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Performance Modeling and Automatic Ghost Zone Optimization for Iterative Stencil Loops on GPUs
- ICS ’09: Proceedings of the 23rd international conference on Supercomputing (2009
"... Iterative stencil loops (ISLs) are used in many applications and tiling is a well-known technique to localize their computation. When ISLs are tiled across a parallel architecture, there are usually halo regions that need to be updated and exchanged among different processing elements (PEs). In addi ..."
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Cited by 42 (9 self)
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Iterative stencil loops (ISLs) are used in many applications and tiling is a well-known technique to localize their computation. When ISLs are tiled across a parallel architecture, there are usually halo regions that need to be updated and exchanged among different processing elements (PEs). In addition, synchronization is often used to signal the completion of halo exchanges. Both communication and synchronization may incur significant overhead on parallel architectures with shared memory. This is especially true in the case of graphics processors (GPUs), which do not preserve the state of the per-core L1 storage across global synchronizations. To reduce these overheads, ghost zones can be created to replicate stencil operations, reducing communication and synchronization costs at the expense of redundantly computing some values on multiple PEs. However, the selection of the optimal ghost zone size depends on the characteristics of both the architecture and the application, and it has only been studied for message-passing systems in a grid environment. To automate this process on shared memory systems, we establish a performance model using NVIDIA’s Tesla architecture as a case study and propose a framework that uses the performance model to automatically select the ghost zone size that performs best and generate appropriate code. The modeling is validated by four diverse ISL applications, for which the predicted ghost zone configurations are able to achieve a speedup no less than 98 % of the optimal speedup. 1.
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.
A multilevel parallelization framework for high-order stencil computations,” in Euro-Par
, 2009
"... Abstract. Stencil based computation on structured grids is a common kernel to broad scientific applications. The order of stencils increases with the required precision, and it is a challenge to optimize such high-order stencils on multicore architectures. Here, we propose a multilevel parallelizati ..."
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Cited by 11 (1 self)
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Abstract. Stencil based computation on structured grids is a common kernel to broad scientific applications. The order of stencils increases with the required precision, and it is a challenge to optimize such high-order stencils on multicore architectures. Here, we propose a multilevel parallelization framework that combines: (1) inter-node parallelism by spatial decomposition; (2) intra-chip parallelism through multithreading; and (3) data-level parallelism via singleinstruction multiple-data (SIMD) techniques. The framework is applied to a 6 th order stencil based seismic wave propagation code on a suite of multicore architectures. Strong-scaling scalability tests exhibit superlinear speedup due to increasing cache capacity on Intel Harpertown and AMD Barcelona based clusters, whereas weak-scaling parallel efficiency is 0.92 on 65,536 BlueGene/P processors. Multithreading+SIMD optimizations achieve 7.85-fold speedup on a dual quad-core Intel Clovertown, and the data-level parallel efficiency is found to depend on the stencil order.
Optimization Principles for Collective Neighborhood Communications
"... Abstract — Many scientific applications operate in a bulksynchronous mode of iterative communication and computation steps. Even though the communication steps happen at the same logical time, important patterns such as stencil computations cannot be expressed as collective communications in MPI. We ..."
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Cited by 8 (3 self)
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Abstract — Many scientific applications operate in a bulksynchronous mode of iterative communication and computation steps. Even though the communication steps happen at the same logical time, important patterns such as stencil computations cannot be expressed as collective communications in MPI. We demonstrate how neighborhood collective operations allow to specify arbitrary collective communication relations during runtime and enable optimizations similar to traditional collective calls. We show a number of optimization opportunities and algorithms for different communication scenarios. We also show how users can assert constraints that provide additional optimization opportunities in a portable way. We demonstrate the utility of all described optimizations in a highly optimized implementation of neighborhood collective operations. Our communication and protocol optimizations result in a performance improvement of up to a factor of two for small stencil communications. We found that, for some patterns, our optimization heuristics automatically generate communication schedules that are comparable to handtuned collectives. With those optimizations in place, we are able to accelerate arbitrary collective communication patterns, such as regular and irregular stencils with optimization methods for collective communications. We expect that our methods will influence the design of future MPI libraries and provide a significant performance benefit on large-scale systems. I.
A Performance Study for Iterative Stencil Loops on GPUs with Ghost Zone Optimizations
"... Abstract Iterative stencil loops (ISLs) are used in many applications and tiling is a well-known technique to localize their computation. When ISLs are tiled across a parallel architecture, there are usually halo regions that need to be updated and exchanged among different processing elements (PEs) ..."
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Cited by 8 (0 self)
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Abstract Iterative stencil loops (ISLs) are used in many applications and tiling is a well-known technique to localize their computation. When ISLs are tiled across a parallel architecture, there are usually halo regions that need to be updated and exchanged among different processing elements (PEs). In addition, synchronization is often used to signal the completion of halo exchanges. Both communication and synchronization may incur significant overhead on parallel architectures with shared memory. This is especially true in the case of graphics processors (GPUs), which do not preserve the state of the per-core L1 storage across global synchronizations. To reduce these overheads, ghost zones can be created to replicate stencil operations, reducing communication and synchronization costs at the expense of redundantly computing some values on multiple PEs. However, the selection of the optimal ghost zone size depends on the characteristics of both the architecture and the application, and it has only been studied for message-passing systems in distributed environments. To automate this process on shared memory systems, we establish a performance model using NVIDIA’s Tesla architecture as a case study and propose a framework that uses the performance model to automatically select the ghost zone size that performs best and generate appropriate code. The modeling is validated by four diverse ISL applications, for which the predicted ghost zone configurations are able to achieve a speedup no less than 95 % of the optimal speedup.
1 Cache Accurate Time Skewing in Iterative Stencil Computations
"... Abstract—We present a time skewing algorithm that breaks the memory wall for certain iterative stencil computations. A stencil computation, even with constant weights, is a completely memory-bound algorithm. For example, for a large 3D domain of 500 3 doubles and 100 iterations on a quad-core Xeon X ..."
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Cited by 7 (1 self)
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Abstract—We present a time skewing algorithm that breaks the memory wall for certain iterative stencil computations. A stencil computation, even with constant weights, is a completely memory-bound algorithm. For example, for a large 3D domain of 500 3 doubles and 100 iterations on a quad-core Xeon X5482 3.2GHz system, a hand-vectorized and parallelized naive 7-point stencil implementation achieves only 1.4 GFLOPS because the system memory bandwidth limits the performance. Although many efforts have been undertaken to improve the performance of such nested loops, for large data sets they still lag far behind synthetic benchmark performance. The state-of-art automatic locality optimizer PluTo [1] achieves 3.7 GFLOPS for the above stencil, whereas a parallel benchmark executing the inner stencil computation directly on registers performs at 25.1 GFLOPS. In comparison, our algorithm achieves 13.0 GFLOPS (52 % of the stencil peak benchmark). We present results for 2D and 3D domains in double precision including problems with gigabyte large data sets. The results are compared against hand-optimized naive schemes, PluTo, the stencil peak benchmark and results from literature. For constant stencils of slope one we break the dependence on the low system bandwidth and achieve at least 50 % of the stencil peak, thus performing within a factor two of an ideal system with infinite bandwidth (the benchmark runs on registers without memory access). For large stencils and banded matrices the additional data transfers let the limitations of the system bandwidth come into play again, however, our algorithm still gains a large improvement over the other schemes. Keywords-memory wall, memory bound, stencil, banded matrix, time skewing, temporal blocking, wavefront I.
Integrative Scientific
"... Abstract—Temporal blocking in iterative stencil computations allows to surpass the performance of peak system bandwidth that holds for a single stencil computation. However, the effectiveness of temporal blocking depends strongly on the tiling scheme, which must account for the contradicting goals o ..."
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Abstract—Temporal blocking in iterative stencil computations allows to surpass the performance of peak system bandwidth that holds for a single stencil computation. However, the effectiveness of temporal blocking depends strongly on the tiling scheme, which must account for the contradicting goals of spatio-temporal data locality, regular memory access patterns, parallelization into many independent tasks, and datato-core affinity for NUMA-aware data distribution. Despite the prevalence of cache coherent non-uniform memory access (ccNUMA) in todays many-core systems, this latter aspect has been largely ignored in the development of temporal blocking algorithms. Building upon previous cache-aware [1] and cacheoblivious [2] schemes, this paper develops their NUMA-aware variants, explaining why the incorporation of data-to-core affinity as an equally important goal necessitates also new tiling and parallelization strategies. Results are presented on an 8 socket dual-core and a 4 socket oct-core systems and compared against an optimized naive scheme, various peak performance characteristics, and related schemes from literature. Keywords-stencil computation; temporal blocking; NUMAaware data distribution; affinity; cache-oblivious; cache-aware; parallelism and locality I.
Automatic Data Movement and Computation Mapping for Multi-level Parallel Architectures with Explicitly Managed Memories
, 2008
"... Several parallel architectures such as GPUs and the Cell processor have fast explicitly managed on-chip memories, in addition to slow off-chip memory. They also have very high computational power with multiple levels of parallelism. A significant challenge in programming these architectures is to ef ..."
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Several parallel architectures such as GPUs and the Cell processor have fast explicitly managed on-chip memories, in addition to slow off-chip memory. They also have very high computational power with multiple levels of parallelism. A significant challenge in programming these architectures is to effectively exploit the parallelism available in the architecture and manage the fast memories to maximize performance. In this paper we develop an approach to effective automatic data management for on-chip memories, including creation of buffers in on-chip (local) memories for holding portions of data accessed in a computational block, automatic determination of array access functions of local buffer references, and generation of code that moves data between slow off-chip memory and fast local memories. We also address the problem of mapping computation in regular programs to multi-level parallel architectures using a multi-level tiling approach, and study the impact of on-chip memory availability on the selection of tile sizes at various levels. Experimental results on a GPU demonstrate the effectiveness of the proposed approach.
BREAKING THE MEMORY WALL FOR HIGHLY MULTI-THREADED CORES
, 2010
"... Emerging applications such as scientific computation, media processing, machine learning and data mining are commonly computation- and data- intensive [1], and they usually exhibit abundant parallelism. These applications motivate the design of throughputoriented many- and multi-core architectures t ..."
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Emerging applications such as scientific computation, media processing, machine learning and data mining are commonly computation- and data- intensive [1], and they usually exhibit abundant parallelism. These applications motivate the design of throughputoriented many- and multi-core architectures that employ many small and simple cores and scale up to large thread counts. The cores themselves are also typically multi-threaded. Such organizations are sometimes referred to as Chip Multi-Threading (CMT). However, with tens or hundreds of concurrent threads running on a single chip, throughput is not limited by the computation resources, but by the overhead in data movement. In fact, adding more cores or threads is likely to harm performance due to contention in the memory system. It is therefore important to improve data management to either reduce or tolerate data movement and associated latencies. Several techniques have been proposed for conventional multi-core organizations. However, the large thread count per core in CMT poses new challenges: much lower cache capacity per thread, nonuniform overhead in thread communication, inability of aggressive out-of-order execution to hide latency, and additional memory latency caused by SIMD constraints. To address the above challenges, we propose several techniques. Some reduce contention in either private caches or shared caches; some identify the right amount of computation to replicate to reduce communication, and some reconfigure SIMD architectures at runtime. Our objective is to allow CMTs 4 to achieve scalable performance along with the thread count, despite limited energy budget for their memory system. 5
