Enhancing speed and scalability of the ParFlow simulation code

Regional hydrology studies are often supported by high resolution simulations of subsurface flow that require expensive and extensive computations. Efficient usage of the latest high performance parallel computing systems becomes a necessity. The simulation software ParFlow has been demonstrated to meet this requirement and shown to have excellent solver scalability for up to 16,384 processes. In the present work we show that the code requires further enhancements in order to fully take advantage of current petascale machines. We identify ParFlow's way of parallelization of the computational mesh as a central bottleneck. We propose to reorganize this subsystem using fast mesh partition algorithms provided by the parallel adaptive mesh refinement library p4est. We realize this in a minimally invasive manner by modifying selected parts of the code to reinterpret the existing mesh data structures. We evaluate the scaling performance of the modified version of ParFlow, demonstrating good weak and strong scaling up to 458k cores of the Juqueen supercomputer, and test an example application at large scale.Comment: The final publication is available at link.springer.co

Implementation and scaling of the fully coupled Terrestrial Systems Modeling Platform (TerrSysMP) in a massively parallel supercomputing environment – a case study on JUQUEEN (IBM Blue Gene/Q)

Continental-scale hyper-resolution simulations constitute a grand challenge in characterizing non-linear feedbacks of states and fluxes of the coupled water, energy, and biogeochemical cycles of terrestrial systems. Tackling this challenge requires advanced coupling and supercomputing technologies for earth system models that are discussed in this study, utilizing the example of the implementation of the newly developed Terrestrial Systems Modeling Platform (TerrSysMP) on JUQUEEN (IBM Blue Gene/Q) of the Jülich Supercomputing Centre, Germany. The applied coupling strategies rely on the Multiple Program Multiple Data (MPMD) paradigm and require memory and load balancing considerations in the exchange of the coupling fields between different component models and allocation of computational resources, respectively. These considerations can be reached with advanced profiling and tracing tools leading to the efficient use of massively parallel computing environments, which is then mainly determined by the parallel performance of individual component models. However, the problem of model I/O and initialization in the peta-scale range requires major attention, because this constitutes a true big data challenge in the perspective of future exa-scale capabilities, which is unsolved

Forage yield and chemical composition of pearl millet varieties (Pennisetum glaucum (L.) R. BR.)

O experimento foi realizado para avaliar a produtividade, o perfilhamento, a porcentagem de lâmina/haste e a composição bromatológica (PB, FDN e FDA) de três variedades (Africano, Americano e BN-2) de milheto (Pennisetum glaucum (L) R. Br.) em três idades de corte (35, 42 e 49 dias). Na primeira fase da pesquisa, foi utilizado delineamento experimental em blocos casualizados, em um esquema de parcelas subdivididas no tempo, com quatro repetições. Na fase de rebrota, o delineamento foi inteiramente casualizado, com o mesmo número de repetições. As parcelas principais foram representadas pelas variedades e as subparcelas, pelas três idades de corte. A produção média de MS durante a fase de corte foi similar entre as variedades (4.360, 4.204 e 3.247 kg/MS/ha para as variedades Africano, Americano e BN-2, respectivamente), ao passo que os teores de PB, FDN e FDA e a relação lâmina/haste diferiram (Americano: 16,71% PB; 56,29% FDN e 30,04% FDA; BN-2: 16,30% PB; 55,93% FDN e 30,98% FDA; Africano: 15,36% PB; 60,55% FDN e 34,55% FDA). Com o avançar da idade de corte, a produtividade e os teores de FDN e FDA aumentaram, enquanto a relação lâmina/haste e o teor de PB decresceram linearmente. Na rebrota, a produtividade diminuiu, mas os teores médios de PB, FDN e FDA não diferiram entre as variedades (Americano: 20,21% PB; 53,19% FDN e 26,72% FDA; BN-2: 20,43% PB; 53,42% FDN e 27,06% FDA; Africano: 19,75% PB; 52,45% FDN e 27,44% FDA), observando-se diferença para a relação média lâmina/haste. O valor nutritivo da forragem na rebrota manteve-se acima dos encontrados na primeira fase de corte. As maiores porcentagens de lâminas foram observadas nas variedades Americano e BN-2 e as maiores de hastes, na variedade AFRICANO. As melhores variedades para uso na alimentação animal são: Americano e BN-2 e a melhor idade de corte é de 49 dias. __________________________________________________________________________________ ABSTRACTThe objective of this experiment was to evaluate the productivity, tillering, leaf blade/stem ratio and chemical composition (CP, NDF and ADF) of three pearl millet (Pennisetum glaucum (L.) R. BR.) varieties (African, American and BN-2) submitted to three different cutting ages (35, 42 and 49 days). During the first growth period, a split-plot arrangement in a complete randomized block design was used with varieties being the main plots and cutting ages the subplots. During regrowth, a complete randomized design was used. In both cases, there were four replications per treatment. Dry matter yield among varieties was similar (4,360, 4,204, and 3,247 kg/DM/ha) for the varieties African, American and BN-2, respectively. The CP (15.36, 16.71, and 16.3%), NDF (60.55, 56.29, and 55.93%) and ADF (34.55, 30.04, and 30.98%) concentrations as well as the leaf blade/stem percentages differed among African, American and BN-2 varieties, respectively. Dry matter productivity, NDF, and ADF concentrations increased with the advance of cutting age while leaf blade/stem ratio and CP decreased linearly. Productivity was reduced during regrowth, however, the average CP (19.75, 20.21, and 20.43%), NDF (52.45, 53.19, and 53.42%) and ADF (27.44, 26.72, and 27.06%) concentrations did not differ among African, American and BN-2 varieties during this period, respectively. The leaf blade/stem ratio, however, differed among them during regrowth. Forage nutritive value at regrowth was greater than during first growth period. American and BN-2 varieties presented the highest leaf blade percentage while the African variety showed the highest stem percentage. Thus, the best forage varieties are American and BN-2 and the best cutting age is 49 days

Brucella and Osteoarticular Cell Activation: Partners in Crime

Osteoarticular brucellosis is the most common presentation of human active disease although its prevalence varies widely. The three most common forms of osteoarticular involvement are sacroiliitis, spondylitis, and peripheral arthritis. The molecular mechanisms implicated in bone damage have been recently elucidated. B. abortus induces bone damage through diverse mechanisms in which TNF-α and the receptor activator of nuclear factor kappa-B ligand (RANKL)-the natural modulator of bone homeostasis are involved. These processes are driven by inflammatory cells, like monocytes/macrophages, neutrophils, Th17 CD4+ T, and B cells. In addition, Brucella abortus has a direct effect on osteoarticular cells and tilts homeostatic bone remodeling. These bacteria inhibit bone matrix deposition by osteoblasts (the only bone cells involved in bone deposition), and modify the phenotype of these cells to produce matrix metalloproteinases (MMPs) and cytokine secretion, contributing to bone matrix degradation. B. abortus also affects osteoclasts (cells naturally involved in bone resorption) by inducing an increase in osteoclastogenesis and osteoclast activation; thus, increasing mineral and organic bone matrix resorption, contributing to bone damage. Given that the pathology induced by Brucella species involved joint tissue, experiments conducted on synoviocytes revealed that besides inducing the activation of these cells to secrete chemokines, proinflammatory cytokines and MMPS, the infection also inhibits synoviocyte apoptosis. Brucella is an intracellular bacterium that replicates preferentially in the endoplasmic reticulum of macrophages. The analysis of B. abortus-infected synoviocytes indicated that bacteria also replicate in their reticulum suggesting that they could use this cell type for intracellular replication during the osteoarticular localization of the disease. Finally, the molecular mechanisms of osteoarticular brucellosis discovered recently shed light on how the interaction between B. abortus and immune and osteoarticular cells may play an important role in producing damage in joint and bone.Fil: Giambartolomei, Guillermo Hernan. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Inmunología, Genética y Metabolismo. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Inmunología, Genética y Metabolismo; ArgentinaFil: Arriola Benitez, Paula Constanza. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Inmunología, Genética y Metabolismo. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Inmunología, Genética y Metabolismo; ArgentinaFil: Delpino, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Inmunología, Genética y Metabolismo. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Inmunología, Genética y Metabolismo; Argentin

Reply to comment by H. Lough, Department of Civil Engineering, University of Canterbury, Christchurch, New Zealand, on the paper “Stream depletion predictions using pumping test data from a heterogeneous stream–aquifer system (a case study from the Great Plains, USA)”

1. General remark 2. The study by Kollet and Zlotnik (2003) 3. Remark on the explanation of the drawdown behavior 4. Remark on the re-analysis of the data from piezometer C2d 5. Summar

Response of Convective Boundary Layer and Shallow Cumulus to Soil Moisture Heterogeneity: A Large‐Eddy Simulation Study

In this study, the impact of varying soil moisture heterogeneity (spatial variance and structure) on the development of the convective boundary layer and shallow cumulus clouds was investigated. Applying soil moisture heterogeneity generated via spatially correlated Gaussian random fields based on a power law model and idealized atmospheric vertical profiles as initial conditions, three sets of large‐eddy simulations provide insight in the influence of soil moisture heterogeneity on the ensuing growth of the convective boundary layer and development of shallow cumulus clouds. A sensitivity on the strong, weak, and unstructured soil moisture heterogeneity is investigated. The simulation results show that domain‐averaged land surface sensible heat and latent heat flux change strongly with changing soil moisture variance because of the interactions between surface heterogeneity and induced circulations, while domain means of soil moisture are identical. Vertical profiles of boundary layer characteristics are strongly influenced by the surface energy partitioning and induced circulations, especially the profiles of liquid water and liquid water flux. The amount of liquid water and liquid water flux increases with increasing structure. In addition, the liquid water path is higher in case of strongly‐structured heterogeneity because more available energy is partitioned into latent heat and more intensive updrafts exist. Interestingly, the increase of liquid water path with increasing soil moisture variance only occurs in the strongly structured cases, which suggests that soil moisture variance and structure work conjunctively in the surface energy partitioning and the cloud formation

Infiltration from the pedon to global grid scales: an overview and outlook for land surface modelling

Infiltration in soils is a key process that partitions precipitation at the land surface in surface runoff and water that enters the soil profile. We reviewed the basic principles of water infiltration in soils and we analyzed approaches commonly used in Land Surface Models (LSMs) to quantify infiltration as well as its numerical implementation and sensitivity to model parameters. We reviewed methods to upscale infiltration from the point to the field, hill slope, and grid cell scale of LSMs. Despite the progress that has been made, upscaling of local scale infiltration processes to the grid scale used in LSMs is still far from being treated rigorously. We still lack a consistent theoretical framework to predict effective fluxes and parameters that control infiltration in LSMs. Our analysis shows, that there is a large variety in approaches used to estimate soil hydraulic properties. Novel, highly resolved soil information at higher resolutions than the grid scale of LSMs may help in better quantifying subgrid variability of key infiltration parameters. Currently, only a few land surface models consider the impact of soil structure on soil hydraulic properties. Finally, we identified several processes not yet considered in LSMs that are known to strongly influence infiltration. Especially, the impact of soil structure on infiltration requires further research. In order to tackle the above challenges and integrate current knowledge on soil processes affecting infiltration processes on land surface models, we advocate a stronger exchange and scientific interaction between the soil and the land surface modelling communities

Bone marrow injection stimulates hepatic ductular reactions in the absence of injury via macrophage-mediated TWEAK signaling

Tissue progenitor cells are an attractive target for regenerative therapy. In various organs, bone marrow cell (BMC) therapy has shown promising preliminary results, but to date no definite mechanism has been demonstrated to account for the observed benefit in organ regeneration. Tissue injury and regeneration is invariably accompanied by macrophage infiltration, but their influence upon the progenitor cells is incompletely understood, and direct signaling pathways may be obscured by the multiple roles of macrophages during organ injury. We therefore examined a model without injury; a single i.v. injection of unfractionated BMCs in healthy mice. This induced ductular reactions (DRs) in healthy mice. We demonstrate that macrophages within the unfractionated BMCs are responsible for the production of DRs, engrafting in the recipient liver and localizing to the DRs. Engrafted macrophages produce the cytokine TWEAK (TNF-like weak inducer of apoptosis) in situ. We go on to show that recombinant TWEAK activates DRs and that BMC mediated DRs are TWEAK dependent. DRs are accompanied by liver growth, occur in the absence of liver tissue injury and hepatic progenitor cells can be isolated from the livers of mice with DRs. Overall these results reveal a hitherto undescribed mechanism linking macrophage infiltration to DRs in the liver and highlight a rationale for macrophage derived cell therapy in regenerative medicine

Processos de comunicação e educação ambiental na formação de multiplicadores em resíduos sólidos no CIPAE G8 do Vale do Taquari-RS

O G8 é um consórcio de pequenos municípios do Rio Grande do Sul que atua coletivamente para o enfrentamento de questões da gestão pública e através do Programa Intermunicipal de Gestão Integrada de Resíduos – PIGIRS atende às exigências previstas, para o âmbito municipal, na Política Nacional de Resíduos Sólidos, a qual prevê e aponta para a responsabilidade compartilhada pelo ciclo de vida dos produtos e gestão integrada dos resíduos. Com a necessidade de ações que contribuam para a construção de sociedades sustentáveis e com a cobrança do Ministério Público para o cumprimento do PIGIRS (2013) pelo G8, no que se refere à educação ambiental, se dá início a um processo de formação, o qual segue as prerrogativas propostas pelo Ministério do Meio Ambiente quando cria a metodologia dos Coletivos Educadores. Os coletivos são constituídos por instituições e grupos que passam por processos formativos permanentes, participativos, continuados e voltados à diversidade de habitantes de um território, caso do G8. O Coletivo Educador está articulado ao que está posto no Programa Nacional de Educação Ambiental (ProNEA). Para tanto, problematiza-se a metodologia de formação, a apropriação do conhecimento pelos participantes e os modos de multiplicação em cada um dos municípios onde ocorreram formações. O objetivo do estudo é investigar processos de intervenção para a formação de multiplicadores em comunicação e educação ambiental em ambiente não-formal, voltados para a área de resíduos sólidos domésticos no âmbito do G8. O estudo atrela-se a um dos Objetivos de Desenvolvimento Sustentável, ODS 11: Tornar as cidades e os assentamentos humanos inclusivos, seguros, resilientes e sustentáveis, especificamente à meta de, até 2030, reduzir o impacto ambiental negativo per capita das cidades, inclusive prestando especial atenção à qualidade do ar, gestão de resíduos municipais e outros. A metodologia caracteriza-se como qualitativa, estudo de caso e, quanto aos fins a pesquisa é exploratória, descritiva e aplicada, baseada no estudo bibliográfico, documental e de campo, essa de caráter intervencionista. O tratamento de dados apoia-se na análise textual. Como resultados apresenta-se a análise das categorias de apropriações metodológicas e apropriações da formação nas quais é possível evidenciar que a formação de multiplicadores por meio de práticas colaborativas é potente, gera possibilidades de apropriação diversas pelos multiplicadores, o que se pode visualizar nas intervenções viabilizadas pela formação, além disso verificou-se suas possibilidades de potencializar a criação de Coletivos de Educação Ambiental. No entanto, esta possibilidade diferencia-se em cada município, já que em alguns a motivação foi maior que em outros, ademais a situação de pandemia dificultou a continuidade das ações, desfavorecendo a criação efetiva dos Coletivos Educadores. Mas evidenciou-se que o processo de formação de multiplicadores em resíduos sólidos do CIPAE G8 resultou na capacitação dos multiplicadores em educação ambiental e esses realizaram práticas de intervenção, as quais passaram a constituir parte de sua experiência de vida. Depois da formação estão mais próximos da formação de Coletivos Educadores que antes, considerando-se que, ao menos temporariamente e com o apoio dos pesquisadores, organizaram-se como tal.The G8 is a consortium of small municipalities in Rio Grande do Sul that works collectively to face public management issues and through the Intermunicipal Program for Integrated Waste Management - PIGIRS meets the requirements foreseen, for the municipal scope, in the National Policy for Solid Waste, which provides for and points to shared responsibility for the life cycle of products and integrated waste management. With the need for actions that contribute to the construction of sustainable societies and the collection of the Public Ministry for the fulfillment of PIGIRS (2013) by the G8, with regard to environmental education, a training process begins, which it follows the prerogatives proposed by the Ministry of the Environment when it creates the methodology of Collective Educators. The collectives are made up of institutions and groups that undergo permanent, participatory, continuous training processes and focused on the diversity of inhabitants of a territory, as in the case of the G8. The Educative Collective is linked to what is included in the National Environmental Education Program (ProNEA). To this end, the training methodology, the appropriation of knowledge by the participants and the multiplication modes that in each of the municipalities where training took place are problematized. The objective of the study is to investigate intervention processes for the formation of multipliers in communication and environmental education in a non-formal environment, focused on the area of domestic solid waste within the scope of the G8. The study is linked to one of the Sustainable Development Goals, SDG 11: Making cities and human settlements inclusive, safe, resilient and sustainable, specifically to the goal of, by 2030, reducing the negative environmental impact per capita of cities, including paying special attention to air quality, municipal waste management and others. The methodology is characterized as qualitative, case study and, as for the purposes, the research is exploratory, descriptive and applied, based on bibliographic, documentary and field study, this is of an interventionist character. Data processing is supported by textual analysis