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  1. Joint Nonnegative Matrix Factorization (JointNMF) is a hybrid method for mining information from datasets that contain both feature and connection information. We propose distributed-memory parallelizations of three algorithms for solving the JointNMF problem based on Alternating Nonnegative Least Squares, Projected Gradient Descent, and Projected Gauss-Newton. We extend well-known communication-avoiding algorithms using a single processor grid case to our coupled case on two processor grids. We demonstrate the scalability of the algorithms on up to 960 cores (40 nodes) with 60\% parallel efficiency. The more sophisticated Alternating Nonnegative Least Squares (ANLS) and Gauss-Newton variants outperform the first-order gradient descent method in reducing the objective on large-scale problems. We perform a topic modelling task on a large corpus of academic papers that consists of over 37 million paper abstracts and nearly a billion citation relationships, demonstrating the utility and scalability of the methods. 
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    Free, publicly-accessible full text available June 21, 2024
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    As systems and applications grow more complex, detailed computer architecture simulation takes an ever increasing amount of time. Longer simulation times result in slower design iterations which then force architects to use simpler models, such as spreadsheets, when they want to iterate quickly on a design. Simple models are not easy to work with though, as architects must rely on intuition to choose representative models, and the path from the simple models to a detailed hardware simulation is not always clear. In this work, we present a method of bridging the gap between simple and detailed simulation by monitoring simulation behavior online and automatically swapping out detailed models with simpler statistical approximations. We demonstrate the potential of our methodology by implementing it in the open-source simulator SVE-Cachesim to swap out the level one data cache (L1D) within a memory hierarchy. This proof of concept demonstrates that our technique can train simple models to match real program behavior in the L1D and can swap them in without destructive side-effects for the performance of downstream models. Our models introduce only 8% error in the overall cycle count, while being used for over 90% of the simulation and using models that require two to eight times less computation per cache access. 
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    We are motivated by newly proposed methods for data mining large-scale corpora of scholarly publications, such as the full biomedical literature, which may consist of tens of millions of papers spanning decades of research. In this setting, analysts seek to discover how concepts relate to one another. They construct graph representations from annotated text databases and then formulate the relationship-mining problem as one of computing all-pairs shortest paths (APSP), which becomes a significant bottleneck. In this context, we present a new high-performance algorithm and implementation of the Floyd-Warshall algorithm for distributed-memory parallel computers accelerated by GPUs, which we call DSNAPSHOT (Distributed Accelerated Semiring All-Pairs Shortest Path). For our largest experiments, we ran DSNAPSHOT on a connected input graph with millions of vertices using 4, 096nodes (24,576GPUs) of the Oak Ridge National Laboratory's Summit supercomputer system. We find DSNAPSHOT achieves a sustained performance of 136×1015 floating-point operations per second (136petaflop/s) at a parallel efficiency of 90% under weak scaling and, in absolute speed, 70% of the best possible performance given our computation (in the single-precision tropical semiring or “min-plus” algebra). Looking forward, we believe this novel capability will enable the mining of scholarly knowledge corpora when embedded and integrated into artificial intelligence-driven natural language processing workflows at scale. 
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    We present an optimized Floyd-Warshall (Floyd-Warshall) algorithm that computes the All-pairs shortest path (APSP) for GPU accelerated clusters. The Floyd-Warshall algorithm due to its structural similarities to matrix-multiplication is well suited for highly parallel GPU architectures. To achieve high parallel efficiency, we address two key algorithmic challenges: reducing high communication overhead and addressing limited GPU memory. To reduce high communication costs, we redesign the parallel (a) to expose more parallelism, (b) aggressively overlap communication and computation with pipelined and asynchronous scheduling of operations, and (c) tailored MPI-collective. To cope with limited GPU memory, we employ an offload model, where the data resides on the host and is transferred to GPU on-demand. The proposed optimizations are supported with detailed performance models for tuning. Our optimized parallel Floyd-Warshall implementation is up to 5x faster than a strong baseline and achieves 8.1 PetaFLOPS/sec on 256~nodes of the Summit supercomputer at Oak Ridge National Laboratory. This performance represents 70% of the theoretical peak and 80% parallel efficiency. The offload algorithm can handle 2.5x larger graphs with a 20% increase in overall running time. 
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    We show how to exploit graph sparsity in the Floyd-Warshall algorithm for the all-pairs shortest path (Apsp) problem.Floyd-Warshall is an attractive choice for APSP on high-performing systems due to its structural similarity to solving dense linear systems and matrix multiplication. However, if sparsity of the input graph is not properly exploited,Floyd-Warshall will perform unnecessary asymptotic work and thus may not be a suitable choice for many input graphs. To overcome this limitation, the key idea in our approach is to use the known algebraic relationship between Floyd-Warshall and Gaussian elimination, and import several algorithmic techniques from sparse Cholesky factorization, namely, fill-in reducing ordering, symbolic analysis, supernodal traversal, and elimination tree parallelism. When combined, these techniques reduce computation, improve locality and enhance parallelism. We implement these ideas in an efficient shared memory parallel prototype that is orders of magnitude faster than an efficient multi-threaded baseline Floyd-Warshall that does not exploit sparsity. Our experiments suggest that the Floyd-Warshall algorithm can compete with Dijkstra’s algorithm (the algorithmic core of Johnson’s algorithm) for several classes sparse graphs. 
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  8. This paper describes a new benchmark tool, Spatter, for assessing memory system architectures in the context of a specific category of indexed accesses known as gather and scatter. These types of operations are increasingly used to express sparse and irregular data access patterns, and they have widespread utility in many modern HPC applications including scientific simulations, data mining and analysis computations, and graph processing. However, many traditional benchmarking tools like STREAM, STRIDE, and GUPS focus on characterizing only uniform stride or fully random accesses despite evidence that modern applications use varied sets of more complex access patterns. Spatter is an open-source benchmark that provides a tunable and configurable framework to benchmark a variety of indexed access patterns, including variations of gather / scatter that are seen in HPC mini-apps evaluated in this work. The design of Spatter includes backends for OpenMP and CUDA, and experiments show how it can be used to evaluate 1) uniform access patterns for CPU and GPU, 2) prefetching regimes for gather / scatter, 3) compiler implementations of vectorization for gather / scatter, and 4) trace-driven "proxy patterns" that reflect the patterns found in multiple applications. The results from Spatter experiments show, for instance, that GPUs typically outperform CPUs for these operations in absolute bandwidth but not fraction of peak bandwidth, and that Spatter can better represent the performance of some cache-dependent mini-apps than traditional STREAM bandwidth measurements. 
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