (32.2%), glucides (19.8%) and minor lipids (3.6%). The fatty acid profile is 40.7% PUFAs, 29.7% MUFAs and 29.5% SAFAs, and the most abundant acids are Eicosapentaenoic (18.8%), Oleic (6.8%) and Palmitic (16.6%), respectively. H. crenulatus has highest level of proteins, lipids and PUFAs among the species of the Brachyura infraorder

La economía rural en Chile: entre la pobreza y el desarrollo

El trabajo ofrece la visión de la economía rural chilena. Una realidad dicotómica que se mueve entre un medio rural diversificado (turismo, frutales, madera, pesca y vino, fundamentalmente), innovador, que exporta, dominado por empresas transnacionales, y la pequeña agricultura campesina, que se asocia con elevados índices de pobreza y que, en estos momentos, se encuentra ante un futuro incierto. Es hacia este sector de la población rural hacia donde deben dirigirse determinadas políticas de desarrollo encaminadas a lograr la reducción de la pobreza.The paper offers a view of rural economy in Chile. A dichotomical reality between a rural diversified sector (tourism, fruit trees, wood, fishing and wine, mainly), innovator, exporter, under control by transnational enterprises, and the short farming agriculture which shows high levels of poverty and it has an uncertain future at this moment. Specific development policies must be implemented to affect this kind of rural population and to reduce poverty

Parallel SFC-based mesh partitioning and load balancing

Modern supercomputers allow the simulation of complex phenomena with increased accuracy. Eventually, this requires finer geometric discretizations with larger numbers of mesh elements. In this context, and extrapolating to the Exascale paradigm, meshing operations such as generation, adaptation or partition, become a critical issue within the simulation workflow. In this paper, we focus on mesh partitioning. In particular, we present some improvements carried out on an in-house parallel mesh partitioner based on the Hilbert Space-Filling Curve. Additionally, taking advantage of its performance, we present the application of the SFC-based partitioning for dynamic load balancing. This method is based on the direct monitoring of the imbalance at runtime and the subsequent re-partitioning of the mesh. The target weights for the optimized partitions are evaluated using a least-squares approximation considering all measurements from previous iterations. In this way, the final partition corresponds to the average performance of the computing devices engaged.This work is partially supported by the BSC-IBM Deep Learning Research Agreement, under JSA “Application porting, analysis and optimization for POWER and POWERAI”. It has also been partially supported by the EXCELLERAT project funded by the European Commission’s ICT activity of the H2020 Programme under grant agreement number: 823691. It has also received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement number: 846139 (Exa-FireFlows). This paper expresses the opinions of the authors and not necessarily those of the European Commission. The European Commission is not liable for any use that may be made of the information contained in this paper. This work has also been financially supported by the Ministerio de Economia, Industria y Competitividad, of Spain (TRA2017-88508-R). The computing experiments of this paper have been performed on the resources of the Barcelona Supercomputing Center.Peer ReviewedPostprint (author's final draft