[SoC] [GRASS-dev] GSoC 2021 - Final Report [Parallelization of raster modules for GRASS GIS]

[Aaron Saw Min Sern]

Hi all,

Thanks Vero for spotting the mistakes on the links. The formatting of the links must have gone wrong, but here's the links to the respective PR.

  *   r.univar - 1634<https://github.com/OSGeo/grass/pull/1634>
  *   r.neighbors - 1724<https://github.com/OSGeo/grass/pull/1724>
  *   r.mfilter - 1708<https://github.com/OSGeo/grass/pull/1708>
  *   r.resamp.filter - 1759<https://github.com/OSGeo/grass/pull/1759>
  *   r.resamp.interp - 1771<https://github.com/OSGeo/grass/pull/1771>
  *   r.slope.aspect - 1767<https://github.com/OSGeo/grass/pull/1767>
  *   r.series - 1776<https://github.com/OSGeo/grass/pull/1776>
  *   r.patch - 1782<https://github.com/OSGeo/grass/pull/1782>

I will still be working on getting the checklists completed in the next few weeks.

Warmest regards,
Aaron
________________________________
From: Veronica Andreo <veroandreo at gmail.com>
Sent: Tuesday, August 24, 2021 8:48 PM
To: Aaron Saw Min Sern <aaronsms at u.nus.edu>
Cc: soc at lists.osgeo.org <soc at lists.osgeo.org>; grass-dev at lists.osgeo.org <grass-dev at lists.osgeo.org>
Subject: Re: [GRASS-dev] [SoC] GSoC 2021 - Final Report [Parallelization of raster modules for GRASS GIS]

        - External Email -



Dear Aaron,

Thanks for your report and all your work to make GRASS raster modules run faster, we like that :) Huge thanks as well to Vaclav, Huidae and Maris for their commitment to the project and mentoring! You all did a great team work!

One question: are these changes planned to be merged before the creation of grass 8 branch or will they remain for 8+? Maybe add a milestone to clarify?
One minor observation: all links currently point to the same PR

We hope to keep seeing you around, Aaron!

All the best,
Vero

El mar, 24 ago 2021 a las 3:18, Aaron Saw Min Sern (<aaronsms at u.nus.edu<mailto:aaronsms at u.nus.edu>>) escribió:
Hello everyone,

Here is my final report for GSoC 2021 project, Parallelization of Raster Modules for GRASS GIS.

Abstract
The goal of this project is to introduce parallelization to existing raster modules in GRASS GIS using OpenMP. This will allow users to take advantage of more cores in their hardware to speed up the computation time especially for large raster files with large computation cost. The key challenge of this project is to separate the parallelizable components from the sequential part of the modules without introducing too much overhead in terms of memory, disk or computation resources.

Milestones

In total, I have introduced OpenMP support to 8 raster modules in GRASS GIS. The pull requests to each module are as follows:

  *   r.univar - https://github.com/OSGeo/grass/pull/1634
  *   r.neighbors - https://github.com/OSGeo/grass/pull/<https://github.com/OSGeo/grass/pull/1634>1724<https://github.com/OSGeo/grass/pull/1724>
  *   r.mfilter - https://github.com/OSGeo/grass/pull/<https://github.com/OSGeo/grass/pull/1634>1708<https://github.com/OSGeo/grass/pull/1708>
  *   r.resamp.filter - https://github.com/OSGeo/grass/pull/<https://github.com/OSGeo/grass/pull/1634>1759<https://github.com/OSGeo/grass/pull/1759>
  *   r.resamp.interp - https://github.com/OSGeo/grass/pull/<https://github.com/OSGeo/grass/pull/1634>1771<https://github.com/OSGeo/grass/pull/1771>
  *   r.slope.aspect - https://github.com/OSGeo/grass/pull/<https://github.com/OSGeo/grass/pull/1634>1767<https://github.com/OSGeo/grass/pull/1767>
  *   r.series - https://github.com/OSGeo/grass/pull/<https://github.com/OSGeo/grass/pull/1634>1776<https://github.com/OSGeo/grass/pull/1776>
  *   r.patch - https://github.com/OSGeo/grass/pull/<https://github.com/OSGeo/grass/pull/1634>1782<https://github.com/OSGeo/grass/pull/1782>

Firstly, I have greatly underestimated the complexity of the work. Up to 20 modules were initially proposed at first but after the second week. However, it became clear that we had to cut down on the number of target modules and focus more on designing the algorithms. The modules we targeted behave differently as compared to some modules that had received OpenMP support in the past such as r.sun. In particular, the modules need to keep the same of behavior of having low memory footprint even after the parallelization, unlike r.sun which loads the entire raster map in-memory.


During the first half of the GSoC, with the mentors’ discussion, we have come out with three different approaches to introducing parallel support to r.neighbors. After benchmarking their performance and taking account of their memory/disk usage, we decided to settle with the last approach which requires us to add an extra parameter memory to allow users to adjust their memory consumption. With this approach, we have to allow the modules to process the raster map by chunks. Once we settled about the design, we started applying the same approach to other similar modules with low memory footprints.

For more information regarding the implementation, see https://grasswiki.osgeo.org/wiki/Raster_Parallelization_with_OpenMP.


Furthermore, test scripts were included in the modules to ensure the consistency of the results. Benchmark scripts were added to allow users to easily benchmark the performance of the parallelization to monitor the speedup in their own local machine. User documentations were also modified to include sections detailing how to make use of the newly added features.

Future Work


In the future, more raster modules can be parallelized using similar approach. Then, we can consider tackling more complex modules such as r.watershed and r.mapcalc. Also, we could consider exploring 3D raster modules as well.


Furthermore, when we implement parallelization for r.univar, we notice that modules that produce statistics involving arithmetic can often have floating point discrepancies when dealing with large summation. Because of this, computation using different number of threads will now produce different results due to having different order of arithmetic. One idea would be to introduce Kahan Summation algorithm to reduce the floating-point discrepancies. However, this still would not guarantee the consistency of results.

Permanent Links

For the project overview, please visit the https://summerofcode.withgoogle.com/dashboard/project/6280792767987712/overview<https://summerofcode.withgoogle.com/dashboard/project/6280792767987712/overview/>/.
For the project timeline and logs, please visit the https://trac.osgeo.org/grass/wiki/GSoC/2021/RasterParallelization.

I would like to huge thanks to Huidae Cho, Vaclav Petras and Māris Nartišs for their valuable guidance. And I would like to thank the GRASS community for the valuable feedbacks and support. Lastly, I would like to thank the GSoC team for this opportunity.

Thanks all!

Warmest regards,
Aaron Saw Min Sern



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