[Bug]: flepimop notebooks do not render on HPC

[pearsonca]

Label

bug, meta/workflow

Priority Label

high priority

Describe the bug/issue

Users report that they are unable to render notebooks on the rockfish / longleaf clusters to work with flepimop outputs (examples to follow in response comments @saraloo @MacdonaldJoshuaCaleb).

To verify: issues with both Rmarkdown and ipynb

To Reproduce

No response

Environment, if relevant

HPC

Desired Behavior

TBD, but roughly (ala this SO post):

$ jupyter nbconvert --execute <notebook>

or for R (ala this SO post):

$ Rscript -e "rmarkdown::render('example.Rmd',params=list(args = myarg))"

this is the MVP soln for rendering, with configs hard coded, etc

[saraloo]

I can't locate specific error messages, but from past runs the scripts being run automatically after batch runs are listed in https://github.com/HopkinsIDD/flepiMoP/blob/main/batch/postprocessing-scripts.sh
Usually they run out memory or time so a 137 error or just get cancelled.

[MacdonaldJoshuaCaleb]

The issue here, which I've only experienced on rockfish, seems to be a memory allocation error. Mainly seems to occur when too many walkers or iterations are specified. We did try and change some memory flags IIRC, but it didn't seem to fix the problem.