User-scripts can't run module use/load

[jo-basevi]

Running module use / module load in user-scripts results in /bin/sh: module: command not found

In payu, $MODULEHOMES/bin/modulecmd is used to run any module commands. The $MODULEHOMES/bin/modulecmd python load <module> generates commands that can be executed to run the module load command.

payu/payu/envmod.py

Lines 102 to 108 in 6ee85bb

	modulecmd = ('{0}/bin/modulecmd'.format(os.environ['MODULESHOME']))
	cmd = '{0} python {1} {2}'.format(modulecmd, command, ' '.join(args))
	envs, _ = subprocess.Popen(shlex.split(cmd),
	stdout=subprocess.PIPE).communicate()
	exec(envs)

Payu PBS jobs are submitted with a format similar to qsub -- /path/to/env/bin/python /path/to/env/bin/payu-run. The qsub man page noted had the following for using -- to run commands:

When you run qsub this way, it runs the executable directly. It does not start a shell, so no shell initialization scripts are run, and execution paths and other environment variables are not set.

So the shell initialisation scripts might be what is setting up the module commands? I don't know if it possible to avoid using $MODULEHOMES/bin/modulecmd commands in envmod.py as modules need to be loaded in the same process that python is running (unless copying back the changes to environment in a subprocess call). However when running bash user-scripts should payu first run an shell initialisation script in the subprocess to setup module commands? My ~/.bashrc has the following which I've tested works for setting up the module command (at least on gadi - this might be platform specific?)

# Source global definitions (Required for modules)
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

This might not be a major issue, as workarounds is to specify any required modules in config.yaml, under modules: load:, or run a shell initialisation script or use modulecmd in the user-scripts.

[anton-seaice]

It looks like the modules get initialised in

/opt/Modules/v4.3.0/init/bash