理化学研究所 計算科学研究センター

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第133回 第一部

第133回 第一部
日時: 2018年3月6日(火)、14:30 – 16:30(第一部開始から第二部終了まで)
場所: AICS 6階講堂

講演題目:Efficient Gather-Scatter Operations in NEK5000 using PGAS
講演者:Niclas Jansson (KTH Stockholm)
※発表・スライド共に英語

講演要旨: 詳細を見る

Gather-scatter operations are one of the key communication kernels used in the computation fluid dynamics (CFD) application Nek5000 for fetching data dependencies (gather), and spreading results to other nodes (scatter). The current implementation used in Nek5000 is the Gather-Scatter library, GS, which utilises different communication strategies: nearest neighbour exchange, message aggregation, and collectives, to efficiently perform communication on a given platform. GS is implemented using non-blocking, two-sided message passing via MPI and the library has proven to scale well to hundreds of thousands of cores. However, the necessity to match sending and receiving messages in the two-sided communication abstraction can quickly increase latency and synchronisation costs for very fine grained parallelism, in particular for the unstructured communication patterns created by unstructured CFD problems. ExaGS is are-implementation of the Gather-Scatter library, with the intent to use the best available programming model for a given architecture. We present our current implementation of ExaGS, based on the one-sided programming model provided by the Partitioned Global Address Space (PGAS) abstraction, using Unified Parallel C (UPC). Using a lock-free design with efficient point-to-point synchronisation primitives, ExaGS is able to reduce communication latency compared to the current two-sided MPI implementation. A detailed description of the library and implemented algorithms are given, together with a performance study of ExaGS when used together with Nek5000, and its co-design benchmarking application Nekbone.