Heterogeneous computing with an algorithmic skeleton framework

The Graphics Processing Unit (GPU) is present in almost every modern day personal computer. Despite its specific purpose design, they have been increasingly used for general computations with very good results. Hence, there is a growing effort from the community to seamlessly integrate this kind of devices in everyday computing. However, to fully exploit the potential of a system comprising GPUs and CPUs, these devices should be presented to the programmer as a single platform. The efficient combination of the power of CPU and GPU devices is highly dependent on each device’s characteristics, resulting in platform specific applications that cannot be ported to different systems. Also, the most efficient work balance among devices is highly dependable on the computations to be performed and respective data sizes. In this work, we propose a solution for heterogeneous environments based on the abstraction level provided by algorithmic skeletons. Our goal is to take full advantage of the power of all CPU and GPU devices present in a system, without the need for different kernel implementations nor explicit work-distribution.To that end, we extended Marrow, an algorithmic skeleton framework for multi-GPUs, to support CPU computations and efficiently balance the work-load between devices. Our approach is based on an offline training execution that identifies the ideal work balance and platform configurations for a given application and input data size. The evaluation of this work shows that the combination of CPU and GPU devices can significantly boost the performance of our benchmarks in the tested environments, when compared to GPU-only executions

Efficiently and Transparently Maintaining High SIMD Occupancy in the Presence of Wavefront Irregularity

Demand is increasing for high throughput processing of irregular streaming applications; examples of such applications from scientific and engineering domains include biological sequence alignment, network packet filtering, automated face detection, and big graph algorithms. With wide SIMD, lightweight threads, and low-cost thread-context switching, wide-SIMD architectures such as GPUs allow considerable flexibility in the way application work is assigned to threads. However, irregular applications are challenging to map efficiently onto wide SIMD because data-dependent filtering or replication of items creates an unpredictable data wavefront of items ready for further processing. Straightforward implementations of irregular applications on a wide-SIMD architecture are prone to load imbalance and reduced occupancy, while more sophisticated implementations require advanced use of parallel GPU operations to redistribute work efficiently among threads. This dissertation will present strategies for addressing the performance challenges of wavefront- irregular applications on wide-SIMD architectures. These strategies are embodied in a developer framework called Mercator that (1) allows developers to map irregular applications onto GPUs ac- cording to the streaming paradigm while abstracting from low-level data movement and (2) includes generalized techniques for transparently overcoming the obstacles to high throughput presented by wavefront-irregular applications on a GPU. Mercator forms the centerpiece of this dissertation, and we present its motivation, performance model, implementation, and extensions in this work

Enhancing a Neurosurgical Imaging System with a PC-based Video Processing Solution

This work presents a PC-based prototype video processing application developed to be used with a specific neurosurgical imaging device, the OPMI® PenteroTM operating microscope, in the Department of Neurosurgery of Helsinki University Central Hospital at Töölö, Helsinki. The motivation for implementing the software was the lack of some clinically important features in the imaging system provided by the microscope. The imaging system is used as an online diagnostic aid during surgery. The microscope has two internal video cameras; one for regular white light imaging and one for near-infrared fluorescence imaging, used for indocyanine green videoangiography. The footage of the microscope’s current imaging mode is accessed via the composite auxiliary output of the device. The microscope also has an external high resolution white light video camera, accessed via a composite output of a separate video hub. The PC was chosen as the video processing platform for its unparalleled combination of prototyping and high-throughput video processing capabilities. A thorough analysis of the platform and efficient video processing methods was conducted in the thesis and the results were used in the design of the imaging station. The features found feasible during the project were incorporated into a video processing application running on a GNU/Linux distribution Ubuntu. The clinical usefulness of the implemented features was ensured beforehand by consulting the neurosurgeons using the original system. The most significant shortcomings of the original imaging system were mended in this work. The key features of the developed application include: live streaming, simultaneous streaming and recording, and playing back of upto two video streams. The playback mode provides full media player controls, with a frame-by-frame precision rewinding, in an intuitive and responsive interface. A single view and a side-by-side comparison mode are provided for the streams. The former gives more detail, while the latter can be used, for example, for before-after and anatomic-angiographic comparisons.fi=Opinnäytetyö kokotekstinä PDF-muodossa.|en=Thesis fulltext in PDF format.|sv=Lärdomsprov tillgängligt som fulltext i PDF-format