Example scripts for running ISOFIT

• get-test-data.sh -- Downloads some example datasets from JPL server and unzips them into the test_data folder.
• run-apply-oe.sh -- Example bash script for running Isofit apply_oe workflow (the "default" way to perform atmospheric correction using Isofit). Includes SBATCH directives for NCCS DISCOVER (you must be a member of project s3673, "SBG DO"). Also serves as an effective template script for running the workflow on other images.

Running on NCCS DISCOVER

It is best practice to run Isofit workflows as batch jobs. Because run-apply-oe.sh already has all the SBATCH flags you need, you can simply do the following to submit a job.

sbatch run-apply-oe.sh

If you need to do some interactive runs (e.g., for testing or debugging), best practice is to do so on an interactive compute node. You can request a compute node for, e.g., 48 minutes, with a command like the following:

srun -A s3673 -t 48 --pty bash 

This command will request the compute resources and, when ready, will automatically log you into the compute node when resources are available.

From there, you can just run bash run-apply-oe.sh.

For more fine-grained debugging, start by loading the Python 3.9 module (which includes conda and mamba pre-installed).

module load python/GEOSpyD/Min4.11.0_py3.9

Next, activate the pre-installed isofit-master conda environment.

mamba activate /discover/nobackup/projects/SBG-DO/conda-envs/isofit-master 

NOTE: If this command fails with an error about your shell not being configured, run mamba init to configure your shell. You should only have to do this step once per system.

Finally, use this environment to run whatever code you need to for testing.