High-performance and hardware-aware computing: proceedings of the first International Workshop on New Frontiers in High-performance and Hardware-aware Computing (HipHaC\u2708)

The HipHaC workshop aims at combining new aspects of parallel, heterogeneous, and reconfigurable microprocessor technologies with concepts of high-performance computing and, particularly, numerical solution methods. Compute- and memory-intensive applications can only benefit from the full hardware potential if all features on all levels are taken into account in a holistic approach

Efficient Geometry and Illumination Representations for Interactive Protein Visualization

This dissertation explores techniques for interactive simulation and visualization for large protein datasets. My thesis is that using efficient representations for geometric and illumination data can help in developing algorithms that achieve better interactivity for visual and computational proteomics. I show this by developing new algorithms for computation and visualization for proteins. I also show that the same insights that resulted in better algorithms for visual proteomics can also be turned around and used for more efficient graphics rendering. Molecular electrostatics is important for studying the structures and interactions of proteins, and is vital in many computational biology applications, such as protein folding and rational drug design. We have developed a system to efficiently solve the non-linear Poisson-Boltzmann equation governing molecular electrostatics. Our system simultaneously improves the accuracy and the efficiency of the solution by adaptively refining the computational grid near the solute-solvent interface. In addition, we have explored the possibility of mapping the PBE solution onto GPUs. We use pre-computed accumulation of transparency with spherical-harmonics-based compression to accelerate volume rendering of molecular electrostatics. We have also designed a time- and memory-efficient algorithm for interactive visualization of large dynamic molecules. With view-dependent precision control and memory-bandwidth reduction, we have achieved real-time visualization of dynamic molecular datasets with tens of thousands of atoms. Our algorithm is linearly scalable in the size of the molecular datasets. In addition, we present a compact mathematical model to efficiently represent the six-dimensional integrals of bidirectional surface scattering reflectance distribution functions (BSSRDFs) to render scattering effects in translucent materials interactively. Our analysis first reduces the complexity and dimensionality of the problem by decomposing the reflectance field into non-scattered and subsurface-scattered reflectance fields. While the non-scattered reflectance field can be described by 4D bidirectional reflectance distribution functions (BRDFs), we show that the scattered reflectance field can also be represented by a 4D field through pre-processing the neighborhood scattering radiance transfer integrals. We use a novel reference-points scheme to compactly represent the pre-computed integrals using a hierarchical and progressive spherical harmonics representation. Our algorithm scales linearly with the number of mesh vertices

Real-Time deep image rendering and order independent transparency

In computer graphics some operations can be performed in either object space or image space. Image space computation can be advantageous, especially with the high parallelism of GPUs, improving speed, accuracy and ease of implementation. For many image space techniques the information contained in regular 2D images is limiting. Recent graphics hardware features, namely atomic operations and dynamic memory location writes, now make it possible to capture and store all per-pixel fragment data from the rasterizer in a single pass in what we call a deep image. A deep image provides a state where all fragments are available and gives a more complete image based geometry representation, providing new possibilities in image based rendering techniques. This thesis investigates deep images and their growing use in real-time image space applications. A focus is new techniques for improving fundamental operation performance, including construction, storage, fast fragment sorting and sampling. A core and driving application is order-independent transparency (OIT). A number of deep image sorting improvements are presented, through which an order of magnitude performance increase is achieved, significantly advancing the ability to perform transparency rendering in real time. In the broader context of image based rendering we look at deep images as a discretized 3D geometry representation and discuss sampling techniques for raycasting and antialiasing with an implicit fragment connectivity approach. Using these ideas a more computationally complex application is investigated — image based depth of field (DoF). Deep images are used to provide partial occlusion, and in particular a form of deep image mipmapping allows a fast approximate defocus blur of up to full screen size

Finite-difference time-domain solver for room acoustics using graphics processing units

Erilaisia akustisia simulaatiomenetelmiä on kehitetty viime vuosikymmenien aikana. Yhtenä vaihtoehtona on käytetty aaltopohjaisia ratkaisijoita, mutta laskennallinen tehokkuus on usein rajoittava tekijä niiden käytölle. Viimevuosina grafiikkaprosessoreiden ja ohjelmistorajapintojen kehitys on mahdollistanut erilaisten aaltopohjaisten menetelmien käytön. Tässä työssä toteutetaan aaltoyhtälön ratkaisija aika-alueen differenssimenetelmällä. Toteutuksen tehokkuutta parannetaan hyödyntämällä grafiikkaprosessoreita ja eri toteutusvaihtoehtoja verrataan. Jäjestelmällä estimoituja vasteita verrataan tunnettuihin analyyttisiin ratkaisuihin. Toteutettu järjestelmä on C++-ohjelma jota voidaan käyttää Matlab-ympäristöstä hyödyntäen Matlab-ohjelmiston mex-rajapintaa. Päivitysyhtälö jossa reunaehdot on toteutettu etenevällä differenssillä todetaan tehokkaimmaksi vaihtoehdoki. Simulaation tehokkuus alenee huomattavasti käytettäessä kaksinkertaista laskentatarkuutta. Voidaan todeta, että järjestelmän estimoimat vasteet toteuttavat odotetulla tavalla analyyttiset ratkaisut, poislukien etenevällä differenssillä toteutetun reunaehdon heijastusominaisuudet, jotka eroavat analyyttisestä mallista.Several acoustic simulation methods have been introduced during the past decades. Wave-based simulation methods have been one of the alternatives, but their applicability for wideband acoustic simulation has been limited by the computing power of available hardware. During recent years, the processing power and programmability of graphics processing units have improved, and therefore several wave-based simulation methods have become potential alternatives. In this thesis, a finite-difference time-domain solver is implemented. The performance of the solver is accelerated with the use of graphics processing units. Different performance considerations are reviewed and the system is evaluated by comparing the simulated responses to known analytic solutions. The resulting system is C++ software, which is interfaced with Matlab with the use of a mex-function. It is found that the forward difference boundary formulation is the most efficient for parallel implementation due to a lesser number of operations. The usage of double precision data type in the simulation decreases the performance significantly. The system is found to follow the analytical solutions with accuracy expected of the method, apart from the reflection characteristics of the forward difference boundary formulation that deviate slightly from the analytical solution

GPU-friendly marching cubes.

Xie, Yongming.Thesis (M.Phil.)--Chinese University of Hong Kong, 2008.Includes bibliographical references (leaves 77-85).Abstracts in English and Chinese.Abstract --- p.iAcknowledgement --- p.iiChapter 1 --- Introduction --- p.1Chapter 1.1 --- Isosurfaces --- p.1Chapter 1.2 --- Graphics Processing Unit --- p.2Chapter 1.3 --- Objective --- p.3Chapter 1.4 --- Contribution --- p.3Chapter 1.5 --- Thesis Organization --- p.4Chapter 2 --- Marching Cubes --- p.5Chapter 2.1 --- Introduction --- p.5Chapter 2.2 --- Marching Cubes Algorithm --- p.7Chapter 2.3 --- Triangulated Cube Configuration Table --- p.12Chapter 2.4 --- Summary --- p.16Chapter 3 --- Graphics Processing Unit --- p.18Chapter 3.1 --- Introduction --- p.18Chapter 3.2 --- History of Graphics Processing Unit --- p.19Chapter 3.2.1 --- First Generation GPU --- p.20Chapter 3.2.2 --- Second Generation GPU --- p.20Chapter 3.2.3 --- Third Generation GPU --- p.20Chapter 3.2.4 --- Fourth Generation GPU --- p.21Chapter 3.3 --- The Graphics Pipelining --- p.21Chapter 3.3.1 --- Standard Graphics Pipeline --- p.21Chapter 3.3.2 --- Programmable Graphics Pipeline --- p.23Chapter 3.3.3 --- Vertex Processors --- p.25Chapter 3.3.4 --- Fragment Processors --- p.26Chapter 3.3.5 --- Frame Buffer Operations --- p.28Chapter 3.4 --- GPU CPU Analogy --- p.31Chapter 3.4.1 --- Memory Architecture --- p.31Chapter 3.4.2 --- Processing Model --- p.32Chapter 3.4.3 --- Limitation of GPU --- p.33Chapter 3.4.4 --- Input and Output --- p.34Chapter 3.4.5 --- Data Readback --- p.34Chapter 3.4.6 --- FramebufFer --- p.34Chapter 3.5 --- Summary --- p.35Chapter 4 --- Volume Rendering --- p.37Chapter 4.1 --- Introduction --- p.37Chapter 4.2 --- History of Volume Rendering --- p.38Chapter 4.3 --- Hardware Accelerated Volume Rendering --- p.40Chapter 4.3.1 --- Hardware Acceleration Volume Rendering Methods --- p.41Chapter 4.3.2 --- Proxy Geometry --- p.42Chapter 4.3.3 --- Object-Aligned Slicing --- p.43Chapter 4.3.4 --- View-Aligned Slicing --- p.45Chapter 4.4 --- Summary --- p.48Chapter 5 --- GPU-Friendly Marching Cubes --- p.49Chapter 5.1 --- Introduction --- p.49Chapter 5.2 --- Previous Work --- p.50Chapter 5.3 --- Traditional Method --- p.52Chapter 5.3.1 --- Scalar Volume Data --- p.53Chapter 5.3.2 --- Isosurface Extraction --- p.53Chapter 5.3.3 --- Flow Chart --- p.54Chapter 5.3.4 --- Transparent Isosurfaces --- p.56Chapter 5.4 --- Our Method --- p.56Chapter 5.4.1 --- Cell Selection --- p.59Chapter 5.4.2 --- Vertex Labeling --- p.61Chapter 5.4.3 --- Cell Indexing --- p.62Chapter 5.4.4 --- Interpolation --- p.65Chapter 5.5 --- Rendering Translucent Isosurfaces --- p.67Chapter 5.6 --- Implementation and Results --- p.69Chapter 5.7 --- Summary --- p.74Chapter 6 --- Conclusion --- p.76Bibliography --- p.7

Accelerating and simulating detected physical interations

The aim of this doctoral thesis is to present a body of work aimed at improving performance and developing new methods for animating physical interactions using simulation in virtual environments. To this end we develop a number of novel parallel collision detection and fracture simulation algorithms. Methods for traversing and constructing bounding volume hierarchies (BVH) on graphics processing units (GPU) have had a wide success. In particular, they have been adopted widely in simulators, libraries and benchmarks as they allow applications to reach new heights in terms of performance. Even with such a development however, a thorough adoption of techniques has not occurred in commercial and practical applications. Due to this, parallel collision detection on GPUs remains a relatively niche problem and a wide number of applications could benefit from a significant boost in proclaimed performance gains. In fracture simulations, explicit surface tracking methods have a good track record of success. In particular they have been adopted thoroughly in 3D modelling and animation software like Houdini [124] as they allow accurate simulation of intricate fracture patterns with complex interactions, which are generated using physical laws. Even so, existing methods can pose restrictions on the geometries of simulated objects. Further, they often have tight dependencies on implicit surfaces (e.g. level sets) for representing cracks and performing cutting to produce rigid-body fragments. Due to these restrictions, catering to various geometries can be a challenge and the memory cost of using implicit surfaces can be detrimental and without guarantee on the preservation of sharp features. We present our work in four main chapters. We first tackle the problem in the accelerating collision detection on the GPU via BVH traversal - one of the most demanding components during collision detection. Secondly, we show the construction of a new representation of the BVH called the ostensibly implicit tree - a layout of nodes in memory which is encoded using the bitwise representation of the number of enclosed objects in the tree (e.g. polygons). Thirdly, we shift paradigm to the task of simulating breaking objects after collision: we show how traditional finite elements can be extended as a way to prevent frequent re-meshing during fracture evolution problems. Finally, we show how the fracture surface–represented as an explicit (e.g. triangulated) surface mesh–is used to generate rigid body fragments using a novel approach to mesh cutting

Large Model Visualization : Techniques and Applications

The size of datasets in scientific computing is rapidly increasing. This increase is caused by a boost of processing power in the past years, which in turn was invested in an increase of the accuracy and the size of the models. A similar trend enabled a significant improvement of medical scanners; more than 1000 slices of a resolution of 512x512 can be generated by modern scanners in daily practice. Even in computer-aided engineering typical models eas-ily contain several million polygons. Unfortunately, the data complexity is growing faster than the rendering performance of modern computer systems. This is not only due to the slower growing graphics performance of the graphics subsystems, but in particular because of the significantly slower growing memory bandwidth for the transfer of the geometry and image data from the main memory to the graphics accelerator. Large model visualization addresses this growing divide between data complexity and rendering performance. Most methods focus on the reduction of the geometric or pixel complexity, and hence also the memory bandwidth requirements are reduced. In this dissertation, we discuss new approaches from three different research areas. All approaches target at the reduction of the processing complexity to achieve an interactive visualization of large datasets. In the second part, we introduce applications of the presented ap-proaches. Specifically, we introduce the new VIVENDI system for the interactive virtual endoscopy and other applications from mechanical engineering, scientific computing, and architecture.The size of datasets in scientific computing is rapidly increasing. This increase is caused by a boost of processing power in the past years, which in turn was invested in an increase of the accuracy and the size of the models. A similar trend enabled a significant improvement of medical scanners; more than 1000 slices of a resolution of 512x512 can be generated by modern scanners in daily practice. Even in computer-aided engineering typical models eas-ily contain several million polygons. Unfortunately, the data complexity is growing faster than the rendering performance of modern computer systems. This is not only due to the slower growing graphics performance of the graphics subsystems, but in particular because of the significantly slower growing memory bandwidth for the transfer of the geometry and image data from the main memory to the graphics accelerator. Large model visualization addresses this growing divide between data complexity and rendering performance. Most methods focus on the reduction of the geometric or pixel complexity, and hence also the memory bandwidth requirements are reduced. In this dissertation, we discuss new approaches from three different research areas. All approaches target at the reduction of the processing complexity to achieve an interactive visualization of large datasets. In the second part, we introduce applications of the presented ap-proaches. Specifically, we introduce the new VIVENDI system for the interactive virtual endoscopy and other applications from mechanical engineering, scientific computing, and architecture

vorgelegt von

Prof. Dr. N. NavabTo my familyAcknowledgements I am deeply grateful that I had the opportunity to write this thesis while working at the Chair for Pattern Recognition within the project B6 of the Sonderforschungsbereich 603 (funded by Deutsche Forschungsgemeinschaft). Many people contributed to this work and I want to express my gratitude to all of them

Visual-auditory visualisation of dynamic multi-scale heterogeneous objects.

The multi-scale phenomena analysis is an area of active research that is connecting simulations with experiments to get a correct insight into the compound dynamic structure. Visualisation is a challenging task due to a large amount of data and a wide range of complex data representations. The analysis of dynamic multi-scale phenomena requires a combination of geometric modelling and rendering techniques for the analysis of the changes in the internal structure in the case of data coming from different sources of various nature. Moreover, the area often addresses the limitations of solely visual data representation and considers the introduction of other sensory stimuli as a well-known tool to enhance visual analysis. However, there is a lack of software tools allowing perform an advanced real-time analysis of heterogeneous phenomena properties. The hardware-accelerated volume rendering allows getting insight into the internal structure of complex multi-scale phenomena. The technique is convenient for detailed visual analysis and highlights the features of interest in complex structures and is an area of active research. However, the conventional volume visualisation is limited to the use of transfer functions that operate on homogeneous material and, as a result, does not provide flexibility in geometry and material distribution modelling that is crucial for the analysis of heterogeneous objects. Moreover, the extension to visual-auditory analysis emphasises the necessity to review the entire conventional volume visualisation pipeline. The multi-sensory feedback highly depends on the use of modern hardware and software advances for real-time modelling and evaluation. In this work, we explore the aspects of the design of visual-auditory pipelines for the analysis of dynamic multi-scale properties of heterogeneous objects that can allow overcoming well-known problems of complex representations solely visual analysis. We consider the similarities between light and sound propagation as a solution to the problem. The approach benefits from a combination of GPU accelerated ray-casting, geometry, optical and auditory properties modelling. We discuss how the modern GPU techniques application in those areas allows introducing a unified approach to the visual-auditory analysis of dynamic multi-scale heterogeneous objects. Similarly to the conventional volume rendering technique based on light propagation, we model auditory feedback as a result of initial impulse propagation through 3D space and its digital representation as a sampled sound wave obtained with the ray-casting procedure. The auditory stimuli can complement visual ones in the analysis of the dynamic multi-scale heterogeneous object. We propose a framework that facilitates the design of dynamic multi-scale heterogeneous objects visual-auditory pipeline and discuss the framework application for two case studies. The first is a molecular phenomena study that is a result of molecular dynamics simulation and quantum simulation. The second explores microstructures in digital fabrication with an arbitrary irregular lattice structure. For considered case studies, the visual-auditory techniques facilitate the interactive analysis of both spatial structure and internal multi-scale properties of volume nature in complex heterogeneous objects. A GPU-accelerated framework for visual-auditory analysis of heterogeneous objects can be applied and extend beyond this research. Thus, to specify the main direction of such extension from the point of view of the potential users, strengthen the value of this research as well as to evaluate the vision of the application of the techniques described above, we carry out a preliminary evaluation. The user study aims to compare our expectations on the visual-auditory approach with the views of the potential users of this system if it is implemented as a software product. A preliminary evaluation study was carried out with limitations imposed by 2020/2021 restrictions. However, it confirms that the main direction for the visual-auditory analysis of heterogeneous objects has been identified correctly and visual and auditory stimuli can complement each other in the analysis of both volume and spatial distribution properties of heterogeneous phenomena. The user reviews also highlight the necessary enhancements that should be introduced to the approach in terms of the design of more complex user interfaces and consideration of additional application cases. To provide a more detailed picture on evaluation results and recommendations introduced, we also identify the key factors that define the user vision of the approach further enhancement and its possible application areas, such as users experience in the area of complex physical phenomena analysis or multi-sensory area. The discussed in this work aspects of heterogeneous objects analysis task, theoretical and practical solutions allow considering the application, further development and enhancement of the results in multidisciplinary areas of GPU accelerated High-performance visualisation pipelines design and multi-sensory analysis