16,111 research outputs found
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
GROMACS is a widely used package for biomolecular simulation, and over the
last two decades it has evolved from small-scale efficiency to advanced
heterogeneous acceleration and multi-level parallelism targeting some of the
largest supercomputers in the world. Here, we describe some of the ways we have
been able to realize this through the use of parallelization on all levels,
combined with a constant focus on absolute performance. Release 4.6 of GROMACS
uses SIMD acceleration on a wide range of architectures, GPU offloading
acceleration, and both OpenMP and MPI parallelism within and between nodes,
respectively. The recent work on acceleration made it necessary to revisit the
fundamental algorithms of molecular simulation, including the concept of
neighborsearching, and we discuss the present and future challenges we see for
exascale simulation - in particular a very fine-grained task parallelism. We
also discuss the software management, code peer review and continuous
integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin
Scaling Monte Carlo Tree Search on Intel Xeon Phi
Many algorithms have been parallelized successfully on the Intel Xeon Phi
coprocessor, especially those with regular, balanced, and predictable data
access patterns and instruction flows. Irregular and unbalanced algorithms are
harder to parallelize efficiently. They are, for instance, present in
artificial intelligence search algorithms such as Monte Carlo Tree Search
(MCTS). In this paper we study the scaling behavior of MCTS, on a highly
optimized real-world application, on real hardware. The Intel Xeon Phi allows
shared memory scaling studies up to 61 cores and 244 hardware threads. We
compare work-stealing (Cilk Plus and TBB) and work-sharing (FIFO scheduling)
approaches. Interestingly, we find that a straightforward thread pool with a
work-sharing FIFO queue shows the best performance. A crucial element for this
high performance is the controlling of the grain size, an approach that we call
Grain Size Controlled Parallel MCTS. Our subsequent comparing with the Xeon
CPUs shows an even more comprehensible distinction in performance between
different threading libraries. We achieve, to the best of our knowledge, the
fastest implementation of a parallel MCTS on the 61 core Intel Xeon Phi using a
real application (47 relative to a sequential run).Comment: 8 pages, 9 figure
An investigation of the performance portability of OpenCL
This paper reports on the development of an MPI/OpenCL implementation of LU, an application-level benchmark from the NAS Parallel Benchmark Suite. An account of the design decisions addressed during the development of this code is presented, demonstrating the importance of memory arrangement and work-item/work-group distribution strategies when applications are deployed on different device types. The resulting platform-agnostic, single source application is benchmarked on a number of different architectures, and is shown to be 1.3–1.5× slower than native FORTRAN 77 or CUDA implementations on a single node and 1.3–3.1× slower on multiple nodes. We also explore the potential performance gains of OpenCL’s device fissioning capability, demonstrating up to a 3× speed-up over our original OpenCL implementation
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