On the performance of two-sided MPI, MPI-3 RMA and SHMEM in a Lagrangian particle cluster algorithm
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arXiv
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| Format: | Preprint |
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2024
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| _version_ | 1866910948916199424 |
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| author | Frey, Matthias Shanks, Douglas Böing, Steven Apóstolo, Rui F. G. |
| author_facet | Frey, Matthias Shanks, Douglas Böing, Steven Apóstolo, Rui F. G. |
| contents | In this paper, we compare the parallel performance of three distributed-memory communication models for a cluster algorithm based on a nearest neighbour search algorithm for N-body simulations. The nearest neighbour is defined by the Euclidean distance in three-dimensional space. The resulting directed nearest neighbour graphs that are used to define the clusters are pruned in an iterative procedure where we use either point-to-point message passing interface (MPI), MPI-3 remote memory access (RMA), or SHMEM communication. The original algorithm has been developed and implemented as part of the elliptical parcel-in-cell (EPIC) method targeting geophysical fluid flows. The parallel scalability of the algorithm is discussed by means of an artificial and a standard fluid dynamics test case. Performance measurements were carried out on three different computing systems with InfiniBand FDR, Hewlett Packard Enterprise (HPE) Slingshot 10 or HPE Slingshot 200 interconnect. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2408_15348 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | On the performance of two-sided MPI, MPI-3 RMA and SHMEM in a Lagrangian particle cluster algorithm Frey, Matthias Shanks, Douglas Böing, Steven Apóstolo, Rui F. G. Distributed, Parallel, and Cluster Computing In this paper, we compare the parallel performance of three distributed-memory communication models for a cluster algorithm based on a nearest neighbour search algorithm for N-body simulations. The nearest neighbour is defined by the Euclidean distance in three-dimensional space. The resulting directed nearest neighbour graphs that are used to define the clusters are pruned in an iterative procedure where we use either point-to-point message passing interface (MPI), MPI-3 remote memory access (RMA), or SHMEM communication. The original algorithm has been developed and implemented as part of the elliptical parcel-in-cell (EPIC) method targeting geophysical fluid flows. The parallel scalability of the algorithm is discussed by means of an artificial and a standard fluid dynamics test case. Performance measurements were carried out on three different computing systems with InfiniBand FDR, Hewlett Packard Enterprise (HPE) Slingshot 10 or HPE Slingshot 200 interconnect. |
| title | On the performance of two-sided MPI, MPI-3 RMA and SHMEM in a Lagrangian particle cluster algorithm |
| topic | Distributed, Parallel, and Cluster Computing |
| url | https://arxiv.org/abs/2408.15348 |