Doctor of Philosophy

dissertationMemory access irregularities are a major bottleneck for bandwidth limited problems on Graphics Processing Unit (GPU) architectures. GPU memory systems are designed to allow consecutive memory accesses to be coalesced into a single memory access. Noncontiguous accesses within a parallel group of threads working in lock step may cause serialized memory transfers. Irregular algorithms may have data-dependent control flow and memory access, which requires runtime information to be evaluated. Compile time methods for evaluating parallelism, such as static dependence graphs, are not capable of evaluating irregular algorithms. The goals of this dissertation are to study irregularities within the context of unstructured mesh and sparse matrix problems, analyze the impact of vectorization widths on irregularities, and present data-centric methods that improve control flow and memory access irregularity within those contexts. Reordering associative operations has often been exploited for performance gains in parallel algorithms. This dissertation presents a method for associative reordering of stencil computations over unstructured meshes that increases data reuse through caching. This novel parallelization scheme offers considerable speedups over standard methods. Vectorization widths can have significant impact on performance in vectorized computations. Although the hardware vector width is generally fixed, the logical vector width used within a computation can range from one up to the width of the computation. Significant performance differences can occur due to thread scheduling and resource limitations. This dissertation analyzes the impact of vectorization widths on dense numerical computations such as 3D dG postprocessing. It is difficult to efficiently perform dynamic updates on traditional sparse matrix formats. Explicitly controlling memory segmentation allows for in-place dynamic updates in sparse matrices. Dynamically updating the matrix without rebuilding or sorting greatly improves processing time and overall throughput. This dissertation presents a new sparse matrix format, dynamic compressed sparse row (DCSR), which allows for dynamic streaming updates to a sparse matrix. A new method for parallel sparse matrix-matrix multiplication (SpMM) that uses dynamic updates is also presented

Efficient Machine Learning Approach for Optimizing Scientific Computing Applications on Emerging HPC Architectures

Efficient parallel implementations of scientific applications on multi-core CPUs with accelerators such as GPUs and Xeon Phis is challenging. This requires - exploiting the data parallel architecture of the accelerator along with the vector pipelines of modern x86 CPU architectures, load balancing, and efficient memory transfer between different devices. It is relatively easy to meet these requirements for highly-structured scientific applications. In contrast, a number of scientific and engineering applications are unstructured. Getting performance on accelerators for these applications is extremely challenging because many of these applications employ irregular algorithms which exhibit data-dependent control-flow and irregular memory accesses. Furthermore, these applications are often iterative with dependency between steps, and thus making it hard to parallelize across steps. As a result, parallelism in these applications is often limited to a single step. Numerical simulation of charged particles beam dynamics is one such application where the distribution of work and memory access pattern at each time step is irregular. Applications with these properties tend to present significant branch and memory divergence, load imbalance between different processor cores, and poor compute and memory utilization. Prior research on parallelizing such irregular applications have been focused around optimizing the irregular, data-dependent memory accesses and control-flow during a single step of the application independent of the other steps, with the assumption that these patterns are completely unpredictable. We observed that the structure of computation leading to control-flow divergence and irregular memory accesses in one step is similar to that in the next step. It is possible to predict this structure in the current step by observing the computation structure of previous steps. In this dissertation, we present novel machine learning based optimization techniques to address the parallel implementation challenges of such irregular applications on different HPC architectures. In particular, we use supervised learning to predict the computation structure and use it to address the control-flow and memory access irregularities in the parallel implementation of such applications on GPUs, Xeon Phis, and heterogeneous architectures composed of multi-core CPUs with GPUs or Xeon Phis. We use numerical simulation of charged particles beam dynamics simulation as a motivating example throughout the dissertation to present our new approach, though they should be equally applicable to a wide range of irregular applications. The machine learning approach presented here use predictive analytics and forecasting techniques to adaptively model and track the irregular memory access pattern at each time step of the simulation to anticipate the future memory access pattern. Access pattern forecasts can then be used to formulate optimization decisions during application execution which improves the performance of the application at a future time step based on the observations from earlier time steps. In heterogeneous architectures, forecasts can also be used to improve the memory performance and resource utilization of all the processing units to deliver a good aggregate performance. We used these optimization techniques and anticipation strategy to design a cache-aware, memory efficient parallel algorithm to address the irregularities in the parallel implementation of charged particles beam dynamics simulation on different HPC architectures. Experimental result using a diverse mix of HPC architectures shows that our approach in using anticipation strategy is effective in maximizing data reuse, ensuring workload balance, minimizing branch and memory divergence, and in improving resource utilization

SONIC: streaming overlapping community detection

A community within a graph can be broadly defined as a set of vertices that exhibit high cohesiveness (relatively high number of edges within the set) and low conductance (relatively low number of edges leaving the set). Community detection is a fundamental graph processing analytic that can be applied to several application domains, including social networks. In this context, communities are often overlapping, as a person can be involved in more than one community (e.g., friends, and family); and evolving, since the structure of the network changes. We address the problem of streaming overlapping community detection, where the goal is to maintain communities in the presence of streaming updates. This way, the communities can be updated more efficiently. To this end, we introduce SONIC—a find-and-merge type of community detection algorithm that can efficiently handle streaming updates. SONIC first detects when graph updates yield significant community changes. Upon the detection, it updates the communities via an incremental merge procedure. The SONIC algorithm incorporates two additional techniques to speed-up the incremental merge; min-hashing and inverted indexes. Results show that SONIC can provide high quality overlapping communities, while handling streaming updates several orders of magnitude faster than the alternatives performing from-scratch computation. © 2015, The Author(s)

Performance-efficient mechanisms for managing irregularity in throughput processors

textRecent graphics processing units (GPUs) have emerged as a promising platform for general purpose computing and have been shown to be very efficient in executing parallel applications with regular control and memory access behavior. Current GPU architectures primarily adopt the single-instruction multiple-thread (SIMT) programming model that balances programmability and hardware efficiency. With SIMT, the programmer writes application code to be executed by scalar threads and each thread is supported with conditional branch and fine-grained load/store instruction for ease of programming. At the same time, the hardware and software collaboratively enable the grouping of scalar threads to be executed in a vectorized single-instruction multiple-data (SIMD) in-order pipeline, simplifying hardware design. As GPUs gain momentum in being utilized in various application domains, these throughput processors will increasingly demand more efficient execution of irregular applications. Current GPUs, however, suffer from reduced thread-level parallelism, underutilization of compute resources, inefficient on-chip caching, and waste in off-chip memory bandwidth utilization for highly irregular programs with divergent control and memory accesses. In this dissertation, I develop techniques that enable simple, robust, and highly effective performance optimizations for SIMT-based throughput processor architectures such that they can better manage irregularity. I first identify that previously suggested optimizations to the divergent control flow problem suffers from the following limitations: 1) serialized execution of diverging paths, 2) lack of robustness across regular/irregular codes, and 3) limited applicability. Based on such observations, I propose and evaluate three novel mechanisms that resolve the aforementioned issues, providing significant performance improvements while minimizing implementation overhead. In the second half of the dissertation, I observe that conventional coarse-grained memory hierarchy designs do not take into account the massively multi-threaded nature of GPUs, which leads to substantial waste in off-chip memory bandwidth utilization. I design and evaluate a locality-aware memory hierarchy for throughput processors, which retains the advantages of coarse-grained accesses for spatially and temporally local programs while permitting selective fine-grained access to memory. By adaptively adjusting the access granularity, memory bandwidth and energy consumption are reduced for data with low spatial/temporal locality without wasting control overheads or prefetching potential for data with high spatial locality.Electrical and Computer Engineerin