Accelerating data-intensive scientific visualization and computing through parallelization

Many extreme-scale scientific applications generate colossal amounts of data that require an increasing number of processors for parallel processing. The research in this dissertation is focused on optimizing the performance of data-intensive parallel scientific visualization and computing. In parallel scientific visualization, there exist three well-known parallel architectures, i.e., sort-first/middle/last. The research in this dissertation studies the composition stage of the sort-last architecture for scientific visualization and proposes a generalized method, namely, Grouping More and Pairing Less (GMPL), for order-independent image composition workflow scheduling in sort-last parallel rendering. The technical merits of GMPL are two-fold: i) it takes a prime factorization-based approach for processor grouping, which not only obviates the common restriction in existing methods on the total number of processors to fully utilize computing resources, but also breaks down processors to the lowest level with a minimum number of peers in each group to achieve high concurrency and save communication cost; ii) within each group, it employs an improved direct send method to narrow down each processor’s pairing scope to further reduce communication overhead and increase composition efficiency. The performance superiority of GMPL over existing methods is evaluated through rigorous theoretical analysis and further verified by extensive experimental results on a high-performance visualization cluster. The research in this dissertation also parallelizes the over operator, which is commonly used for α-blending in various visualization techniques. Compared with its predecessor, the fully generalized over operator is n-operator compatible. To demonstrate the advantages of the proposed operator, the proposed operator is applied to the asynchronous and order-dependent image composition problem in parallel visualization. In addition, the dissertation research also proposes a very-high-speed pipeline-based architecture for parallel sort-last visualization of big data by developing and integrating three component techniques: i) a fully parallelized per-ray integration method that significantly reduces the number of iterations required for image rendering; ii) a real-time over operator that not only eliminates the restriction of pre-sorting and order-dependency, but also facilitates a high degree of parallelization for image composition. In parallel scientific computing, the research goal is to optimize QR decomposition, which is one primary algebraic decomposition procedure and plays an important role in scientific computing. QR decomposition produces orthogonal bases, i.e.,“core” bases for a given matrix, and oftentimes can be leveraged to build a complete solution to many fundamental scientific computing problems including Least Squares Problem, Linear Equations Problem, Eigenvalue Problem. A new matrix decomposition method is proposed to improve time efficiency of parallel computing and provide a rigorous proof of its numerical stability. The proposed solutions demonstrate significant performance improvement over existing methods for data-intensive parallel scientific visualization and computing. Considering the ever-increasing data volume in various science domains, the research in this dissertation have a great impact on the success of next-generation large-scale scientific applications

Inviwo -- A Visualization System with Usage Abstraction Levels

The complexity of today's visualization applications demands specific visualization systems tailored for the development of these applications. Frequently, such systems utilize levels of abstraction to improve the application development process, for instance by providing a data flow network editor. Unfortunately, these abstractions result in several issues, which need to be circumvented through an abstraction-centered system design. Often, a high level of abstraction hides low level details, which makes it difficult to directly access the underlying computing platform, which would be important to achieve an optimal performance. Therefore, we propose a layer structure developed for modern and sustainable visualization systems allowing developers to interact with all contained abstraction levels. We refer to this interaction capabilities as usage abstraction levels, since we target application developers with various levels of experience. We formulate the requirements for such a system, derive the desired architecture, and present how the concepts have been exemplary realized within the Inviwo visualization system. Furthermore, we address several specific challenges that arise during the realization of such a layered architecture, such as communication between different computing platforms, performance centered encapsulation, as well as layer-independent development by supporting cross layer documentation and debugging capabilities

Scalable Interactive Volume Rendering Using Off-the-shelf Components

This paper describes an application of a second generation implementation of the Sepia architecture (Sepia-2) to interactive volu-metric visualization of large rectilinear scalar fields. By employingpipelined associative blending operators in a sort-last configuration a demonstration system with 8 rendering computers sustains 24 to 28 frames per second while interactively rendering large data volumes (1024x256x256 voxels, and 512x512x512 voxels). We believe interactive performance at these frame rates and data sizes is unprecedented. We also believe these results can be extended to other types of structured and unstructured grids and a variety of GL rendering techniques including surface rendering and shadow map-ping. We show how to extend our single-stage crossbar demonstration system to multi-stage networks in order to support much larger data sizes and higher image resolutions. This requires solving a dynamic mapping problem for a class of blending operators that includes Porter-Duff compositing operators

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