Shingle 2.0: generalising self-consistent and automated domain discretisation for multi-scale geophysical models

The approaches taken to describe and develop spatial discretisations of the domains required for geophysical simulation models are commonly ad hoc, model or application specific and under-documented. This is particularly acute for simulation models that are flexible in their use of multi-scale, anisotropic, fully unstructured meshes where a relatively large number of heterogeneous parameters are required to constrain their full description. As a consequence, it can be difficult to reproduce simulations, ensure a provenance in model data handling and initialisation, and a challenge to conduct model intercomparisons rigorously. This paper takes a novel approach to spatial discretisation, considering it much like a numerical simulation model problem of its own. It introduces a generalised, extensible, self-documenting approach to carefully describe, and necessarily fully, the constraints over the heterogeneous parameter space that determine how a domain is spatially discretised. This additionally provides a method to accurately record these constraints, using high-level natural language based abstractions, that enables full accounts of provenance, sharing and distribution. Together with this description, a generalised consistent approach to unstructured mesh generation for geophysical models is developed, that is automated, robust and repeatable, quick-to-draft, rigorously verified and consistent to the source data throughout. This interprets the description above to execute a self-consistent spatial discretisation process, which is automatically validated to expected discrete characteristics and metrics.Comment: 18 pages, 10 figures, 1 table. Submitted for publication and under revie

Population structure of chum salmon (Oncorhynchus keta) across the Pacific Rim, determined from microsatellite analysis

The Pacific Rim population structure of chum salmon (Oncorhynchus keta) was examined with a survey of microsatellite variation to describe the distribution of genetic variation and to evaluate whether chum salmon may have originated from two or more glacial refuges following dispersal to newly available habitat after glacial retreat. Variation at 14 microsatellite loci was surveyed for over 53,000 chum salmon sampled from over 380 localities ranging from Korea through Washington State. An index of genetic differentiation, FST, over all populations and loci was 0.033, with individual locus values ranging from 0.009 to 0.104. The most genetically diverse chum salmon were observed from Asia, particularly Japan, whereas chum salmon from the Skeena River and Queen Charlotte Islands in northern British Columbia and those from Washington State displayed the fewest number of alleles compared with chum salmon in other regions. Differentiation in chum salmon allele frequencies among regions and populations within regions was approximately 18 times greater than that of annual variation within populations. A regional structuring of populations was the general pattern observed, with chum salmon spawning in different tributaries within a major river drainage or spawning in smaller rivers in a geographic area generally more similar to each other than to populations in different major river drainages or geographic areas. Population structure of chum salmon on a Pacific Rim basis supports the concept of a minimum of two refuges, northern and southern, during the last glaciation, but four possible refuges fit better the observed distribution of genetic variation. The distribution of microsatellite variation of chum salmon on a Pacific Rim basis likely reflects the origins of salmon radiating from refuges after the last glaciation period

Numerical solution of perturbed Kepler problem using a split operator technique

An efficient geometric integrator is proposed for solving the perturbed Kepler motion. This method is stable and accurate over long integration time, which makes it appropriate for treating problems in astrophysics, like solar system simulations, and atomic and molecular physics, like classical simulations of highly excited atoms in external fields. The key idea is to decompose the hamiltonian in solvable parts and propagate the system according to each term. Two case studies, the Kepler atom in an uniform field and in a monochromatic field, are presented and the errors are analyzed.Comment: 17 pages, 5 figures, submitted to the Journal of Computational Physic

Macrogol (polyethylene glycol) laxatives in children with functional constipation and faecal impaction: a systematic review

As the evidence base supporting the use of laxatives in children is very limited, we undertook an updated systematic review to clarify the issue. A comprehensive literature search was carried out to identify randomised controlled trials of polyethylene glycol (PEG) versus either placebo or active comparator, in patients aged <18 years with primary chronic constipation. Outcomes were assessed as either global assessments of effectiveness or differences in defaecation rates. Seven qualifying studies involving 594 children were identified. Five were comparisons of PEG with lactulose, one with milk of magnesia and one with placebo. Study duration ranged from 2 weeks to 12 months. PEG was significantly more effective than placebo and either equivalent to (two studies) or superior to (four studies) active comparator. Differences in study design precluded meaningful meta-analysis. Lack of high quality studies has meant that the management of childhood constipation has tended to rely on anecdote and empirical treatment choice. Recent publication of well designed randomised trials now permits a more evidence-based approach, with PEG-based treatments having been proven to be effective and well-tolerated first-line treatment

Dividing population genetic distance data with the software Partitioning Optimization with Restricted Growth Strings (PORGS): an application for Chinook salmon (Oncorhynchus tshawytscha), Vancouver Island, British Columbia

A new method of finding the optimal group membership and number of groupings to partition population genetic distance data is presented. The software program Partitioning Optimization with Restricted Growth Strings (PORGS), visits all possible set partitions and deems acceptable partitions to be those that reduce mean intracluster distance. The optimal number of groups is determined with the gap statistic which compares PORGS results with a reference distribution. The PORGS method was validated by a simulated data set with a known distribution. For efficiency, where values of n were larger, restricted growth strings (RGS) were used to bipartition populations during a nested search (bi-PORGS). Bi-PORGS was applied to a set of genetic data from 18 Chinook salmon (Oncorhynchus tshawytscha) populations from the west coast of Vancouver Island. The optimal grouping of these populations corresponded to four geographic locations: 1) Quatsino Sound, 2) Nootka Sound, 3) Clayoquot +Barkley sounds, and 4) southwest Vancouver Island. However, assignment of populations to groups did not strictly reflect the geographical divisions; fish of Barkley Sound origin that had strayed into the Gold River and close genetic similarity between transferred and donor populations meant groupings crossed geographic boundaries. Overall, stock structure determined by this partitioning method was similar to that determined by the unweighted pair-group method with arithmetic averages (UPGMA), an agglomerative clustering algorithm

Let It Out (LIO) study: protocol for a mixed-methods study to optimise the design and assess the feasibility of an online emotional disclosure-based intervention in UK hospices

INTRODUCTION: The current COVID-19 pandemic has forced hospices to look for more ways to support people remotely, including psychological support. Emotional disclosure-based interventions hold potential as a way of providing support remotely. However, evidence of their efficacy in people with terminal illness is mixed. Reviews have highlighted this may be due to interventions not being tailored to the unique needs of this population. In response to this, we are developing Let It Out (LIO), an online, self-guided emotional disclosure-based intervention tailored for people living with terminal illness. AIMS: The primary objective of the study is to optimise the design of the LIO intervention. Secondary objectives include assessing its acceptability and feasibility; exploring potential impact on well-being; identifying potential adverse effects; and informing choice of outcome measures for potential future evaluation. METHODS AND ANALYSIS: A single arm, mixed-methods, multisite, longitudinal study. Up to 40 people living with a terminal illness under the care of hospices in England and Scotland will receive the online LIO intervention. LIO consists of 3, self-guided expression sessions over 2 weeks. The primary outcome measures are (1) a structured feedback form completed by participants after the final expression session; and (2) semi-structured interviews and focus groups with ≤15 patient participants, ≤30 hospice staff and ≤15 informal carers. These quantitative and qualitative data will be triangulated via process evaluation to inform optimisation of the intervention design. Secondary outcome measures include validated measures of physical and psychological health collected at baseline and after the final expression session (immediately, 1, 4 and 8 weeks after); and data on recruitment, retention and fidelity. ETHICS AND DISSEMINATION: The study is approved by the University College London Research Ethics Committee (reference: 15281/002). The findings will be shared through peer-reviewed scientific journals and conferences, and traditional, online and social media platforms

An Enhanced Nonlinear Critical Gradient for Electron Turbulent Transport due to Reversed Magnetic Shear

The first nonlinear gyrokinetic simulations of electron internal transport barriers (e-ITBs) in the National Spherical Torus Experiment show that reversed magnetic shear can suppress thermal transport by increasing the nonlinear critical gradient for electron-temperature-gradient-driven turbulence to three times its linear critical value. An interesting feature of this turbulence is nonlinearly driven off-midplane radial streamers. This work reinforces the experimental observation that magnetic shear is likely an effective way of triggering and sustaining e-ITBs in magnetic fusion devices.Comment: 4 pages, 5 figure

An Enhanced Nonlinear Critical Gradient for Electron Turbulent Transport due to Reversed Magnetic Shear

The first nonlinear gyrokinetic simulations of electron internal transport barriers (e-ITBs) in the National Spherical Torus Experiment show that reversed magnetic shear can suppress thermal transport by increasing the nonlinear critical gradient for electron-temperature-gradient-driven turbulence to three times its linear critical value. An interesting feature of this turbulence is nonlinearly driven off-midplane radial streamers. This work reinforces the experimental observation that magnetic shear is likely an effective way of triggering and sustaining e-ITBs in magnetic fusion devices.Comment: 4 pages, 5 figure

Optimization and Portability of a Fusion OpenACC-based FORTRAN HPC Code from NVIDIA to AMD GPUs

NVIDIA has been the main provider of GPU hardware in HPC systems for over a decade. Most applications that benefit from GPUs have thus been developed and optimized for the NVIDIA software stack. Recent exascale HPC systems are, however, introducing GPUs from other vendors, e.g. with the AMD GPU-based OLCF Frontier system just becoming available. AMD GPUs cannot be directly accessed using the NVIDIA software stack, and require a porting effort by the application developers. This paper provides an overview of our experience porting and optimizing the CGYRO code, a widely-used fusion simulation tool based on FORTRAN with OpenACC-based GPU acceleration. While the porting from the NVIDIA compilers was relatively straightforward using the CRAY compilers on the AMD systems, the performance optimization required more fine-tuning. In the optimization effort, we uncovered code sections that had performed well on NVIDIA GPUs, but were unexpectedly slow on AMD GPUs. After AMD-targeted code optimizations, performance on AMD GPUs has increased to meet our expectations. Modest speed improvements were also seen on NVIDIA GPUs, which was an unexpected benefit of this exercise.Comment: 6 pages, 4 figures, 2 tables, To be published in Proceedings of PEARC2