Abstract
Initial optimization strategies and results on MFDn, a large-scale nuclear physics application code, running on a single KNL node are presented. This code consists of the construction of a very large sparse real symmetric matrix and computing a few lowest eigenvalues and eigenvectors of this matrix through iterative methods. Challenges addressed include effectively utilizing MCDRAM with representative input data for production runs on 5,000 KNL nodes that require over 80 GB of memory per node, using OpenMP 4 to parallelize functions in the construction phase of the sparse matrices, and vectorizing those functions in spite of while-loops, conditionals, and lookup tables with indirect indexing. Moreover, hybrid MPI/OpenMP is employed not only to maximize the total problem size that can be solved per node, but also to eventually minimize parallel scaling overhead through the best scaling combination of MPI ranks per node with OpenMP threads. We describe a vectorized version of a popcount operation to avoid serialization on intrinsic popcnt which only operates on scalar registers. Additionally we leverage SSE 4.2 string comparison instructions to determine nonzero matrix elements. By utilizing MCDRAM, we achieve excellent Sparse Matrix–Matrix multiplication performance; in particular, using blocks of 8 vectors lead to a speedup of 6.4\(\times \) on KNL and 2.9\(\times \) on Haswell compared to the performance of repeated SpMV’s. This optimization was essential in achieving a 1.6\(\times \) improvement on KNL over Haswell.
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Notes
- 1.
The optimal choice of this number is certainly architecture dependent.
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Acknowledgments
This work is supported in part by U.S. DOE Grant Number DESC0008485 (SciDAC/NUCLEI). This research used resources of the National Energy Research Scientific Computing Center (NERSC), a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
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Cook, B. et al. (2016). High Performance Optimizations for Nuclear Physics Code MFDn on KNL. In: Taufer, M., Mohr, B., Kunkel, J. (eds) High Performance Computing. ISC High Performance 2016. Lecture Notes in Computer Science(), vol 9945. Springer, Cham. https://doi.org/10.1007/978-3-319-46079-6_26
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DOI: https://doi.org/10.1007/978-3-319-46079-6_26
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