Model runs for phase 1b

[infotroph]

Scripts and documentation for the model execution portion of 1b. See README for details.

[dlebauer]

This looks good for the modeling component of our phase 1b deliverables.

Below are some suggestions for the next iteration(s) (update: moved to ccmmf/organization#118):

• README Clarifications:

  • Describe all files and directories
    • What goes in tools/ vs the higher level directory?
    • I found it helpful for scripts to be numbered as they were in 1a, why are they no longer numbered?
  • Many of the 'tools/' are not mentioned in README (make_site_info, read_dwr_planting, slurm_array_submit, run_getERA5)
  • Describe the overall workflow.

• Scripts

  • It would be helpful to identify functions that are intended to be added to PEcAn, and which are ccmmf or script specific.
    • Note: The function read_ncdir overlaps with line 79 ff in downscale/02_extract_sipnet_output.R (see PR #2).
  • Are separate versions of install_pecan.sh and install_sipnet.sh necessary?

[infotroph]

What goes in tools/ vs the higher level directory?

root dir: Does one distinct step of the workflow; probably called once per model run.
tools/: Does one specific task; probably called each time that task needs doing (which might be <1x per run for setup tasks or >1x for helpers called from multiple steps).

why are they no longer numbered?

Wasn't obvious as I developed how many separate steps there would be, nor whether all of them would be mandatory to run each time (e.g. as currently written the inputs tarball contains some of the files created by ic_build but then the user has to run it again to finish setup). I'll number them in the order currently mentioned in README

It would be helpful to identify functions that are intended to be added to PEcAn

Easy: If it's here, I think it's CCMMF-specific. Otherwise I would have added to PEcAn to start with. If you see any candidates for relocation, flag them and we can consider.

Are separate versions of install_pecan.sh and install_sipnet.sh necessary?

Not essential, but copying them was an easy way to preserve the principle that one workflow directory contains everything you need to run the workflow. I think that's valuable enough to accept some duplication of simple files.