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使用分布式共享内存中的 HDF5 文件进行高性能计算应用的并行计算指导。

Parallel computational steering for HPC applications using HDF5 files in distributed shared memory.

机构信息

CSCS Swiss National Supercomputing Centre, Galleria 2, Via Cantonale, Manno 6928, Switzerland.

出版信息

IEEE Trans Vis Comput Graph. 2012 Jun;18(6):852-64. doi: 10.1109/TVCG.2012.63.


DOI:10.1109/TVCG.2012.63
PMID:22350196
Abstract

Interfacing a GUI driven visualization/analysis package to an HPC application enables a supercomputer to be used as an interactive instrument. We achieve this by replacing the IO layer in the HDF5 library with a custom driver which transfers data in parallel between simulation and analysis. Our implementation using ParaView as the interface, allows a flexible combination of parallel simulation, concurrent parallel analysis, and GUI client, either on the same or separate machines. Each MPI job may use different core counts or hardware configurations, allowing fine tuning of the amount of resources dedicated to each part of the workload. By making use of a distributed shared memory file, one may read data from the simulation, modify it using ParaView pipelines, write it back, to be reused by the simulation (or vice versa). This allows not only simple parameter changes, but complete remeshing of grids, or operations involving regeneration of field values over the entire domain. To avoid the problem of manually customizing the GUI for each application that is to be steered, we make use of XML templates that describe outputs from the simulation (and inputs back to it) to automatically generate GUI controls for manipulation of the simulation.

摘要

将图形用户界面 (GUI) 驱动的可视化/分析包与高性能计算 (HPC) 应用程序接口,可以使超级计算机成为交互式仪器。我们通过用自定义驱动程序替换 HDF5 库中的 I/O 层来实现这一点,该驱动程序在模拟和分析之间并行传输数据。我们使用 ParaView 作为接口的实现,允许在同一台或不同的机器上灵活组合并行模拟、并发并行分析和 GUI 客户端。每个 MPI 作业可以使用不同的核心数或硬件配置,从而可以针对工作负载的每个部分精细调整专用资源的数量。通过使用分布式共享内存文件,可以从模拟中读取数据,使用 ParaView 管道对其进行修改,然后将其写回,以供模拟(或反之)重复使用。这不仅允许进行简单的参数更改,还允许对网格进行完全重新划分,或者在整个域上重新生成场值的操作。为避免为要引导的每个应用程序手动定制 GUI 的问题,我们使用 XML 模板来描述模拟的输出(以及回传给它的输入),以自动生成用于模拟操作的 GUI 控件。

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