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Register a new userTemporal blocking of finite-difference stencil operators with sparse off-the-grid sources
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Added by
George Bisbas
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Stencil kernels dominate a range of scientific applications, including seismic and medical imaging, image processing, and neural networks. Temporal blocking is a performance optimization that aims to reduce the required memory bandwidth of stencil computations by re-using data from the cache for multiple time steps. It has already been shown to be beneficial for this class of algorithms. However, applying temporal blocking to practical applications stencils remains challenging. These computations often consist of sparsely located operators not aligned with the computational grid (off-the-grid). Our work is motivated by modeling problems in which source injections result in wavefields that must then be measured at receivers by interpolation from the grided wavefield. The resulting data dependencies make the adoption of temporal blocking much more challenging. We propose a methodology to inspect these data dependencies and reorder the computation, leading to performance gains in stencil codes where temporal blocking has not been applicable. We implement this novel scheme in the Devito domain-specific compiler toolchain. Devito implements a domain-specific language embedded in Python to generate optimized partial differential equation solvers using the finite-difference method from high-level symbolic problem definitions. We evaluate our scheme using isotropic acoustic, anisotropic acoustic, and isotropic elastic wave propagators of industrial significance. After auto-tuning, performance evaluation shows that this enables substantial performance improvement through temporal blocking over highly-optimized vectorized spatially-blocked code of up to 1.6x.
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We propose two novel techniques for overcoming load-imbalance encountered when implementing so-called look-ahead mechanisms in relevant dense matrix factorizations for the solution of linear systems. Both techniques target the scenario where two thread teams are created/activated during the factorization, with each team in charge of performing an independent task/branch of execution. The first technique promotes worker sharing (WS) between the two tasks, allowing the threads of the task that completes first to be reallocated for use by the costlier task. The second technique allows a fast task to alert the slower task of completion, enforcing the early termination (ET) of the second task, and a smooth transition of the factorization procedure into the next iteration. The two mechanisms are instantiated via a new malleable thread-level implementation of the Basic Linear Algebra Subprograms (BLAS), and their benefits are illustrated via an implementation of the LU factorization with partial pivoting enhanced with look-ahead. Concretely, our experimental results on a six core Intel-Xeon processor show the benefits of combining WS+ET, reporting competitive performance in comparison with a task-parallel runtime-based solution.
We present FPDetect, a low overhead approach for detecting logical errors and soft errors affecting stencil computations without generating false positives. We develop an offline analysis that tightly estimates the number of floating-point bits preserved across stencil applications. This estimate rigorously bounds the values expected in the data space of the computation. Violations of this bound can be attributed with certainty to errors. FPDetect helps synthesize error detectors customized for user-specified levels of accuracy and coverage. FPDetect also enables overhead reduction techniques based on deploying these detectors coarsely in space and time. Experimental evaluations demonstrate the practicality of our approach.
Empirical Dynamic Modeling (EDM) is a state-of-the-art non-linear time-series analysis framework. Despite its wide applicability, EDM was not scalable to large datasets due to its expensive computational cost. To overcome this obstacle, researchers have attempted and succeeded in accelerating EDM from both algorithmic and implementational aspects. In previous work, we developed a massively parallel implementation of EDM targeting HPC systems (mpEDM). However, mpEDM maintains different backends for different architectures. This design becomes a burden in the increasingly diversifying HPC systems, when porting to new hardware. In this paper, we design and develop a performance-portable implementation of EDM based on the Kokkos performance portability framework (kEDM), which runs on both CPUs and GPUs while based on a single codebase. Furthermore, we optimize individual kernels specifically for EDM computation, and use real-world datasets to demonstrate up to $5.5times$ speedup compared to mpEDM in convergent cross mapping computation.
The growth of data to be processed in the Oil & Gas industry matches the requirements imposed by evolving algorithms based on stencil computations, such as Full Waveform Inversion and Reverse Time Migration. Graphical processing units (GPUs) are an attractive architectural target for stencil computations because of its high degree of data parallelism. However, the rapid architectural and technological progression makes it difficult for even the most proficient programmers to remain up-to-date with the technological advances at a micro-architectural level. In this work, we present an extension for an open source compiler designed to produce highly optimized finite difference kernels for use in inversion methods named Devito. We embed it with the Oxford Parallel Domain Specific Language (OP-DSL) in order to enable automatic code generation for GPU architectures from a high-level representation. We aim to enable users coding in a symbolic representation level to effortlessly get their implementations leveraged by the processing capacities of GPU architectures. The implemented backend is evaluated on a NVIDIA GTX Titan Z, and on a NVIDIA Tesla V100 in terms of operational intensity through the roof-line model for varying space-order discretization levels of 3D acoustic isotropic wave propagation stencil kernels with and without symbolic optimizations. It achieves approximately 63% of V100s peak performance and 24% of Titan Zs peak performance for stencil kernels over grids with 256 points. Our study reveals that improving memory usage should be the most efficient strategy for leveraging the performance of the implemented solution on the evaluated architectures.
A parallel and nested version of a frequency filtering preconditioner is proposed for linear systems corresponding to diffusion equation on a structured grid. The proposed preconditioner is found to be robust with respect to jumps in the diffusion coefficients. The storage requirement for the preconditioner is O(N),where N is number of rows of matrix, hence, a fairly large problem of size more than 42 million unknowns has been solved on a quad core machine with 64GB RAM. The parallelism is achieved using twisted factorization and SIMD operations. The preconditioner achieves a speedup of 3.3 times on a quad core processor clocked at 4.2 GHz, and compared to a well known algebraic multigrid method, it is significantly faster in both setup and solve times for diffusion equations with jumps.
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