A low memory, highly concurrent multigrid algorithm

We examine what is an efficient and scalable nonlinear solver, with low work and memory complexity, for many classes of discretized partial differential equations (PDEs) - matrix-free Full multigrid (FMG) with a Full Approximation Storage (FAS) - in the context of current trends in computer architectures. Brandt proposed an extremely low memory FMG-FAS algorithm over 25 years ago that has several attractive properties for reducing costs on modern - memory centric -- machines and has not been developed to our knowledge. This method, segmental refinement (SR), has very low memory requirements because the finest grids need not be held in memory at any one time but can be "swept" through, computing coarse grid correction and any quantities of interest, allowing for orders of magnitude reduction in memory usage. This algorithm has two useful ideas for effectively exploiting future architectures: improved data locality and reuse via "vertical" processing of the multigrid algorithms and the method of $\tau$-corrections, which allows for not storing the entire fine grids at any one time. This report develops this algorithm for a model problem and a parallel generalization of the original sweeping technique. We show that FMG-FAS-SR can work as originally predicted, solving systems accurately enough to maintain the convergence rate of the discretization with one FMG iteration, and that the parallel algorithm provides a natural approach to fully exploiting the available parallelism of FMG

A performance portable, fully implicit Landau collision operator with batched linear solvers

Modern accelerators use hierarchically parallel programming models that enable massive multithreading within a processing element (PE), with multiple PEs per device driven by traditional processes. Batching is a technique for exposing PE-level parallelism in algorithms that previously ran on entire processes or multiple threads within a single MPI process. Kinetic discretizations of magnetized plasmas, for example, advance the Vlasov-Maxwell system, which is then followed by a fully implicit time advance of a collision operator. These collision advances are independent at each spatial point and are well suited to batch processing. This paper builds on previous work on a high-performance, fully nonlinear Landau collision operator by batching the linear solver, as well as batching the spatial point problems and adding new support for multiple grids for highly multiscale, multi-species problems. An anisotropic relaxation verification test that agrees well with previous published results and analytical solutions is presented. The performance of the NVIDIA A100 and AMD MI250X nodes is evaluated, with a detailed hardware utilization analysis on the A100. For portability, the entire Landau operator time advance is implemented in Kokkos and is available in the PETSc numerical library

Modelling nasal high flow therapy effects on upper airway resistance and resistive work of breathing

Aim The goal of this paper is to quantify upper airway resistance with and without nasal high flow (NHF) therapy. For adults, NHF therapy feeds 30–60 L/min of warm humidified air into the nose through short cannulas which do not seal the nostril. NHF therapy has been reported to increase airway pressure, increase tidal volume (Vt) and decrease respiratory rate (RR), but it is unclear how these findings affect the work done to overcome airway resistance to air flow during expiration. Also, there is little information on how the choice of nasal cannula size may affect work of breathing. In this paper, estimates of airway resistance without and with different NHF flow (applied via different cannula sizes) were made. The breathing efforts required to overcome airway resistance under these conditions were quantified. Method NHF was applied via three different cannula sizes to a 3-D printed human upper airway. Pressure drop and flow rate were measured and used to estimate inspiratory and expiratory upper airway resistances. The resistance information was used to compute the muscular work required to overcome the resistance of the upper airway to flow. Results NHF raises expiratory resistance relative to spontaneous breathing if the breathing pattern does not change but reduces work of breathing if peak expiratory flow falls. Of the cannula sizes used, the large cannula produced the greatest resistance and the small cannula produced the least. The work required to cause tracheal flow through the upper airway was reduced if the RR and minute volume are reduced by NHF. NHF has been observed to do so in COPD patients (Bräunlich et al., 2013). A reduction in I:E ratio due to therapy was found to reduce work of breathing if the peak inspiratory flow is less than the flow below which no inspiratory effort is required to overcome upper airway resistance. Conclusion NHF raises expiratory resistance but it can reduce the work required to overcome upper airway resistance via a fall in inspiratory work of breathing, RR and minute volume

Moving polewards in winter: a recent change in the migratory strategy of a pelagic seabird?

Background: During the non-breeding period, many birds migrate to milder areas, found closer to the equator than their breeding sites. Opposite movements are very rare. In the Southern Ocean, the abundance of C-13 declines markedly with more southern latitude, providing a characteristic C-13 isoscape. This can be used as a tracer for the movement of seabirds between breeding and inter-breeding areas, by comparing stable isotope ratios of feathers grown at different times of the year. Results: We studied seasonal movements of Thin-billed prions (Aves, Procellariiformes), breeding at the Subantarctic Falkland/Malvinas Islands, compared with those of Wilson's storm-petrels breeding in the Antarctic South Shetland Islands. The two species showed opposite migratory movements. While Wilson's storm-petrels moved to warmer waters north of the Drake Passage in winter, Thin-billed prions showed a reversed movement towards more polar waters. Carbon stable isotope ratios in recent and historical feathers indicated that poleward winter movements of Thin-billed prions were less common historically (45% in 1913-1915), and have only recently become dominant (92% in 2003-2005), apparently in response to warming sea temperatures. Conclusions: This study shows that pelagic seabirds can rapidly change migration strategies within populations, including migration towards more poleward waters in winte

Genome-by-Trauma Exposure Interactions in Adults With Depression in the UK Biobank

IMPORTANCE: Self-reported trauma exposure has consistently been found to be a risk factor for major depressive disorder (MDD), and several studies have reported interactions with genetic liability. To date, most studies have examined gene-environment interactions with trauma exposure using genome-wide variants (single-nucleotide variations [SNVs]) or polygenic scores, both typically capturing less than 3% of phenotypic risk variance. OBJECTIVE: To reexamine genome-by-trauma interaction associations using genetic measures using all available genotyped data and thus, maximizing accounted variance. DESIGN, SETTING, AND PARTICIPANTS: The UK Biobank study was conducted from April 2007 to May 1, 2016 (follow-up mental health questionnaire). The current study used available cross-sectional genomic and trauma exposure data from UK Biobank. Participants who completed the mental health questionnaire and had available genetic, trauma experience, depressive symptoms, and/or neuroticism information were included. Data were analyzed from April 1 to August 30, 2021. EXPOSURES: Trauma and genome-by-trauma exposure interactions. MAIN OUTCOMES AND MEASURES: Measures of self-reported depression, neuroticism, and trauma exposure with whole-genome SNV data are available from the UK Biobank study. Here, a mixed-model statistical approach using genetic, trauma exposure, and genome-by-trauma exposure interaction similarity matrices was used to explore sources of variation in depression and neuroticism. RESULTS: Analyses were conducted on 148 129 participants (mean [SD] age, 56 [7] years) of which 76 995 were female (52.0%). The study approach estimated the heritability (SE) of MDD to be approximately 0.160 (0.016). Subtypes of self-reported trauma exposure (catastrophic, adult, childhood, and full trauma) accounted for a significant proportion of the variance of MDD, with heritability (SE) ranging from 0.056 (0.013) to 0.176 (0.025). The proportion of MDD risk variance accounted for by significant genome-by-trauma interaction revealed estimates (SD) ranging from 0.074 (0.006) to 0.201 (0.009). Results from sex-specific analyses found genome-by-trauma interaction variance estimates approximately 5-fold greater for MDD in male participants (0.441 [0.018]) than in female participants (0.086 [0.009]). CONCLUSIONS AND RELEVANCE: This cross-sectional study used an approach combining all genome-wide SNV data when exploring genome-by-trauma interactions in individuals with MDD; findings suggest that such interactions were associated with depression manifestation. Genome-by-trauma interaction accounts for greater trait variance in male individuals, which points to potential differences in depression etiology between the sexes. The methodology used in this study can be extrapolated to other environmental factors to identify modifiable risk environments and at-risk groups to target with interventions