Survey on Combinatorial Register Allocation and Instruction Scheduling

Register allocation (mapping variables to processor registers or memory) and instruction scheduling (reordering instructions to increase instruction-level parallelism) are essential tasks for generating efficient assembly code in a compiler. In the last three decades, combinatorial optimization has emerged as an alternative to traditional, heuristic algorithms for these two tasks. Combinatorial optimization approaches can deliver optimal solutions according to a model, can precisely capture trade-offs between conflicting decisions, and are more flexible at the expense of increased compilation time. This paper provides an exhaustive literature review and a classification of combinatorial optimization approaches to register allocation and instruction scheduling, with a focus on the techniques that are most applied in this context: integer programming, constraint programming, partitioned Boolean quadratic programming, and enumeration. Researchers in compilers and combinatorial optimization can benefit from identifying developments, trends, and challenges in the area; compiler practitioners may discern opportunities and grasp the potential benefit of applying combinatorial optimization

Predictive analysis and optimisation of pipelined wavefront applications using reusable analytic models

Pipelined wavefront computations are an ubiquitous class of high performance parallel algorithms used for the solution of many scientific and engineering applications. In order to aid the design and optimisation of these applications, and to ensure that during procurement platforms are chosen best suited to these codes, there has been considerable research in analysing and evaluating their operational performance. Wavefront codes exhibit complex computation, communication, synchronisation patterns, and as a result there exist a large variety of such codes and possible optimisations. The problem is compounded by each new generation of high performance computing system, which has often introduced a previously unexplored architectural trait, requiring previous performance models to be rewritten and reevaluated. In this thesis, we address the performance modelling and optimisation of this class of application, as a whole. This differs from previous studies in which bespoke models are applied to specific applications. The analytic performance models are generalised and reusable, and we demonstrate their application to the predictive analysis and optimisation of pipelined wavefront computations running on modern high performance computing systems. The performance model is based on the LogGP parameterisation, and uses a small number of input parameters to specify the particular behaviour of most wavefront codes. The new parameters and model equations capture the key structural and behavioural differences among different wavefront application codes, providing a succinct summary of the operations for each application and insights into alternative wavefront application design. The models are applied to three industry-strength wavefront codes and are validated on several systems including a Cray XT3/XT4 and an InfiniBand commodity cluster. Model predictions show high quantitative accuracy (less than 20% error) for all high performance configurations and excellent qualitative accuracy. The thesis presents applications, projections and insights for optimisations using the model, which show the utility of reusable analytic models for performance engineering of high performance computing codes. In particular, we demonstrate the use of the model for: (1) evaluating application configuration and resulting performance; (2) evaluating hardware platform issues including platform sizing, configuration; (3) exploring hardware platform design alternatives and system procurement and, (4) considering possible code and algorithmic optimisations

Parallelization of dynamic programming recurrences in computational biology

The rapid growth of biosequence databases over the last decade has led to a performance bottleneck in the applications analyzing them. In particular, over the last five years DNA sequencing capacity of next-generation sequencers has been doubling every six months as costs have plummeted. The data produced by these sequencers is overwhelming traditional compute systems. We believe that in the future compute performance, not sequencing, will become the bottleneck in advancing genome science. In this work, we investigate novel computing platforms to accelerate dynamic programming algorithms, which are popular in bioinformatics workloads. We study algorithm-specific hardware architectures that exploit fine-grained parallelism in dynamic programming kernels using field-programmable gate arrays: FPGAs). We advocate a high-level synthesis approach, using the recurrence equation abstraction to represent dynamic programming and polyhedral analysis to exploit parallelism. We suggest a novel technique within the polyhedral model to optimize for throughput by pipelining independent computations on an array. This design technique improves on the state of the art, which builds latency-optimal arrays. We also suggest a method to dynamically switch between a family of designs using FPGA reconfiguration to achieve a significant performance boost. We have used polyhedral methods to parallelize the Nussinov RNA folding algorithm to build a family of accelerators that can trade resources for parallelism and are between 15-130x faster than a modern dual core CPU implementation. A Zuker RNA folding accelerator we built on a single workstation with four Xilinx Virtex 4 FPGAs outperforms 198 3 GHz Intel Core 2 Duo processors. Furthermore, our design running on a single FPGA is an order of magnitude faster than competing implementations on similar-generation FPGAs and graphics processors. Our work is a step toward the goal of automated synthesis of hardware accelerators for dynamic programming algorithms

Effective Performance Analysis and Debugging

Performance is once again a first-class concern. Developers can no longer wait for the next generation of processors to automatically optimize their software. Unfortunately, existing techniques for performance analysis and debugging cannot cope with complex modern hardware, concurrent software, or latency-sensitive software services. While processor speeds have remained constant, increasing transistor counts have allowed architects to increase processor complexity. This complexity often improves performance, but the benefits can be brittle; small changes to a program’s code, inputs, or execution environment can dramatically change performance, resulting in unpredictable performance in deployed software and complicating performance evaluation and debugging. Developers seeking to improve performance must resort to manual performance tuning for large performance gains. Software profilers are meant to guide developers to important code, but conventional profilers do not produce actionable information for concurrent applications. These profilers report where a program spends its time, not where optimizations will yield performance improvements. Furthermore, latency is a critical measure of performance for software services and interactive applications, but conventional profilers measure only throughput. Many performance issues appear only when a system is under high load, but generating this load in development is often impossible. Developers need to identify and mitigate scalability issues before deploying software, but existing tools offer developers little or no assistance. In this dissertation, I introduce an empirically-driven approach to performance analysis and debugging. I present three systems for performance analysis and debugging. Stabilizer mitigates the performance variability that is inherent in modern processors, enabling both predictable performance in deployment and statistically sound performance evaluation. Coz conducts performance experiments using virtual speedups to create the effect of an optimization in a running application. This approach accurately predicts the effect of hypothetical optimizations, guiding developers to code where optimizations will have the largest effect. Amp allows developers to evaluate system scalability using load amplification to create the effect of high load in a testing environment. In combination, Amp and Coz allow developers to pinpoint code where manual optimizations will improve the scalability of their software

High Performance Reconfigurable Computing for Linear Algebra: Design and Performance Analysis

Field Programmable Gate Arrays (FPGAs) enable powerful performance acceleration for scientific computations because of their intrinsic parallelism, pipeline ability, and flexible architecture. This dissertation explores the computational power of FPGAs for an important scientific application: linear algebra. First of all, optimized linear algebra subroutines are presented based on enhancements to both algorithms and hardware architectures. Compared to microprocessors, these routines achieve significant speedup. Second, computing with mixed-precision data on FPGAs is proposed for higher performance. Experimental analysis shows that mixed-precision algorithms on FPGAs can achieve the high performance of using lower-precision data while keeping higher-precision accuracy for finding solutions of linear equations. Third, an execution time model is built for reconfigurable computers (RC), which plays an important role in performance analysis and optimal resource utilization of FPGAs. The accuracy and efficiency of parallel computing performance models often depend on mean maximum computations. Despite significant prior work, there have been no sufficient mathematical tools for this important calculation. This work presents an Effective Mean Maximum Approximation method, which is more general, accurate, and efficient than previous methods. Together, these research results help address how to make linear algebra applications perform better on high performance reconfigurable computing architectures