Dataflow methods in HPC, visualisation and analysis

The processing power available to scientists and engineers using supercomputers over the last few decades has grown exponentially, permitting significantly more sophisticated simulations, and as a consequence, generating proportionally larger output datasets. This change has taken place in tandem with a gradual shift in the design and implementation of simulation and post-processing software, with a shift from simulation as a first step and visualisation/analysis as a second, towards in-situ on the fly methods that provide immediate visual feedback, place less strain on file-systems and reduce overall data-movement and copying. Concurrently, processor speed increases have dramatically slowed and multi and many-core architectures have instead become the norm for virtually all High Performance computing (HPC) machines. This in turn has led to a shift away from the traditional distributed one rank per node model, to one rank per process, using multiple processes per multicore node, and then back towards one rank per node again, using distributed and multi-threaded frameworks combined. This thesis consists of a series of publications that demonstrate how software design for analysis and visualisation has tracked these architectural changes and pushed the boundaries of HPC visualisation using dataflow techniques in distributed environments. The first publication shows how support for the time dimension in parallel pipelines can be implemented, demonstrating how information flow within an application can be leveraged to optimise performance and add features such as analysis of time-dependent flows and comparison of datasets at different timesteps. A method of integrating dataflow pipelines with in-situ visualisation is subsequently presented, using asynchronous coupling of user driven GUI controls and a live simulation running on a supercomputer. The loose coupling of analysis and simulation allows for reduced IO, immediate feedback and the ability to change simulation parameters on the fly. A significant drawback of parallel pipelines is the inefficiency caused by improper load-balancing, particularly during interactive analysis where the user may select between different features of interest, this problem is addressed in the fourth publication by integrating a high performance partitioning library into the visualization pipeline and extending the information flow up and down the pipeline to support it. This extension is demonstrated in the third publication (published earlier) on massive meshes with extremely high complexity and shows that general purpose visualization tools such as ParaView can be made to compete with bespoke software written for a dedicated task. The future of software running on many-core architectures will involve task-based runtimes, with dynamic load-balancing, asynchronous execution based on dataflow graphs, work stealing and concurrent data sharing between simulation and analysis. The final paper of this thesis presents an optimisation for one such runtime, in support of these future HPC applications

Addressing the welfare needs of farmed lumpfish: knowledge gaps, challenges and solutions

Lumpfish (Cyclopterus lumpus L.) are increasingly being used as cleaner fish to control parasitic sea lice, one of the most important threats to salmon farming. However, lumpfish cannot survive feeding solely on sea lice, and their mortality in salmon net pens can be high, which has welfare, ethical and economic implications. The industry is under increasing pressure to improve the welfare of lumpfish, but little guidance exists on how this can be achieved. We undertook a knowledge gap and prioritisa tion exercise using a Delphi approach with participants from the fish farming sector, animal welfare, academia and regulators to assess consensus on the main challenges and potential solutions for improving lumpfish welfare. Consensus among participants on the utility of 5 behavioural and 12 physical welfare indicators was high (87–89%), reliable (Cronbach's alpha = 0.79, 95CI = 0.69–0.92) and independent of participant background. Participants highlighted fin erosion and body damage as the most use ful and practical operational welfare indicators, and blood parameters and behav ioural indicators as the least practical. Species profiling revealed profound differences between Atlantic salmon and lumpfish in relation to behaviour, habitat preferences, nutritional needs and response to stress, suggesting that applying a common set of welfare standards to both species cohabiting in salmon net-pens may not work well for lumpfish. Our study offers 16 practical solutions for improving the welfare of lumpfish and illustrates the merits of the Delphi approach for achieving consensus among stakeholders on welfare needs, targeting research where is most needed and generating workable solutions.info:eu-repo/semantics/publishedVersio

Cerebrospinal fluid dynamics in the human cranial subarachnoid space: an overlooked mediator of cerebral disease. I. Computational model

Abnormal cerebrospinal fluid (CSF) flow is suspected to be a contributor to the pathogenesis of neurodegenerative diseases such as Alzheimer's through the accumulation of toxic metabolites, and to the malfunction of intracranial pressure regulation, possibly through disruption of neuroendocrine communication. For the understanding of transport processes involved in either, knowledge of in vivo CSF dynamics is important. We present a three-dimensional, transient, subject-specific computational analysis of CSF flow in the human cranial subarachnoid space (SAS) based on in vivo magnetic resonance imaging. We observed large variations in the spatial distribution of flow velocities with a temporal peak of 5 cm s−1 in the anterior SAS and less than 4 mm s−1 in the superior part. This could reflect dissimilar flushing requirements of brain areas that may show differences in susceptibility to pathological CSF flow. Our methods can be used to compare the transport of metabolites and neuroendocrine substances in healthy and diseased brains

Harnessing billions of tasks for a scalable portable hydrodynamic simulation of the merger of two stars

We present a highly scalable demonstration of a portable asynchronous many-task programming model and runtime system applied to a grid-based adaptive mesh refinement hydrodynamic simulation of a double white dwarf merger with 14 levels of refinement that spans 17 orders of magnitude in astrophysical densities. The code uses the portable C++ parallel programming model that is embodied in the HPX library and being incorporated into the ISO C++ standard. The model represents a significant shift from existing bulk synchronous parallel programming models under consideration for exascale systems. Through the use of the Futurization technique, seemingly sequential code is transformed into wait-free asynchronous tasks. We demonstrate the potential of our model by showing results from strong scaling runs on National Energy Research Scientific Computing Center’s Cori system (658,784 Intel Knight’s Landing cores) that achieve a parallel efficiency of 96.8% using billions of asynchronous tasks

Standardization of Techniques for Using Planar (2D) Imaging for Aerosol Deposition Assessment of Orally Inhaled Products

Two-dimensional (2D or planar) imaging with 99mTc radiolabels enables quantification of whole-lung and regional lung depositions for orally inhaled drug products. This article recommends standardized methodology for 2D imaging studies. Simultaneous anterior and posterior imaging with a dual-headed gamma camera is preferred, but imaging with a single-headed gamma camera is also acceptable. Correction of raw data for the effects of gamma ray attenuation is considered essential for accurate quantification, for instance, using transmission scanning with a flood-field source of 99mTc or 57Co. Evidence should be provided of the accuracy of the quantification method, for instance, by determining “mass balance.” Lung deposition may be expressed as a percentage of ex-valve or ex-device dose, but should also be given as mass of drug when possible. Assessment of regional lung deposition requires delineation of the lung borders, using X-ray computed tomography, radioactive gas scans (133Xe or 81mKr), or transmission scans. When quantifying regional lung deposition, the lung should be divided into outer (O) and inner (I) zones. A penetration index should be calculated, as the O/I ratio for aerosol, normalized to that for a radioactive gas or transmission scan. A variety of methods can be used to assess lung deposition and distribution. Methodology and results should be documented in detail, so that data from different centers may be compared. The use of appropriate methodology will provide greater confidence in the results of 2D imaging studies, and should allay concerns that such studies are qualitative or semiquantitative in nature