Review DeGAUSS containerized platforms

[sigmafelix]

TODO

• [x] Check if it runs -- runs smoothly on apptainer
• [x] Check its scalability: review the code and run test scripts with 10K+ points
• [ ] Adopt design ideas
• [ ] Include container build-run scripts into Scalable_GIS package

Points of consideration

• DeGAUSS is a special platform for calculating geomarkers in relatively local areas (i.e., accessibility is evaluated at affiliated medical centers); our target is the mainland US, so the scalability is more important than the existing platform
• They hosted their files on Amazon S3; each container includes minimal base system components and scripts. Our system needs to map the fixed (or parametrized) locations in ddn for reproducibility
• Basic design
  • A text file to read user information for SLURM submission: e-mail, job alias, output and error log file names
  • A container with postscripts that install required packages we often use (i.e., exactextractr, terra, etc.)
  • A fixed script that includes default arguments, which will make users have no trouble with entering incorrect/invalid arguments in calculation functions

[sigmafelix]

Looking at the codes from degauss-org, I found that the container included very small pre-calculated datasets (e.g., for isochrones --polygons representing the same travel time) or pointed preprocessed datasets at S3 storage (e.g., NDVI). Each container serves a very specialized function and not other than that, where users only need to consider what they want to calculate. For our use cases, this design would be easily adopted as we mainly consider vector-raster overlay in this package. For example, a container will accept two to three parameters (of course, in terminal):

apptainer run _image.sif_ satellite_imagery.tif input_locations.gpkg 30000

where each argument is a satellite imagery, a data of input locations, and buffer radius, respectively.

[sigmafelix]

This platform will be referred to as an existing solution for local / study-specific geocomputation needs.