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Stencil computation optimization and autotuning on state-of-the-art multicore architectures
- In (submitted to) Proc. SC2008: High performance computing, networking, and storage conference
, 2008
"... Understanding the most efficient design and utilization of emerging multicore systems is one of the most challenging questions faced by the mainstream and scientific computing industries in several decades. Our work explores multicore stencil (nearest-neighbor) computations — a class of algorithms a ..."
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Cited by 136 (16 self)
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Understanding the most efficient design and utilization of emerging multicore systems is one of the most challenging questions faced by the mainstream and scientific computing industries in several decades. Our work explores multicore stencil (nearest-neighbor) computations — a class of algorithms at the heart of many structured grid codes, including PDE solvers. We develop a number of effective optimization strategies, and build an auto-tuning environment that searches over our optimizations and their parameters to minimize runtime, while maximizing performance portability. To evaluate the effectiveness of these strategies we explore the broadest set of multicore architectures in the current HPC literature, including the
A practical automatic polyhedral parallelizer and locality optimizer
- In PLDI ’08: Proceedings of the ACM SIGPLAN 2008 conference on Programming language design and implementation
, 2008
"... We present the design and implementation of an automatic polyhedral source-to-source transformation framework that can optimize regular programs (sequences of possibly imperfectly nested loops) for parallelism and locality simultaneously. Through this work, we show the practicality of analytical mod ..."
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Cited by 122 (8 self)
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We present the design and implementation of an automatic polyhedral source-to-source transformation framework that can optimize regular programs (sequences of possibly imperfectly nested loops) for parallelism and locality simultaneously. Through this work, we show the practicality of analytical model-driven automatic transformation in the polyhedral model.Unlike previous polyhedral frameworks, our approach is an end-to-end fully automatic one driven by an integer linear optimization framework that takes an explicit view of finding good ways of tiling for parallelism and locality using affine transformations. The framework has been implemented into a tool to automatically generate OpenMP parallel code from C program sections. Experimental results from the tool show very high performance for local and parallel execution on multi-cores, when compared with state-of-the-art compiler frameworks from the research community as well as the best native production compilers. The system also enables the easy use of powerful empirical/iterative optimization for general arbitrarily nested loop sequences.
3D finite difference computation on GPUs using CUDA
- Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, ACM International Conference Proceeding Series
, 2009
"... In this paper we describe a GPU parallelization of the 3D finite difference computation using CUDA. Data access redundancy is used as the metric to determine the optimal implementation for both the stencil-only computation, as well as the discretization of the wave equation, which is currently of gr ..."
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Cited by 75 (0 self)
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In this paper we describe a GPU parallelization of the 3D finite difference computation using CUDA. Data access redundancy is used as the metric to determine the optimal implementation for both the stencil-only computation, as well as the discretization of the wave equation, which is currently of great interest in seismic computing. For the larger stencils, the described approach achieves the throughput of between 2,400 to over 3,000 million of output points per second on a single Tesla 10-series GPU. This is roughly an order of magnitude higher than a 4-core Harpertown CPU running a similar code from seismic industry. Multi-GPU parallelization is also described, achieving linear scaling with GPUs by overlapping inter-GPU communication with computation.
Lattice Boltzmann simulation optimization on leading multicore platforms
- in Interational Conference on Parallel and Distributed Computing Systems (IPDPS
, 2008
"... We present an auto-tuning approach to optimize application performance on emerging multicore architectures. The methodology extends the idea of searchbased performance optimizations, popular in linear algebra and FFT libraries, to application-specific computational kernels. Our work applies this str ..."
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Cited by 48 (16 self)
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We present an auto-tuning approach to optimize application performance on emerging multicore architectures. The methodology extends the idea of searchbased performance optimizations, popular in linear algebra and FFT libraries, to application-specific computational kernels. Our work applies this strategy to a lattice Boltzmann application (LBMHD) that historically has made poor use of scalar microprocessors due to its complex data structures and memory access patterns. We explore one of the broadest sets of multicore architectures in the HPC literature, including the Intel Clovertown, AMD Opteron X2, Sun Niagara2, STI Cell, as well as the single core Intel Itanium2. Rather than hand-tuning LBMHD for each system, we develop a code generator that allows us identify a highly optimized version for each platform, while amortizing the human programming effort. Results show that our autotuned LBMHD application achieves up to a 14 × improvement compared with the original code. Additionally, we present detailed analysis of each optimization, which reveal surprising hardware bottlenecks and software challenges for future multicore systems and applications. 1
OPTIMIZATION AND PERFORMANCE MODELING OF STENCIL COMPUTATIONS ON MODERN MICROPROCESSORS
"... Stencil-based kernels constitute the core of many important scientific applications on block-structured grids. Unfortunately, these codes achieve a low fraction of peak performance, due primarily to the disparity between processor and main memory speeds. In this paper, we explore the impact of tre ..."
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Cited by 45 (8 self)
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Stencil-based kernels constitute the core of many important scientific applications on block-structured grids. Unfortunately, these codes achieve a low fraction of peak performance, due primarily to the disparity between processor and main memory speeds. In this paper, we explore the impact of trends in memory subsystems on a variety of stencil optimization techniques and develop performance models to analytically guide our optimizations. Our work targets cache reuse methodologies across single and multiple stencil sweeps, examining cache-aware algorithms as well as cache-oblivious techniques on the Intel Itanium2, AMD Opteron, and IBM Power5. Additionally, we consider stencil computations on the heterogeneous multi-core design of the Cell processor, a machine with an explicitly-managed memory hierarchy. Overall our work represents one of the most extensive analyses of stencil optimizations and performance modeling to date. Results demonstrate that recent trends in memory system organization have reduced the efficacy of traditional cacheblocking optimizations. We also show that a cache-aware implementation is significantly faster than a cache-oblivious approach, while the explicitly managed memory on Cell enables the highest overall efficiency: Cell attains 88 % of algorithmic peak while the best competing cache-based processor only achieves 54 % of algorithmic peak performance.
The Pochoir Stencil Compiler
"... A stencil computation repeatedly updates each point of a d-dimensionalgridasafunctionofitselfanditsnearneighbors. Parallel cache-efficient stencil algorithms based on “trapezoidal decompositions” are known, but most programmers find them difficult to write. The Pochoir stencil compiler allows a prog ..."
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Cited by 43 (2 self)
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A stencil computation repeatedly updates each point of a d-dimensionalgridasafunctionofitselfanditsnearneighbors. Parallel cache-efficient stencil algorithms based on “trapezoidal decompositions” are known, but most programmers find them difficult to write. The Pochoir stencil compiler allows a programmer to write a simple specification of a stencil in a domain-specific stencil language embedded in C++ which the Pochoir compiler then translates into high-performing Cilk code that employs an efficient parallel cache-oblivious algorithm. Pochoir supports general d-dimensional stencils and handles both periodic and aperiodic boundary conditions in one unified algorithm. The Pochoir system provides a C++ template library that allows the user’s stencilspecificationtobeexecuteddirectlyinC++withoutthePochoir compiler(albeitmoreslowly),whichsimplifiesuserdebuggingand greatly simplified the implementation of the Pochoir compiler itself. A host of stencil benchmarks run on a modern multicore machine demonstrates that Pochoir outperforms standard parallelloop implementations, typically running 2–10 times faster. The algorithm behind Pochoir improves on prior cache-efficient algorithms on multidimensional grids by making “hyperspace ” cuts, which yield asymptotically more parallelism for the same cache efficiency. Categories andSubjectDescriptors
Sketching Stencils
"... Performance of stencil computations can be significantly improved through smart implementations that improve memory locality, computation reuse, or parallelize the computation. Unfortunately, efficient implementations are hard to obtain because they often involve non-traditional transformations, whi ..."
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Cited by 41 (6 self)
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Performance of stencil computations can be significantly improved through smart implementations that improve memory locality, computation reuse, or parallelize the computation. Unfortunately, efficient implementations are hard to obtain because they often involve non-traditional transformations, which means that they cannot be produced by optimizing the reference stencil with a compiler. In fact, many stencils are produced by code generators that were tediously handcrafted. In this paper, we show how stencil implementations can be produced with sketching. Sketching is a software synthesis approach where the programmer develops a partial implementation— a sketch—and a separate specification of the desired functionality given by a reference (unoptimized) stencil. The synthesizer then completes the sketch to behave like the specification, filling in code fragments that are difficult to develop manually. Existing sketching systems work only for small finite programs, i.e., programs that can be represented as small Boolean circuits. In this paper, we develop a sketching synthesizer that works for stencil computations, a large class of programs that, unlike circuits, have unbounded inputs and outputs, as well as an unbounded number of computations. The key contribution is a reduction algorithm that turns a stencil into a circuit, allowing us to synthesize stencils using an existing sketching synthesizer.
3.5d blocking optimization for stencil computations on modern CPUs and GPUs
- in Proc. of the 2010 ACM/IEEE Int’l Conf. for High Performance Computing, Networking, Storage and Analysis, 2010
"... Abstract—Stencil computation sweeps over a spatial grid over multiple time steps to perform nearest-neighbor computations. The bandwidth-to-compute requirement for a large class of stencil kernels is very high, and their performance is bound by the available memory bandwidth. Since memory bandwidth ..."
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Cited by 36 (1 self)
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Abstract—Stencil computation sweeps over a spatial grid over multiple time steps to perform nearest-neighbor computations. The bandwidth-to-compute requirement for a large class of stencil kernels is very high, and their performance is bound by the available memory bandwidth. Since memory bandwidth grows slower than compute, the performance of stencil kernels will not scale with increasing compute density. We present a novel 3.5D-blocking algorithm that performs 2.5D-spatial and temporal blocking of the input grid into on-chip memory for both CPUs and GPUs. The resultant algorithm is amenable to both threadlevel and data-level parallelism, and scales near-linearly with the SIMD width and multiple-cores. Our performance numbers are faster or comparable to state-of-the-art-stencil implementations on CPUs and GPUs. Our implementation of 7-point-stencil is 1.5X-faster on CPUs, and 1.8X faster on GPUs for singleprecision floating point inputs than previously reported numbers. For Lattice Boltzmann methods, the corresponding speedup number on CPUs is 2.1X.
Efficient Computation of Sum-products on GPUs Through Software-Managed Cache
, 2008
"... We present a technique for designing memory-bound algorithms with high data reuse on Graphics Processing Units (GPUs) equipped with close-to-ALU software-managed memory. The approach is based on the efficient use of this memory through the implementation of a software-managed cache. We also present ..."
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Cited by 35 (1 self)
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We present a technique for designing memory-bound algorithms with high data reuse on Graphics Processing Units (GPUs) equipped with close-to-ALU software-managed memory. The approach is based on the efficient use of this memory through the implementation of a software-managed cache. We also present an analytical model for performance analysis of such algorithms. We apply this technique to the implementation of the GPU-based solver of the sum-product or marginalize a product of functions (MPF) problem, which arises in a wide variety of real-life applications in artificial intelligence, statistics, image processing, and digital communications. Our motivation to accelerate MPF originated in the context of the analysis of genetic diseases, which in some cases requires years to complete on modern CPUs. Computing MPF is similar to computing the chain matrix product of multi-dimensional matrices, but is more difficult due to a complex data-dependent access pattern, high data reuse, and a low computeto-memory access ratio. Our GPU-based MPF solver achieves up to 2700-fold speedup on random data and 270-fold on real-life genetic analysis datasets on GeForce 8800GTX GPU from NVIDIA over the optimized CPU version on an Intel 2.4 GHz Core 2 with a 4 MB L2 cache.
