Zonation
Zonation is a spatial conservation prioritization framework for large-scale conservation planning. It identifies areas, or landscapes, important for retaining high habitat quality and connectivity for multiple biodiversity features (eg. species), providing a quantitative method for enhancing species' long term persistence.
Available
Zonation is available in Puhti with following versions:
- 4.0.0
Usage
Zonation is available in the zonation module and can be loaded with
module load zonation
Zonation 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 Zonation module you can run normal zonation commands in the following way:
srun singularity_wrapper exec <zonation command>
Here is an example with the zonation-tutorial data. With the Singularity wrapper, you need to have the data in your project's projappl or scratch folder.
srun singularity_wrapper exec \
zig4 -r 01_core_area_zonation/01_core_area_zonation.dat 01_core_area_zonation/01_core_area_zonation.spp \
basic_output/01_core_area_zonation/01_core_area_zonation.txt 0.0 0 1.0 1
Note
The installation of Zonation in Puhti does not include the graphical user interface
Example batch job script
#!/bin/bash
#SBATCH --account=<YOUR-PROJECT>
#SBATCH --cpus-per-task=1
#SBATCH --partition=test
#SBATCH --time=00:10:00
#SBATCH --mem=2G
module load zonation
cd /scratch/<your_project>
srun singularity_wrapper exec \
zig4 -r 01_core_area_zonation/01_core_area_zonation.dat 01_core_area_zonation/01_core_area_zonation.spp \
basic_output/01_core_area_zonation/01_core_area_zonation.txt 0.0 0 1.0 1
Note
Please note that Zonation can use only one CPU core so reserving more won't speed up the processing
License and citing
Zonation computational core (zig4) is distributed under the GNU General Public License (GPL) version 3. 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).”