Hi Aaron,
I have a use case for which I would like to try the parallelized
r.neighbors. Do I just have to apply PR 1724 to current main to be able
to do this, or do I have to do something else ?
Moritz
Am 25.08.2021 15:59 schrieb 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 [1]
* r.neighbors - 1724 [2]
* r.mfilter - 1708 [3]
* r.resamp.filter - 1759 [4]
* r.resamp.interp - 1771 [5]
* r.slope.aspect - 1767 [6]
* r.series - 1776 [7]
* r.patch - 1782 [8]
I will still be working on getting the checklists completed in the
next few weeks.
Warmest regards,
Aaron
-------------------------
FROM: Veronica Andreo <veroand...@gmail.com>
SENT: Tuesday, August 24, 2021 8:48 PM
TO: Aaron Saw Min Sern <aaron...@u.nus.edu>
CC: s...@lists.osgeo.org <s...@lists.osgeo.org>;
grass-dev@lists.osgeo.org <grass-dev@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
(<aaron...@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 [1]
* r.neighbors - https://github.com/OSGeo/grass/pull/ [1]1724 [2]
* r.mfilter - https://github.com/OSGeo/grass/pull/ [1]1708 [3]
* r.resamp.filter - https://github.com/OSGeo/grass/pull/ [1]1759
[4]
* r.resamp.interp - https://github.com/OSGeo/grass/pull/ [1]1771
[5]
* r.slope.aspect - https://github.com/OSGeo/grass/pull/ [1]1767 [6]
* r.series - https://github.com/OSGeo/grass/pull/ [1]1776 [7]
* r.patch - https://github.com/OSGeo/grass/pull/ [1]1782 [8]
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
[9].
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
[10]/.
For the project timeline and logs, please visit the
https://trac.osgeo.org/grass/wiki/GSoC/2021/RasterParallelization
[11].
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
_______________________________________________
grass-dev mailing list
grass-dev@lists.osgeo.org
https://lists.osgeo.org/mailman/listinfo/grass-dev [12]
Links:
------
[1] https://github.com/OSGeo/grass/pull/1634
[2] https://github.com/OSGeo/grass/pull/1724
[3] https://github.com/OSGeo/grass/pull/1708
[4] https://github.com/OSGeo/grass/pull/1759
[5] https://github.com/OSGeo/grass/pull/1771
[6] https://github.com/OSGeo/grass/pull/1767
[7] https://github.com/OSGeo/grass/pull/1776
[8] https://github.com/OSGeo/grass/pull/1782
[9] https://grasswiki.osgeo.org/wiki/Raster_Parallelization_with_OpenMP
[10]
https://summerofcode.withgoogle.com/dashboard/project/6280792767987712/overview/
[11] https://trac.osgeo.org/grass/wiki/GSoC/2021/RasterParallelization
[12] https://lists.osgeo.org/mailman/listinfo/grass-dev
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