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WhiteboxTools

WhiteboxTools is an advanced geospatial data analysis platform which includes more than 420 tools.

Available

WhiteboxTools is available in Puhti with following versions:

  • 0.15.0

Usage

WhiteboxTools is available in the WhiteboxTools module and can be loaded with

module load whiteboxtools

WhiteboxTools usage in Puhti happens through a container system called Singularity which is very similar as Docker. CSC provides a singularity_wrapper command that makes running these containers simpler for the user.

After loading the WhiteboxTools module you can run normal WhiteboxTools commands on the computing nodes with the following way:

srun singularity_wrapper exec <whiteboxtools command>

Note

For now, the Graphical user interface (Whitebox GAT) and the Python interface are not available on Puhti

Here is an example of calculating Hillshade for a 2m DEM.

singularity_wrapper exec whitebox_tools -r=Hillshade -v --wd="<INPUT-DATA-FOLDER>" -i=T4323D.tif -o=test_hillshade.tif --azimuth=315.0 --altitude=30.0

Note

The --wd (working directory) parameter requires quotation marks " " around the path

Example batch job script

#!/bin/bash
#SBATCH --account=<YOUR-PROJECT>
#SBATCH --cpus-per-task=1
#SBATCH --partition=small
#SBATCH --time=00:10:00
#SBATCH --mem=2G

module load whiteboxtools
singularity_wrapper exec whitebox_tools -r=Hillshade -v --wd="<INPUT-DATA-FOLDER>" -i=T4323D.tif -o=test_hillshade.tif --azimuth=315.0 --altitude=30.0

License and citing

The WhiteboxTools project has been developed using a permissive MIT license, which allows for the tools to be readily incorporated into other GIS software. Full license here

In your publications please acknowledge also oGIIR and CSC, for example β€œThe authors wish to acknowledge for computational resources CSC – IT Center for Science, Finland (urn:nbn:fi:research-infras-2016072531) and the Open Geospatial Information Infrastructure for Research (oGIIR, urn:nbn:fi:research-infras-2016072513).”

References

Last edited Mon Jan 11 2021