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Register a new userMulti-GPU Performance Optimization of a CFD Code using OpenACC on Different Platforms
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Added by
Weicheng Xue
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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This paper investigates the multi-GPU performance of a 3D buoyancy driven cavity solver using MPI and OpenACC directives on different platforms. The paper shows that decomposing the total problem in different dimensions affects the strong scaling performance significantly for the GPU. Without proper performance optimizations, it is shown that 1D domain decomposition scales poorly on multiple GPUs due to the noncontiguous memory access. The performance using whatever decompositions can be benefited from a series of performance optimizations in the paper. Since the buoyancy driven cavity code is latency-bounded on the clusters examined, a series of optimizations both agnostic and tailored to the platforms are designed to reduce the latency cost and improve memory throughput between hosts and devices efficiently. First, the parallel message packing/unpacking strategy developed for noncontiguous data movement between hosts and devices improves the overall performance by about a factor of 2. Second, transferring different data based on the stencil sizes for different variables further reduces the communication overhead. These two optimizations are general enough to be beneficial to stencil computations having ghost changes on all of the clusters tested. Third, GPUDirect is used to improve the communication on clusters which have the hardware and software support for direct communication between GPUs without staging CPUs memory. Finally, overlapping the communication and computations is shown to be not efficient on multi-GPUs if only using MPI or MPI+OpenACC. Although we believe our implementation has revealed enough overlap, the actual running does not utilize the overlap well due to a lack of asynchronous progression.
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This paper is focused on improving multi-GPU performance of a research CFD code on structured grids. MPI and OpenACC directives are used to scale the code up to 16 GPUs. This paper shows that using 16 P100 GPUs and 16 V100 GPUs can be 30$times$ and 70$times$ faster than 16 Xeon CPU E5-2680v4 cores for three different test cases, respectively. A series of performance issues related to the scaling for the multi-block CFD code are addressed by applying various optimizations. Performance optimizations such as the pack/unpack message method, removing temporary arrays as arguments to procedure calls, allocating global memory for limiters and connected boundary data, reordering non-blocking MPI I_send/I_recv and Wait calls, reducing unnecessary implicit derived type member data movement between the host and the device and the use of GPUDirect can improve the compute utilization, memory throughput, and asynchronous progression in the multi-block CFD code using modern programming features.
Much of the current focus in high-performance computing is on multi-threading, multi-computing, and graphics processing unit (GPU) computing. However, vectorization and non-parallel optimization techniques, which can often be employed additionally, are less frequently discussed. In this paper, we present an analysis of several optimizations done on both central processing unit (CPU) and GPU implementations of a particular computationally intensive Metropolis Monte Carlo algorithm. Explicit vectorization on the CPU and the equivalent, explicit memory coalescing, on the GPU are found to be critical to achieving good performance of this algorithm in both environments. The fully-optimized CPU version achieves a 9x to 12x speedup over the original CPU version, in addition to speedup from multi-threading. This is 2x faster than the fully-optimized GPU version.
Performance and energy are the two most important objectives for optimisation on modern parallel platforms. Latest research demonstrated the importance of workload distribution as a decision variable in the bi-objective optimisation for performance and energy on homogeneous multicore clusters. We show in this work that bi-objective optimisation for performance and energy on heterogeneous processors results in a large number of Pareto-optimal optimal solutions (workload distributions) even in the simple case of linear performance and energy profiles. We then study performance and energy profiles of real-life data-parallel applications and find that their shapes are non-linear, complex and non-smooth. We, therefore, propose an efficient and exact global optimisation algorithm, which takes as an input most general discrete performance and dynamic energy profiles of the heterogeneous processors and solves the bi-objective optimisation problem. The algorithm is also used as a building block to solve the bi-objective optimisation problem for performance and total energy. We also propose a novel methodology to build discrete dynamic energy profiles of individual computing devices, which are input to the algorithm. The methodology is based purely on system-level measurements and addresses the fundamental challenge of accurate component-level energy modelling of a hybrid data-parallel application running on a heterogeneous platform integrating CPUs and accelerators. We experimentally validate the proposed method using two data-parallel applications, matrix multiplication and 2D fast Fourier transform (2D-FFT).
Hardware-aware design and optimization is crucial in exploiting emerging architectures for PDE-based computational fluid dynamics applications. In this work, we study optimizations aimed at acceleration of OpenFOAM-based applications on emerging hybrid heterogeneous platforms. OpenFOAM uses MPI to provide parallel multi-processor functionality, which scales well on homogeneous systems but does not fully utilize the potential per-node performance on hybrid heterogeneous platforms. In our study, we use two OpenFOAM applications, icoFoam and laplacianFoam, both based on Krylov iterative methods. We propose a number of optimizations of the dominant kernel of the Krylov solver, aimed at acceleration of the overall execution of the applications on modern GPU-accelerated heterogeneous platforms. Experimental results show that the proposed hybrid implementation significantly outperforms the state-of-the-art implementation.
We present new results on the strong parallel scaling for the OpenACC-accelerated implementation of the high-order spectral element fluid dynamics solver Nek5000. The test case considered consists of a direct numerical simulation of fully-developed turbulent flow in a straight pipe, at two different Reynolds numbers $Re_tau=360$ and $Re_tau=550$, based on friction velocity and pipe radius. The strong scaling is tested on several GPU-enabled HPC systems, including the Swiss Piz Daint system, TACCs Longhorn, Julichs JUWELS Booster, and Berzelius in Sweden. The performance results show that speed-up between 3-5 can be achieved using the GPU accelerated version compared with the CPU version on these different systems. The run-time for 20 timesteps reduces from 43.5 to 13.2 seconds with increasing the number of GPUs from 64 to 512 for $Re_tau=550$ case on JUWELS Booster system. This illustrates the GPU accelerated version the potential for high throughput. At the same time, the strong scaling limit is significantly larger for GPUs, at about $2000-5000$ elements per rank; compared to about $50-100$ for a CPU-rank.
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