Genetic improvement of GPU software

We survey genetic improvement (GI) of general purpose computing on graphics cards. We summarise several experiments which demonstrate four themes. Experiments with the gzip program show that genetic programming can automatically port sequential C code to parallel code. Experiments with the StereoCamera program show that GI can upgrade legacy parallel code for new hardware and software. Experiments with NiftyReg and BarraCUDA show that GI can make substantial improvements to current parallel CUDA applications. Finally, experiments with the pknotsRG program show that with semi-automated approaches, enormous speed ups can sometimes be had by growing and grafting new code with genetic programming in combination with human input

Multi-GPU support on the marrow algorithmic skeleton framework

Dissertação para obtenção do Grau de Mestre em Engenharia InformáticaWith the proliferation of general purpose GPUs, workload parallelization and datatransfer optimization became an increasing concern. The natural evolution from using a single GPU, is multiplying the amount of available processors, presenting new challenges, as tuning the workload decompositions and load balancing, when dealing with heterogeneous systems. Higher-level programming is a very important asset in a multi-GPU environment, due to the complexity inherent to the currently used GPGPU APIs (OpenCL and CUDA), because of their low-level and code overhead. This can be obtained by introducing an abstraction layer, which has the advantage of enabling implicit optimizations and orchestrations such as transparent load balancing mechanism and reduced explicit code overhead. Algorithmic Skeletons, previously used in cluster environments, have recently been adapted to the GPGPU context. Skeletons abstract most sources of code overhead, by defining computation patterns of commonly used algorithms. The Marrow algorithmic skeleton library is one of these, taking advantage of the abstractions to automate the orchestration needed for an efficient GPU execution. This thesis proposes the extension of Marrow to leverage the use of algorithmic skeletons in the modular and efficient programming of multiple heterogeneous GPUs, within a single machine. We were able to achieve a good balance between simplicity of the programming model and performance, obtaining good scalability when using multiple GPUs, with an efficient load distribution, although at the price of some overhead when using a single-GPU.projects PTDC/EIA-EIA/102579/2008 and PTDC/EIA-EIA/111518/200

An automated OpenCL FPGA compilation framework targeting a configurable, VLIW chip multiprocessor

Modern system-on-chips augment their baseline CPU with coprocessors and accelerators to increase overall computational capacity and power efficiency, and thus have evolved into heterogeneous systems. Several languages have been developed to enable this paradigm shift, including CUDA and OpenCL. This thesis discusses a unified compilation environment to enable heterogeneous system design through the use of OpenCL and a customised VLIW chip multiprocessor (CMP) architecture, known as the LE1. An LLVM compilation framework was researched and a prototype developed to enable the execution of OpenCL applications on the LE1 CPU. The framework fully automates the compilation flow and supports work-item coalescing to better utilise the CPU cores and alleviate the effects of thread divergence. This thesis discusses in detail both the software stack and target hardware architecture and evaluates the scalability of the proposed framework on a highly precise cycle-accurate simulator. This is achieved through the execution of 12 benchmarks across 240 different machine configurations, as well as further results utilising an incomplete development branch of the compiler. It is shown that the problems generally scale well with the LE1 architecture, up to eight cores, when the memory system becomes a serious bottleneck. Results demonstrate superlinear performance on certain benchmarks (x9 for the bitonic sort benchmark with 8 dual-issue cores) with further improvements from compiler optimisations (x14 for bitonic with the same configuration

Three-Dimensional Processing-In-Memory-Architectures: A Holistic Tool For Modeling And Simulation

Die gemeinhin als Memory Wall bekannte, sich stetig weitende Leistungslücke zwischen Prozessor- und Speicherarchitekturen erfordert neue Konzepte, um weiterhin eine Skalierung der Rechenleistung zu ermöglichen. Da Speicher als die Beschränkung innerhalb einer Von-Neumann-Architektur identifiziert wurden, widmet sich die Arbeit dieser Problemstellung. Obgleich dreidimensionale Speicher zu einer Linderung der Memory Wall beitragen können, sind diese alleinig für die zukünftige Skalierung ungenügend. Aufgrund höherer Effizienzen stellt die Integration von Rechenkapazität in den Speicher (Processing-In-Memory, PIM) ein vielversprechender Ausweg dar, jedoch existiert ein Mangel an PIM-Simulationsmodellen. Daher wurde ein flexibles Simulationswerkzeug für dreidimensionale Speicherstapel geschaffen, welches zur Modellierung von dreidimensionalen PIM erweitert wurde. Dieses kann Speicherstapel wie etwa Hybrid Memory Cube standardkonform simulieren und bietet zugleich eine hohe Genauigkeit indem auf elementaren Datenpaketen in Kombination mit dem Hardware validierten Simulator BOBSim modelliert wird. Ein eigens entworfener Simulationstaktbaum ermöglicht zugleich eine schnelle Ausführung. Messungen weisen im funktionalen Modus eine 100-fache Beschleunigung auf, wohingegen eine Verdoppelung der Ausführungsgeschwindigkeit mit Taktgenauigkeit erzielt wird. Anhand eines eigens implementierten, binärkompatiblen GPU-Beschleunigers wird die Modellierung einer vollständig dreidimensionalen PIM-Architektur demonstriert. Dabei orientieren sich die maximalen Hardwareressourcen an einem PIM-Beschleuniger aus der Literatur. Evaluiert wird einerseits das GPU-Simulationsmodell eigenständig, andererseits als PIM-Verbund jeweils mit Hilfe einer repräsentativ gewählten, speicherbeschränkten geophysikalischen Bildverarbeitung. Bei alleiniger Betrachtung des GPU-Simulationsmodells weist dieses eine signifikant gesteigerte Simulationsgeschwindigkeit auf, bei gleichzeitiger Abweichung von 6% gegenüber dem Verilator-Modell. Nachfolgend werden innerhalb dieser Arbeit unterschiedliche Konfigurationen des integrierten PIM-Beschleunigers evaluiert. Je nach gewählter Konfiguration kann der genutzte Algorithmus entweder bis zu 140GFLOPS an tatsächlicher Rechenleistung abrufen oder eine maximale Recheneffizienz von synthetisch 30% bzw. real 24,5% erzielen. Letzteres stellt eine Verdopplung des Stands der Technik dar. Eine anknüpfende Diskussion erläutert eingehend die Resultate.The steadily widening performance gap between processor- and memory-architectures - commonly known as the Memory Wall - requires novel concepts to achieve further scaling in processing performance. As memories were identified as the limitation within a Von-Neumann-architecture, this work addresses this constraining issue. Although three-dimensional memories alleviate the effects of the Memory Wall, the sole utilization of such memories would be insufficient. Due to higher efficiencies, the integration of processing capacity into memories (so-called Processing-In-Memory, PIM) depicts a promising alternative. However, a lack of PIM simulation models still remains. As a consequence, a flexible simulation tool for three-dimensional stacked memories was established, which was extended for modeling three-dimensional PIM architectures. This tool can simulate stacked memories such as Hybrid Memory Cube standard-compliant and simultaneously offers high accuracy by modeling on elementary data packets (FLIT) in combination with the hardware validated BOBSim simulator. To this, a specifically designed simulation clock tree enables an rapid simulation execution. A 100x speed up in simulation execution can be measured while utilizing the functional mode, whereas a 2x speed up is achieved during clock-cycle accuracy mode. With the aid of a specifically implemented, binary compatible GPU accelerator and the established tool, the modeling of a holistic three-dimensional PIM architecture is demonstrated within this work. Hardware resources used were constrained by a PIM architecture from literature. A representative, memory-bound, geophysical imaging algorithm was leveraged to evaluate the GPU model as well as the compound PIM simulation model. The sole GPU simulation model depicts a significantly improved simulation performance with a deviation of 6% compared to a Verilator model. Subsequently, various PIM accelerator configurations with the integrated GPU model were evaluated. Depending on the chosen PIM configuration, the utilized algorithm achieves 140GFLOPS of processing performance or a maximum computing efficiency of synthetically 30% or realistically 24.5%. The latter depicts a 2x improvement compared to state-of-the-art. A following discussion showcases the results in depth

Doctor of Philosophy in Computing

dissertationThe aim of direct volume rendering is to facilitate exploration and understanding of three-dimensional scalar fields referred to as volume datasets. Improving understanding is done by improving depth perception, whereas facilitating exploration is done by speeding up volume rendering. In this dissertation, improving both depth perception and rendering speed is considered. The impact of depth of field (DoF) on depth perception in direct volume rendering is evaluated by conducting a user study in which the test subjects had to choose which of two features, located at different depths, appeared to be in front in a volume-rendered image. Whereas DoF was expected to improve perception in all cases, the user study revealed that if used on the back feature, DoF reduced depth perception, whereas it produced a marked improvement when used on the front feature. We then worked on improving the speed of volume rendering on distributed memory machines. Distributed volume rendering has three stages: loading, rendering, and compositing. In this dissertation, the focus is on image compositing, more specifically, trying to optimize communication in image compositing algorithms. For that, we have developed the Task Overlapped Direct Send Tree image compositing algorithm, which works on both CPU- and GPU-accelerated supercomputers, which focuses on communication avoidance and overlapping communication with computation; the Dynamically Scheduled Region-Based image compositing algorithm that uses spatial and temporal awareness to efficiently schedule communication among compositing nodes, and a rendering and compositing pipeline that allows both image compositing and rendering to be done on GPUs of GPU-accelerated supercomputers. We tested these on CPU- and GPU-accelerated supercomputers and explain how these improvements allow us to obtain better performance than image compositing algorithms that focus on load-balancing and algorithms that have no spatial and temporal awareness of the rendering and compositing stages

Efficient Scheduling and High-Performance Graph Partitioning on Heterogeneous CPU-GPU Systems

Heterogeneous CPU-GPU systems have emerged as a power-efficient platform for high performance parallelization of the applications. However, effectively exploiting these architectures faces a number of challenges including differences in the programming models of the CPU (MIMD) and the GPU (SIMD), GPU memory constraints, and comparatively low communication bandwidth between the CPU and GPU. As a consequence, high performance execution of applications on these platforms requires designing new adaptive parallelizing methods. In this thesis, first we explore embarrassingly parallel applications where tasks have no inter-dependencies. Although the massive processing power of GPUs provides an attractive opportunity for high-performance execution of embarrassingly parallel tasks on CPU-GPU systems, minimized execution time can only be obtained by optimally distributing the tasks between the processors. In contemporary CPU-GPU systems, the scheduler cannot decide about the appropriate rate distribution. Hence it requires high programming effort to manually divide the tasks among the processors. Herein, we design and implement a new dynamic scheduling heuristic to minimize the execution time of embarrassingly parallel applications on a heterogeneous CPU-GPU system. The scheduler is integrated into a scheduling framework that provides pre-implemented automated scheduling modules, liberating the user from the complexities of scheduling details. The experimental results show that our scheduling approach achieves better to similar performance compared to some of the scheduling algorithms proposed for CPU-GPU systems. We then investigate task dependent applications, where the tasks have data dependencies. The computational tasks and their communication patterns are expressed by a task interaction graph. Scheduling of the task interaction graph on a cluster can be done by first partitioning the graph into a set of computationally balanced partitions in such a way that the communication cost among the partitions is minimized, and subsequently mapping the partitions onto physical processors. Aside from scheduling, graph partitioning is a common computation phase in many application domains, including social network analysis, data mining, and VLSI design. However, irregular and data-dependent graph partitioning sub-tasks pose multiple challenges for efficient GPU utilization, which favors regularity. We design and implement a multilevel graph partitioner on a heterogeneous CPU-GPU system that takes advantage of the high parallel processing power of GPUs by executing the computation-intensive parts of the partitioning sub-tasks on the GPU and assigning the parts with less parallelism to the CPU. Our partitioner aims to overcome some of the challenges arising due to the irregular nature of the algorithm, and memory constraints on GPUs. We present a lock-free scheme since fine-grained synchronization among thousands of GPU threads imposes too high a performance overhead. Experimental results demonstrate that our partitioner outperforms serial and parallel MPI-based partitioners. It performs similar to shared-memory CPU-based parallel graph partitioner. To optimize the graph partitioner performance, we describe an effective and methodological approach to enable a GPU-based multi-level graph partitioning that is tailored specifically for the SIMD architecture. Our solution avoids thread divergence and balances the load over GPU threads by dynamically assigning an appropriate number of threads to process the graph vertices and irregular sized neighbors. Our optimized design is autonomous as all the steps are carried out by the GPU with minimal CPU interference. We show that this design outperforms CPU-based parallel graph partitioner. Finally, we apply some of our partitioning techniques to another graph processing algorithm, minimum spanning tree (MST), that exhibits load imbalance characteristics. We show that extending these techniques helps in achieving a high performance implementation of MST on the GPU

Optimal program variant generation for hybrid manycore systems

Field Programmable Gate Arrays promise to deliver superior energy efficiency in heterogeneous high performance computing, as compared to multicore CPUs and GPUs. The rate of adoption is however hampered by the relative difficulty of programming FPGAs. High-level synthesis tools such as Xilinx Vivado, Altera OpenCL or Intel's HLS address a large part of the programmability issue by synthesizing a Hardware Description Languages representation from a high-level specification of the application, given in programming languages such as OpenCL C, typically used to program CPUs and GPUs. Although HLS solutions make programming easier, they fail to also lighten the burden of optimization. Application developers must rely on expert knowledge to manually optimize their applications for each target device, meaning that traditional HLS solutions do not offer a solution to the issue of performance portability. This state of fact prompted the development of compiler frameworks such as TyTra that operate at an even higher level of abstraction that is amenable to the use of Design Space Exploration (DSE). With DSE the initial program specification can be seen as the starting location in a search-space of correct-by-construction program transformations. In TyTra the search-space is generated from the transitive-closure of term-level transformations derived from type-level transformations. Compiler frameworks such as TyTra theoretically solve the issue of performance portability by providing a way to automatically generate alternative correct program variants. They however suffer from the very practical issue that the generated space is often too large to fully explore. As a consequence, the globally optimal solution may be overlooked. In this work we provide a novel solution to issue performance portability by deriving an efficient yet effective DSE strategy for the TyTra compiler framework. We make use of categorical data types to derive categorical semantics for the formal languages that describe the terms, types, cost-performance estimates and their transformations. From these we define a category of interpretations for TyTra applications, from which we derive a DSE strategy that finds the globally optimal transformation sequence in polynomial time. This is achieved by reducing the size of the generated search space. We formally state and prove a theorem for this claim and then show that the polynomial run-time for our DSE strategy has practically negligible coefficients leading to sub-second exploration times for realistic applications

XSEDE: eXtreme Science and Engineering Discovery Environment Third Quarter 2012 Report

The Extreme Science and Engineering Discovery Environment (XSEDE) is the most advanced, powerful, and robust collection of integrated digital resources and services in the world. It is an integrated cyberinfrastructure ecosystem with singular interfaces for allocations, support, and other key services that researchers can use to interactively share computing resources, data, and expertise.This a report of project activities and highlights from the third quarter of 2012.National Science Foundation, OCI-105357