Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
allowing some temporary fixes to be reverted.
* removes upp submodule
* uses upp from the ufs-weather-model
* restores the build and link that were hacked during the Hera Rocky 8
transition to allow for UPP submodule
* Removes forecast directories in clean-up

Resolves NOAA-EMC#2617 
Resolves NOAA-EMC#2437

---------

Co-authored-by: Rahul Mahajan <[email protected]>

…OAA-EMC#2632)

This PR enables linking both global-nest fix files and non-nest ones at
the same time and users can run both nesting and non-nesting experiments
at the same time without worries about what fix files to be linked.

Resolves NOAA-EMC#2631

Adds a COM template to define a path to store obs processed for JEDI.
This will allow UFSDA to stop writing to COM_OBS, which should be
read-only as it belongs to obsproc in operations.

No functional change yet.

This PR addresses issue NOAA-EMC#2444. The following is accomplished:

- All `sleep` statements are replaced with `wait_for_file` for the
relevant scripts beneath `scripts` and `ush`;
- Indentation and shell-norms are updated where applicable. 

Note: The WAFS scripts are not updated as per @aerorahul direction.

Resolves NOAA-EMC#2444

---------

Co-authored-by: henrywinterbottom-wxdev <[email protected]>
Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

The PR allows the use of ICs from PSL's replay analysis. These replay
ICs will be used for GEFS reforecasting and SFS. Two main changes are
associated with these updates: (1) replay ICs being valid at 3Z, and (2)
the use of warm starts.

Resolves NOAA-EMC#1838

---------

Co-authored-by: Jessica Meixner <[email protected]>
Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
Co-authored-by: Rahul Mahajan <[email protected]>

This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
build for gsi_utils.
 
Resolves NOAA-EMC#2640

…#2685)

This quick-fix PR is to update the Jenkins Pipeline's configurable
parameter list to include the **Hercules-EMC** node.
This allows Jenkins users to restart Jobs in the controller when no
updates have been made.

needed a comma

This PR removes the ocn_daily files that are produced by the ocean
component. These files can be recreated by averaging data that exists in
the 6 hour aveaged files if needed.

Fixes NOAA-EMC#2675
Fixes NOAA-EMC#2659 (by
removing them and making this obsolete)

…#2624)

Add a prepaeroobs job to prepare aerosol obs files for DA.

This job does quality control of the VIIRS aerosol raw observations and
convert them to ioda format.

Resolves NOAA-EMC#2623 
---------

Co-authored-by: ypwang19 <[email protected]>
Co-authored-by: TerrenceMcGuinness-NOAA <[email protected]>
Co-authored-by: Cory Martin <[email protected]>
Co-authored-by: David Huber <[email protected]>

This PR moves JCB into GDASapp. The PR
also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
which at time of writing is develop plus the absorption of JCB into
GDASapp.
Note that I also took the changes from
NOAA-EMC#2641 to follow the
testing @RussTreadon-NOAA has done.

Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs

This is done by
1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
- performing operations on all files at once instead of looping over
each file
    - removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
    - combining `sed` and `grep` calls when possible
    - adding logic to `awk` calls instead of handling that logic in bash
2) minimizing as much as possible the amount of data on disk that has to
be read in (e.g. limiting sed to read only the line numbers it needs)
---------

Co-authored-by: Walter Kolczynski - NOAA <[email protected]>

Turns on high-frequency (hourly) output in the extended products test to
exercise that aspect of the code. This test only runs on WCOSS.

Also adds the hooks to optionally turn on the metplus jobs, but that is
deferred as they are not currently working correctly.

NCO has requested that each COM variable specify whether it is an input
or an output. This completes that process for the global-workflow
archive task.

Refs NOAA-EMC#2451 
---------

Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
Co-authored-by: Rahul Mahajan <[email protected]>
Co-authored-by: David Huber <[email protected]>

This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
template.
Resolves NOAA-EMC#2696 
Refs NOAA-EMC#2451

…put files (NOAA-EMC#2688)

This PR addresses issue NOAA-EMC#1252. The following is accomplished:

- Prior to removing files, the existence of a file is checked prior to
attempting to remove; this is performed as noted
[here](NOAA-EMC#1252 (comment));
this PR only addresses the the `chgrp` issue.

Refs NOAA-EMC#1252

---------

Co-authored-by: David Huber <[email protected]>

Eliminates the post groups used for upp and products jobs so that each
task only processes one forecast hour. This is more efficient and
greatly simplifies downstream dependencies that depend on a specific
forecast hour.

Resolves NOAA-EMC#2666
Refs NOAA-EMC#2642

…#2687)

This fixes the online archiving portion of the `*arch` and `*earc00`
jobs, a prerequisite for running METplus.  This also reenables
METplus by default.

The approach previously taken created `FileHandler` dictionaries at
varying levels within the resulting yaml, which was not properly parsed
by `exglobal_archive.py`. This approach creates a single `FileHandler`
dictionary and is much less complicated overall.

Resolves NOAA-EMC#2673 NOAA-EMC#2647

Adds a table to HPC documentation stating the minimum support versions