Add `moosetainer` (Apptainer) instructions #27744

milljm · 2024-05-30T13:36:29Z

Add information about not using the visualization machines for build MOOSE/MOOSE-based applications (the real reason for this PR).

Add moosetainer (or possibly apptainer) instructions.

Modernize the HPC OnDemand page, which was making use of these instructions.

This is a work in progress.

Closes #27731

Add information about not using the visualization machines for build MOOSE/MOOSE-based applications (the real reason for this PR). Add moosetainer (or possibly apptainer) instructions. Modernize the HPC OnDemand page, which was making use of these instructions. This is a work in progress. Closes idaholab#27731

modules/doc/content/application_development/build_system.md

modules/doc/content/getting_started/installation/build_petsc_and_libmesh.md.template

milljm · 2024-06-27T15:28:35Z

modules/doc/content/help/faq/apptainer.md

+Beyond the initial cloning of the application, most steps are barred from network access. You
+can mimmic these behaviors if need be. See [Apptainer Features](help/faq/apptainer.md#features)
+below for details.
+!alert-end!


TODO: I need to add how to enable this feature.

cticenhour · 2024-06-27T15:07:15Z

framework/doc/acronyms.yml

@@ -63,3 +63,4 @@ FAR: Failure Analysis Report
 QLD: Quality Level Determination
 QP: quadrature point
 QPs: quadrature points
+URI: Uniform resource identifier


Suggested change

URI: Uniform resource identifier

URI: uniform resource identifier

cticenhour · 2024-06-27T15:10:55Z

modules/doc/content/application_development/build_system.md

+!style! halign=left
+The MOOSE build system is a hierarchical Makefile based system. The idea is that no matter where
+you are in the hierarchy of MOOSE applications/modules/framework, simply typing `make` will rebuild
+everything that needs to be rebuilt. The basic way to build any MOOSE application is simply to do
+a:
+!style-end!


FYI - if you wanted to reduce new line count, simply placing !style halign=left in front of the paragraph and not the full "start-to-end" syntax is sufficient to get the spacing right after a heading. Mentioning it in case you wanted to adjust as you're working through other parts of this review, but I will not require it, as this is good syntax as well.

Oh! I didn't know that. Yes I'd much rather not need the style-end syntax.

cticenhour · 2024-06-27T15:14:39Z

modules/doc/content/application_development/build_system.md

-`METHODS`.
+`METHODS` is used to specify the full set (space separated) of the above options that you will
+ _ever_ want to used.  It is used in the build of `libMesh` to build a `libMesh` library for each of
+ the `METHODS`.


Suggested change

the `METHODS`.

the `METHODS`, so that a rebuild of `libMesh` is not required every time a rebuild of MOOSE

with a new `METHOD` is performed.

cticenhour · 2024-06-27T15:18:26Z

modules/doc/content/application_development/build_system.md


+!style! halign=left


Suggested change

!style! halign=left

!alert! note

Let's make this stand out a bit more since the section isn't strictly necessary.

cticenhour · 2024-06-27T15:18:43Z

modules/doc/content/application_development/build_system.md

 This is advanced information meant to inform you of optimizations that happen within the MOOSE build
-system.  This is not necessary to understand how to use and build MOOSE.
+system. This is not necessary to understand how to use and build MOOSE.
+!style-end!


Suggested change

!style-end!

!alert-end!

Tied to my previous comment.

cticenhour · 2024-06-27T15:51:17Z

modules/doc/content/help/faq/apptainer.md

+If you're still unable to reproduce the error, please keep in mind one golden truth:
+Containers are immutable+. The lack of reproducibility is being caused by *something* that is
+different in your environment compared to Civet's. Things like Network connectivity, shell flavor
+(tsch, zsh, bash), CPU microachitechture (extremely rare), and the like.


Suggested change

(tsch, zsh, bash), CPU microachitechture (extremely rare), and the like.

(tsch, zsh, bash), CPU microarchitecture (extremely rare), and the like.

cticenhour · 2024-06-27T15:52:06Z

modules/doc/content/help/faq/apptainer.md

+#### Paths and Mounts
+
+!style! halign=left
+You can instruct Apptainer to mount any path you have access to, to be made available inside the


Suggested change

You can instruct Apptainer to mount any path you have access to, to be made available inside the

You can instruct Apptainer to mount any path you have access to, so that it is available inside the

cticenhour · 2024-06-27T15:52:32Z

modules/doc/content/help/faq/apptainer.md

+[moose-dev][~]> ls /scratch  # contents of scratch is displayed
+```
+
+Do you want to mount something somewhere else? Also with read-only permissions?


Suggested change

Do you want to mount something somewhere else? Also with read-only permissions?

Do you want to mount something somewhere else - perhaps also with read-only permissions?

cticenhour · 2024-06-27T15:53:26Z

modules/doc/content/help/faq/apptainer.md

+```
+
+!alert! tip title=Custom Prompt
+There is an all encompasing `$CUSTOM_PROMPT` variable that allows you to pass your own prompt:


Suggested change

There is an all encompasing `$CUSTOM_PROMPT` variable that allows you to pass your own prompt:

There is an all-encompassing `$CUSTOM_PROMPT` variable that allows you to pass your own prompt:

cticenhour · 2024-06-27T15:53:41Z

modules/doc/content/help/faq/apptainer.md

+[my-container][12:17:43]>
+```
+
+<!-- NOTE to editor: sub children elements require less top possitioning (-15 vs -7) -->


Suggested change

moosebuild · 2024-06-27T17:12:26Z

Job Documentation on 6a6c758 wanted to post the following:

View the site here

This comment will be updated on new commits.

milljm requested review from loganharbour and cticenhour as code owners May 30, 2024 13:36

GiudGiud assigned milljm Jun 11, 2024

WIP awesomeness

6a6c758

milljm changed the title ~~WIP: Add moosetainer (Apptainer) instructions~~ Add moosetainer (Apptainer) instructions Jun 27, 2024

milljm commented Jun 27, 2024

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Add `moosetainer` (Apptainer) instructions #27744

Add `moosetainer` (Apptainer) instructions #27744

milljm commented May 30, 2024

milljm Jun 27, 2024

cticenhour Jun 27, 2024

cticenhour Jun 27, 2024

milljm Jun 27, 2024

cticenhour Jun 27, 2024

cticenhour Jun 27, 2024

cticenhour Jun 27, 2024

cticenhour Jun 27, 2024

cticenhour Jun 27, 2024

cticenhour Jun 27, 2024

cticenhour Jun 27, 2024

cticenhour Jun 27, 2024

moosebuild commented Jun 27, 2024

	URI: Uniform resource identifier
	URI: uniform resource identifier

	the `METHODS`.
	the `METHODS`, so that a rebuild of `libMesh` is not required every time a rebuild of MOOSE
	with a new `METHOD` is performed.

	(tsch, zsh, bash), CPU microachitechture (extremely rare), and the like.
	(tsch, zsh, bash), CPU microarchitecture (extremely rare), and the like.

	You can instruct Apptainer to mount any path you have access to, to be made available inside the
	You can instruct Apptainer to mount any path you have access to, so that it is available inside the

	Do you want to mount something somewhere else? Also with read-only permissions?
	Do you want to mount something somewhere else - perhaps also with read-only permissions?

	There is an all encompasing `$CUSTOM_PROMPT` variable that allows you to pass your own prompt:
	There is an all-encompassing `$CUSTOM_PROMPT` variable that allows you to pass your own prompt:

	<!-- NOTE to editor: sub children elements require less top possitioning (-15 vs -7) -->
	<!-- NOTE to editor: sub children elements require less top positioning (-15 vs -7) -->

Add moosetainer (Apptainer) instructions #27744

Are you sure you want to change the base?

Add moosetainer (Apptainer) instructions #27744

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milljm commented May 30, 2024

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moosebuild commented Jun 27, 2024

Add `moosetainer` (Apptainer) instructions #27744

Add `moosetainer` (Apptainer) instructions #27744