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Geoconda

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

Additionally geoconda includes:

  • spyder - Scientific Python Development Environment with graphical interface (similar to RStudio for R).
  • GDAL/OGR commandline tools
  • GMT The Generic Mapping Tools
  • PDAL Point Data Abstraction Library
  • ncview for visualizing netcdf files

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 servicedesk@csc.fi.

Available

The geoconda module is available in Puhti:

  • 3.10.6

Version number is the same as the Python version.

Usage

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

module load geoconda

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

module load geoconda/[VERSION]

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

list-packages

You can add more Python packages to geoconda, see instructions from CSC Python page.

You can edit your Python code in Puhti with:

To open Spyder in Puhti web interface with remote desktop:

  1. Log in to Puhti web interface.
  2. Open Remote desktop: Apps -> Desktop, choose Desktop: mate or xfce.
  3. After launcing the remote desktop open Host Terminal (Desktop icon) and start Spyder:
module geoconda
spyder

Using Allas from Python

There are two Python libraries installed in Geoconda that can interact with Allas. Swiftclient uses the swift protocol and boto3 uses S3 protocol. You can find CSC examples how to use both here. With large quantities of data in Allas, virtual rasters should be considered. More information on how to create and use virtual rasters can be found here.

License and acknowledgement

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

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".

References



Last update: January 24, 2023