The Topology ToolKit

This system paper presents the Topology ToolKit (TTK), a software platform designed for topological data analysis in scientific visualization. TTK provides a unified, generic, efficient, and robust implementation of key algorithms for the topological analysis of scalar data, including: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces, and more. TTK is easily accessible to end users due to a tight integration with ParaView. It is also easily accessible to developers through a variety of bindings (Python, VTK/C++) for fast prototyping or through direct, dependence-free, C++, to ease integration into pre-existing complex systems. While developing TTK, we faced several algorithmic and software engineering challenges, which we document in this paper. In particular, we present an algorithm for the construction of a discrete gradient that complies to the critical points extracted in the piecewise-linear setting. This algorithm guarantees a combinatorial consistency across the topological abstractions supported by TTK, and importantly, a unified implementation of topological data simplification for multi-scale exploration and analysis. We also present a cached triangulation data structure, that supports time efficient and generic traversals, which self-adjusts its memory usage on demand for input simplicial meshes and which implicitly emulates a triangulation for regular grids with no memory overhead. Finally, we describe an original software architecture, which guarantees memory efficient and direct accesses to TTK features, while still allowing for researchers powerful and easy bindings and extensions. TTK is open source (BSD license) and its code, online documentation and video tutorials are available on TTK's website

Parallelized Rigid Body Dynamics

Physics engines are collections of API-like software designed for video games, movies and scientific simulations. While physics engines often come in many shapes and designs, all engines can benefit from an increase in speed via parallelization. However, despite this need for increased speed, it is uncommon to encounter a parallelized physics engine today. Many engines are long-standing projects and changing them to support parallelization is too costly to consider as a practical matter. Parallelization needs to be considered from the design stages through completion to ensure adequate implementation. In this project we develop a realistic approach to simulate physics in a parallel environment. Utilizing many techniques we establish a practical approach to significantly reduce the run-time on a standard physics engine

Bringing UMAP Closer to the Speed of Light with GPU Acceleration

The Uniform Manifold Approximation and Projection (UMAP) algorithm has become widely popular for its ease of use, quality of results, and support for exploratory, unsupervised, supervised, and semi-supervised learning. While many algorithms can be ported to a GPU in a simple and direct fashion, such efforts have resulted in inefficient and inaccurate versions of UMAP. We show a number of techniques that can be used to make a faster and more faithful GPU version of UMAP, and obtain speedups of up to 100x in practice. Many of these design choices/lessons are general purpose and may inform the conversion of other graph and manifold learning algorithms to use GPUs. Our implementation has been made publicly available as part of the open source RAPIDS cuML library (https://github.com/rapidsai/cuml)

Trusted content-based publish/subscribe trees

Publish/Subscribe systems hold strong assumptions of the expected behaviour of clients and routers, as it is assumed they all abide by the matching and routing protocols. Assumptions of implicit trust between the components of the publish/subscribe infrastructure are acceptable where the underlying event distribution service is under the control of a single or multiple co-operating administrative entities and contracts between clients and these authorities exist, however there are application contexts where these presumptions do not hold. In such environments, such as ad hoc networks, there is the possibility of selfish and malicious behaviour that can lead to disruption of the routing and matching algorithms. The most commonly researched approach to security in publish/subscribe systems is role-based access control (RBAC). RBAC is suitable for ensuring confidentiality, but due to the assumption of strong identities associated with well defined roles and the absence of monitoring systems to allow for adaptable policies in response to the changing behaviour of clients, it is not appropriate for environments where: identities can not be assigned to roles in the absence of a trusted administrative entity; long-lived identities of entities do not exist; and where the threat model consists of highly adaptable malicious and selfish entities. Motivated by recent work in the application of trust and reputation to Peer-to-Peer networks, where past behaviour is used to generate trust opinions that inform future transactions, we propose an approach where the publish/subscribe infrastructure is constructed and re-configured with respect to the trust preferences of clients and routers. In this thesis, we show how Publish/Subscribe trees (PSTs) can be constructed with respect to the trust preferences of publishers and subscribers, and the overhead costs of event dissemination. Using social welfare theory, it is shown that individual trust preferences over clients and routers, which are informed by a variety of trust sources, can be aggregated to give a social preference over the set of feasible PSTs. By combining this and the existing work on PST overheads, the Maximum Trust PST with Overhead Budget problem is defined and is shown to be in NP-complete. An exhaustive search algorithm is proposed that is shown to be suitable only for very small problem sizes. To improve scalability, a faster tabu search algorithm is presented, which is shown to scale to larger problem instances and gives good approximations of the optimal solutions. The research contributions of this work are: the use of social welfare theory to provide a mechanism to establish the trustworthiness of PSTs; the finding that individual trust is not interpersonal comparable as is considered to be the case in much of the trust literature; the Maximum Trust PST with Overhead Budget problem; and algorithms to solve this problem

Computing graph neural networks: A survey from algorithms to accelerators

Graph Neural Networks (GNNs) have exploded onto the machine learning scene in recent years owing to their capability to model and learn from graph-structured data. Such an ability has strong implications in a wide variety of fields whose data are inherently relational, for which conventional neural networks do not perform well. Indeed, as recent reviews can attest, research in the area of GNNs has grown rapidly and has lead to the development of a variety of GNN algorithm variants as well as to the exploration of ground-breaking applications in chemistry, neurology, electronics, or communication networks, among others. At the current stage research, however, the efficient processing of GNNs is still an open challenge for several reasons. Besides of their novelty, GNNs are hard to compute due to their dependence on the input graph, their combination of dense and very sparse operations, or the need to scale to huge graphs in some applications. In this context, this article aims to make two main contributions. On the one hand, a review of the field of GNNs is presented from the perspective of computing. This includes a brief tutorial on the GNN fundamentals, an overview of the evolution of the field in the last decade, and a summary of operations carried out in the multiple phases of different GNN algorithm variants. On the other hand, an in-depth analysis of current software and hardware acceleration schemes is provided, from which a hardware-software, graph-aware, and communication-centric vision for GNN accelerators is distilled.This work is possible thanks to funding from the European Union’s Horizon 2020 research and innovation programme under Grant No. 863337 (WiPLASH project) and the Spanish Ministry of Economy and Competitiveness under contract TEC2017-90034-C2-1-R (ALLIANCE project) that receives funding from FEDER.Peer ReviewedPostprint (published version

Using The Software Adapter To Connect Legacy Simulation Models To The Rti

The establishment of a network of persistent shared simulations depends on the presence of a robust standard for communicating state information between those simulations. The High Level Architecture (HLA) can serve as the basis for such a standard. While the HLA is architecture, not software, use of Run Time Infrastructure (RTI) software is required to support operations of a federation execution. The integration of RTI with existing simulation models is complex and requires a lot of expertise. This thesis implements a less complex and effective interaction between a legacy simulation model and RTI using a middleware tool known as Distributed Manufacturing Simulation (DMS) adapter. Shuttle Model, an Arena based discrete-event simulation model for shuttle operations, is connected to the RTI using the DMS adapter. The adapter provides a set of functions that are to be incorporated within the Shuttle Model, in a procedural manner, in order to connect to RTI. This thesis presents the procedure when the Shuttle Model connects to the RTI, to communicate with the Scrub Model for approval of its shuttle\u27s launch