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Warning!

Puhti and Mahti are being decommissioned in stages, and their storage areas will become fully unavailable from 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

Puhti scratch is very full: keep only active data there and move or delete everything else. No new Puhti scratch quota will be granted.

Python-geo

Python-geo is a collection of python packages that facilitate the development of python scripts for geoinformatics applications. It includes following python packages:

Additionally python-geo includes:

Python has multiple packages for parallel computing, for example multiprocessing, joblib and dask. In our Puhti Python examples there are examples how to utilize these different parallelisation libraries.

If you think that some important GIS package for Python is missing from here, you can ask for installation from CSC Service Desk.

Available

The python-geo module is available:

  • 3.14.3 (Python 3.14.3, PDAL 2.10.0, GDAL 3.12.2, created April 2026), in Roihu-CPU

The version number is the same as the Python version.

In Puhti, Mahti and LUMI python-geo is named geoconda

Usage

For using Python packages and other tools listed above, you can initialize them with:

module load python-geo

By default the latest python-geo module is loaded. If you want a specific version you can specify the version number of python-geo:

module load python-geo/[VERSION]

To check the exact packages and versions included in the loaded module:

list-packages

You can add more Python packages to python-geo by following the instructions in our Python usage guide.

You can edit your Python code with web interface or LUMI web interface :

r5py memory settings

r5py by default does not correctly understand how much memory it has available in a supercomputer so, it has to be defined manually. It is using Java in the background, so add environmental variable to set maximum memory available for Java:

  • export _JAVA_OPTIONS="-Xmx4g" from command-line before starting Python OR
  • os.environ["_JAVA_OPTIONS"] = "-Xmx4g" in the beginning of your Python code.

Google Earth Engine authentication set up

For using Google Earth Engine (GEE) API with earthengine-api package, GEE account and project are needed. Before first usage, also set up GEE authentication:

module load python-geo allas
earthengine authenticate --quiet

This prints out a long link and asks for a code. Copy the link to the web browser of your local laptop. Follow the instructions on the web page and finally copy the created code back to Terminal.

Using Allas or LUMI-O from Python

There are two Python libraries installed in Python-geo that can interact with Allas or LUMI-O. Swiftclient uses the swift protocol and boto3 uses S3 protocol. You can find CSC examples how to use both here.

It is also possible to read and write files from and to Allas or other cloud object storage directly with GDAL-based packages such as geopandas and rasterio. Please check our Using geospatial files directly from cloud, inc Allas tutorial for instructions and examples.

With large quantities of raster data, consider using virtual rasters.

License

All packages are licensed under various free and open source licenses (FOSS), see the linked pages above for exact details.

Citation

Please see the above linked package pages for citation information per package.

Acknowledgement

Please acknowledge CSC and Geoportti in your publications, it is important for project continuation and funding reports. As an example, you can write "The authors wish to thank CSC - IT Center for Science, Finland (urn:nbn:fi:research-infras-2016072531) and the Open Geospatial Information Infrastructure for Research (Geoportti, urn:nbn:fi:research-infras-2016072513) for computational resources and support".

Installation

Python-geo was installed to Roihu using Tykkys conda-containerize functionality. In LUMI, geoconda was installed using LUMI container wrapper. The functionality of the tools is almost identical with --post option being --post-install on LUMI container wrapper. The WhiteboxTools conda package installs only WhiteboxTools installer, therefore for proper installation of Whiteboxtools required additional post installation command and folder to wrap commandline tools.

conda-containerize new --mamba \
  --prefix install_dir --post download_wbt \
  -w miniconda/envs/env1/lib/python3.11/site-packages/whitebox/WBT/whitebox_tools \
  python-geo_3.11.10.yml

Python-geo conda environment files and download_wbt and start_wbt.py needed for WhiteboxTools are available in CSCs geocomputing repository. Note that for reproducibility, you'll need to define the package versions in the environment file, which can be checked using list-packages command after loading the python-geo module.

References