Add R2D2 mysql dependencies and complete site config updates for unified environment

[climbfuji]

Description

Changes in this PR:

• Add dependencies for the upcoming R2D2 mysql backend implementation to various configs files,
• Update the submodule pointer for spack for the corresponding changes there
• Update CI scripts and documentation - avoid using the padded_length logic for now, too many issues. Instead, alwaus install in same location (env-name/env-dir)
• Add Ubuntu CI on AWS EC2, currently only with Intel on the AWS Parallelcluster head node of JCSDA
• Also update remaining site configs with changes required for the unified environment. The unified environment was introduced in Create template for unified environment, test install on orion and AWS parallelcluster #454, PR Update compiler/MPI entries in site configs for the UE #480 updated some of the site configs, this PR adds the remaining site configurations for fully supported sites

With this PR and previous PRs, the following sites have updated compiler/package files for (a) the unified environment and (b) mysql. For sites marked with an asterisk *, the updated unified-environment was built successfully (manually).

• Orion (Intel, GNU) *
• S4 (Intel, GNU) *
• Cheyenne (Intel, GNU) *
• Casper (Intel)
• Discover (Intel, GNU) *
• Hera (Intel, GNU)
• Jet (Intel, GNU)
• AWS Parallelcluster (Intel) *
• Narwhal (Intel, GNU)
• Gaea
• noaa-aws
• noaa-azure
• noaa-gcloud

The following sites are still missing, but we can do those in a follow-up PR (as long as before we roll out the spack-stack 1.3.0 release) - but may want to consider moving this to a different "category" of support, as discussed in the last spack-stack meeting:

• Acorn
• Gaea c5
• emc-rhel (if building the unified-dev env)
• frontera
• comet

Dependencies

• Waiting on Add R2D2 mysql dependencies, remove ncl from global-workflow-env, Intel bug fix from spack repo spack#220

Issues

Fixes #383

Testing

• New Ubuntu and macOS CI tests passed for 45c5520
• Manual tests on platforms listed above and on Dom's macOS

[srherbener]

In the documentation updates I'm not seeing updated instructions for the Mac regarding the need to install mysql with homebrew and to mark mysql as an external package. Should brew install mysql be added to the list showing the other brew install commands? Also add the spack --not-buildable --scope system mysql to the list of spack find commands?

Also, should we put in the tip about shutting off the auto updates of dependencies in the Mac instructions. Ie, add export HOMEBREW_NO_AUTO_UPDATE=1 to your environment before running brew installs?

[climbfuji]

In the documentation updates I'm not seeing updated instructions for the Mac regarding the need to install mysql with homebrew and to mark mysql as an external package. Should brew install mysql be added to the list showing the other brew install commands? Also add the spack --not-buildable --scope system mysql to the list of spack find commands?

Also, should we put in the tip about shutting off the auto updates of dependencies in the Mac instructions. Ie, add export HOMEBREW_NO_AUTO_UPDATE=1 to your environment before running brew installs?

Indeed. Now the instructions are there. See 7952569.

[srherbener]

Looks great. Thanks!

[srherbener]

I'm testing on my Mac now with the proper handling of the mysql package. I should have a result later this afternoon.

[ericlingerfelt]

Thanks, @climbfuji!

[ulmononian]

5stars. seems ready to roll!