Integration of High-Performance Task-Based In Situ for Molecular Dynamics on Exascale Computers

Estelle Dirand 1, 2
2 DATAMOVE - Data Aware Large Scale Computing
Inria Grenoble - Rhône-Alpes, LIG - Laboratoire d'Informatique de Grenoble
Abstract : The exascale era will widen the gap between data generation rate and the time to manage their output and analysis in a post-processing way, dramatically increasing the end-to-end time to scientific discovery and calling for a shift toward new data processing methods. The in situ paradigm proposes to analyze data while still resident in the supercomputer memory to reduce the need for data storage. Several techniques already exist, by executing simulation and analytics on the same nodes (in situ), by using dedicated nodes (in transit) or by combining the two approaches (hybrid). Most of the in situ techniques target simulations that are not able to fully benefit from the ever growing number of cores per processor but they are not designed for the emerging manycore processors.Task-based programming models on the other side are expected to become a standard for these architectures but few task-based in situ techniques have been developed so far. This thesis proposes to study the design and integration of a novel task-based in situ framework inside a task-based molecular dynamics code designed for exascale supercomputers. We take benefit from the composability properties of the task-based programming model to implement the TINS hybrid framework. Analytics workflows are expressed as graphs of tasks that can in turn generate children tasks to be executed in transit or interleaved with simulation tasks in situ. The in situ execution is performed thanks to an innovative dynamic helper core strategy that uses the work stealing concept to finely interleave simulation and analytics tasks inside a compute node with a low overhead on the simulation execution time.TINS uses the Intel® TBB work stealing scheduler and is integrated into ExaStamp, a task-based molecular dynamics code. Various experiments have shown that TINS is up to 40% faster than state-of-the-art in situ libraries. Molecular dynamics simulations of up to 2 billions particles on up to 14,336 cores have shown that TINS is able to execute complex analytics workflows at a high frequency with an overhead smaller than 10%.
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Estelle Dirand. Integration of High-Performance Task-Based In Situ for Molecular Dynamics on Exascale Computers. Distributed, Parallel, and Cluster Computing [cs.DC]. Université Grenoble Alpes, 2018. English. ⟨NNT : 2018GREAM065⟩. ⟨tel-01949170v2⟩



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