C-Star is a python package for setting up and running ocean model simulations, with a particular focus on marine carbon dioxide removal (mCDR) applications.
This PR fixes several issues uncovered while running on NERSC's Perlmutter system (particularly in the context of using C-Star in a jupyterlab job)
use importlib to import the Linux Environment Modules python module for environment management
capture output when using lmod and only print if fail or error found in stderr (several system messages are otherwise printed when import cstar is run)
Define a _CSTAR_ENVIRONMENT_VARIABLES global to track environment variables set by C-Star. This is used to reconstruct the C-Star specific environment inside a slurm job with --export=NONE
Create text files in additional_files specifying the modules to be loaded on different machines. These files are parsed by C-Star and used to call module , rather than hardcoding the environment into the C-Star python code.
rename set_local_config to get_user_environment and do not update environment variables within the function anymore (just append to _CSTAR_ENVIRONMENT_VARIABLES
add a queue option to Case.run and Component.run
Remove SLURM_ prefixed environment variables from subprocess environment when submitting to the queue (even with --export=NONE these were slipping through, causing conflicts if a job was started from within another job)
This PR fixes several issues uncovered while running on NERSC's Perlmutter system (particularly in the context of using C-Star in a jupyterlab job)
importlibto import the Linux Environment Modules python module for environment managementfailorerrorfound in stderr (several system messages are otherwise printed whenimport cstaris run)_CSTAR_ENVIRONMENT_VARIABLESglobal to track environment variables set by C-Star. This is used to reconstruct the C-Star specific environment inside a slurm job with--export=NONEadditional_filesspecifying the modules to be loaded on different machines. These files are parsed by C-Star and used to callmodule, rather than hardcoding the environment into the C-Star python code.set_local_configtoget_user_environmentand do not update environment variables within the function anymore (just append to_CSTAR_ENVIRONMENT_VARIABLESqueueoption toCase.runandComponent.runSLURM_prefixed environment variables from subprocess environment when submitting to the queue (even with--export=NONEthese were slipping through, causing conflicts if a job was started from within another job)post_run