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Launching Python Applications on Peta-scale Massively Parallel Systems

Yu Feng
Berkeley Center for Cosmological Physics, University of California, Berkeley CA 94720
Berkeley Institute for Data Science, University of California, Berkeley CA 94720

Nick Hand
Berkeley Center for Cosmological Physics, University of California, Berkeley CA 94720

Video: https://youtu.be/CfrRDI71vTc

Abstract

We introduce a method to launch Python applications at near native speed on large high performance computing systems. The Python run-time and other dependencies are bundled and delivered to computing nodes via a broadcast operation. The interpreter is instructed to use the local version of the files on the computing node, removing the shared file system as a bottleneck during the application start-up. Our method can be added as a preamble to the traditional job script, improving the performance of user applications in a non-invasive way. Furthermore, we find it useful to implement a three-tier system for the supporting components of an application, reducing the overhead of runs during the development phase of an application. The method launches applications on Cray XC30 and Cray XT systems up to full machine capacity with an overhead of typically less than 2 minutes. We expect the method to be portable to similar applications in Julia or R. We also hope the three-tier system for the supporting components provides some insight for the container based solutions for launching applications in a development environment. We provide the full source code of an implementation of the method at https://github.com/rainwoodman/python-mpi-bcast. Now that large scale Python applications can launch extremely efficiently on state-of-the-art super-computing systems, it is time for the high performance computing community to seriously consider building complicated computational applications at large scale with Python.

Keywords

Python, high performance computing, development environment, application

Bibtex entry

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