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 “The 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 Fri Jan 24 2020