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"Rasmussen, Craig E"
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A Network-Failure-Tolerant Message-Passing System for Terascale Clusters
The Los Alamos Message Passing Interface (LA-MPI) is an end-to-end network-failure-tolerant message-passing system designed for terascale clusters. LA-MPI is a standard-compliant implementation of MPI designed to tolerate network-related failures including I/O bus errors, network card errors, and wire-transmission errors. This paper details the distinguishing features of LA-MPI, including support for concurrent use of multiple types of network interface, and reliable message transmission utilizing multiple network paths and routes between a given source and destination. In addition, performance measurements on production-grade platforms are presented. [PUBLICATION ABSTRACT]
Journal Article
ForOpenCL: Transformations Exploiting Array Syntax in Fortran for Accelerator Programming
Emerging GPU architectures for high performance computing are well suited to a data-parallel programming model. This paper presents preliminary work examining a programming methodology that provides Fortran programmers with access to these emerging systems. We use array constructs in Fortran to show how this infrequently exploited, standardized language feature is easily transformed to lower-level accelerator code. The transformations in ForOpenCL are based on a simple mapping from Fortran to OpenCL. We demonstrate, using a stencil code solving the shallow-water fluid equations, that the performance of the ForOpenCL compiler-generated transformations is comparable with that of hand-optimized OpenCL code.
Paper
Beyond clay
Improved quantification of the factors controlling soil organic matter (SOM) stabilization at continental to global scales is needed to inform projections of the largest actively cycling terrestrial carbon pool on Earth, and its response to environmental change. Biogeochemical models rely almost exclusively on clay content to modify rates of SOM turnover and fluxes of climate-active CO₂ to the atmosphere. Emerging conceptual understanding, however, suggests other soil physicochemical properties may predict SOM stabilization better than clay content. We addressed this discrepancy by synthesizing data from over 5,500 soil profiles spanning continental scale environmental gradients. Here, we demonstrate that other physicochemical parameters are much stronger predictors of SOM content, with clay content having relatively little explanatory power. We show that exchangeable calcium strongly predicted SOM content in water-limited, alkaline soils, whereas with increasing moisture availability and acidity, iron- and aluminum-oxyhydroxides emerged as better predictors, demonstrating that the relative importance of SOM stabilization mechanisms scales with climate and acidity. These results highlight the urgent need to modify biogeochemical models to better reflect the role of soil physicochemical properties in SOM cycling.
Journal Article
Adolescence and the next generation
Adolescent growth and social development shape the early development of offspring from preconception through to the post-partum period through distinct processes in males and females. At a time of great change in the forces shaping adolescence, including the timing of parenthood, investments in today’s adolescents, the largest cohort in human history, will yield great dividends for future generations.
Investing in adolescents as the parents of the next generation is important for the wellbeing of current and future generations.
The afterlife of adolescence
Adolescence is increasingly recognized as a developmental period that has a potential for influencing life-course trajectories that is second only to early life, but that could also shape the growth and development of the following generation. George Patton and colleagues review the evidence around how an individual's health, growth and nutrition during adolescence may affect the early growth of their offspring, and consider potential mechanisms for transmission. The current generation of adolescents—now considered to be all those aged between 10 and 24—will be the largest in human history to become parents. The greatest dividends from investments in today's adolescents may be seen in the health and human capabilities of the next generation.
Journal Article
The trans-ancestral genomic architecture of glycemic traits
Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel;
P
< 5 × 10
−8
), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution.
A trans-ancestry meta-analysis of GWAS of glycemic traits in up to 281,416 individuals identifies 99 novel loci, of which one quarter was found due to the multi-ancestry approach, which also improves fine-mapping of credible variant sets.
Journal Article
Analysis of single-Alter-shielded and unshielded measurements of mixed and solid precipitation from WMO-SPICE
Although precipitation has been measured for many centuries, precipitation measurements are still beset with significant inaccuracies. Solid precipitation is particularly difficult to measure accurately, and wintertime precipitation measurement biases between different observing networks or different regions can exceed 100 %. Using precipitation gauge results from the World Meteorological Organization Solid Precipitation Intercomparison Experiment (WMO-SPICE), errors in precipitation measurement caused by gauge uncertainty, spatial variability in precipitation, hydrometeor type, crystal habit, and wind were quantified. The methods used to calculate gauge catch efficiency and correct known biases are described. Adjustments, in the form of transfer functions that describe catch efficiency as a function of air temperature and wind speed, were derived using measurements from eight separate WMO-SPICE sites for both unshielded and single-Alter-shielded precipitation-weighing gauges. For the unshielded gauges, the average undercatch for all eight sites was 0.50 mm h−1 (34 %), and for the single-Alter-shielded gauges it was 0.35 mm h−1 (24 %). After adjustment, the mean bias for both the unshielded and single-Alter measurements was within 0.03 mm h−1 (2 %) of zero. The use of multiple sites to derive such adjustments makes these results unique and more broadly applicable to other sites with various climatic conditions. In addition, errors associated with the use of a single transfer function to correct gauge undercatch at multiple sites were estimated.
Journal Article
Dermal appendage-dependent patterning of zebrafish atoh1a+ Merkel cells
Touch system function requires precise interactions between specialized skin cells and somatosensory axons, as exemplified by the vertebrate mechanosensory Merkel cell-neurite complex. Development and patterning of Merkel cells and associated neurites during skin organogenesis remain poorly understood, partly due to the in utero development of mammalian embryos. Here, we discover Merkel cells in the zebrafish epidermis and identify Atonal homolog 1a (Atoh1a) as a marker of zebrafish Merkel cells. We show that zebrafish Merkel cells derive from basal keratinocytes, express neurosecretory and mechanosensory machinery, extend actin-rich microvilli, and complex with somatosensory axons, all hallmarks of mammalian Merkel cells. Merkel cells populate all major adult skin compartments, with region-specific densities and distribution patterns. In vivo photoconversion reveals that Merkel cells undergo steady loss and replenishment during skin homeostasis. Merkel cells develop concomitant with dermal appendages along the trunk and loss of Ectodysplasin signaling, which prevents dermal appendage formation, reduces Merkel cell density by affecting cell differentiation. By contrast, altering dermal appendage morphology changes the distribution, but not density, of Merkel cells. Overall, our studies provide insights into touch system maturation during skin organogenesis and establish zebrafish as an experimentally accessible in vivo model for the study of Merkel cell biology.
Journal Article
Refactoring the elastic–viscous–plastic solver from the sea ice model CICE v6.5.1 for improved performance
This study focuses on the performance of the elastic–viscous–plastic (EVP) dynamical solver within the sea ice model, CICE v6.5.1. The study has been conducted in two steps. First, the standard EVP solver was extracted from CICE for experiments with refactored versions, which are used for performance testing. Second, one refactored version was integrated and tested in the full CICE model to demonstrate that the new algorithms do not significantly impact the physical results.The study reveals two dominant bottlenecks, namely (1) the number of Message Parsing Interface (MPI) and Open Multi-Processing (OpenMP) synchronization points required for halo exchanges during each time step combined with the irregular domain of active sea ice points and (2) the lack of single-instruction, multiple-data (SIMD) code generation.The standard EVP solver has been refactored based on two generic patterns. The first pattern exposes how general finite differences on masked multi-dimensional arrays can be expressed in order to produce significantly better code generation by changing the memory access pattern from random access to direct access. The second pattern takes an alternative approach to handle static grid properties.The measured single-core performance improvement is more than a factor of 5 compared to the standard implementation. The refactored implementation of strong scales on the Intel® Xeon® Scalable Processors series node until the available bandwidth of the node is used. For the Intel® Xeon® CPU Max series, there is sufficient bandwidth to allow the strong scaling to continue for all the cores on the node, resulting in a single-node improvement factor of 35 over the standard implementation. This study also demonstrates improved performance on GPU processors.
Journal Article
Soil organic carbon is not just for soil scientists
Soil organic carbon (SOC) regulates terrestrial ecosystem functioning, provides diverse energy sources for soil microorganisms, governs soil structure, and regulates the availability of organically bound nutrients. Investigators in increasingly diverse disciplines recognize how quantifying SOC attributes can provide insight about ecological states and processes. Today, multiple research networks collect and provide SOC data, and robust, new technologies are available for managing, sharing, and analyzing large data sets. We advocate that the scientific community capitalize on these developments to augment SOC data sets via standardized protocols. We describe why such efforts are important and the breadth of disciplines for which it will be helpful, and outline a tiered approach for standardized sampling of SOC and ancillary variables that ranges from simple to more complex. We target scientists ranging from those with little to no background in soil science to those with more soil-related expertise, and offer examples of the ways in which the resulting data can be organized, shared, and discoverable.
Journal Article