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Register a new userDesign and Optimization of OpenFOAM-based CFD Applications for Hybrid and Heterogeneous HPC Platforms
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Added by
Alexey Lastovetsky
Publication date
2015
fields
Informatics Engineering
and research's language is
English
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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.
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Traditional heterogeneous parallel algorithms, designed for heterogeneous clusters of workstations, are based on the assumption that the absolute speed of the processors does not depend on the size of the computational task. This assumption proved inaccurate for modern and perspective highly heterogeneous HPC platforms. New class of algorithms based on the functional performance model (FPM), representing the speed of the processor by a function of problem size, has been recently proposed. These algorithms cannot be however employed in self-adaptable applications because of very high cost of construction of the functional performance model. The paper presents a new class of parallel algorithms for highly heterogeneous HPC platforms. Like traditional FPM-based algorithms, these algorithms assume that the speed of the processors is characterized by speed functions rather than speed constants. Unlike the traditional algorithms, they do not assume the speed functions to be given. Instead, they estimate the speed functions of the processors for different problem sizes during their execution. These algorithms do not construct the full speed function for each processor but rather build and use their partial estimates sufficient for optimal distribution of computations with a given accuracy. The low execution cost of distribution of computations between heterogeneous processors in these algorithms make them suitable for employment in self-adaptable applications. Experiments with parallel matrix multiplication applications based on this approach are performed on local and global heterogeneous computational clusters. The results show that the execution time of optimal matrix distribution between processors is significantly less, by orders of magnitude, than the total execution time of the optimized application.
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.
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).
High-Performance Big Data Analytics (HPDA) applications are characterized by huge volumes of distributed and heterogeneous data that require efficient computation for knowledge extraction and decision making. Designers are moving towards a tight integration of computing systems combining HPC, Cloud, and IoT solutions with artificial intelligence (AI). Matching the application and data requirements with the characteristics of the underlying hardware is a key element to improve the predictions thanks to high performance and better use of resources. We present EVEREST, a novel H2020 project started on October 1st, 2020 that aims at developing a holistic environment for the co-design of HPDA applications on heterogeneous, distributed, and secure platforms. EVEREST focuses on programmability issues through a data-driven design approach, the use of hardware-accelerated AI, and an efficient runtime monitoring with virtualization support. In the different stages, EVEREST combines state-of-the-art programming models, emerging communication standards, and novel domain-specific extensions. We describe the EVEREST approach and the use cases that drive our research.
In this paper we would like to share our experience for transforming a parallel code for a Computational Fluid Dynamics (CFD) problem into a parallel version for the RedisDG workflow engine. This system is able to capture heterogeneous and highly dynamic environments, thanks to opportunistic scheduling strategies. We show how to move to the field of HPC as a Service in order to use heterogeneous platforms. We mainly explain, through the CFD use case, how to transform the parallel code and we exhibit challenges to unfold the task graph dynamically in order to improve the overall performance (in a broad sense) of the workflow engine. We discuss in particular of the impact on the workflow engine of such dynamic feature. This paper states that new models for High Performance Computing are possible, under the condition we revisit our mind in the direction of the potential of new paradigms such as cloud, edge computing.
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