Enabling System Wide Shared Memory for Performance Improvement in PyCOMPSs Applications

Python has been gaining some traction for years in the world of scientific applications. However, the high-level abstraction it provides may not allow the developer to use the machines to their peak performance. To address this, multiple strategies, sometimes complementary, have been developed to enrich the software ecosystem either by relying on additional libraries dedicated to efficient computation (e.g., NumPy) or by providing a framework to better use HPC scale infrastructures (e.g., PyCOMPSs).In this paper, we present a Python extension based on SharedArray that enables the support of system-provided shared memory and its integration into the PyCOMPSs programming model as an example of integration to a complex Python environment. We also evaluate the impact such a tool may have on performance in two types of distributed execution-flows, one for linear algebra with a blocked matrix multiplication application and the other in the context of data-clustering with a k-means application. We show that with very little modification of the original decorator (3 lines of code to be modified) of the task-based application the gain in performance can rise above 40% for tasks relying heavily on data reuse on a distributed environment, especially when loading the data is prominent in the execution time.This work was partly funded by the EXPERTISE project (http://www.msca-expertise.eu/), which has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 721865. BSC authors have also been supported by the Spanish Government through contracts SEV2015-0493 and TIN2015-65316-P, and by Generalitat de Catalunya through contract 2014-SGR-1051.Peer ReviewedPostprint (author's final draft