Add hook for custom apptainer environment

[dschwen]

Reason

I'm missing my aliases in the apptainer shells.

Design

Add an apptainer env script that sources $HOME/.bashrc_apptainer if it exists.

Impact

Permit users to set up familiar environments in apptainer containers.

[milljm]

I can address this in #28813

[loganharbour]

Need to bump the whole conda stack due to changing mpi.def (which is versioned alongside moose-mpi)

[loganharbour]

Please do a chmod +x on this file if you haven't. and while you're at it, do one on 01-fix-exec.sh too because I think we forgot it

[dschwen]

x is not really necessary for source, but I can make that change

[milljm]

Can you try the following, see if alias work:

apptainer shell -B /path/to/your/.bashrc_apptainer:/init_env oras://theimage

I am finding many things don't work by simply sourcing the file, as you are suggesting to do.

If the above works, then this feature is already present. We just need to be more clear as to its availability.

Edit:
Seems to work for me.

Edit2:
Seems to only work in the lowest level container (rocky:8.9-0). So, the test I performed here should be ignored. It does not work for the rest of our containers.

[dschwen]

Can you try the following, see if alias work:

apptainer shell -B /path/to/your/.bashrc_apptainer:/init_env oras://theimage

I'm using vscode_container, so unless that script passes through cli args, this script would need to be patched.

[dschwen]

I am finding many things don't work by simply sourcing the file, as you are suggesting to do.

Why wouldn't that work?!

[moosebuild]

Job Precheck, step Conda build config check on 3b38a76 wanted to post the following:

A change of the following file(s) triggered this check:

conda/peacock

The following file(s) are unchanged:

conda/mpi/conda_build_config.yaml

The conda build config was not changed but one or more of its dependencies have changed

[milljm]

I am finding many things don't work by simply sourcing the file, as you are suggesting to do.

Why wouldn't that work?!

Here has been my experience:

$ apptainer shell -B /home/milljm/.testing:/init_env oras://mooseharbor.hpc.inl.gov/moose-dev/moose-dev-mpich-x86_64:28a1964
INFO:    Using cached SIF image
moose-dev-mpich-x86_64:28a1964 [milljm@rod: ~ ]
$ cat /init_env 
function my_test(){
  echo 'hello from my_test function'
}
alias jas='ls -latrh'

So the file exists inside the container well enough. But...

moose-dev-mpich-x86_64:28a1964 [milljm@rod: ~ ]
$ my_test 
bash: my_test: command not found
moose-dev-mpich-x86_64:28a1964 [milljm@rod: ~ ]
$ jas
bash: jas: command not found

no dice. Not until I source it again

moose-dev-mpich-x86_64:28a1964 [milljm@rod: ~ ]
$ . /init_env 
moose-dev-mpich-x86_64:28a1964 [milljm@rod: ~ ]
$ my_test
hello from my_test function
moose-dev-mpich-x86_64:28a1964 [milljm@rod: ~ ]
$ jas
total 195M
-rw-------  1 milljm milljm  256 Sep 18  2013 .pulse-cookie
<trimmed>

All the while we do seem to be doing it:

moose/apptainer/mpi.def

Lines 52 to 55 in a35543b

	# Load a custom environment if it exists
	if [ -e /init_env ]; then
	source /init_env
	fi

Perhaps what you are doing may work. As I have been experiencing different results as to when this file gets sourced.

[milljm]

I am trying what you are suggesting, and it won't work. My PR I am working on should fix this. But simply "sourcing" files doesn't seem to be enough. Don't ask me why, lol.

editing the atrocious PS prompt...

$ apptainer shell moose-dev-mpich-x86_64_28a1964.sifw 
$ jas
bash: jas: command not found

$ my_test
bash: my_test: command not found

$ echo $MYVAR  # exports work!?
foobar

$ cat /.singularity.d/env/02-bashrc-apptainer.sh 
if [ -e $HOME/.bashrc_apptainer ]; then
    source $HOME/.bashrc_apptainer
fi

$ cat $HOME/.bashrc_apptainer
function my_test(){
  echo 'hello from my_test function'
}
alias jas='ls -latrh'
export MYVAR=foobar

$ . /.singularity.d/env/02-bashrc-apptainer.sh  # sourcing it again works. 🤷 
$ my_test
hello from my_test function

$ jas
total 2.2G
<trimmed>
drwxr-xr-x  3 milljm milljm   60 Oct 14 12:56 ..
$ 

[dschwen]

Hm... I suppose that env stuff is not sourced in my current shell, and aliases are not inherited. But why is the bash not sourcing my .bashrc then?

[moosebuild]

Job Precheck, step Conda build config check on e44885a wanted to post the following:

A change of the following file(s) triggered this check:

conda/peacock

The following file(s) are unchanged:

conda/mpi/conda_build_config.yaml

The conda build config was not changed but one or more of its dependencies have changed

[loganharbour]

Isn't this due to the --norc option or whatever we pass bash?