A parallel edge orientation algorithm for quadrilateral meshes

One approach to achieving correct finite element assembly is to ensure that the local orientation of facets relative to each cell in the mesh is consistent with the global orientation of that facet. Rognes et al. have shown how to achieve this for any mesh composed of simplex elements, and deal.II contains a serial algorithm to construct a consistent orientation of any quadrilateral mesh of an orientable manifold. The core contribution of this paper is the extension of this algorithm for distributed memory parallel computers, which facilitates its seamless application as part of a parallel simulation system. Furthermore, our analysis establishes a link between the well-known Union-Find algorithm and the construction of a consistent orientation of a quadrilateral mesh. As a result, existing work on the parallelisation of the Union-Find algorithm can be easily adapted to construct further parallel algorithms for mesh orientations.Comment: Second revision: minor change

Consistent Point Data Assimilation in Firedrake and Icepack

We present methods and tools that significantly improve the ability to estimate quantities and fields which are difficult to directly measure, such as the fluidity of ice, using point data sources, such as satellite altimetry. These work with both sparse and dense point data with estimated quantities and fields becoming more accurate as the number of measurements are increased. Such quantities and fields are often used as inputs to mathematical models that are used to make predictions so improving their accuracy is of vital importance. We demonstrate how our methods and tools can increase the accuracy of results, ensure posterior consistency, and aid discourse between modellers and experimenters. To do this, we bring point data into the finite element method ecosystem as discontinuous fields on meshes of disconnected vertices. Point evaluation can then be formulated as a finite element interpolation operation (dual-evaluation). Our new abstractions are well-suited to automation. We demonstrate this by implementing them in Firedrake, which generates highly optimised code for solving PDEs with the finite element method. Our solution integrates with dolfin-adjoint/pyadjoint which allows PDE-constrained optimisation problems, such as data assimilation, to be solved through forward and adjoint mode automatic differentiation. We demonstrate our new functionality through examples in the fields of groundwater hydrology and glaciology

checkpoint_schedules: schedules for incremental checkpointing of adjoint simulations

checkpoint_schedules provides schedules for step-based incremental checkpointing of the adjoints to computer models. The schedules contain instructions indicating the sequence of forward and adjoint steps to be executed, and the data storage and retrieval to be performed.These instructions are independent of the model implementation, which enables the model authors to switch between checkpointing algorithms without recoding. Conversely, checkpointing_schedules provides developers of checkpointing algorithms a direct mechanism to convey their work to model authors. checkpointing_schedules has been integrated into tlm_adjoint (James R. Maddison et al., 2019), a Python library designed for the automated derivationof higher-order tangent-linear and adjoint models and work is ongoing to integrate it with pyadjoint (Mitusch et al., 2019). This package can be incorporated into other gradient solvers based on adjoint methods, regardless of the specific approach taken to generate the adjoint model

Occupation and workplace policies predict smoking behaviors: Analysis of national data from the current population survey

OBJECTIVE: Describe differences in smoking behaviors associated with occupation, workplace rules against smoking, and workplace smoking cessation programs. METHODS: We analyzed data from the Current Population Survey- Tobacco Use Supplement surveys from 1992 through 2007. RESULTS: After adjusting for demographic factors, blue-collar workers were at higher risk than white-collar workers for ever smoking, current smoking, and persistent smoking (current smoking among ever smokers). Construction workers were more likely to be current daily smokers than other blue-collar workers. Among ever smokers, current daily smoking was more common in the absence of both workplace rules against smoking and workplace smoking cessation programs. CONCLUSIONS: Social or cultural effects related to occupation are important determinants of smoking. More aggressive promotion of smoking cessation programs and workplace rules prohibiting smoking could have a significant public health impact

Dose-Response Evaluation of Braslet-M Occlusion Cuffs

Introduction: Braslet-M is a set of special elasticized thigh cuffs used by the Russian space agency to reduce the effects of the head-ward fluid shift during early adaptation to microgravity by sequestering fluid in the lower extremities. Currently, no imaging modalities are used in the calibration of the device, and the pressure required to produce a predictable physiological response is unknown. This investigation intends to relate the pressure exerted by the cuffs to the extent of fluid redistribution and commensurate physiological effects. Materials and Methods: Ten healthy subjects with standardized fluid intake participated in the study. Data collection included femoral and internal jugular vein imaging in two orthogonal planes, pulsed Doppler of cervical and femoral vessels and middle cerebral artery, optic nerve imaging, and echocardiography. Braslet-M cuff pressure was monitored at the skin interface using pre-calibrated pressure sensors. Using 6 and 30 head-down tilt in two separate sessions, the effect of Braslet-M was assessed while incrementally tightening the cuffs. Cuffs were then simultaneously released to document the resulting hemodynamic change. Results: Preliminary analysis shows correlation between physical pressure exerted by the Braslet-M device and several parameters such as jugular and femoral vein cross-sections, resistivity of the lower extremity vascular bed, and others. A number of parameters reflect blood redistribution and will be used to determine the therapeutic range of the device and to prevent unsafe application. Conclusion: Braslet-M exerts a physical effect that can be measured and correlated with many changes in central and peripheral hemodynamics. Analysis of the full data set will be required to make definitive recommendations regarding the range of safe therapeutic application. Objective data and subjective responses suggest that a safer and equally effective use of Braslet can be achieved when compared with the current non-imaging calibration techniques

A structure-exploiting numbering algorithm for finite elements on extruded meshes, and its performance evaluation in Firedrake

We present a generic algorithm for numbering and then efficiently iterating over the data values attached to an extruded mesh. An extruded mesh is formed by replicating an existing mesh, assumed to be unstructured, to form layers of prismatic cells. Applications of extruded meshes include, but are not limited to, the representation of three-dimensional high aspect ratio domains employed by geophysical finite element simulations. These meshes are structured in the extruded direction. The algorithm presented here exploits this structure to avoid the performance penalty traditionally associated with unstructured meshes. We evaluate the implementation of this algorithm in the Firedrake finite element system on a range of low compute intensity operations which constitute worst cases for data layout performance exploration. The experiments show that having structure along the extruded direction enables the cost of the indirect data accesses to be amortized after 10–20 layers as long as the underlying mesh is well ordered. We characterize the resulting spatial and temporal reuse in a representative set of both continuous-Galerkin and discontinuous-Galerkin discretizations. On meshes with realistic numbers of layers the performance achieved is between 70 and 90 % of a theoretical hardware-specific limit