Manycore high-performance computing in bioinformatics

Mining the increasing amount of genomic data requires having very efficient tools. Increasing the efficiency can be obtained with better algorithms, but one could also take advantage of the hardware itself to reduce the application runtimes. Since a few years, issues with heat dissipation prevent the processors from having higher frequencies. One of the answers to maintain Moore's Law is parallel processing. Grid environments provide tools for effective implementation of coarse grain parallelization. Recently, another kind of hardware has attracted interest: multicore processors. Graphic processing units (GPUs) are a first step towards massively multicore processors. They allow everyone to have some teraflops of cheap computing power in its personal computer. The CUDA library (released in 2007) and the new standard OpenCL (specified in 2008) make programming of such devices very convenient. OpenCL is likely to gain a wide industrial support and to become a standard of choice for parallel programming. In all cases, the best speedups are obtained when combining precise algorithmic studies with a knowledge of the computing architectures. This is especially true with the memory hierarchy: the algorithms have to find a good balance between using large (and slow) global memories and some fast (but small) local memories. In this chapter, we will show how those manycore devices enable more efficient bioinformatics applications. We will first give some insights into architectures and parallelism. Then we will describe recent implementations specifically designed for manycore architectures, including algorithms on sequence alignment and RNA structure prediction. We will conclude with some thoughts about the dissemination of those algorithms and implementations: are they today available on the bookshelf for everyone

An enhanced GPU architecture for not-so-regular parallelism with special implications for database search

textGraphics Processing Units (GPUs) have become a popular platform for executing general purpose (i.e., non-graphics) applications. To run efficiently on a GPU, applications must be parallelized into many threads, each of which performs the same task but operates on different data (i.e., data parallelism). Previous work has shown that some applications experience significant speedup when executed on a GPU instead of a CPU. The applications that benefit most tend to have certain characteristics such as high computational intensity, regular control-flow and memory access patterns, and little to no communication among threads. However, not all parallel applications have these characteristics. Applications with a more balanced compute to memory ratio, divergent control flow, irregular memory accesses, and/or frequent communication (i.e., not-so-regular applications) will not take full advantage of the GPU's resources, resulting in performance far short of what could be delivered. The goal of this dissertation is to enhance the GPU architecture to better handle not-so-regular parallelism. This is accomplished in two parts. First, I analyze a diverse set of data parallel applications that suffer from divergent control-flow and/or significant stall time due to memory. I propose two microarchitectural enhancements to the GPU called the Large Warp Microarchitecture and Two-Level Warp Scheduling to address these problems respectively. When combined, these mechanisms increase performance by 19% on average. Second, I examine one of the most important and fundamental applications in computing: database search. Database search is an excellent example of an application that is rich in parallelism, but rife with not-so-regular characteristics. I propose enhancements to the GPU architecture including new instructions that improve intra-warp thread communication and decision making, and also a row-buffer locality hint bit to better handle the irregular memory access patterns of index-based tree search. These proposals improve performance by 21% for full table scans, and 39% for index-based search. The result of this dissertation is an enhanced GPU architecture that better handles not-so-regular parallelism. This increases the scope of applications that run efficiently on the GPU, making it a more viable platform not only for current parallel workloads such as databases, but also for future and emerging parallel applications.Electrical and Computer Engineerin

High throughput image compression and decompression on GPUs

Diese Arbeit befasst sich mit der Entwicklung eines GPU-freundlichen, intra-only, Wavelet-basierten Videokompressionsverfahrens mit hohem Durchsatz, das für visuell verlustfreie Anwendungen optimiert ist. Ausgehend von der Beobachtung, dass der JPEG 2000 Entropie-Kodierer ein Flaschenhals ist, werden verschiedene algorithmische Änderungen vorgeschlagen und bewertet. Zunächst wird der JPEG 2000 Selective Arithmetic Coding Mode auf der GPU realisiert, wobei sich die Erhöhung des Durchsatzes hierdurch als begrenzt zeigt. Stattdessen werden zwei nicht standard-kompatible Änderungen vorgeschlagen, die (1) jede Bitebebene in nur einem einzelnen Pass verarbeiten (Single-Pass-Modus) und (2) einen echten Rohcodierungsmodus einführen, der sample-weise parallelisierbar ist und keine aufwendige Kontextmodellierung erfordert. Als nächstes wird ein alternativer Entropiekodierer aus der Literatur, der Bitplane Coder with Parallel Coefficient Processing (BPC-PaCo), evaluiert. Er gibt Signaladaptivität zu Gunsten von höherer Parallelität auf und daher wird hier untersucht und gezeigt, dass ein aus verschiedensten Testsequenzen gemitteltes statisches Wahrscheinlichkeitsmodell eine kompetitive Kompressionseffizienz erreicht. Es wird zudem eine Kombination von BPC-PaCo mit dem Single-Pass-Modus vorgeschlagen, der den Speedup gegenüber dem JPEG 2000 Entropiekodierer von 2,15x (BPC-PaCo mit zwei Pässen) auf 2,6x (BPC-PaCo mit Single-Pass-Modus) erhöht auf Kosten eines um 0,3 dB auf 1,0 dB erhöhten Spitzen-Signal-Rausch-Verhältnis (PSNR). Weiter wird ein paralleler Algorithmus zur Post-Compression Ratenkontrolle vorgestellt sowie eine parallele Codestream-Erstellung auf der GPU. Es wird weiterhin ein theoretisches Laufzeitmodell formuliert, das es durch Benchmarking von einer GPU ermöglicht die Laufzeit einer Routine auf einer anderen GPU vorherzusagen. Schließlich wird der erste JPEG XS GPU Decoder vorgestellt und evaluiert. JPEG XS wurde als Low Complexity Codec konzipiert und forderte erstmals explizit GPU-Freundlichkeit bereits im Call for Proposals. Ab Bitraten über 1 bpp ist der Decoder etwa 2x schneller im Vergleich zu JPEG 2000 und 1,5x schneller als der schnellste hier vorgestellte Entropiekodierer (BPC-PaCo mit Single-Pass-Modus). Mit einer GeForce GTX 1080 wird ein Decoder Durchsatz von rund 200 fps für eine UHD-4:4:4-Sequenz erreicht.This work investigates possibilities to create a high throughput, GPU-friendly, intra-only, Wavelet-based video compression algorithm optimized for visually lossless applications. Addressing the key observation that JPEG 2000’s entropy coder is a bottleneck and might be overly complex for a high bit rate scenario, various algorithmic alterations are proposed. First, JPEG 2000’s Selective Arithmetic Coding mode is realized on the GPU, but the gains in terms of an increased throughput are shown to be limited. Instead, two independent alterations not compliant to the standard are proposed, that (1) give up the concept of intra-bit plane truncation points and (2) introduce a true raw-coding mode that is fully parallelizable and does not require any context modeling. Next, an alternative block coder from the literature, the Bitplane Coder with Parallel Coefficient Processing (BPC-PaCo), is evaluated. Since it trades signal adaptiveness for increased parallelism, it is shown here how a stationary probability model averaged from a set of test sequences yields competitive compression efficiency. A combination of BPC-PaCo with the single-pass mode is proposed and shown to increase the speedup with respect to the original JPEG 2000 entropy coder from 2.15x (BPC-PaCo with two passes) to 2.6x (proposed BPC-PaCo with single-pass mode) at the marginal cost of increasing the PSNR penalty by 0.3 dB to at most 1 dB. Furthermore, a parallel algorithm is presented that determines the optimal code block bit stream truncation points (given an available bit rate budget) and builds the entire code stream on the GPU, reducing the amount of data that has to be transferred back into host memory to a minimum. A theoretical runtime model is formulated that allows, based on benchmarking results on one GPU, to predict the runtime of a kernel on another GPU. Lastly, the first ever JPEG XS GPU-decoder realization is presented. JPEG XS was designed to be a low complexity codec and for the first time explicitly demanded GPU-friendliness already in the call for proposals. Starting at bit rates above 1 bpp, the decoder is around 2x faster compared to the original JPEG 2000 and 1.5x faster compared to JPEG 2000 with the fastest evaluated entropy coder (BPC-PaCo with single-pass mode). With a GeForce GTX 1080, a decoding throughput of around 200 fps is achieved for a UHD 4:4:4 sequence

An efficient multi-core SIMD implementation for H.264/AVC encoder

The optimization process of a H.264/AVC encoder on three different architectures is presented. The architectures are multi- and singlecore and SIMD instruction sets have different vector registers size. The need of code optimization is fundamental when addressing HD resolutions with real-time constraints. The encoder is subdivided in functional modules in order to better understand where the optimization is a key factor and to evaluate in details the performance improvement. Common issues in both partitioning a video encoder into parallel architectures and SIMD optimization are described, and author solutions are presented for all the architectures. Besides showing efficient video encoder implementations, one of the main purposes of this paper is to discuss how the characteristics of different architectures and different set of SIMD instructions can impact on the target application performance. Results about the achieved speedup are provided in order to compare the different implementations and evaluate the more suitable solutions for present and next generation video-coding algorithms