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Convert modulefiles to LUA format (develop) #670

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KateFriedman-NOAA opened this issue Mar 1, 2022 · 2 comments · Fixed by #756
Closed

Convert modulefiles to LUA format (develop) #670

KateFriedman-NOAA opened this issue Mar 1, 2022 · 2 comments · Fixed by #756
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@WalterKolczynski-NOAA
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feature New feature or request
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WCOSS2 - GFSv16.2.x

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@KateFriedman-NOAA
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Description

Related to work done for issue #639, convert modulefiles from TCL to LUA format in the develop branch. This came from a requirement during the WCOSS2 port and has already been done in the operations/dev_v16/feature/ops-wcoss2 branches.

Acceptance Criteria (Definition of Done)

  1. All workflow modulefiles are in LUA format and have the .lua file extension.
  2. Scripts that invoke modulefiles replace source with module load.
  3. Modules in modulefiles properly load on currently supported platforms.

This will be just a straight-up format conversion. Follow-up work will introduce version files and module version usage in LUA format modulefiles (related WCOSS2 port requirements).
@KateFriedman-NOAA KateFriedman-NOAA added the feature New feature or request label Mar 1, 2022
@KateFriedman-NOAA KateFriedman-NOAA self-assigned this Mar 1, 2022
This was referenced Mar 1, 2022
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@KateFriedman-NOAA
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Branch for this work: https://github.com/KateFriedman-NOAA/global-workflow/tree/feature/lua

KateFriedman-NOAA added a commit to KateFriedman-NOAA/global-workflow that referenced this issue Mar 1, 2022
@KateFriedman-NOAA
Rename modulefiles to include .lua extension
49e1f65 
- modulefiles need to include the ".lua" filename extension
for the conversion to LUA format
- rename modulefiles to include that extension

Refs: NOAA-EMC#670
@KateFriedman-NOAA KateFriedman-NOAA added this to the WCOSS2 - GFSv16.2.0 milestone Mar 7, 2022
KateFriedman-NOAA added a commit to KateFriedman-NOAA/global-workflow that referenced this issue Apr 19, 2022
@KateFriedman-NOAA
Convert module_base files to LUA format
f15b33e 
Refs: NOAA-EMC#670
KateFriedman-NOAA added a commit to KateFriedman-NOAA/global-workflow that referenced this issue Apr 19, 2022
@KateFriedman-NOAA
Convert modulefile.ww3 files to LUA format
1744339 
Refs: NOAA-EMC#670
KateFriedman-NOAA added a commit to KateFriedman-NOAA/global-workflow that referenced this issue Apr 19, 2022
@KateFriedman-NOAA
Convert workflow_utils modulefiles to LUA format
1a31f31 
Refs: NOAA-EMC#670
KateFriedman-NOAA added a commit to KateFriedman-NOAA/global-workflow that referenced this issue Apr 19, 2022
@KateFriedman-NOAA
Update build_workflow_utils.sh for LUA format loading
d5bf6d1 
- adjust build_workflow_utils.sh to replace sourcing with module load
- since LUA format loading doesn't include ".lua" in the command,
update the build script to check existence with ".lua" but not use the
extension at module load time

Refs: NOAA-EMC#670
KateFriedman-NOAA added a commit to KateFriedman-NOAA/global-workflow that referenced this issue Apr 19, 2022
@KateFriedman-NOAA
Update build_ww3prepost.sh for LUA format module load
a654070 
- change build_ww3prepost.sh to use "module load" instead of "source"

Refs: NOAA-EMC#670
KateFriedman-NOAA added a commit to KateFriedman-NOAA/global-workflow that referenced this issue Apr 19, 2022
@KateFriedman-NOAA
Remove module use and module load statements from machine-setup.sh
4b0b311 
- The module use and module load statements now happen in the modulefiles
that have been converted to LUA format.

Refs: NOAA-EMC#670
@KateFriedman-NOAA
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@WalterKolczynski-NOAA My fork branch for this is: https://github.com/KateFriedman-NOAA/global-workflow/tree/feature/lua

I tested the updates for the build but didn't get to testing at runtime yet. This branch will need to be synced with develop branch updates since early March. Thanks!

Note...this work converts the modulefiles to LUA format but doesn't also take the step of adding the _ver variables within these files. That is the next step after this issue is complete.

@KateFriedman-NOAA KateFriedman-NOAA removed their assignment Apr 19, 2022
WalterKolczynski-NOAA added a commit to WalterKolczynski-NOAA/global-workflow that referenced this issue Apr 26, 2022
@WalterKolczynski-NOAA
Fix cmake version on Dell
ffb7cb8 
The incorrect version of cmake was being requested on Dell (the one
requested is not available).

Refs: NOAA-EMC#670
Merged
9 tasks
WalterKolczynski-NOAA added a commit that referenced this issue Apr 27, 2022
@WalterKolczynski-NOAA
Convert module files from Tcl to Lua (#756)
88b1b15 
Converts all module files from Tcl format to Lua. As a side effect, this change enforces using the files as modules rather than improperly sourcing them instead of loading.

Fixes #670
jkhender added a commit to jkhender/global-workflow that referenced this issue Jun 17, 2022
@jkhender
Merged NOAA-EMC/develop 30May22 branch into gslv16_dev
68a10c5 
Squashed commit of the following:

commit dbd9fa93ced07f39accf7ff4eec2859f0ed5d35f
Author: ChunxiZhang-NOAA <[email protected]>
Date:   Mon May 30 21:50:56 2022 -0400

    Updated SDFs and namelist settings for P8c (#795)

    Updates the model version in preparation for prototype 8c, along with commensurate setting updates. Some CCPP suites are removed from the UFS build as they are no longer available.

    Also updates the coupled initial conditions, and there is a simultaneous update to fixed orography files.

    Refs: #736

commit 05accc1c72b1311ae9689bef5e7a1291dc12a96a
Author: RussTreadon-NOAA <[email protected]>
Date:   Mon May 23 17:36:51 2022 -0400

    Correct incorrect increment prefix variable (#805)

    One instance of the increment prefix variable in `ush/forecast_postdet.sh` used `PREFIX_INC` instead of the `PREFIX_ATMINC` used elsewhere.

    Fixes #804

commit ac7cb1000d5c1d31babd36f4c3e17f643f30fd4d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Sun May 22 16:50:30 2022 -0400

    Remove separate UPP clone (#803)

    Now that UPP is cloned within UFS, there is no need to create an independent clone in global-workflow. Scripts are updated to use the UPP within UFS. In addition to removing redundancy, this will avoid version mismatch issues when UFS and global-workflow checkout different versions. The upp directory is now linked from within UFS to sorc as upp.fd (instead of the gfs_post.fd the clone was placed in). Additionally, the build script is renamed to build_upp.sh.

    Fixes #770
    Moots #797

commit 58728fb2c689c11335f4bf8ac371e18070c6fbd2
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri May 20 10:14:58 2022 -0400

    Fix build script options (#801)

    There was an issue where if build_all.sh was called with only options that are not used by partial_build.sh, partial_build.sh would see those options because $@ was not overwritten. The script have been updated to consume those options so they are no longer present if $@ isn't overwritten in the new script call.

    Also fixed the getopts statement in partial_build.sh so we handle errors instead of bash (bash would report the wrong script if the script is sourced)

    Fixes #800

commit fa12db279cf829b861d08c06e3e3534a335e9fd7
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed May 18 01:04:32 2022 -0400

    Refactor some build scripts (#794)

    Refactors the build_ufs script to allow the build of any UFS app to support future expansion of global-workflow capability. The default should be sufficient for most users, as S2SWA can be used for ATM, ATMA, S2S, and S2SW as well. The new format of the command is now:
    ```
    build_ufs.sh [-a UFS_app][-v]
      -a UFS_app:
        Specify the UFS application to build. The default if none is provided is S2SWA
      -v:
        Turn on verbose mode (BUILD_VERBOSE)
    ```

    build_all.sh is similarly refactored to include the same options. Also, a new `-c build_config` option is added to specify an alternative list of programs to build.
    ```
    build_all.sh [-a UFS_app][-c build_config][-h][-v]
      -a UFS_app:
        Build a specific UFS app instead of the default
      -c build_config:
        Selectively build based on the provided config instead of the default config
      -h:
        Print usage message and exit
      -v:
        Run all scripts in verbose mode
    ```

    partial_build.sh is also updated to take the new `-c` option to specify a build config.
    ```
    partial_build.sh [-c config_file][-h][-v]
      -c config_file:
        Selectively build based on the provided config. The default if none is specified is gfs_build.cfg
      -h:
        Print usage message and exit
      -v:
        Run in verbose mode
    ```

    In addition to the above, build_all and partial_build had their indentation redone and their usage/help statement updated/added. Also, the build configuration file was renamed to from fv3gfs_build.cfg to gfs_build.cfg.

    Fixes #745
    Fixes #751

commit 2abee02765a3bae48f2b4e6a900400d6731eda06
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed May 18 01:02:57 2022 -0400

    Add continuous aerosols support (#693)

    Adds support for continuous aerosols when running with GOCART (using the forecast aerosol tracers from the previous cycle as initial tracer fields). This adds a new task to the workflow mesh in forecast-only mode. The new task does not run in the first cycle, though it will appear in rocotostat/rocotoviewer. In subsequent cycles, the task will launch as soon as the needed restart files from the previous cycle are available and gfs_init has completed. There is currently no mechanism to have aerosol_init run for the first cycle (for instance, continuing from a previous experiment); users would have to run the scripts off-line to add aerosols to the initial conditions.

    To support the introduction of the necessary python scripts, a new python environment is added to provide necessary libraries. This virtual environment is temporarily being housed in personal space, but an issue has been opened with hpc-stack to add it to the standard stack installations. The introduction of miniconda also caused the conversion of all of the rocoto entry scripts (the ones rocoto calls to run the job) to bash. Most of them had been in korne.

    To make sure the needed restart files are produced, config.fcst now makes sure the forecast cadence is included in the list of restart times. This may need more testing to ensure it works properly with other restart lists. As part of this, STEP_GFS was updated to properly determine the step from gfs_cyc instead of being a set value.

    Closes #366
    Fixes #516
    Fixes #630

commit 69b39ee5af8cfbb5cbf5cf62c92d01958b697652
Author: Kate Friedman <[email protected]>
Date:   Thu May 12 12:18:50 2022 -0400

    Add --init to GSI submodule command (#781)

    Needed to obtain libsrc submodule during checkout and allows the GSI to build correctly since this GSI hash still needs the libsrc submodule during build.

    Refs: #780

commit b09f92c21028ea37e4663ce4c304935a2dc45b33
Author: lgannoaa <[email protected]>
Date:   Thu May 12 08:20:16 2022 -0400

    Update field_table to be consistent with UFS (#778)

    Changes the fixed surface value of hydrometeor number concentrations and sub-grid TKE to 0. Also renames the field table. Both changes are consistent with changes made in UFS.

    Fixes #676

commit d72a62d6c0ab2e9f53ca3e6133148f29982f9d32
Author: lgannoaa <[email protected]>
Date:   Thu May 12 08:15:23 2022 -0400

    Remove special MOD_PATH from build scripts (#775)

    We always use pre-installed libraries and special MOD_PATHs are no longer necessary, so these are removed from build scripts. MOD_PATH. This also moots MOD_PATHs that were hard-coded to Hera locations in some scripts. The MOD_PATH in build_ufs.sh remains as it is still needed and is a relative path into the UFS repo.

    Fixes #298

commit 2adf123814a2f29e9cca54a11fbb2807b3f6cf1b
Author: Kate Friedman <[email protected]>
Date:   Wed May 4 12:31:20 2022 -0400

    Revert g2tmpl back to 1.10.0 (#773)

    Resolves bug with mismatch between hpc-ips and g2tmpl versions on the WCOSS-Dells. Also revert back to 1.10.0 on Hera and Orion to be consistent.

    Refs: #772

commit b90f4e99bc42f9a8afbeaa9479e674fb75e096ea
Author: lgannoaa <[email protected]>
Date:   Tue May 3 09:45:19 2022 -0400

    Remove git submodule update for upp checkout (#768)

    UPP no longer has a CMakeModules submodule, so the submodule update
    is removed from the checkout script.

    Fixes: #767

commit ad2b14d9b1ed0fe89fe59bfb96cc03630e8457de
Author: lgannoaa <[email protected]>
Date:   Tue May 3 09:44:57 2022 -0400

    Remove duplicate file linking for Thompson MP (#765)

    Files for Thompson MP were being copied twice by the link script: once by checking imp_physics, then again checking the CCPP Suite. This is now reduced to one check.

    Fixes: #675

commit a9fc0033b908aefb42d5b2d191c65af5cb7660c4
Author: Kate Friedman <[email protected]>
Date:   Thu Apr 28 15:17:22 2022 -0400

    Remove unneeded/outdated modulefiles (#762)

    Remove unneeded modulefiles for WCOSS-Cray and GSI monitoring.

commit 3333dee304b6b53d3d716c60d0c87ad06d629c1c
Author: lgannoaa <[email protected]>
Date:   Thu Apr 28 14:35:57 2022 -0400

    Remove prepbufr_pre-qc from archive lists (#753)

    The prepbuft_pre-qc file does not need to be archived, so it no longer is.

    Fixes #361

commit 88b1b1591d3201709f5f981908aaf7890d3021bd
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Apr 26 20:40:41 2022 -0400

    Convert module files from Tcl to Lua (#756)

    Converts all module files from Tcl format to Lua. As a side effect, this change enforces using the files as modules rather than improperly sourcing them instead of loading.

    Fixes #670

commit ca80aeb86cb221263611605ba23858448bce0bad
Author: lgannoaa <[email protected]>
Date:   Mon Apr 25 06:23:06 2022 -0400

    Ensure hourly files when GLDAS is on (#740)

    GLDAS requires hourly output, so make sure FHOUT is 1 when GLDAS is on.

    Fixes #695

commit 9d00239088651b73a9667b70bd6247b34e35046f
Author: lgannoaa <[email protected]>
Date:   Tue Apr 19 21:22:22 2022 -0400

    Update cyclone tracker to handle return code correctly #642

    Updates the cyclone tracker call to correctly exit with an error code if the tracker script reports one.

    Fixes #507

commit 33d3dd14d6df8109274dde4606bb7a50e4638fa2
Author: Jessica Meixner <[email protected]>
Date:   Tue Apr 19 21:18:56 2022 -0400

    Update ww3 pre and post exe build to use cmake (#731)

    Updates the WW3 pre/post build system to use cmake.

    Fixes #688

commit 39facec1e03a404f84fd05b8739cd8e4010a0779
Author: Kate Friedman <[email protected]>
Date:   Tue Apr 12 11:36:30 2022 -0400

    Add WCOSS2 GFSv16.2 operational def files into develop (#717)

    Add WCOSS2 operational GFS def files.

    Refs: #399

commit 0a85223e48a1a8dcced163791d8e7ae5a42a4fab
Author: Xianwu Xue - NOAA <[email protected]>
Date:   Tue Apr 12 11:34:17 2022 -0400

    Initialize "err" to avoid potential task fail (#715)

    If not initialize err, and change "set -x" to "set -xue", then the waveinit task will fail with error message:
        "line 234: err: unbound variable"

     On branch bugfix/issue_714
     Changes to be committed:
    	modified:   scripts/exgfs_wave_init.sh

    Refs: #714

commit fc6e1c3316397432d2da218b3c4fc0ea1fe70644
Author: Rahul Mahajan <[email protected]>
Date:   Tue Apr 5 11:07:21 2022 -0400

    config.base should not exist in the repository unless it is in ops.  template only exists in the repo, the experiment directory should not contain the templated config.base.emc.dyn (#707)

commit cabf437044cb937caf7a7830068fd9e413c5921f
Author: Jessica Meixner <[email protected]>
Date:   Wed Mar 30 21:28:50 2022 -0400

    Update model and settings for Prototype P8b (#681)

    Updates model and setting defaults for prototype 8b.

    The UFS version is updated to a recent version of UFS (tag Prototype-P8b). As part of this, the print_esmf option is removed from the model configure file and replaced with a new setting in nems.configure. We have not made this option user-configurable at this point, but that may come in the future.

    The default CCPP suites have been updated for all modes to either FV3_GFS_v17_p8 or FV3_GFS_v17_coupled_p8. This involves changing the microphysics to Thompson and changes the gravity wave drag version (knob_ugwp_version) to 0. This change breaks cycled mode for the time being. A future PR will revert the defaults to ones that allow cycled to run along with a more robust system for changing settings.

    Tiled fix files are now used for all modes instead of just coupled.

    Cellular automata now defaults on ON.

    There are also other miscellaneous settings that have had their defaults changed.

    Fixes #641, #687

commit e3f707cb9c05b45e9d4019679e406f54008279a5
Author: XuLi-NOAA <[email protected]>
Date:   Thu Mar 24 05:43:31 2022 -0400

    Modify eobs for EnKF thinning

    In the Hybrid EnKF GSI, the thinning box size, dmesh, is different for the full resolution analysis and EnKF respectively. There are set in GSI scripts for the full resolution analysis, and reset in global workflow in config.eobs.
    Only two thinning box sizes, dmesh(1) & dmesh(2), are defined in GSI scripts before, recently, two more, dmesh(3) & dmesh(4) are added. Accordingly, these two need to be added in config.eobs as well.

    Specifically, add dmesh(3)=225.0,demsh(4)=100.0 to config.eobs.

    Fixes #595

commit c32eea459af3177cee28e151b43fe5e12bdfc412
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Mar 22 11:18:10 2022 -0400

    Update ocean resolution for C48 (#651)

    The ocean resolution for C48 was set as 1-deg, but the fractional
    grid fix files available at C48 are for a 4-deg ocean grid. The
    ocean resolution is now set to this value when FV3 is C48.

    Also commented out a currently redundant block setting OCNRES in
    config.ocn. The one in ecfs has to stay as it recalculates the
    ocean resolution based on the EnKF resolution.

    Fixes #650

commit d758e8b227fca7b5a3320adc43c29ba492c3bfe9
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Mar 10 05:54:49 2022 -0500

    Add single forecast GOCART support (#659)

    Adds support for running single coupled free forecasts with GOCART aerosols. Support for continuous aerosol fields from cycle to cycle will be added in a future PR.

    To turn on aerosols, there is a new --aerosols option for setup_expt.py. The option takes no arguments. When it is used, aerosols will be turned on by setting DO_AERO="YES" in config.base.

    GOCART output files are placed in the chem directory in COM.

    There is a new tarball archived, chem.tar, that contains the GOCART output.

    Partially addresses #516
    Fixes #403

commit a0e23e254c7c881b20d66c1c53cd36de509e6d69
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Mar 1 10:50:39 2022 -0500

    Specify memory for init job (#669)

    The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed.

    Fixes #631

commit 6874e8939211fdc07143450bfd1b6a2863172e10
Author: arun chawla <[email protected]>
Date:   Fri Feb 25 16:39:45 2022 -0500

    Cleanup of utils directory (#660)

    Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo.

    Fixes #618

commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Feb 24 22:49:45 2022 -0500

    Fix bug with partition_batch on WCOSS (#668)

    partition_batch was not being defined for WCOSS machines, but was
    being used in a substitution for config.base.

    Fixes #667

commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Mon Feb 21 02:10:00 2022 -0500

    Split output filetype variable into atm and sfc (#602)

    The determination of the FV3 output filetype was a bit unwieldy as it
    contained two different settings (one for the atmosphere and one for
    the surface) that were not necessarily changed at the same time. They
    were also being determined in a different location than other settings
    based on the model resolution.

    Now the old OUTPUT_FILETYPES variable has been split into two different
    variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi-
    nation was also moved into the config.fv3 file, where other resolution-
    dependent computational settings are set.

    This has resulted in some functional change on WCOSS Dell, as the EnKF
    was using different chunking settings and never used parallel output
    for the surface likely because wasn't being run at a low enough resolu-
    tion to consider it. However, there is no reason to believe the two
    forecast modes should have different chunk or output settings. So, I've
    used the EnKF chunking settings and the free forecast switchover point
    for the surface output mode.

    The new filetype settings are now also divorced from the OUTPUT_FILE
    setting. However, that setting will soon be unnecessary as nemsio
    is removed from the code as an option (see Issue #601).

    Fixes #600
    Refs #601

commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Feb 17 15:55:24 2022 -0500

    Correct MODE comparisons for forecast only (#658)

    When the setup_expt scripts were combined, the forecast mode became a mandatory
    argument. The value of this option is then directly used for the MODE variable,
    but the argument name (forecast-only) does not match what was previously used
    for MODE in the forecast-only script (free) and some scripts were still testing
    against the old value instead of the new one. Those comparisons have now been
    updated to use the new MODE name.

    Fixes #657

commit f8867d3f0b1f3b5d238dced412996c56e30d31a1
Author: David Huber <[email protected]>
Date:   Thu Feb 10 20:23:54 2022 -0500

    Add LOCALARCH option (#628)

    Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR.

    Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO).

    Fixes #624.

commit 2950c7b97f99341caa738526138022987f665627
Author: Jessica Meixner <[email protected]>
Date:   Thu Feb 10 18:07:43 2022 -0500

    Turn on fractional grid by default for uncoupled forecasts (#638)

    Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true.

    Fixes #571

commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4
Author: David Huber <[email protected]>
Date:   Wed Feb 9 17:02:39 2022 -0500

    Specify warm start as .true. or .false. (#644)

    Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`.

    Fixes #643

commit e537f0cecabc8e16e26b14e606558de906b19e3f
Author: David Huber <[email protected]>
Date:   Tue Feb 8 23:33:21 2022 -0500

    Archive TC tracking logs if produced (#627)

    The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track.

    Fixes #625.

commit 32f93becde5ffa07c162252b95417845f2ab5159
Author: David Huber <[email protected]>
Date:   Tue Feb 8 20:59:37 2022 -0500

    Fix separate threading for GFS and GDAS forecasts. (#621)

    Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs.

    Fixes #610

commit 9bb09a92c55d4534feca5d521fbbd1c664730317
Author: David Huber <[email protected]>
Date:   Tue Feb 8 20:58:05 2022 -0500

    Updated the RadMon and OznMon links. #596 (#597)

commit 97ebc4d4e6483b135468d85cd9ed974f88955914
Author: Rahul Mahajan <[email protected]>
Date:   Thu Feb 3 02:56:34 2022 -0500

    Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537)

    `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name.

    The user is now required to provide a `mode` as the first positional argument to `setup.py`.  Valid options are `cycled` and `forecast-only`.

    ```
    ❯ python3 setup_expt.py -h
    usage: setup_expt.py [-h] {cycled,forecast-only} ...

    Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link
    initial condition files from $ICSDIR to $COMROT

    positional arguments:
      {cycled,forecast-only}
        cycled              arguments for cycled mode
        forecast-only       arguments for forecast-only mode

    optional arguments:
      -h, --help            show this help message and exit
    ```

    Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively.

    ```
    ❯ python3 setup_expt.py forecast-only -h                                                                  feature/unify-setups
    usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE
                                       [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}]
                                       [--app {ATM,ATMW,S2S,S2SW}]

    optional arguments:
      -h, --help            show this help message and exit
      --pslot PSLOT         parallel experiment name
      --resdet RESDET       resolution of the deterministic model forecast
      --comrot COMROT       full path to COMROT
      --expdir EXPDIR       full path to EXPDIR
      --idate IDATE         starting date of experiment, initial conditions must exist!
      --edate EDATE         end date experiment
      --icsdir ICSDIR       full path to initial condition directory
      --configdir CONFIGDIR
                            full path to directory containing the config files
      --cdump CDUMP         CDUMP to start the experiment
      --gfs_cyc {0,1,2,4}   GFS cycles to run
      --start {warm,cold}   restart mode: warm or cold
      --app {ATM,ATMW,S2S,S2SW}
                            UFS application
    ```

    ```
    ❯ python3 setup_expt.py cycled -h                                                                         feature/unify-setups
    usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE
                                [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}]
                                [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}]

    optional arguments:
      -h, --help            show this help message and exit
      --pslot PSLOT         parallel experiment name
      --resdet RESDET       resolution of the deterministic model forecast
      --comrot COMROT       full path to COMROT
      --expdir EXPDIR       full path to EXPDIR
      --idate IDATE         starting date of experiment, initial conditions must exist!
      --edate EDATE         end date experiment
      --icsdir ICSDIR       full path to initial condition directory
      --configdir CONFIGDIR
                            full path to directory containing the config files
      --cdump CDUMP         CDUMP to start the experiment
      --gfs_cyc {0,1,2,4}   GFS cycles to run
      --start {warm,cold}   restart mode: warm or cold
      --resens RESENS       resolution of the ensemble model forecast
      --nens NENS           number of ensemble members
      --app {ATM,ATMW}      UFS application
    ```

    Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications.

    The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing.

    The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source.

    The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation.

    There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR.   It will be cleaned up in subsequent PR's.

    Another unnecessary complication is the argument of `--start`.  The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot.  It is left unchanged.

commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Feb 2 11:19:43 2022 -0500

    Stop archiving gfsarch.log as it is being written (#581)

    The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group.

    Fixes: #558

commit 1b300dbf98eccdf03117b3795a2d8da3310a6126
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Feb 2 11:18:55 2022 -0500

    Fix build on non-WCOSS2 machines (#612)

    The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions.

    Also updates the UFS_UTILS repository to its new location under UFS instead of EMC.

    Fixes #476, #561

commit d3028b9d8268028226f9c27800fcd6655e9e4bb8
Author: David Huber <[email protected]>
Date:   Wed Jan 19 14:29:51 2022 -0500

    Fix setting of OUTPUT_FILETYPES (#589)

    The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine.

    Fixes #588

commit 13421b01a07e5d1cca32ee7579a4094d8209b072
Author: Rahul Mahajan <[email protected]>
Date:   Wed Jan 19 12:16:29 2022 -0500

    Update PR template

commit 322a61a61238e8486cb42d7d26282b2728d0c32f
Author: Rahul Mahajan <[email protected]>
Date:   Wed Jan 19 12:13:33 2022 -0500

    Move PR template MD file. Update issue templates

commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013
Author: Rahul Mahajan <[email protected]>
Date:   Wed Jan 19 11:32:51 2022 -0500

    rename pull_request_template.md

commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c
Author: Rahul Mahajan <[email protected]>
Date:   Wed Jan 19 10:34:54 2022 -0500

    make changes to the templates

commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Jan 19 10:08:45 2022 -0500

    Fix lfrac entry in diag table (#570)

    Land fraction was listed in the wrong module, keeping it from being
    written to output.

    Refs: #562

commit e2657adbdadaac7089591390428324c6aec260a9
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jan 18 17:04:04 2022 -0500

    Update NCO_bug_report.md

commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jan 18 16:59:18 2022 -0500

    Update bug report issue template

commit 2fab8b4213645b79b3fea8127e7d4ab21044188e
Author: Rahul Mahajan <[email protected]>
Date:   Tue Jan 18 15:13:53 2022 -0500

    Add templates for Github (#560)

    Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included.

commit 03be05309b184421c473f1b43082b766b114fd46
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Jan 18 10:02:02 2022 -0500

    Fix toggle for building workflow_utils (#580)

    The fv3gfs_build.cfg did not have a space between the periods and
    the setting for workflow_utils, which means the setting was ignored
    and the default of yes was always used.

    Fixes: #577

commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Jan 18 10:01:24 2022 -0500

    Remove redundant toggle for gldas build (#579)

    The build cfg files controlling which components are built and the
    partial_build.sh script all have two instances trying to set the
    value for gldas. This means one of the settings did nothing when
    changed.

    Fixes: #578

commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Jan 14 01:05:59 2022 -0500

    Update config missed in last GSI update (#569)

    When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489).

    Refs: PR #530

commit 33308ea3b477db17a5db455a4c4887e3d5cbc711
Author: Jessica Meixner <[email protected]>
Date:   Thu Jan 6 00:44:43 2022 -0500

    Updates for P8a (#538)

    Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype.

    Updates include:

    Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml )
    Updates to CA namelists
    Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2

    Closes #525

commit ae7092405e7552f76674b33fc81cb3973a68ad4e
Author: David Huber <[email protected]>
Date:   Mon Jan 3 17:28:47 2022 -0500

    Reordered CDUMP_LIST Refs #541 (#542)

commit 033b1d8ef29b7c829e8131758135b372ae61de26
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Sun Dec 19 22:18:48 2021 -0500

    Update GSI version to 2021 Dec 14 (#530)

commit b187e2aa15bfd7600c49627fd4c2d02915b50abe
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Thu Dec 16 22:15:45 2021 -0500

    Replace all backticks for command substitution (#526)

    All instances where backticks are used for command substitution are
    replaced with $( ). This standardizes usage around $( ), which can
    be nested and does not be confused with single quotation marks.

    Refs: #397

commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Fri Dec 10 15:35:00 2021 -0500

    Add coupled support and update UFS (#500)

    Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon.

    This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously.

    Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed.

    Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum:
    ```
    ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc
    ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc
    ```

    A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested.

    When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file.

    Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location.

    There are new options available for the checkout.sh, build_all, and link_fv3 scripts:
    - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out.
    - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg.
    - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files.

    ### To run in coupled mode with prototype settings/inputs
    1. Clone as usual
    2. Run checkout.sh
    3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary)
    4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled`
    5. Run setup_expt_fcstonly.py using the --app option S2SW
    6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW
    7. Run setup_workflow_fcstonly.py as usual
    8. Setup rocoto to run your experiment

    ### Technical udpates
    Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on.

    The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination.

    Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm.

    The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs.

    The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/

    The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh.

    Error checking was added to the build_ww3prepost.sh script.

    The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517).

    rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use.

    For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0).

    Co-authored-by: jikuang <[email protected]>
    Co-authored-by: Kate.Friedman <[email protected]>
    Co-authored-by: Rahul Mahajan <[email protected]>
    Co-authored-by: JessicaMeixner-NOAA <[email protected]>
    Co-authored-by: JianKuang-UMD <[email protected]>
    Co-authored-by: lgannoaa <[email protected]>

commit 8abe1dfa8d613f9398cd86564046b53235f62749
Author: lgannoaa <[email protected]>
Date:   Wed Dec 8 16:36:52 2021 -0500

    Fix resource assignment issue found in analysis job running global_cycle (#467)

    Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere.

commit fdffeaaf013f638ac43ad421981e48fabf7a7070
Author: malloryprow <[email protected]>
Date:   Thu Nov 18 14:17:02 2021 -0500

    Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508)

    * Update gfsmetp and gfsarch dependencies
    * Update EMC_verif-global tag to verif_global_v2.8.0

    Refs: #437, #472

commit 108abc589b746b2ba585d18a6b6587e5a0d89f39
Merge: f6f1bb702 e5cd63693
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Tue Nov 16 10:11:39 2021 -0500

    Merge pull request #497 from NOAA-EMC/feature/shebang

    Update ush/ script files with "python3" in shebang

commit e5cd636930b0e36ae9b2b25697cda317a2df996d
Author: jikuang <[email protected]>
Date:   Fri Nov 12 11:50:53 2021 -0600

    update the following files with "python3" in shebang

commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724
Author: lgannoaa <[email protected]>
Date:   Wed Nov 10 10:08:42 2021 -0500

    Add flag to launcher command to prepend task number to lines in stdout/err (#493)

    Modified env file settings for launcher variable to prepend task number label with "-l" flag.

commit 096fc1fb76ee01aff7908b91adc9851da9235cad
Author: Rahul Mahajan <[email protected]>
Date:   Tue Nov 9 08:47:22 2021 -0500

    Update NSSTBUFR file logic in prep job (#469)

    Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh.  Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow.  NSSTBUFR is created with different DTYPS_nsst before 2020102200.

commit 84194a735b46c907656fe2b2cca3ca97799396f0
Merge: a39cb11ef 0740b5b6c
Author: Walter Kolczynski - NOAA <[email protected]>
Date:   Wed Oct 27 11:52:55 2021 -0400

    Merge pull request #474 from NOAA-EMC/feature/setx2

    Hide module load commands

commit 0740b5b6c622d64b770c73aa47d9789494d94a99
Author: jikuang <[email protected]>
Date:   Tue Oct 26 13:19:07 2021 -0500

    wrap module load commands with set +x

commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22
Author: Kate Friedman <[email protected]>
Date:   Wed Sep 29 09:36:31 2021 -0400

    Update EMC_verif-global tag to verif_global_v2.5.2 (#450)

    New tag provides the following updates since the verif_global_v2.2.1 tag:
    - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards)
    - Added capability to produce fit-to-obs plots
    - Added support for Jet
    - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids
    - Hot fix for new METviewer AWS host name
    - Hot fix for reorganizing precipitation verification input files

    Refs: #438

commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30
Author: JianKuang-UMD <[email protected]>
Date:   Tue Sep 28 09:53:16 2021 -0400

    Remove firstcyc job (#440)

    The need for the firstcyc job has gone away, removing redundant job.

commit 1ca27148d776eedf96636a845feb95881cfaa138
Author: Kate Friedman <[email protected]>
Date:   Thu Sep 9 11:53:11 2021 -0400

    Update repository name for EMC_post component to UPP (#441)

    - the "EMC_post" repository was renamed to "UPP" on September 6th 2021
    - update repository url in checkout script and Externals.cfg

    Refs: #433

commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4
Author: Kate Friedman <[email protected]>
Date:   Mon Aug 23 11:22:26 2021 -0400

    Add rstprod support to Orion (#421)

    - Update EMC_verif-global tag to verif_global_v2.2.1
    - Turn on rstprod support by default on Orion
    - Change default DMPDIR path on Orion to new rstprod-supported GDA

    Refs: #347

commit 20c331dd9678834b980ccc932b6235a8266d4a88
Author: Kate Friedman <[email protected]>
Date:   Thu Aug 19 13:01:07 2021 -0400

    Update obsproc package versions for TAC2BUFR implementation (#423)

    Update obsproc package versions for TAC2BUFR implementation:

    - obsproc_prep v5.5.0
    - obsproc_global v3.4.2
    - new packages installed on WCOSS-Dell, Hera, Jet, Orion

    Refs: #341

commit 7f0f7400520b031e2428238a9741d4d8bfb8207a
Author: Kate Friedman <[email protected]>
Date:   Wed Aug 18 12:41:09 2021 -0400

    Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414)

    Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs

    Refs: #401

commit 9233d965cd19a94ee649b4ee8c117bb587b78923
Author: Kate Friedman <[email protected]>
Date:   Tue Aug 17 12:48:12 2021 -0400

    Update workflow_utils build modules and remove ncio module hack (#412)

    Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline.
    Refs: #407

commit df26e953792913669698ba64b414b3be5184f43d
Author: Kate Friedman <[email protected]>
Date:   Tue Aug 17 11:15:38 2021 -0400

    UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410)

    * Update UFS_UTILS tag to ufs_utils_1_6_0
    * Update HPSS path for real-time GFSv16 pre-implementation parallels

    Refs: #400

commit 34427f560c729ee3b7cc91ff357b3ad908a7486a
Author: lgannoaa <[email protected]>
Date:   Mon Aug 9 15:47:27 2021 -0400

    Free-forecast mode support on Jet (#394)

    Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported.

commit 8c777ad04bce0555bed9f6666b808515b0a3766d
Merge: ce66c74bb fc48af56d
Author: Kate Friedman <[email protected]>
Date:   Tue Jul 20 15:53:45 2021 -0400

    Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3

    Convert setup scripts to python3

commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b
Author: Brian Curtis <[email protected]>
Date:   Mon Jul 19 20:48:05 2021 +0000

    Missed a set of raw_input(), in py3 they are just input()

commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82
Author: Brian Curtis <[email protected]>
Date:   Mon Jul 19 19:59:54 2021 +0000

    revert rocoto_viewer as its being worked on elsewhere

commit 37f25384c29f6697be5c851868ce98d8b6c31207
Author: Brian Curtis <[email protected]>
Date:   Mon Jul 19 19:27:32 2021 +0000

    Fixes from testing

commit c0716f41f2446fec9a441b285d9033f73345c5d4
Author: Brian Curtis <[email protected]>
Date:   Mon Jul 19 10:28:06 2021 -0400

    Merge w/upstream and update those changes to py3

commit cf8758f84418c236fb45913912491a1c27b2829f
Merge: f9013decd ce66c74bb
Author: Brian Curtis <[email protected]>
Date:   Mon Jul 19 09:21:25 2021 -0400

    fix merge conflict in workflow_fcstonly

commit ce66c74bbc43e997bae66a2c2035f2412d3f602b
Merge: 96347ea52 7a166da9f
Author: Kate Friedman <[email protected]>
Date:   Wed Jul 14 16:18:55 2021 -0400

    Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres

    Correct wrong settings for high-res warm-start free-forecast

commit 7a166da9f20a59729be39fff953bfe367987f046
Author: Kate.Friedman <[email protected]>
Date:   Wed Jul 14 19:19:45 2021 +0000

    Reduce C768 npe_wav_gfs from ops 440 to dev 140

    Refs: #353

commit b34c581c3b19ecdcdb4eff463e855597e5c08d80
Author: Kate.Friedman <[email protected]>
Date:   Wed Jul 14 19:15:31 2021 +0000

    Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step

    - remove default value for start (EXP_WARM_START)
    - if user provides start flag then use it for EXP_WARM_START
    - if user doesn't provide start flag then make a decision for them based on resolution
    - if start=None and res=768 then start=warm
    - if start=None and res!=768 then start=cold

    Refs: #353

commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572
Author: Kate.Friedman <[email protected]>
Date:   Thu Jun 24 16:38:25 2021 +0000

    Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768

    - have free-forecast setup_expt script check if resolution is operational resolution (C768)
      and if so, set EXP_WARM_START=.true.
    - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting
    - the --start argument still works but new check will override if res=768
    - users can still change config.base setting as needed for special scenarios

    Refs: #353

commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09
Author: Kate.Friedman <[email protected]>
Date:   Wed Jun 23 21:21:51 2021 +0000

    Revert EXP_WARM_START if-block addition in config.getic

    - need to determine better way to set EXP_WARM_START

    Refs: #353

commit 1c03067ca570295b65f967467ef2329fb7999578
Author: Kate.Friedman <[email protected]>
Date:   Wed Jun 23 19:33:18 2021 +0000

    Revert config.base EXP_WARM_START check change

    Refs: #353

commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1
Author: Kate.Friedman <[email protected]>
Date:   Wed Jun 23 19:12:27 2021 +0000

    Add checks for EXP_WARM_START in config.base and config.getic

    - add OPS_RES variable to both config.base.emc.dyn and config.getic
    - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops)
    - check in config.base helps with later IAU checks
    - help catch when user doesn't set EXP_WARM_START=true when running v16 C768

    Refs: #353

commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2
Author: Kate.Friedman <[email protected]>
Date:   Wed Jun 23 19:10:17 2021 +0000

    Add cd to ROTDIR when pulling ops warm starts

    - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs
    - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR

    Refs: #353

commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882
Author: Kate.Friedman <[email protected]>
Date:   Wed Jun 23 19:06:42 2021 +0000

    Reduce C768 resource settings to fit node limits

    - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job
    - bring C768 settings in config.fv3 down to 148 nodes (on Hera)
    - tested new settings in free-forecast mode on Hera

    Refs: #353

commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c
Merge: cfca8bb2c 5c042e087
Author: Kate Friedman <[email protected]>
Date:   Wed Jun 23 11:13:06 2021 -0400

    Merge pull request #316 from NOAA-EMC/feature/hpc-stack

    GFS components update for hpc-stack support

commit 5c042e087c02cb82fe24ce666e477791f5e2417e
Merge: b36414e4c cfca8bb2c
Author: kate.friedman <[email protected]>
Date:   Thu Jun 17 19:33:03 2021 +0000

    Merge remote-tracking branch 'origin/develop' into feature/hpc-stack

commit cfca8bb2ca0dc0105b905c536f346002408db771
Merge: e08f55583 fba8cef5b
Author: Kate Friedman <[email protected]>
Date:   Thu Jun 17 14:40:18 2021 -0400

    Merge pull request #342 from KateFriedman-NOAA/issue178

    Free-forecast integration with chgres_cube and resolve know mode bugs

commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf
Author: Kate.Friedman <[email protected]>
Date:   Wed Jun 16 13:57:14 2021 +0000

    Remove wave restart pull in getic script

    Refs: #178

commit 921838feb9f6fd3fc3c69579c677ffdd7175a103
Author: Kate.Friedman <[email protected]>
Date:   Wed Jun 16 13:18:35 2021 +0000

    Remove old compile command from build_fv3.sh

    Refs: #178

commit b36414e4ce49579c5db1829fab46e1a4ef302569
Merge: 9cf615d11 e08f55583
Author: kate.friedman <[email protected]>
Date:   Tue Jun 15 18:36:55 2021 +0000

    Merge remote-tracking branch 'origin/develop' into feature/hpc-stack

    Refs: #164

commit 65ff48e049a651e74be8be121163c20957bf1c44
Author: kate.friedman <[email protected]>
Date:   Thu Jun 10 18:37:24 2021 +0000

    Add v16 pgb anl pull to getic script

    Refs: #178

commit 37e7c2e0806678c93a11bae682f48da172940fd6
Author: kate.friedman <[email protected]>
Date:   Thu Jun 10 18:36:59 2021 +0000

    Add OPS_RES variable to init script

    Refs: #178

commit db18627960d2def7bbfee30994f4be6586babe1c
Author: kate.friedman <[email protected]>
Date:   Thu Jun 10 18:36:10 2021 +0000

    Increase init job walltime to 30 mins from 15 mins

    Refs: #178

commit 30aefb11dd8130f1d4a1e6eb951e1fa400fdc361
Author: kate.friedman <[email protected]>
Date:   Thu Jun 10 15:43:27 2021 +0000

    Update/fix pull of v14/v15 pgrb2 anl files in getic job

    Refs: #178

commit 18970c716d79922fa02b86165996bb47fb42d3fa
Author: kate.friedman <[email protected]>
Date:   Wed Jun 9 12:04:01 2021 -0500

    Disconnect archive job in workflow from HPSS access check

    - remove dependency on HPSS access to check for adding gdas[gfs]arch job to workflow
    - add HPSSARCH variable to ARCHIVE_TO_HPSS definition in cycled workflow, similar to prior addition to free-forecast script

    Refs: #178

commit b52d2f0b82e0e376905c64daa593362396f8da1b
Author: kate.friedman <[email protected]>
Date:   Tue Jun 8 13:06:30 2021 -0500

    Update UFS_UTILS checkout to ufs_utils_1_4_0 tag

    - new ufs_utils_1_4_0 tag includes updates to support this branch
    - From tag release notes:
      - Update the GDAS initialization utility to ingest GFS v16 data.
      - Update to process either the GFS or GDAS CDUMPs.

    Refs: #178

commit 4c858c0f059abd0ff4c937c7bab692d7b13a8163
Author: kate.friedman <[email protected]>
Date:   Tue Jun 8 13:05:08 2021 -0500

    Adjust comments in getic job script

    Refs: #178

commit 898a43fb74005e969ecb5baf28ecf2d51f7c5dda
Author: Kate.Friedman <[email protected]>
Date:   Tue Jun 8 15:57:32 2021 +0000

    Adjust getic/init job scripts

    - adjust EXTRACT_DIR, DATA, and ROTDIR usage in getic and init jobs
    - remove duplicate pgb file pull from init job

    Refs: #178

commit 1cdc2a44c6d29cfb8f06a50238ea29d28642c1f1
Author: Kate.Friedman <[email protected]>
Date:   Tue Jun 8 15:56:46 2021 +0000

    Add cmake module load to Hera block in machine-setup.sh

    Refs: #178

commit fe448ff29aedca6a40a748ee47ae001b1639188c
Author: kate.friedman <[email protected]>
Date:   Thu Jun 3 19:32:15 2021 +0000

    Set DO_WAVE to NO

    - turning off waves by default in config.base

    Refs: #178

commit bfb0a33305a46d87f62c4a5c8bd7799a60362678
Author: kate.friedman <[email protected]>
Date:   Thu Jun 3 13:13:08 2021 -0500

    Remove RUN_CCPP option, force CCPP now

    - remove RUN_CCPP case option from build_all.sh
    - remove RUN_CCPP option in build_fv3.sh, force CCPP build now
    - remove pre-CCPP GFS ops tag checkout option in checkout.sh, forcing CCPP hash checkout now

    Refs: #178

commit 771782f109de15f9f0214bcceb852b51bb4b0e02
Author: kate.friedman <[email protected]>
Date:   Thu Jun 3 13:09:42 2021 -0500

    Replace Orion checks with hpssarch checks for getic job

    - add hpssarch variable to setup_workflow_fcstonly.py
    - replace Orion checks with hpssarch=YES checks

    Refs: #178

commit e2ac5872ca482eb335bc6294e00594dc3a806718
Author: kate.friedman <[email protected]>
Date:   Wed Jun 2 14:23:35 2021 +0000

    Update WCOSS-Dell section of machine-setup.sh

    - needed cmake module loaded for building
    - added cmake module load and prereq stack loads

    Refs: #178

commit f0afb91bae738413539ee2f1fdc63b79e93b3e52
Author: kate.friedman <[email protected]>
Date:   Wed Jun 2 14:22:43 2021 +0000

    Change BDATE to GDATE in getic.sh

    Refs: #178

commit 69ac287062512b929a5193ebc86e4c7fcbbb1917
Merge: e62cefb39 e08f55583
Author: Kate Friedman <[email protected]>
Date:   Wed Jun 2 10:17:52 2021 -0400

    Merge branch 'NOAA-EMC:develop' into issue178

commit e62cefb3943a87a90fd40234f08845534df818a1
Author: Kate.Friedman <[email protected]>
Date:   Tue Jun 1 16:50:28 2021 +0000

    Correct gdas operational tarball name in getic job script

    Refs: #178

commit 127723adfde2b7b7c79bd4d346cafcb1f265dc1c
Author: Kate.Friedman <[email protected]>
Date:   Tue Jun 1 16:44:37 2021 +0000

    getic job updates to add OPS_RES variable and pull from operational tarballs for warm starting

    - add OPS_RES variable to define current operational resolution; use variable where needed now
    - updated getic job script to use OPS_RES variable in if-block check
    - updated getic job script with new operational tarballs to pull for warm starting high res runs

    Refs: #178

commit 499f217f92b5bb0fad9e71de221937d9973046ce
Author: Kate.Friedman <[email protected]>
Date:   Tue Jun 1 15:49:41 2021 +0000

    Resolve bug in wavepostpnt jobs when DOBLL_WAV=NO

    - change DOBNDPNT_WAV=YES and CFP_MP=YES if-block to only prepare cmdtarfile for CFP
    when DOBLL_WAV=YES to avoid scenario where only a single command is added to cmdtarfile

    Refs: #178

commit e08f5558372d43d88890ca639e70ab923071361b
Merge: e09a398f1 b2879fe9f
Author: Kate Friedman <[email protected]>
Date:   Wed May 26 12:27:40 2021 -0400

    Merge pull request #327 from NOAA-EMC/operations

    Operations updates for GFSv16.1.1

commit 824ff7254fba04a0b3726316d300f9fa6282c937
Author: Kate.Friedman <[email protected]>
Date:   Tue May 25 20:42:25 2021 +0000

    Change UFS_UTILS version to feature branch for testing

    Refs: #178

commit 151e0b56b6e38f40449c9eb0807ffa92b6aa46f9
Author: Kate.Friedman <[email protected]>
Date:   Tue May 25 20:41:32 2021 +0000

    Correct if-statement syntax in config.init

    Refs: #178

commit 005d33d7b100b279e0db5290824c3e7acabfa4ba
Merge: 5ec376bab e09a398f1
Author: Kate Friedman <[email protected]>
Date:   Mon May 24 15:23:05 2021 -0400

    Merge branch 'NOAA-EMC:develop' into issue178

commit b2879fe9f90def631047f533db2144858d827023
Merge: 68b9157bd a8ed770d9
Author: Kate Friedman <[email protected]>
Date:   Mon May 24 10:07:05 2021 -0400

    Merge pull request #326 from NOAA-EMC/release/gfsv16.1.1

    GFSv16.1.1

commit e09a398f1cedc7252219e75bf0b319d2601bc8df
Merge: e3fcfebc1 6bad810bc
Author: Kate Friedman <[email protected]>
Date:   Fri May 21 09:58:49 2021 -0400

    Merge pull request #317 from malloryprow/feature/EMC_verif-global_upgrade

    EMC_verif-global v2.0.0 major release updates

commit 6bad810bccdfc893fd51b8b55c60c1f732547c3a
Author: Mallory Row <[email protected]>
Date:   Fri May 21 13:55:13 2021 +0000

    Update Externals.cfg EMC_verif-global tag to verif_global_v2.0.2

    Refs: #315

commit 9cf615d11b096ea4843f4e5938a6a65f3500df49
Author: kate.friedman <[email protected]>
Date:   Thu May 20 20:10:18 2021 +0000

    Modulefile updates for testing with waves on

    - updated ww3 and base modulefiles to add modules and update some
    - added new: pio/2.5.2i, fms/2020.04.03
    - updated esmf module to esmf/8_1_1 and nceppost/dceca26 to upp/10.0.6

    Refs: #164

commit b155ff37040658703168268d4e58fe4e6b45a50d
Author: Mallory Row <[email protected]>
Date:   Thu May 20 15:00:04 2021 +0000

    Update EMC_verif-global tag to verif_global_v2.0.2

    Refs: #315

commit cae62e3f47e245e70fcf3721fb4c022ea11c059f
Merge: 8def77afd e3fcfebc1
Author: kate.friedman <[email protected]>
Date:   Wed May 19 19:45:05 2021 +0000

    Sync merge with develop and WW3 build updates

    - Merge remote-tracking branch 'origin/develop' into feature/hpc-stack
    - WW3 build updates: revert back to separate module files for build;
      address modulefile reorganization in separate issue
    - remove CCPP option with system build, doing CCPP by default now

    Refs: #164

commit 5ec376bababd935e4f3b15c4754105f5bd750657
Merge: 6b6b9ed39 e3fcfebc1
Author: Kate.Friedman <[email protected]>
Date:   Wed May 19 18:24:31 2021 +0000

    Merge remote-tracking branch 'origin/develop' into issue178

    * origin/develop:
      change fv3gfs checkout head
      fixed a compilation error, NEMs/exe existing, in hera
      build_fv3.sh with ATM
      fixed line 43 of link_fv3gfs.sh, build_fv3.sh v15 to v16
      bugfix for not removing last point from list in wave post pnt jobs
      changes added in link_fv3gfs for fix_aer
      changed fix dir for link_fv3gfs
      changes on build_fv3.sh and symlinks to optical data files instead of cp
      Update util_shared module version to 1.3.0 for wave footer fix
      Revert addition of ecflow trigger for wavepostbndpntbll job
      update ufs-weather-model tag to GFS.v16.0.16
      add ecflow updates for new wave bndpntbll job
      Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8
      Back out updates to add config.resources.nco.static
      WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg
      WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes
      fix for missing wave boundary cbull and bull files
      Fix cycle date in bull and cbull wave files
      Reverting transfer parm file changes committed at 39bab45
      Component tag updates for nwprod/gfsv16.0.7
      Updated transfer parm files for gdas, enkf, and gfs dissemination
      updated config.fcst
      testing merra2 workflow in hera
      update merra2 before a new pull request
      Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions
      udate config.base.emc.dyn
      high resolution MERRA2 data used
      fixed a bug related to orion
      added merra2 input and update diag_table
      merra2 workflow for orion
      Clean up commments
      Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes )

commit 4641c5d206a95e0e66276fa86d46ecd580213fd5
Merge: eff8a1258 e3fcfebc1
Author: Mallory Row <[email protected]>
Date:   Wed May 19 14:51:19 2021 +0000

    Merge branch 'develop' into feature/EMC_verif-global_upgrade

commit e3fcfebc1ff9c9f9ceda7b775de0c34117de6459
Merge: 95e0dffea fa5d1e2ba
Author: Kate Friedman <[email protected]>
Date:   Wed May 19 10:02:19 2021 -0400

    Merge pull request #254 from AnningCheng-NOAA/merra2

    Addition of support for MERRA2

commit fa5d1e2ba242a08e26cb7bac8c68b700a83d1d60
Author: anning.cheng <[email protected]>
Date:   Tue May 18 10:41:16 2021 -0400

    change fv3gfs checkout head

commit 283c4a044847bbadd0cef46e14dde4de97abe986
Author: anning.cheng <[email protected]>
Date:   Mon May 17 15:56:56 2021 -0400

    fixed a compilation error, NEMs/exe existing, in hera

commit 6b574160f94329754677e7f4541ab07c44185bb0
Author: anning.cheng <[email protected]>
Date:   Fri May 14 13:44:18 2021 +0000

    build_fv3.sh with ATM

commit dfc8aa9a2cf5370fff38520d2a28f3960be3b583
Merge: bf5d11063 95e0dffea
Author: anning.cheng <[email protected]>
Date:   Wed May 12 20:11:44 2021 +0000

    Merge remote-tracking branch 'upstream/develop' into merra2

commit eff8a1258aa70c061fe69697388f8914935726ee
Merge: b1ad0b963 95e0dffea
Author: Mallory Row <[email protected]>
Date:   Wed May 12 19:15:17 2021 +0000

    Merge branch 'develop' into feature/EMC_verif-global_upgrade

commit 95e0dffea435af17be9150fcd0c842763768b45f
Merge: fc727f405 dd4d18790
Author: Kate Friedman <[email protected]>
Date:   Wed May 12 14:51:10 2021 -0400

    Merge pull request #323 from NOAA-EMC/sync/operations_v16.0.9

    Bring operations branch v16.0.9 changes into develop

commit dd4d1879093516a7950c9e0e59f6e44e462199f6
Merge: fc727f405 68b9157bd
Author: kate.friedman <[email protected]>
Date:   Mon May 10 16:40:13 2021 +0000

    Merge remote-tracking branch 'origin/operations' into sync/operations_v16.0.9

    * origin/operations:
      bugfix for not removing last point from list in wave post pnt jobs
      Update util_shared module version to 1.3.0 for wave footer fix
      Revert addition of ecflow trigger for wavepostbndpntbll job
      update ufs-weather-model tag to GFS.v16.0.16
      add ecflow updates for new wave bndpntbll job
      Additional WAFS tag update to gfs_wafs.v6.0.21 for GFSv16.0.8
      Back out updates to add config.resources.nco.static
      WAFS tag update to gfs_wafs.v6.0.20 in Externals.cfg
      WAFS tag update (gfs_wafs.v6.0.20) for v16 post-implementation fixes
      fix for missing wave boundary cbull and bull files
      Fix cycle date in bull and cbull wave files
      Reverting transfer parm file changes committed at 39bab45
      Component tag updates for nwprod/gfsv16.0.7
      Updated transfer parm files for gdas, enkf, and gfs dissemination
      Issue #215 - GFSv15.3.5 ops updates for gempak and bufrlib versions
      Clean up commments
      Updated sorc/checkout.sh to pick gfsda.v15.3.3 ( EUM bufr changes )

    Refs: #309

commit 8def77afd4a9f1cd6cdca42c956bc7ebf675a58d
Merge: c6e2a96e8 d46e8cf49
Author: Kate Friedman <[email protected]>
Date:   Mon May 10 11:45:02 2021 -0400

    Merge pull request #322 from JessicaMeixner-NOAA/hpcstackww3

    Updates for ww3 pre and post exec builds for hpc-stack

commit d46e8cf49aff0dbf72e457f1177e10e6f50252a6
Author: Jessica Meixner <[email protected]>
Date:   Mon May 10 15:31:56 2021 +0000

    update for ww3_pre/post build:
    -- remove ww3 specific module files
    -- updated module base files to be in sync with ufs-weather-model
       except that jasper is a more recent version which is needed for ww3_grib
    -- added extra ww3 execs needed for this branch
    -- added ww3prepost build to build_all and partial build

commit c6e2a96e86611cce00455609d9be803d580e7bc0
Author: Kate.Friedman <[email protected]>
Date:   Mon May 10 14:30:13 2021 +0000

    Change fix file linking to scan for possible subfolders in set

    - instead of providing subfolder names, scan for subfolders in FIX_DIR path
    and then create symlinks based on existing subfolders in set
    - will not have to keep updating list of subfolders now

    Refs: #164

commit aa1d1e9ca1d8521ef22e1bdb654d4a70e7b1e29e
Author: Kate.Friedman <[email protected]>
Date:   Mon May 10 14:27:13 2021 +0000

    Change CCPP_SUITE from FV3_GFS_v16beta to FV3_GFS_v16

    - newer ufs-weather-model hash supports FV3_GFS_v16 suite

    Refs: #164

commit a8ed770d9c1e8614c5477d0129d6eaf5fe4e2085
Author: kate.friedman <[email protected]>
Date:   Thu May 6 19:32:36 2021 +0000

    Companion update to Externals.cfg for WAFS tag update to gfs_wafs.v6.0.22

    Refs: #1,#321

commit 68d9b5b5ff072b1f62131a9f7495c33c14c4a850
Author: kate.friedman <[email protected]>
Date:   Thu May 6 19:28:17 2021 +0000

    WAFS tag update to gfs_wafs.v6.0.22 for bug fix

    Refs: #1,#321

commit 68b9157bd59278dc07369d316999d3c8485ebf7c
Merge: 1f5af6283 97fe99096
Author: Kate Friedman <[email protected]>
Date:   Wed May 5 10:50:42 2021 -0400

    Merge pull request #306 from NOAA-EMC/release/gfsv16.0.0_to_ops

    GFSv16.0.9

commit 1aea3ee393c99d4f76556fbbdbebc43f629558c2
Author: kate.friedman <[email protected]>
Date:   Wed May 5 14:30:06 2021 +0000

    Add build script and modulefiles for WW3 build

    - WW3 execs no longer built by FV3 build, need separate build now
    - add new build_ww…
jkhender added a commit to jkhender/global-workflow that referenced this issue Nov 18, 2022
@jkhender
Merged NOAA-EMC/develop 03Aug22 branch into gslv17p8_dev
2fe8513 
commit 71a16e84a4ce59869879dd6c20007d0271521e7b
Author: Judy.K.Henderson <[email protected]>
Date:   Fri Nov 18 01:46:14 2022 +0000

    Squashed commit of the following:

    commit a658e75e579ebc4f454377e5a9cf4c1fc54e4e3d
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Aug 3 18:34:34 2022 +0000

        Updates for P8  (#946)

        These are the final updates for Prototype 8.  These changes include:
        * Updating to the latest ufs-weather-model hash (in progress, waiting for PR) which will update the calculation of 2m T
        * A small update to the organic carbon coefficients for p8, raises them from 0.3 -> 0.4 for oc1 and oc2
        * Uses 10km input files for aerosols
        * Sets do_gsl_drag_tofd=false by default, which helps with stability of the model

        Closes #937

    commit b2155ad3dc999a2f41aeace58f3b199a8ddde65c
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Aug 3 10:04:06 2022 -0400

        Fix GLDAS j-job link (#954)

        The cd was misplaced when checking for the existence of gldas.fd to
        create the link for the j-job, so the directory was never found and
        the job never linked.

    commit 395720cef000ef221c49c93d4f68417b7fda64b6
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Aug 1 17:38:50 2022 -0400

        Add ocean post to archive dependencies (#949)

        The archive job was not waiting for ocean post to complete because
        there was no dependency.

        Fixes #948

    commit 145b67f70f44abbb713e19073016bacfbfcb8184
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Jul 29 13:42:38 2022 -0400

        Initial commit of directory comparison tools (#934)

        Adds a new `test/` directory to the top level. Inside are miscellaneous scripts I have used to test bitwise identicality of experiments.

        Main scripts:
        - `diff_ROTDIR.sh`: Compares two output directories
        - `diff_UFS_rundir.sh`: Compares two UFS run directories

        Other scripts and file are helpers to these two main scripts.

        May eventually form starting point of a global workflow regression test (#267)

        Refs #267

    commit e480093446797e556bc1371f9f80610a7c9a6d4b
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Jul 29 13:42:02 2022 -0400

        Add preamble, convert to bash, and remove env (#929)

        This is the first in a wave of commits to improve and standardize the scripts within global workflow. In this commit, all scripts run during execution are converted to bash and a preamble is added to every script that is not sourced by another script.

        Every script executed during a forecast cycle is converted to bash. This was mostly straightforward, though there were a couple Korne-shell conventions (primarily using `typeset` to format strings) that had to be replaced with bash-compatable alternatives like `printf`. This in turn required a few modification to prevent zero-padded numbers from being treated as octals (other may have been pre-existing bugs).

        The preamble contains a number of feature to standardize code and improve script flow and debugging.

        - First, it uses two variables, `$STRICT` and `$TRACE` to control the behavior of `set`. When `$STRICT` is `"YES"`, error on undefined variables (`set -u`) and exit on non-zero return (`set -e`) are turned on. When `$TRACE` is `"YES"`, command trace (`set -x`) is turned on and a useful string is set to `$PS4` that gives the name and line number of the script. Both `$STRICT` and `$TRACE` default to `"YES"`. They also set up commands, `$ERR_EXIT_ON` and `$TRACE_ON`, that will restore the setting of each in the event a script needs to temporarily turn them off.

        - Second, the preamble sets up primative timing of scripts using Posix `date`.

        - Third, it echos the script is beginning and at what time.

        - Finally, it also establishes a postamble function and sets it to run as a trap of EXIT. The postamble will use the end time to calculate the run time of the script, then print that the script has ended at what time, how long has elapsed, and the exit code. By setting this up as a trap instead of just calling it at the end of the script, it ensures the postamble is called even if the script exits early because there is an error.

        - In response to this standardization, parts of scripts that performed these preamble functions (announcing start/end, `set -x`, etc) have been deleted. For some scripts where temporarily turning off `-x` or `-e` is needed, they now use `$ERR_EXIT_ON` and `$TRACE_ON` to return to the correct state afterwards, instead of blindly turning the setting back on.

        - Additionally, some modifications were needed to comply with `set -eu`. Mostly taking care of undefined variables, but also a couple instances where a non-zero return code had to be dealt with.

        If users wish to use their own preamble script instead, the default script can be overridden by setting `$PREAMBLE_SCRIPT` before the run begins.

        Instance where scripts would print the full list of environment variables have been removed. These can be spot added back in to debug as necessary. Alternatively, a future PR will add them back in in a standardized way.

        `rstprod.sh` is added to the link list from gsi_monitor.fd, as it is needed for the radmon scripts.

        The placeholders for AWIPS and GEMPAK in the Hera and Orion environment scripts were replaced with the correct definitions. There were also other modifications to AWIPS and GEMPAK scripts to get it working for development (AWIPS still isn't and will be fixed in the future).

        GSI scripts that were brought in recently had all of their backticks replaced with `$(  )` as was done with all other script previously.

        Refs: #397

    commit 949513642d33cb3976d0f8e7dd273aedec505a17
    Author: Rahul Mahajan <[email protected]>
    Date:   Thu Jul 28 18:36:58 2022 -0400

        minimal intervention to create a data-atmosphere xml (#936)

    commit e4b01b99f50c674635477ff3e2e962b9d5ed54aa
    Author: Rahul Mahajan <[email protected]>
    Date:   Thu Jul 28 18:28:28 2022 -0400

        Remove Cray, Dell, WCOSS1 from module-setup.sh.inc (#943)

        This file was missed in the initial cleanup.

    commit 1ed89c7d202974bd4ccd2b048fedc56382edc9ec
    Author: Rahul Mahajan <[email protected]>
    Date:   Thu Jul 28 15:35:37 2022 -0400

        bring GDASApp jjobs and exscripts to global-workflow (#941)

    commit f04f3ba4dfd5b358aea425f65f82d40917597776
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 26 22:07:42 2022 -0400

        change gdasechgres dependency to just gdasefcs01 instead of gdasefmn (#933)

        Replaces the dependency of `gdasechgres` on `gdasefmn` with `gdasefcs01`.

        Presently, `gdasechgres` has 2 dependencies:
        - `gdasfcst` - deterministic forecast
        - `gdasefmn` - ensemble forecasts (all of them).

        The work done in `gdasechgres` actually depends only on the `mem001/atmos/gdas.tHHz.atmf006.nc`.
        This file is used as a template as well as obtaining `hgtsfc`.
        As such, there is no reason to depend on the entire ensemble of forecasts to be complete before `gdasechgres` can start.

    commit 490de7bae1322cbaa8ee3d52406034c8edf62dd3
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 26 22:05:59 2022 -0400

        Remove obsolete platforms (WCOSS1, Dell, Cray, Theia) references. (#922)

        Removes code related to decommissioned HPC platforms WCOSS 1 (Dell & Cray) and Theia. Some references remain in scripts outside the global-workflow repo that are cloned as part of `checkout.sh`. Scripts from the `driver` directory that were hard-wired for one of the WCOSS1 platforms are also removed.

        Additionally, this commit also switches to using serial netCDF for resolutions C48. C96, C192.  Running with parallel netCDF (on Hera) gave errors when testing at C96 for the deterministic forecast.  If someone gives a very compelling reason to use parallel netCDF at these resolutions as default, I would be very interested in what they have to say.

        Closes #680

    commit 4eb296f7e82459b1d8188636ca3db60b5fa10091
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Tue Jul 26 14:50:30 2022 -0400

        Optimize DA clone, build, and link (#931)

        The PR contains changes to optimize the DA clone, build, and link.   Changes are made to `checkout.sh`, `build_all.sh`, and `link_workflow.sh` in the g-w `sorc/` directory.  These changes are in g-w branch `feature/clone`

        Two arguments are added to `checkout.sh` to allow the user to specify which DA package to build the global workflow with.  These options are
        - `-g`: clone from the [GSI](https://github.com/NOAA-EMC/GSI) repo and build the g-w for GSI-based DA
        - `-u`:  clone from the [GDASApp](https://github.com/NOAA-EMC/GDASApp) repo and build the g-w for UFS-based DA

        If no option is specified, `checkout.sh` does not clone any DA and DA related repos.  This is the default behavior of `checkout.sh`.   (_DA related_ repos include [GLDAS](https://github.com/NOAA-EMC/GLDAS), [GSI-utils](https://github.com/NOAA-EMC/GSI-utils), and [GSI-Monitor](https://github.com/NOAA-EMC/GSI-Monitor).)

        `build_all.sh` is modified to detect which repos and have been cloned and to build accordingly.   `link_workflow.sh` is modified to detect which directories are present and link/copy accordingly.

        Closes #930

    commit 2cad536551180d25bfcfc2b5d35fe1089de7f3c3
    Author: Kate Friedman <[email protected]>
    Date:   Tue Jul 26 13:25:37 2022 -0400

        WCOSS2 gempak ush scripts updates and cleanup of old release notes (#920)

        * WCOSS2 updates to gempak ush scripts

        - Add /gempak subfolder where needed in gempak ush scripts.
        - Remove unneeded commented out path settings from older iterations.

        * Removing older release notes

        - Cleaning out older GFS version release notes; includes current GFSv16.2.1 release notes, will commit GFSv16.3
        release notes with implementation this fall.
        - Will then keep only the latest release notes moving forward.

        Refs: #419

    commit ffcd5bbde7947902a73eebff7dfe04c2ab045b0a
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Fri Jul 22 16:00:51 2022 -0400

        Add GDASapp (first wave of JEDI changes) (#871)

        Merge changes associated with g-w issue #521 from g-w branch feature/ufsda_gdasapp into develop. feature/ufsda_gdasapp contains g-w extensions for JEDI based atmospheric DA.

        Specifically, this PR adds the option to add JEDI based variational and/or ensemble DA jobs to replace GSI based DA jobs.   The toggling on/off of JEDI_VAR and JEDI_ENS jobs is controlled via two new variables added to `config.base.emc.dyn` and `config.base.nco.static`
        ```
        # DA engine
        export DO_JEDIVAR="NO"
        export DO_JEDIENS="NO"
        ```
        When both variables are `NO`, the global workflow uses GSI based DA jobs.   Thus, the PR does not alter the default behavior of the develop global workflow.

        When `DO_JEDIVAR=YES`, GSI jobs `anal` and `analdiag` are replaced by JEDI_VAR jobs `atmanalprep`, `atmanalrun`, and `atmanalpost`.  When `DO_JEDIENS=YES`, GSI jobs `eobs`, `ediag`, and `eupd` are replaced by JEDI_ENS jobs `atmensanalprep`, `atmensanalrun`, and `atmensanalpost`.

        `checkout.sh`, `build_all.sh`, and `link_workflow.sh` are updated to clone, build, and install the GDASapp in the global workflow.
          Local directory `sorc/gdas.cd` contains the GDASApp superstructure plus the relevant components of JEDI needed to run GDASApp.

        Closes #521

    commit 98f4d16e9bba86d2c433aa0521d960b566062a1f
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Thu Jul 21 16:02:31 2022 -0400

        Add postsnd job when bufrsnd it on (#926)

        In the workflow refactoring, the addition of postsnd to the task list when
        bufrsnd is true was inadvertently left out. It is now added back in.

    commit e2869a1247ad2ba72c1bfe82f7682323d5128f4c
    Author: Kate Friedman <[email protected]>
    Date:   Tue Jul 19 16:16:20 2022 -0400

        Updated GFS transfer*list files from operations (develop) (#918)

        Updated transfer list files from WCOSS2 ops.

        - In move to WCOSS2 the transfer*list files were moved into a new
        transfer folder under the upper-level parm folder.
        - The transfer*list files were updated to clean out unneeded paths
        and the beginning of the paths were updated from:
          `com/gfs/_ENVIR_`
        to:
          `_COMROOT_/gfs/_SHORTVER_`

        Refs: #419

    commit 1651014250a748c8c2e2878663c3e8376639044a
    Author: ChunxiZhang-NOAA <[email protected]>
    Date:   Tue Jul 19 11:18:33 2022 -0400

        Fix history type of cldfra in the diag_tables  (#915)

        The history type of the new cloud fraction field (cldfra) is changed so it is written to the correct output file.

        Fixes #914

    commit 5c9639dba419ef51608aa8962b54ae69c8ad8c60
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 19 11:11:38 2022 -0400

        Combine ecflow and rocoto workflow generation (#916)

        Consolidates the workflow generation systems for ecflow and rocoto.  Further unification will be made to make a choice to use one or the other.  At this time, they are separate and need separate input criteria.

        Moves `ush/rocoto` to `workflow/` at the top level.  Further refining will be performed as needed based on use and need.

    commit b690ed6c7c1a250171484aba267d0724d8c12d11
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jul 18 19:33:36 2022 -0400

        Remove new GSI scripts from gitignore (#917)

        When the scripts were moved over from GSI into global workflow, they
        were never removed from the .gitignore. This has now been addressed.

        Follow-up to PR #904

    commit aa2542eb4c95827bc1fc7a4a76d4d0f5bc701f74
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jul 18 13:49:09 2022 -0400

        Add ecFlow generator to `develop` (#912)

        * merge workflow_generator from dev_v16 at 7b7947e2 and move workflow_generator to ush/ecflow

    commit 5a58fa8a2f75590a671b45bf75a431f2acf2340b
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jul 18 13:02:59 2022 -0400

        Update gsi-utils hash to include bugfix in handling 3D sfc files (#913)

        Update GSI-Utils hash to include bugfix that processed 3D fields in surface netCDF files.

        Fixes #909

    commit e8361cc343743bb5087e75f89406c1265404e359
    Author: Rahul Mahajan <[email protected]>
    Date:   Mon Jul 18 12:44:25 2022 -0400

        Combine setup_workflows scripts (#859)

        `setup_workflow.py` and `setup_workflow_fcstonly.py` are used for setting up the XML for cycled and forecast only configurations.
        They share large parts of the tasks and dependencies.

        This PR unifies the ones listed above and makes room for extending for incoming applications.
        The above two scripts are being replaced by `setup_xml.py`.
        The usage is:

        ```
        $> setup_xml.py /path/to/experiment_directory
        ```

        This PR also removes the handicap of defining hundreds of entities for task resources.  Instead the task resources are placed with the task itself.

        This PR also does the following:
        - moves the declaration of `DOBNDPNT_WAVE="NO"` from `config.wave` to `config.base`
        - reduces timestep at `C48` from `1200s` to `450s` in `config.fv3`.  Several ensemble members failed.  Inspecting `config.fv3.nco.static`, the value there is `450s`
        - `eobs` job times out with a wallclock time of `15m`.  It is increased to `45m` to play it safe.

    commit 13385d9c9018def1fbce6772e53665ccb90b2a2a
    Author: Rahul Mahajan <[email protected]>
    Date:   Fri Jul 15 14:02:12 2022 -0400

        Load `ncdiag` module instead of building it in the GSI, use UFSWM build system, pull sfcanl out from anal. (#905)

        `ncdiag` is no longer being built within the GSI.  It is available as a module on all systems; Hera, Orion and WCOSS2.

        This PR:
        - loads ncdiag module
        - finds the `ncdiag_cat_serial.x` executable from that module (once loaded)
        - updates hashes for GSI, GSI-utils and GSI-monitor.  No code changes were made in these repos.  Only location of `ncdiag` changed.

        In addition, this PR:
        - Uses the ufs-weather-model compilation script.  The global workflow is duplicating and missing configuration options set in the ufs-weather-model.  This also enables a "debug" mode of compiling the model (#300).
        - Fixes #906
        - Fixes an improper link to `fix_gsi`.  It was being linked to a non-existing directory.
        - separates out the creation of Gaussian surface analysis from the GSI atmospheric analysis.  This capability is pulled from PR #871.  It was necessary to pull these changes from PR #871 since the `j-jobs`, `ex-scripts` from the GSI have been brought to global-workflow and the companion PR for PR #871 in the [GSI PR 415](https://github.com/NOAA-EMC/GSI/pull/415) were already merged prior to the updates needed for `ncio` and `ncdiag`.

        I realize all these changes could have been streamlined into smaller atomic PR's.

        **Note:**  This PR also requires a documentation update as a new job `sfcanl` has been added to the workflow.

    commit b61c2375a05daff20805d0216ade8201192c0199
    Author: Fanglin Yang <[email protected]>
    Date:   Thu Jul 14 20:07:54 2022 -0400

        Update ice climo, fix option for non-fractional grid, and add cloud fraction for Thompson (#902)

        Updates the ice climatology from CFSR to IMS_NIC blended.

        Fixes issue in the diag table where the cloud fraction entry for Thompson was not included.

        Adds new coupled mode setting for when fractional grid is not used.

        Fixes #886

        Co-authored-by: Chunxi.Zhang-NOAA <[email protected]>

    commit 680270975e2eb2f09c58a6112a87c0ecaec9e2a5
    Author: Barry Baker <[email protected]>
    Date:   Thu Jul 14 17:03:34 2022 -0400

        Update aerosol variable names and dust alpha (#888)

        The names of some aerosol fields have changed and needed to be updated.

        The dust alpha parameter is updated to improve model performance.

        A typo in the scavenging parameter definition where a string was terminated with a 'smart-quote' instead of a standard one is corrected.

    commit 06b25267b7839808508eed9e91dcd2b76a33c3ca
    Author: Jessica Meixner <[email protected]>
    Date:   Thu Jul 14 18:52:56 2022 +0000

        Allow for wave mesh to be different than the ocean/ice mesh (#897)

        This PR updates the configuration to allow for the wave mesh to be different from the ocean/ice mesh. This PR also changes the default wave grid back to gwes_30m and updates the load-balancing for this change. The ufs-weather-model is updated to use the code that allows for the wave mesh to be different from the ocean/ice mesh.

    commit 4f3e14b59ff6c83fbaaf6888c3a3068eae3d77d7
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jul 13 15:53:18 2022 -0400

        Migrate `jobs/`, `scripts/` and `ush/` from GSI to global-workflow (#904)

        This PR moves the `jobs/`, `scripts/` and `ush/` from NOAA-EMC/GSI into the global-workflow.
        History is preserved.

        Corresponding GSI PR https://github.com/NOAA-EMC/GSI/pull/436

    commit 46f7589807bcb070c8f86601b74f1a84701b669a
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jul 13 15:51:56 2022 -0400

        build GSI utilities from GSI-utils repo (#889)

        **Description**
        The GSI Utilities have been moved to https://github.com/NOAA-EMC/GSI-utils

        This PR:
        - checks out GSI utilities from the above repo
        - builds the utilities from the above repo
        - does not build the utilities from the GSI repo.  In a subsequent PR when the GSI removes the utilities, that option will become redundant.
        - updates gsi-monitor hash and uses `build.sh` from that repository
        - creates links appropriately.

    commit aac2f3a6980cb61a0dbe272b667f602e3051cb16
    Author: Jessica Meixner <[email protected]>
    Date:   Mon Jul 11 06:57:25 2022 +0000

        Replace print_esmf with esmf_logkind (#898)

        Removes print_esmf as it no longer a variable and add the esmf_logkind variable to config.fcst instead which is the equivalent new variable. The change has already been made in nems_configure.sh, so the setting only needed to be changed in the config file.

    commit 4448dd48b2aeebdf4257a2ab08bd147fcb511f92
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Jul 8 13:03:29 2022 -0400

        Restore cycling capability (#895)

        Restores the ability to run in cycled mode. This requires GSI to be built with ncio/1.1.2, so the build script now sets 1.1.2 as the ncio version until either the GSI default version is updated or module version files are added to global-workflow (Issue #671).

        Two new variables, COMIN_OBS and COMIN_GES_OBS, had to be added to the config file in the wake of GSI updates for WCOSS2 to ensure the correct paths are used instead of trying to use the non-functional compath.py.

        Note that, for now, in order to use cycling, the microphysics setting (imp_physics) must be changed in config.base from Thompson (8) back to GFDL (11), along with a corresponding CCPP suite (like FV3_GFS_v16).

        Fixes #711

    commit a39bd6364971894eee4349b028ebf54ab496dee0
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jul 5 16:10:46 2022 -0400

        Merge `ecf` changes from `WCOSS2` into `develop` (#885)

        * moved ecflow/ecf to ecf and with updates from feature/ops-wcoss2

    commit 3076e13ca5976206f1cdab58cca1b6f80fbb7716
    Author: Fanglin Yang <[email protected]>
    Date:   Fri Jul 1 10:33:39 2022 -0400

        Fix settings of dt_inner and lheatstrg (#883)

        For Thompson microphysics, currently dt_inner is set to half of physics timestep. It should be set to the same as the physics timestep if semi-Lag sedimentation is applied to rain and graupel.

        Canopy heat storage is incorrectly turned off for NOAH LSM, and on for NOAH-MP LSM. This setting needs to be reversed.

        Fixes #884

    commit 3b9636c4eadc8c31548e170baeefd358483ec71c
    Author: Ali.Abdolali <[email protected]>
    Date:   Wed Jun 29 18:22:06 2022 +0000

        Update buoy locations (#881)

        Updates buoy locations for those that were incorrect or have been moved.

    commit f0f1025d07a1af216e2125111ae7bd9ac43213c2
    Author: Barry Baker <[email protected]>
    Date:   Tue Jun 28 12:05:31 2022 -0400

        Update dust input files to not include _FillValue = NaN (#873)

        There is an issue with the FENGSHA dust inputs and having the netcdf attribute _FillValue == NaN. This is in relation to ufs-community/ufs-weather-model#1259, ufs-community/ufs-weather-model#1192 and #872

        Some dust emissions files have also been updated. File changes only include the netcdf attribute _FillValue changing from NaN -> something appropriate for each variable.

        Fixes #873

    commit 4c8b388ae4fd1fb618021b5c11d5e9c82c2ee2f7
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jun 27 18:14:39 2022 -0400

        Replace --aerosols with new apps (#854)

        Removes the --aerosols option for setup_expt and replaces it with new apps for aerosols to match the idiom for other components. Currently, ATMA and S2SWA are supported.

    commit 65cdcce2f841f5e3e4926d4dab73fd5a8a97bd84
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Jun 27 17:47:46 2022 -0400

        Update component versions (#851)

        Updates the version of components except UFS and verify to the current tip of their respective develop branches.

        Verify is not yet updated because we are currently on a branch that hasn't been merged to develop yet in order to use the module/py environment fix.

        GSI will still need to be updated further before use after the resolution of NOAA-EMC/GSI/issues/348

        Also updated the GSI and UPP build scripts to take in debug (`-d`), operations (`-o`), and verbose (`-v`) options and apply them as appropriate to the component build scripts. The ops flag for GSI still needs work, as I encountered issues using the [build_4nco_global.sh](https://github.com/NOAA-EMC/GSI/blob/develop/ush/build_4nco_global.sh) or [prune_4nco_global.sh](https://github.com/NOAA-EMC/GSI/blob/develop/ush/prune_4nco_global.sh) scripts.

        Also fixes a typo in the `parm/post` file list.

        Updates are in preparation for the [COM reorg](https://github.com/NOAA-EMC/global-workflow/issues/761)

    commit 2dc2af0e84f52864a719d71d3dbf14f6368f4c0f
    Author: Jessica Meixner <[email protected]>
    Date:   Fri Jun 24 18:49:39 2022 +0000

        Update caculation of restart based on if a wave IC exists (#875)

        Inspect and assert wave initial conditions exist during a RERUN.  Take appropriate action.

    commit b41a36a10b2f949b0c005e48b978261b3d66eb12
    Author: Rahul Mahajan <[email protected]>
    Date:   Thu Jun 16 22:38:28 2022 -0400

        update from dev_v16 utils.f90.  See issue #713 (#868)

    commit a2b9f483c4aaad37e5d26362186b28a782c0541f
    Author: Barry Baker <[email protected]>
    Date:   Tue Jun 14 23:51:47 2022 -0400

        Update GOCART settings for p8/p81 (#818)

        Wet scavenging coefficients for GOCART are updated.

        Fixes a bug where when running atm-aerosol, aerosol settings were not properly read.

        Changes the location of aerosol emissions data on Hera now that Raffaele has moved to a new position.

        Dust inputs for the fengsha dust emission scheme are updated. These updates include a newer soil database (SOILGRIDSv2) and updates for the drag partition and threshold velocity. It also appropriately scales the emissions by modifying the alpha value found in the dust component configuration file.

        Fixes #814
        Fixes #815
        Fixes #816
        Fixes #816

    commit 027eab90e2cb94a1055f9bc54245e7d5979aca3b
    Author: Kate Friedman <[email protected]>
    Date:   Fri Jun 10 09:10:24 2022 -0400

        Retire VSDB (#848)

        Remove VSDB variables, script blocks, and scripts from global-workflow develop.

        Refs: #844

    commit d6705e2564a698eeddf2424bd580482546658788
    Author: Kate Friedman <[email protected]>
    Date:   Fri Jun 10 09:05:36 2022 -0400

        Add "atmos" COMPONENT subfolder to DMPDIR paths (develop) (#847)

        - add atmos to WAVICEFILE DMPDIR path in JGLOBAL_WAVE_PREP
        - add COMPONENT to all DMPDIR paths (COMPONENT=atmos already set)
        - add "atmos" to all DMPDIR paths in config.anal
        - add COMPONENT to COMIN_OBS default that uses DMPDIR in drive_makeprepbufr.sh
        - add COMPONENT to SOURCE_DIR default that uses DMPDIR in getdump.sh
        - add "atmos" to prep job dependency on updated.status.tm00.bufr_d in setup_workflow.py

        Refs: #802

    commit 59604d60a787fc758380a1ef513601d6ffa97566
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Jun 10 03:29:16 2022 -0400

        Move remaining global post scripts over from UPP (#771)

        Several scripts currently located under NOAA-EMC/UPP are only used for global, so they have been moved within global-workflow so they can be managed by the global-workflow team. Scripts are just copied from the current tip of UPP develop, other than some changes to standardize style and indentation.

        Also coming over are four parm files that are used to produce GFS products. As a result, we are no longer linking the entire upp parm directory; instead we are creating individual links for the files we use that still reside in upp.

        Fixes #630
        Fixes #769

    commit d78c942a271e669b1fd5adf4f99af108c9f884fe
    Author: Jessica Meixner <[email protected]>
    Date:   Tue Jun 7 14:56:26 2022 +0000

        update readme for new linking procedure (#843)

    commit 3194f52d1625379e067fd16e84016d45ba5560fc
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Tue Jun 7 01:35:15 2022 -0400

        Consolidate post scripts to eliminate coupled mode of link script (#766)

        The two scripts that had modified versions for the coupled model have been joined with changes to the original scripts, eliminating the need for a special coupled mode for the link script. As part of this, those two scripts are no longer copied from UPP and are now part of the global-workflow repository.

        Fixes: #679
        Fixes: #746
        Refs: #270

    commit d1d2606406aa2deb8d95f348b471770f4388777c
    Author: Jessica Meixner <[email protected]>
    Date:   Mon Jun 6 04:49:38 2022 +0000

        Updates for wave mesh cap (#831)

        Updates to work with the new WW3 mesh cap, including pointing to the new ufs-weather-model tag for p8c slong with associated namelist changes. There is a new setting in config.ww3, `waveMULTIGRID`, that controls whether WW3 uses generic shell (shel) or multigrid.

        The build script for WW3 pre/post has been updated to use the app to determine whether the regular switch file (for ATMW) or the meshcap version (other) is used. In light of this, `build_all.sh` now passes the app to WW3 pre/post as it does with the UFS build.

        A large section of the wave prep script that was a hold-over from running WW3 offline from the atmosphere dealing with pre-processing winds was removed. Another large section was moved out of prep and into a new `parsing_namelists_WW3.sh` script that is called during the forecast job (similar to those for some other components).

        The ability to set `esmf_logkind` for the UFS model is restored (defaults to ESMF_LOGKIND_MULTI).

        The jlog files were removed for the non-pdgen wave script and ush files.

        Resources for the coupled model are rebalanced.

        Fixes #736

    commit 7173fa58f0da831ad181a3afdaf3c861afa49e49
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jun 1 17:05:21 2022 -0400

        Extend `rocoto.py` for handling offsets in data dependencies. (#835)

        Extend rocoto.py data_dep to handle offset to cyclestr in any number of instances.  Remove hack in aerosol_init dependency generation.

    commit a9998af41cb8c2825f34745091a41ea400815d8d
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jun 1 14:11:49 2022 -0400

        Refactor checkout script (#809)

        The checkout script is refactored. First, the repetitive checkout code is abstracted into a function that is called for each component. Second, if the clone already exists, checkout will still checkout the requested commit. Third, a new option (-c) is added that will delete any existing clones a create a fresh clone. These last two options allow updating of versions without needing to manually delete directories (and remembering which are created by checkout)

        Additionally, a usage statement and code documentation are added.

        There is no change to the existing command-line options, only new options. No change is necessary by users (although the checkout order and print messages have changed). The new syntax is as follows:
        ```
        checkout.sh [-c][-h][-m ufs_hash][-o]
          -c:
              Create a fresh clone (delete existing directories)
          -h:
              Print this help message and exit
          -m ufs_hash:
              Check out this UFS hash instead of the default
          -o:
              Check out operational-only code (GTG and WAFS). Only authorized users can check out GTG.
        ```

        Fixes #808

    commit 85bca2479420927d29a1a9db41b542568d527c13
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Jun 1 15:05:07 2022 +0000

        Update IC location for hera because climate moved from (#829)

        The location of the coupled ICs on Hera is changing, so need to update the path in the config.

    commit dbd9fa93ced07f39accf7ff4eec2859f0ed5d35f
    Author: ChunxiZhang-NOAA <[email protected]>
    Date:   Mon May 30 21:50:56 2022 -0400

        Updated SDFs and namelist settings for P8c (#795)

        Updates the model version in preparation for prototype 8c, along with commensurate setting updates. Some CCPP suites are removed from the UFS build as they are no longer available.

        Also updates the coupled initial conditions, and there is a simultaneous update to fixed orography files.

        Refs: #736

    commit 05accc1c72b1311ae9689bef5e7a1291dc12a96a
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Mon May 23 17:36:51 2022 -0400

        Correct incorrect increment prefix variable (#805)

        One instance of the increment prefix variable in `ush/forecast_postdet.sh` used `PREFIX_INC` instead of the `PREFIX_ATMINC` used elsewhere.

        Fixes #804

    commit ac7cb1000d5c1d31babd36f4c3e17f643f30fd4d
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Sun May 22 16:50:30 2022 -0400

        Remove separate UPP clone (#803)

        Now that UPP is cloned within UFS, there is no need to create an independent clone in global-workflow. Scripts are updated to use the UPP within UFS. In addition to removing redundancy, this will avoid version mismatch issues when UFS and global-workflow checkout different versions. The upp directory is now linked from within UFS to sorc as upp.fd (instead of the gfs_post.fd the clone was placed in). Additionally, the build script is renamed to build_upp.sh.

        Fixes #770
        Moots #797

    commit 58728fb2c689c11335f4bf8ac371e18070c6fbd2
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri May 20 10:14:58 2022 -0400

        Fix build script options (#801)

        There was an issue where if build_all.sh was called with only options that are not used by partial_build.sh, partial_build.sh would see those options because $@ was not overwritten. The script have been updated to consume those options so they are no longer present if $@ isn't overwritten in the new script call.

        Also fixed the getopts statement in partial_build.sh so we handle errors instead of bash (bash would report the wrong script if the script is sourced)

        Fixes #800

    commit fa12db279cf829b861d08c06e3e3534a335e9fd7
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 18 01:04:32 2022 -0400

        Refactor some build scripts (#794)

        Refactors the build_ufs script to allow the build of any UFS app to support future expansion of global-workflow capability. The default should be sufficient for most users, as S2SWA can be used for ATM, ATMA, S2S, and S2SW as well. The new format of the command is now:
        ```
        build_ufs.sh [-a UFS_app][-v]
          -a UFS_app:
            Specify the UFS application to build. The default if none is provided is S2SWA
          -v:
            Turn on verbose mode (BUILD_VERBOSE)
        ```

        build_all.sh is similarly refactored to include the same options. Also, a new `-c build_config` option is added to specify an alternative list of programs to build.
        ```
        build_all.sh [-a UFS_app][-c build_config][-h][-v]
          -a UFS_app:
            Build a specific UFS app instead of the default
          -c build_config:
            Selectively build based on the provided config instead of the default config
          -h:
            Print usage message and exit
          -v:
            Run all scripts in verbose mode
        ```

        partial_build.sh is also updated to take the new `-c` option to specify a build config.
        ```
        partial_build.sh [-c config_file][-h][-v]
          -c config_file:
            Selectively build based on the provided config. The default if none is specified is gfs_build.cfg
          -h:
            Print usage message and exit
          -v:
            Run in verbose mode
        ```

        In addition to the above, build_all and partial_build had their indentation redone and their usage/help statement updated/added. Also, the build configuration file was renamed to from fv3gfs_build.cfg to gfs_build.cfg.

        Fixes #745
        Fixes #751

    commit 2abee02765a3bae48f2b4e6a900400d6731eda06
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 18 01:02:57 2022 -0400

        Add continuous aerosols support (#693)

        Adds support for continuous aerosols when running with GOCART (using the forecast aerosol tracers from the previous cycle as initial tracer fields). This adds a new task to the workflow mesh in forecast-only mode. The new task does not run in the first cycle, though it will appear in rocotostat/rocotoviewer. In subsequent cycles, the task will launch as soon as the needed restart files from the previous cycle are available and gfs_init has completed. There is currently no mechanism to have aerosol_init run for the first cycle (for instance, continuing from a previous experiment); users would have to run the scripts off-line to add aerosols to the initial conditions.

        To support the introduction of the necessary python scripts, a new python environment is added to provide necessary libraries. This virtual environment is temporarily being housed in personal space, but an issue has been opened with hpc-stack to add it to the standard stack installations. The introduction of miniconda also caused the conversion of all of the rocoto entry scripts (the ones rocoto calls to run the job) to bash. Most of them had been in korne.

        To make sure the needed restart files are produced, config.fcst now makes sure the forecast cadence is included in the list of restart times. This may need more testing to ensure it works properly with other restart lists. As part of this, STEP_GFS was updated to properly determine the step from gfs_cyc instead of being a set value.

        Closes #366
        Fixes #516
        Fixes #630

    commit 69b39ee5af8cfbb5cbf5cf62c92d01958b697652
    Author: Kate Friedman <[email protected]>
    Date:   Thu May 12 12:18:50 2022 -0400

        Add --init to GSI submodule command (#781)

        Needed to obtain libsrc submodule during checkout and allows the GSI to build correctly since this GSI hash still needs the libsrc submodule during build.

        Refs: #780

    commit b09f92c21028ea37e4663ce4c304935a2dc45b33
    Author: lgannoaa <[email protected]>
    Date:   Thu May 12 08:20:16 2022 -0400

        Update field_table to be consistent with UFS (#778)

        Changes the fixed surface value of hydrometeor number concentrations and sub-grid TKE to 0. Also renames the field table. Both changes are consistent with changes made in UFS.

        Fixes #676

    commit d72a62d6c0ab2e9f53ca3e6133148f29982f9d32
    Author: lgannoaa <[email protected]>
    Date:   Thu May 12 08:15:23 2022 -0400

        Remove special MOD_PATH from build scripts (#775)

        We always use pre-installed libraries and special MOD_PATHs are no longer necessary, so these are removed from build scripts. MOD_PATH. This also moots MOD_PATHs that were hard-coded to Hera locations in some scripts. The MOD_PATH in build_ufs.sh remains as it is still needed and is a relative path into the UFS repo.

        Fixes #298

    commit 2adf123814a2f29e9cca54a11fbb2807b3f6cf1b
    Author: Kate Friedman <[email protected]>
    Date:   Wed May 4 12:31:20 2022 -0400

        Revert g2tmpl back to 1.10.0 (#773)

        Resolves bug with mismatch between hpc-ips and g2tmpl versions on the WCOSS-Dells. Also revert back to 1.10.0 on Hera and Orion to be consistent.

        Refs: #772

    commit b90f4e99bc42f9a8afbeaa9479e674fb75e096ea
    Author: lgannoaa <[email protected]>
    Date:   Tue May 3 09:45:19 2022 -0400

        Remove git submodule update for upp checkout (#768)

        UPP no longer has a CMakeModules submodule, so the submodule update
        is removed from the checkout script.

        Fixes: #767

    commit ad2b14d9b1ed0fe89fe59bfb96cc03630e8457de
    Author: lgannoaa <[email protected]>
    Date:   Tue May 3 09:44:57 2022 -0400

        Remove duplicate file linking for Thompson MP (#765)

        Files for Thompson MP were being copied twice by the link script: once by checking imp_physics, then again checking the CCPP Suite. This is now reduced to one check.

        Fixes: #675

    commit a9fc0033b908aefb42d5b2d191c65af5cb7660c4
    Author: Kate Friedman <[email protected]>
    Date:   Thu Apr 28 15:17:22 2022 -0400

        Remove unneeded/outdated modulefiles (#762)

        Remove unneeded modulefiles for WCOSS-Cray and GSI monitoring.

    commit 3333dee304b6b53d3d716c60d0c87ad06d629c1c
    Author: lgannoaa <[email protected]>
    Date:   Thu Apr 28 14:35:57 2022 -0400

        Remove prepbufr_pre-qc from archive lists (#753)

        The prepbuft_pre-qc file does not need to be archived, so it no longer is.

        Fixes #361

    commit 88b1b1591d3201709f5f981908aaf7890d3021bd
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Tue Apr 26 20:40:41 2022 -0400

        Convert module files from Tcl to Lua (#756)

        Converts all module files from Tcl format to Lua. As a side effect, this change enforces using the files as modules rather than improperly sourcing them instead of loading.

        Fixes #670

    commit ca80aeb86cb221263611605ba23858448bce0bad
    Author: lgannoaa <[email protected]>
    Date:   Mon Apr 25 06:23:06 2022 -0400

        Ensure hourly files when GLDAS is on (#740)

        GLDAS requires hourly output, so make sure FHOUT is 1 when GLDAS is on.

        Fixes #695

    commit 9d00239088651b73a9667b70bd6247b34e35046f
    Author: lgannoaa <[email protected]>
    Date:   Tue Apr 19 21:22:22 2022 -0400

        Update cyclone tracker to handle return code correctly #642

        Updates the cyclone tracker call to correctly exit with an error code if the tracker script reports one.

        Fixes #507

    commit 33d3dd14d6df8109274dde4606bb7a50e4638fa2
    Author: Jessica Meixner <[email protected]>
    Date:   Tue Apr 19 21:18:56 2022 -0400

        Update ww3 pre and post exe build to use cmake (#731)

        Updates the WW3 pre/post build system to use cmake.

        Fixes #688

    commit 39facec1e03a404f84fd05b8739cd8e4010a0779
    Author: Kate Friedman <[email protected]>
    Date:   Tue Apr 12 11:36:30 2022 -0400

        Add WCOSS2 GFSv16.2 operational def files into develop (#717)

        Add WCOSS2 operational GFS def files.

        Refs: #399

    commit 0a85223e48a1a8dcced163791d8e7ae5a42a4fab
    Author: Xianwu Xue - NOAA <[email protected]>
    Date:   Tue Apr 12 11:34:17 2022 -0400

        Initialize "err" to avoid potential task fail (#715)

        If not initialize err, and change "set -x" to "set -xue", then the waveinit task will fail with error message:
            "line 234: err: unbound variable"

         On branch bugfix/issue_714
         Changes to be committed:
        	modified:   scripts/exgfs_wave_init.sh

        Refs: #714

    commit fc6e1c3316397432d2da218b3c4fc0ea1fe70644
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Apr 5 11:07:21 2022 -0400

        config.base should not exist in the repository unless it is in ops.  template only exists in the repo, the experiment directory should not contain the templated config.base.emc.dyn (#707)

    commit cabf437044cb937caf7a7830068fd9e413c5921f
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Mar 30 21:28:50 2022 -0400

        Update model and settings for Prototype P8b (#681)

        Updates model and setting defaults for prototype 8b.

        The UFS version is updated to a recent version of UFS (tag Prototype-P8b). As part of this, the print_esmf option is removed from the model configure file and replaced with a new setting in nems.configure. We have not made this option user-configurable at this point, but that may come in the future.

        The default CCPP suites have been updated for all modes to either FV3_GFS_v17_p8 or FV3_GFS_v17_coupled_p8. This involves changing the microphysics to Thompson and changes the gravity wave drag version (knob_ugwp_version) to 0. This change breaks cycled mode for the time being. A future PR will revert the defaults to ones that allow cycled to run along with a more robust system for changing settings.

        Tiled fix files are now used for all modes instead of just coupled.

        Cellular automata now defaults on ON.

        There are also other miscellaneous settings that have had their defaults changed.

        Fixes #641, #687

    commit e3f707cb9c05b45e9d4019679e406f54008279a5
    Author: XuLi-NOAA <[email protected]>
    Date:   Thu Mar 24 05:43:31 2022 -0400

        Modify eobs for EnKF thinning

        In the Hybrid EnKF GSI, the thinning box size, dmesh, is different for the full resolution analysis and EnKF respectively. There are set in GSI scripts for the full resolution analysis, and reset in global workflow in config.eobs.
        Only two thinning box sizes, dmesh(1) & dmesh(2), are defined in GSI scripts before, recently, two more, dmesh(3) & dmesh(4) are added. Accordingly, these two need to be added in config.eobs as well.

        Specifically, add dmesh(3)=225.0,demsh(4)=100.0 to config.eobs.

        Fixes #595

    commit c32eea459af3177cee28e151b43fe5e12bdfc412
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Tue Mar 22 11:18:10 2022 -0400

        Update ocean resolution for C48 (#651)

        The ocean resolution for C48 was set as 1-deg, but the fractional
        grid fix files available at C48 are for a 4-deg ocean grid. The
        ocean resolution is now set to this value when FV3 is C48.

        Also commented out a currently redundant block setting OCNRES in
        config.ocn. The one in ecfs has to stay as it recalculates the
        ocean resolution based on the EnKF resolution.

        Fixes #650

    commit d758e8b227fca7b5a3320adc43c29ba492c3bfe9
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Thu Mar 10 05:54:49 2022 -0500

        Add single forecast GOCART support (#659)

        Adds support for running single coupled free forecasts with GOCART aerosols. Support for continuous aerosol fields from cycle to cycle will be added in a future PR.

        To turn on aerosols, there is a new --aerosols option for setup_expt.py. The option takes no arguments. When it is used, aerosols will be turned on by setting DO_AERO="YES" in config.base.

        GOCART output files are placed in the chem directory in COM.

        There is a new tarball archived, chem.tar, that contains the GOCART output.

        Partially addresses #516
        Fixes #403

    commit a0e23e254c7c881b20d66c1c53cd36de509e6d69
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Tue Mar 1 10:50:39 2022 -0500

        Specify memory for init job (#669)

        The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed.

        Fixes #631

    commit 6874e8939211fdc07143450bfd1b6a2863172e10
    Author: arun chawla <[email protected]>
    Date:   Fri Feb 25 16:39:45 2022 -0500

        Cleanup of utils directory (#660)

        Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo.

        Fixes #618

    commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Thu Feb 24 22:49:45 2022 -0500

        Fix bug with partition_batch on WCOSS (#668)

        partition_batch was not being defined for WCOSS machines, but was
        being used in a substitution for config.base.

        Fixes #667

    commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Feb 21 02:10:00 2022 -0500

        Split output filetype variable into atm and sfc (#602)

        The determination of the FV3 output filetype was a bit unwieldy as it
        contained two different settings (one for the atmosphere and one for
        the surface) that were not necessarily changed at the same time. They
        were also being determined in a different location than other settings
        based on the model resolution.

        Now the old OUTPUT_FILETYPES variable has been split into two different
        variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi-
        nation was also moved into the config.fv3 file, where other resolution-
        dependent computational settings are set.

        This has resulted in some functional change on WCOSS Dell, as the EnKF
        was using different chunking settings and never used parallel output
        for the surface likely because wasn't being run at a low enough resolu-
        tion to consider it. However, there is no reason to believe the two
        forecast modes should have different chunk or output settings. So, I've
        used the EnKF chunking settings and the free forecast switchover point
        for the surface output mode.

        The new filetype settings are now also divorced from the OUTPUT_FILE
        setting. However, that setting will soon be unnecessary as nemsio
        is removed from the code as an option (see Issue #601).

        Fixes #600
        Refs #601

    commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Thu Feb 17 15:55:24 2022 -0500

        Correct MODE comparisons for forecast only (#658)

        When the setup_expt scripts were combined, the forecast mode became a mandatory
        argument. The value of this option is then directly used for the MODE variable,
        but the argument name (forecast-only) does not match what was previously used
        for MODE in the forecast-only script (free) and some scripts were still testing
        against the old value instead of the new one. Those comparisons have now been
        updated to use the new MODE name.

        Fixes #657

    commit f8867d3f0b1f3b5d238dced412996c56e30d31a1
    Author: David Huber <[email protected]>
    Date:   Thu Feb 10 20:23:54 2022 -0500

        Add LOCALARCH option (#628)

        Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR.

        Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO).

        Fixes #624.

    commit 2950c7b97f99341caa738526138022987f665627
    Author: Jessica Meixner <[email protected]>
    Date:   Thu Feb 10 18:07:43 2022 -0500

        Turn on fractional grid by default for uncoupled forecasts (#638)

        Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true.

        Fixes #571

    commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4
    Author: David Huber <[email protected]>
    Date:   Wed Feb 9 17:02:39 2022 -0500

        Specify warm start as .true. or .false. (#644)

        Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`.

        Fixes #643

    commit e537f0cecabc8e16e26b14e606558de906b19e3f
    Author: David Huber <[email protected]>
    Date:   Tue Feb 8 23:33:21 2022 -0500

        Archive TC tracking logs if produced (#627)

        The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track.

        Fixes #625.

    commit 32f93becde5ffa07c162252b95417845f2ab5159
    Author: David Huber <[email protected]>
    Date:   Tue Feb 8 20:59:37 2022 -0500

        Fix separate threading for GFS and GDAS forecasts. (#621)

        Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs.

        Fixes #610

    commit 9bb09a92c55d4534feca5d521fbbd1c664730317
    Author: David Huber <[email protected]>
    Date:   Tue Feb 8 20:58:05 2022 -0500

        Updated the RadMon and OznMon links. #596 (#597)

    commit 97ebc4d4e6483b135468d85cd9ed974f88955914
    Author: Rahul Mahajan <[email protected]>
    Date:   Thu Feb 3 02:56:34 2022 -0500

        Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537)

        `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name.

        The user is now required to provide a `mode` as the first positional argument to `setup.py`.  Valid options are `cycled` and `forecast-only`.

        ```
        ❯ python3 setup_expt.py -h
        usage: setup_expt.py [-h] {cycled,forecast-only} ...

        Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link
        initial condition files from $ICSDIR to $COMROT

        positional arguments:
          {cycled,forecast-only}
            cycled              arguments for cycled mode
            forecast-only       arguments for forecast-only mode

        optional arguments:
          -h, --help            show this help message and exit
        ```

        Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively.

        ```
        ❯ python3 setup_expt.py forecast-only -h                                                                  feature/unify-setups
        usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE
                                           [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}]
                                           [--app {ATM,ATMW,S2S,S2SW}]

        optional arguments:
          -h, --help            show this help message and exit
          --pslot PSLOT         parallel experiment name
          --resdet RESDET       resolution of the deterministic model forecast
          --comrot COMROT       full path to COMROT
          --expdir EXPDIR       full path to EXPDIR
          --idate IDATE         starting date of experiment, initial conditions must exist!
          --edate EDATE         end date experiment
          --icsdir ICSDIR       full path to initial condition directory
          --configdir CONFIGDIR
                                full path to directory containing the config files
          --cdump CDUMP         CDUMP to start the experiment
          --gfs_cyc {0,1,2,4}   GFS cycles to run
          --start {warm,cold}   restart mode: warm or cold
          --app {ATM,ATMW,S2S,S2SW}
                                UFS application
        ```

        ```
        ❯ python3 setup_expt.py cycled -h                                                                         feature/unify-setups
        usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE
                                    [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}]
                                    [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}]

        optional arguments:
          -h, --help            show this help message and exit
          --pslot PSLOT         parallel experiment name
          --resdet RESDET       resolution of the deterministic model forecast
          --comrot COMROT       full path to COMROT
          --expdir EXPDIR       full path to EXPDIR
          --idate IDATE         starting date of experiment, initial conditions must exist!
          --edate EDATE         end date experiment
          --icsdir ICSDIR       full path to initial condition directory
          --configdir CONFIGDIR
                                full path to directory containing the config files
          --cdump CDUMP         CDUMP to start the experiment
          --gfs_cyc {0,1,2,4}   GFS cycles to run
          --start {warm,cold}   restart mode: warm or cold
          --resens RESENS       resolution of the ensemble model forecast
          --nens NENS           number of ensemble members
          --app {ATM,ATMW}      UFS application
        ```

        Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications.

        The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing.

        The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source.

        The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation.

        There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR.   It will be cleaned up in subsequent PR's.

        Another unnecessary complication is the argument of `--start`.  The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot.  It is left unchanged.

    commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Feb 2 11:19:43 2022 -0500

        Stop archiving gfsarch.log as it is being written (#581)

        The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group.

        Fixes: #558

    commit 1b300dbf98eccdf03117b3795a2d8da3310a6126
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Feb 2 11:18:55 2022 -0500

        Fix build on non-WCOSS2 machines (#612)

        The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions.

        Also updates the UFS_UTILS repository to its new location under UFS instead of EMC.

        Fixes #476, #561

    commit d3028b9d8268028226f9c27800fcd6655e9e4bb8
    Author: David Huber <[email protected]>
    Date:   Wed Jan 19 14:29:51 2022 -0500

        Fix setting of OUTPUT_FILETYPES (#589)

        The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine.

        Fixes #588

    commit 13421b01a07e5d1cca32ee7579a4094d8209b072
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jan 19 12:16:29 2022 -0500

        Update PR template

    commit 322a61a61238e8486cb42d7d26282b2728d0c32f
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jan 19 12:13:33 2022 -0500

        Move PR template MD file. Update issue templates

    commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jan 19 11:32:51 2022 -0500

        rename pull_request_template.md

    commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jan 19 10:34:54 2022 -0500

        make changes to the templates

    commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jan 19 10:08:45 2022 -0500

        Fix lfrac entry in diag table (#570)

        Land fraction was listed in the wrong module, keeping it from being
        written to output.

        Refs: #562

    commit e2657adbdadaac7089591390428324c6aec260a9
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jan 18 17:04:04 2022 -0500

        Update NCO_bug_report.md

    commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jan 18 16:59:18 2022 -0500

        Update bug report issue template

    commit 2fab8b4213645b79b3fea8127e7d4ab21044188e
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jan 18 15:13:53 2022 -0500

        Add templates for Github (#560)

        Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included.

    commit 03be05309b184421c473f1b43082b766b114fd46
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Tue Jan 18 10:02:02 2022 -0500

        Fix toggle for building workflow_utils (#580)

        The fv3gfs_build.cfg did not have a space between the periods and
        the setting for workflow_utils, which means the setting was ignored
        and the default of yes was always used.

        Fixes: #577

    commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Tue Jan 18 10:01:24 2022 -0500

        Remove redundant toggle for gldas build (#579)

        The build cfg files controlling which components are built and the
        partial_build.sh script all have two instances trying to set the
        value for gldas. This means one of the settings did nothing when
        changed.

        Fixes: #578

    commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Jan 14 01:05:59 2022 -0500

        Update config missed in last GSI update (#569)

        When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489).

        Refs: PR #530

    commit 33308ea3b477db17a5db455a4c4887e3d5cbc711
    Author: Jessica Meixner <[email protected]>
    Date:   Thu Jan 6 00:44:43 2022 -0500

        Updates for P8a (#538)

        Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype.

        Updates include:

  …
jkhender added a commit to jkhender/global-workflow that referenced this issue Dec 3, 2022
@jkhender
Created branch gsl_ufs_rt from gfsv16_rt branch
22c7693 
 - merged in gfsv17p8_hfip branch
 - removed HFIP experiment directories for rt_v17p8_mynn and rt_v17_p8_gfonly
 - removed realtime experiment directories rt_ufscam_l127_hera and rt_ufscam_l127_jet

Squashed commit of the following:

commit f63227f238ea0f85154b4b75f085bcdd177bc89b
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Nov 17 00:24:12 2022 +0000

     Corrected syntax error in Externals.cfg

commit 0abbbd0bfcfeb698eeb2ce3d0ee009a1fc812abf
Author: Judy.K.Henderson <[email protected]>
Date:   Sun Sep 18 23:48:42 2022 +0000

     update INFO file

commit 561c194cb4be6cb90013c6768d399efef2183d93
Author: Judy.K.Henderson <[email protected]>
Date:   Sun Sep 18 23:44:04 2022 +0000

     Delete old experiment directory, v17_p8_gf
     Change settings for suites FV3_GFS_v17_p8_gf_mynn and FV3_GFS_v17_p8_mynn
        sedi_semi=.false. (dt_inner will then become 75)
        decfl=8

commit 7e190d844929fd160db5f2db101a244e21de8c5c
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Sep 15 23:50:27 2022 +0000

     Changed dependencies for chkpost and vrfy tasks
      -- add gfspost dependency for chkpost task
      -- add non-zero post grib2 files to dependency for vrfy task

commit d28969d337356310cacb304bd1a87f49f4a6a8a9
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Sep 14 23:46:58 2022 +0000

      Updates to realtime XML files
       - added chkpost task to workflow
         * if post job fails and creates a zero-length file but returns SUCCESFUL state, chkpost task will rerun that forecast hour again
       - changed dependency for vrfy task to look for all non-zero post grib2 files

commit bac474164019b922867cf6c2a9f68ad6e77992eb
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Sep 14 23:43:20 2022 +0000

      Corrected syntax errors in parsing_namelist_FV3.sh
        - fix missing / from gfs_physics_nml
        - remove "" from FV3_GFS_v17_p8_*mynn in CCPP_SUITE case statement

commit c23a9961edd13429c671d79b2c4c02f6aaad6213
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Aug 30 01:11:43 2022 +0000

      Add realtime XML files for hfipPlots and ncl tasks

commit 2d2fe9c323ca3deaa07f47970568c8c03e88a4f9
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Aug 30 01:10:31 2022 +0000

      Updates for experiment directories

       - make paths consistent and use /home/rtfim/GFSv17p8_HFIP instead of /lfs1 or /lfs4 paths
       - add ATCFNAME as environment variable to arch task
       - make ICSDIR consistent and point to /lfs1 path
       - call jobs/rocoto/vrfy_gsl.sh for gfsvrfy task
       - add dependency for gfsvrfy task if running without gfspost task
       - add /lfs4 specific xml files for history

commit 70ed9cab451fb5a968dc53c6ed66457014a71a8c
Author: Judy.K.Henderson <[email protected]>
Date:   Mon Aug 29 18:38:48 2022 +0000

     Updates for realtime experiments

      Update default config files in parm/config
       - turn in-line post off [WRITE_DOPOST=.false.]
       - turn off parallel netcdf if running on jet
       - increase post memory to 50G

      Rename rt_v17p8_gf experiment directory to rt_v17p8_gfonly

      Update experiment directories
       - move to /lfs1 filesystem from /lfs4
       - update config.fcst to handle  v17_p8_gf_mynn suite
       - update XML files to use 50G for memory_post
       - add gfsvrfy dependency to check size of syndat_tcvitals.2022

      Update jet_xml_dir and xml directories
       - add XML files for hfipPlots and ncl tasks which use reservations
       - add non-realtime XML files for hfipPlots and ncl tasks
       - append PSLOT to task/job names for remap and ncl tasks
       - reimplement time dependency of 48h for nclzip task
       - run hfipPlots only for g2 cycles
       - switch to 144h from 168h

commit 106fbada5e117bb52a2e617aec990d2ef37076aa
Author: Judy.K.Henderson <[email protected]>
Date:   Fri Aug 26 18:13:30 2022 +0000

     Update ufs_utils to ufs_utils_1_8_0  [26Aug22 commit, #1001]

commit 366edada59f47cba098ff43c2d3316c78de6a929
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Aug 20 00:57:12 2022 +0000

      Remove files under ufs_model.fd_gsl that are already in the gsl/develop repository

commit 5dc80e326149e3e283df9330b4272221d7983c3d
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Aug 20 00:38:43 2022 +0000

      Additional changes to config.fcst for FV3_GFS_v17_p8_gf_mynn suite
      Added effective date to INFO file

commit 41c756f15bd492fe6aaa9d01cc1f7e5004d4097b
Author: Judy.K.Henderson <[email protected]>
Date:   Fri Aug 19 21:56:54 2022 +0000

     Update to HFIP2022-08-17 gsl/develop tag, b42ca73
       - add FV3_GFS_v17_p8_gf_mynn suite
       - updates to GFS-MYNN configuration
       - update to GF and sgscloud_radpre
       - add regression test for p8+gf+mynn
       - add bl_mynn* namelist parameters for p8+gf+mynn
       - use aerosol-aware Thompson
          * ltaerosol=.true.
          * field_table_thompson_aero_tke
       - set do_gsl_drag_tofd = .false.

commit 48fab18a9e82395f6febafa8fa8593880782615b
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Aug 10 17:12:58 2022 +0000

      Added corrections for post task
        - added nam_micro_lookup.dat to link_workflow.sh
        - corrected typos in link_workflow.sh and .gitignore
        - missing from 10Jun22 initial commit [#771]
        - corrected in 27Jun22 commit [#851] and 08Jul22 commit [#895]

commit 434a1f02e890c81cd16f3d6a929f4be1b4b6eb9a
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jul 23 01:39:17 2022 +0000

     Updates for GSL

     - changed if-statement for netcdf files in GSL archive script to look for a single file (atmf000 netcdf file) instead of multiple files since it now produces errors when running as bash script
     - added GSL archive script for archiving netcdf files only
     - changed getic script to look for atm file instead of sfc file in if-statements since atm file is much larger than sfc file
     - comment out if-statement to check if 0p25 grib2 file already exists in post.sh so post job will run if resubmitted when walltime is exceeded
     - change config.base.emc.dyn link to point to JET version
     # Please enter the commit message for your changes. Lines starting

commit 29bc7b7eeaa8765238af7e6131d41f9c0ebb2b1b
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jul 23 01:19:19 2022 +0000

     Add HFIP experiment directories
       - rt_v17_p8_gf
       - rt_v17_p8_mynn
       - v17_p8_gf
     Add NCL graphics directories
       - jet_xml_dir
       - xml
     Delete gsl_v5 experiment directory

commit 5f58523d4c5be051b4177350f1f9f1f3146f086a
Author: Judy.K.Henderson <[email protected]>
Date:   Fri Jul 1 17:16:38 2022 +0000

    Squashed commit of the following:

    commit 2bde13a6bec1d81375cdc04f1c67f06176de5ba6
    Author: Judy.K.Henderson <[email protected]>
    Date:   Fri Jul 1 17:05:59 2022 +0000

         Remove GFS_SCNV entries from GFS_v7_p8_gf suite definition file

    commit 97515c6866308788c21d98ed80779668e58949b1
    Author: Judy.K.Henderson <[email protected]>
    Date:   Fri Jul 1 17:04:30 2022 +0000

         Update version of ufs_utils.fd to be consistent with what we have been using in our realtime runs, which uses ESMF 8.2.0 library

    commit bb8cb4a729a8021eee6747d6b93e067dca42ab71
    Merge: a1b7d599 845dea70
    Author: Judy.K.Henderson <[email protected]>
    Date:   Fri Jul 1 16:57:46 2022 +0000

        Merge branch '30may_commit' of https://github.com/jkhender/global-workflow into 30may_commit

    commit 845dea70d482e8980d440ecaeba6bba89c433d5f
    Author: Fanglin Yang <[email protected]>
    Date:   Fri Jul 1 10:33:39 2022 -0400

          Fix settings of dt_inner and lheatstrg (#883)

          For Thompson microphysics, currently dt_inner is set to half of physics timestep. It should be set to the same as the physics timestep if semi-Lag sedimentation is applied to rain and graupel.

          Canopy heat storage is incorrectly turned off for NOAH LSM, and on for NOAH-MP LSM. This setting needs to be reversed.

        Fixes #884

commit 4d45b6b9d133a5542955bee4ecf57a400bdaa012
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jun 30 16:46:18 2022 +0000

     Moved GSL-modified post parm files under ufs_model.fd_gsl/FV3/upp/parm

commit 03399b0155f3d2c590fd016dcff13716835521ff
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jun 30 07:02:38 2022 +0000

     Merge in Walter's additional commits for UPP
     Remove gfs_post.fd_gsl/ush/fv3gfs_downstream_nems.sh

        Squashed commit of the following:

        commit aa5c78301b914fb5ab717ec5e74333acb7e587e9
        Author: Walter Kolczynski - NOAA <[email protected]>
        Date:   Fri Jun 10 03:29:16 2022 -0400

            Move remaining global post scripts over from UPP (#771)

            Several scripts currently located under NOAA-EMC/UPP are only used for global, so they have been moved within global-workflow so they can be managed by the global-workflow team. Scripts are just copied from the current tip of UPP develop, other than some changes to standardize style and indentation.

            Also coming over are four parm files that are used to produce GFS products. As a result, we are no longer linking the entire upp parm directory; instead we are creating individual links for the files we use that still reside in upp.

            Fixes #630
            Fixes #769

        commit 8a0a35b707f1d677bcea310030bb54aeeee59c73
        Author: Walter Kolczynski - NOAA <[email protected]>
        Date:   Tue Jun 7 01:35:15 2022 -0400

            Consolidate post scripts to eliminate coupled mode of link script (#766)

            The two scripts that had modified versions for the coupled model have been joined with changes to the original scripts, eliminating the need for a special coupled mode for the link script. As part of this, those two scripts are no longer copied from UPP and are now part of the global-workflow repository.

            Fixes: #679
            Fixes: #746
            Refs: #270

commit 5e776021e28b1a8c87f0f29d4a606531545f3ad3
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jun 30 05:09:49 2022 +0000

     Modify parsing_namelists_FV3.sh

     - added namelist parameters for GFSv17_p8_MYNN
     - set default value for lheatstrg to .false.

commit a18aa5cade877d457b5e01033b84e7bd46cd691e
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jun 30 05:06:11 2022 +0000

     Add WGRIB2 and CRTM_FIX variables to modulefiles/module_base.jet.lua
     Load module ncl in modulefiles/module_base.jet.lua

commit a01f4fc545f2fdd4b2e82863a02c4f3d7d4208ef
Author: Judy.K.Henderson <[email protected]>
Date:   Fri Jun 24 02:03:37 2022 +0000

     Modify srun command to print out memory information

     Request 60G of memory for init task on Jet

commit b538350a481467fa218050074d17b862b40d2e89
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jun 23 01:22:05 2022 +0000

     Updates for running on Jet

     - corrected typos in module_base.jet.lua
     - change DO_VRFY to "YES" for jet
     - create machine-specific files for GSL forecast-only Python workflow scripts to set paths for each machine
     - pass in ATCFNAME variable for vrfy task on Jet

commit 8ff6446102c411e1e344eb6ff925e49aff000b36
Author: Judy.K.Henderson <[email protected]>
Date:   Thu Jun 23 00:32:47 2022 +0000

     Add sedi_semi and decfl namelist parameters to config.fcst

commit 681e4d4704986d242dba43dd1c87059bea6c3db5
Author: Judy.K.Henderson <[email protected]>
Date:   Wed Jun 22 21:59:05 2022 +0000

     Change default workflow_utils.py script to GSL version

commit cd802762e1ba30e49c53cb5b37059ea416a1161a
Author: Judy.K.Henderson <[email protected]>
Date:   Tue Jun 21 22:47:52 2022 +0000

     Update UFS to NOAA-GSL:gsl/develop 14Jun22 branch, 576b58e, in checkout.sh

commit c47265f1f4407e25a11c771fe128bb058457669c
Author: Judy.K.Henderson <[email protected]>
Date:   Sat Jun 18 00:38:19 2022 +0000

    Updates for GSL

    - add Jet changes to JGFS_ATMOS_CYCLONE_TRACKER
    - change GSL scripts to bash
    - have vrfy.sh script link to GSL version
    - delete files leftover from merge

commit 68a10c55428cf5ddb42af56ad23163e307125b52
Author: Judy.K.Henderson <[email protected]>
Date:   Fri Jun 17 09:28:52 2022 +0000

    Merged NOAA-EMC/develop 30May22 branch into gslv16_dev

    Squashed commit of the following:

    commit dbd9fa93ced07f39accf7ff4eec2859f0ed5d35f
    Author: ChunxiZhang-NOAA <[email protected]>
    Date:   Mon May 30 21:50:56 2022 -0400

        Updated SDFs and namelist settings for P8c (#795)

        Updates the model version in preparation for prototype 8c, along with commensurate setting updates. Some CCPP suites are removed from the UFS build as they are no longer available.

        Also updates the coupled initial conditions, and there is a simultaneous update to fixed orography files.

        Refs: #736

    commit 05accc1c72b1311ae9689bef5e7a1291dc12a96a
    Author: RussTreadon-NOAA <[email protected]>
    Date:   Mon May 23 17:36:51 2022 -0400

        Correct incorrect increment prefix variable (#805)

        One instance of the increment prefix variable in `ush/forecast_postdet.sh` used `PREFIX_INC` instead of the `PREFIX_ATMINC` used elsewhere.

        Fixes #804

    commit ac7cb1000d5c1d31babd36f4c3e17f643f30fd4d
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Sun May 22 16:50:30 2022 -0400

        Remove separate UPP clone (#803)

        Now that UPP is cloned within UFS, there is no need to create an independent clone in global-workflow. Scripts are updated to use the UPP within UFS. In addition to removing redundancy, this will avoid version mismatch issues when UFS and global-workflow checkout different versions. The upp directory is now linked from within UFS to sorc as upp.fd (instead of the gfs_post.fd the clone was placed in). Additionally, the build script is renamed to build_upp.sh.

        Fixes #770
        Moots #797

    commit 58728fb2c689c11335f4bf8ac371e18070c6fbd2
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri May 20 10:14:58 2022 -0400

        Fix build script options (#801)

        There was an issue where if build_all.sh was called with only options that are not used by partial_build.sh, partial_build.sh would see those options because $@ was not overwritten. The script have been updated to consume those options so they are no longer present if $@ isn't overwritten in the new script call.

        Also fixed the getopts statement in partial_build.sh so we handle errors instead of bash (bash would report the wrong script if the script is sourced)

        Fixes #800

    commit fa12db279cf829b861d08c06e3e3534a335e9fd7
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 18 01:04:32 2022 -0400

        Refactor some build scripts (#794)

        Refactors the build_ufs script to allow the build of any UFS app to support future expansion of global-workflow capability. The default should be sufficient for most users, as S2SWA can be used for ATM, ATMA, S2S, and S2SW as well. The new format of the command is now:
        ```
        build_ufs.sh [-a UFS_app][-v]
          -a UFS_app:
            Specify the UFS application to build. The default if none is provided is S2SWA
          -v:
            Turn on verbose mode (BUILD_VERBOSE)
        ```

        build_all.sh is similarly refactored to include the same options. Also, a new `-c build_config` option is added to specify an alternative list of programs to build.
        ```
        build_all.sh [-a UFS_app][-c build_config][-h][-v]
          -a UFS_app:
            Build a specific UFS app instead of the default
          -c build_config:
            Selectively build based on the provided config instead of the default config
          -h:
            Print usage message and exit
          -v:
            Run all scripts in verbose mode
        ```

        partial_build.sh is also updated to take the new `-c` option to specify a build config.
        ```
        partial_build.sh [-c config_file][-h][-v]
          -c config_file:
            Selectively build based on the provided config. The default if none is specified is gfs_build.cfg
          -h:
            Print usage message and exit
          -v:
            Run in verbose mode
        ```

        In addition to the above, build_all and partial_build had their indentation redone and their usage/help statement updated/added. Also, the build configuration file was renamed to from fv3gfs_build.cfg to gfs_build.cfg.

        Fixes #745
        Fixes #751

    commit 2abee02765a3bae48f2b4e6a900400d6731eda06
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed May 18 01:02:57 2022 -0400

        Add continuous aerosols support (#693)

        Adds support for continuous aerosols when running with GOCART (using the forecast aerosol tracers from the previous cycle as initial tracer fields). This adds a new task to the workflow mesh in forecast-only mode. The new task does not run in the first cycle, though it will appear in rocotostat/rocotoviewer. In subsequent cycles, the task will launch as soon as the needed restart files from the previous cycle are available and gfs_init has completed. There is currently no mechanism to have aerosol_init run for the first cycle (for instance, continuing from a previous experiment); users would have to run the scripts off-line to add aerosols to the initial conditions.

        To support the introduction of the necessary python scripts, a new python environment is added to provide necessary libraries. This virtual environment is temporarily being housed in personal space, but an issue has been opened with hpc-stack to add it to the standard stack installations. The introduction of miniconda also caused the conversion of all of the rocoto entry scripts (the ones rocoto calls to run the job) to bash. Most of them had been in korne.

        To make sure the needed restart files are produced, config.fcst now makes sure the forecast cadence is included in the list of restart times. This may need more testing to ensure it works properly with other restart lists. As part of this, STEP_GFS was updated to properly determine the step from gfs_cyc instead of being a set value.

        Closes #366
        Fixes #516
        Fixes #630

    commit 69b39ee5af8cfbb5cbf5cf62c92d01958b697652
    Author: Kate Friedman <[email protected]>
    Date:   Thu May 12 12:18:50 2022 -0400

        Add --init to GSI submodule command (#781)

        Needed to obtain libsrc submodule during checkout and allows the GSI to build correctly since this GSI hash still needs the libsrc submodule during build.

        Refs: #780

    commit b09f92c21028ea37e4663ce4c304935a2dc45b33
    Author: lgannoaa <[email protected]>
    Date:   Thu May 12 08:20:16 2022 -0400

        Update field_table to be consistent with UFS (#778)

        Changes the fixed surface value of hydrometeor number concentrations and sub-grid TKE to 0. Also renames the field table. Both changes are consistent with changes made in UFS.

        Fixes #676

    commit d72a62d6c0ab2e9f53ca3e6133148f29982f9d32
    Author: lgannoaa <[email protected]>
    Date:   Thu May 12 08:15:23 2022 -0400

        Remove special MOD_PATH from build scripts (#775)

        We always use pre-installed libraries and special MOD_PATHs are no longer necessary, so these are removed from build scripts. MOD_PATH. This also moots MOD_PATHs that were hard-coded to Hera locations in some scripts. The MOD_PATH in build_ufs.sh remains as it is still needed and is a relative path into the UFS repo.

        Fixes #298

    commit 2adf123814a2f29e9cca54a11fbb2807b3f6cf1b
    Author: Kate Friedman <[email protected]>
    Date:   Wed May 4 12:31:20 2022 -0400

        Revert g2tmpl back to 1.10.0 (#773)

        Resolves bug with mismatch between hpc-ips and g2tmpl versions on the WCOSS-Dells. Also revert back to 1.10.0 on Hera and Orion to be consistent.

        Refs: #772

    commit b90f4e99bc42f9a8afbeaa9479e674fb75e096ea
    Author: lgannoaa <[email protected]>
    Date:   Tue May 3 09:45:19 2022 -0400

        Remove git submodule update for upp checkout (#768)

        UPP no longer has a CMakeModules submodule, so the submodule update
        is removed from the checkout script.

        Fixes: #767

    commit ad2b14d9b1ed0fe89fe59bfb96cc03630e8457de
    Author: lgannoaa <[email protected]>
    Date:   Tue May 3 09:44:57 2022 -0400

        Remove duplicate file linking for Thompson MP (#765)

        Files for Thompson MP were being copied twice by the link script: once by checking imp_physics, then again checking the CCPP Suite. This is now reduced to one check.

        Fixes: #675

    commit a9fc0033b908aefb42d5b2d191c65af5cb7660c4
    Author: Kate Friedman <[email protected]>
    Date:   Thu Apr 28 15:17:22 2022 -0400

        Remove unneeded/outdated modulefiles (#762)

        Remove unneeded modulefiles for WCOSS-Cray and GSI monitoring.

    commit 3333dee304b6b53d3d716c60d0c87ad06d629c1c
    Author: lgannoaa <[email protected]>
    Date:   Thu Apr 28 14:35:57 2022 -0400

        Remove prepbufr_pre-qc from archive lists (#753)

        The prepbuft_pre-qc file does not need to be archived, so it no longer is.

        Fixes #361

    commit 88b1b1591d3201709f5f981908aaf7890d3021bd
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Tue Apr 26 20:40:41 2022 -0400

        Convert module files from Tcl to Lua (#756)

        Converts all module files from Tcl format to Lua. As a side effect, this change enforces using the files as modules rather than improperly sourcing them instead of loading.

        Fixes #670

    commit ca80aeb86cb221263611605ba23858448bce0bad
    Author: lgannoaa <[email protected]>
    Date:   Mon Apr 25 06:23:06 2022 -0400

        Ensure hourly files when GLDAS is on (#740)

        GLDAS requires hourly output, so make sure FHOUT is 1 when GLDAS is on.

        Fixes #695

    commit 9d00239088651b73a9667b70bd6247b34e35046f
    Author: lgannoaa <[email protected]>
    Date:   Tue Apr 19 21:22:22 2022 -0400

        Update cyclone tracker to handle return code correctly #642

        Updates the cyclone tracker call to correctly exit with an error code if the tracker script reports one.

        Fixes #507

    commit 33d3dd14d6df8109274dde4606bb7a50e4638fa2
    Author: Jessica Meixner <[email protected]>
    Date:   Tue Apr 19 21:18:56 2022 -0400

        Update ww3 pre and post exe build to use cmake (#731)

        Updates the WW3 pre/post build system to use cmake.

        Fixes #688

    commit 39facec1e03a404f84fd05b8739cd8e4010a0779
    Author: Kate Friedman <[email protected]>
    Date:   Tue Apr 12 11:36:30 2022 -0400

        Add WCOSS2 GFSv16.2 operational def files into develop (#717)

        Add WCOSS2 operational GFS def files.

        Refs: #399

    commit 0a85223e48a1a8dcced163791d8e7ae5a42a4fab
    Author: Xianwu Xue - NOAA <[email protected]>
    Date:   Tue Apr 12 11:34:17 2022 -0400

        Initialize "err" to avoid potential task fail (#715)

        If not initialize err, and change "set -x" to "set -xue", then the waveinit task will fail with error message:
            "line 234: err: unbound variable"

         On branch bugfix/issue_714
         Changes to be committed:
        	modified:   scripts/exgfs_wave_init.sh

        Refs: #714

    commit fc6e1c3316397432d2da218b3c4fc0ea1fe70644
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Apr 5 11:07:21 2022 -0400

        config.base should not exist in the repository unless it is in ops.  template only exists in the repo, the experiment directory should not contain the templated config.base.emc.dyn (#707)

    commit cabf437044cb937caf7a7830068fd9e413c5921f
    Author: Jessica Meixner <[email protected]>
    Date:   Wed Mar 30 21:28:50 2022 -0400

        Update model and settings for Prototype P8b (#681)

        Updates model and setting defaults for prototype 8b.

        The UFS version is updated to a recent version of UFS (tag Prototype-P8b). As part of this, the print_esmf option is removed from the model configure file and replaced with a new setting in nems.configure. We have not made this option user-configurable at this point, but that may come in the future.

        The default CCPP suites have been updated for all modes to either FV3_GFS_v17_p8 or FV3_GFS_v17_coupled_p8. This involves changing the microphysics to Thompson and changes the gravity wave drag version (knob_ugwp_version) to 0. This change breaks cycled mode for the time being. A future PR will revert the defaults to ones that allow cycled to run along with a more robust system for changing settings.

        Tiled fix files are now used for all modes instead of just coupled.

        Cellular automata now defaults on ON.

        There are also other miscellaneous settings that have had their defaults changed.

        Fixes #641, #687

    commit e3f707cb9c05b45e9d4019679e406f54008279a5
    Author: XuLi-NOAA <[email protected]>
    Date:   Thu Mar 24 05:43:31 2022 -0400

        Modify eobs for EnKF thinning

        In the Hybrid EnKF GSI, the thinning box size, dmesh, is different for the full resolution analysis and EnKF respectively. There are set in GSI scripts for the full resolution analysis, and reset in global workflow in config.eobs.
        Only two thinning box sizes, dmesh(1) & dmesh(2), are defined in GSI scripts before, recently, two more, dmesh(3) & dmesh(4) are added. Accordingly, these two need to be added in config.eobs as well.

        Specifically, add dmesh(3)=225.0,demsh(4)=100.0 to config.eobs.

        Fixes #595

    commit c32eea459af3177cee28e151b43fe5e12bdfc412
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Tue Mar 22 11:18:10 2022 -0400

        Update ocean resolution for C48 (#651)

        The ocean resolution for C48 was set as 1-deg, but the fractional
        grid fix files available at C48 are for a 4-deg ocean grid. The
        ocean resolution is now set to this value when FV3 is C48.

        Also commented out a currently redundant block setting OCNRES in
        config.ocn. The one in ecfs has to stay as it recalculates the
        ocean resolution based on the EnKF resolution.

        Fixes #650

    commit d758e8b227fca7b5a3320adc43c29ba492c3bfe9
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Thu Mar 10 05:54:49 2022 -0500

        Add single forecast GOCART support (#659)

        Adds support for running single coupled free forecasts with GOCART aerosols. Support for continuous aerosol fields from cycle to cycle will be added in a future PR.

        To turn on aerosols, there is a new --aerosols option for setup_expt.py. The option takes no arguments. When it is used, aerosols will be turned on by setting DO_AERO="YES" in config.base.

        GOCART output files are placed in the chem directory in COM.

        There is a new tarball archived, chem.tar, that contains the GOCART output.

        Partially addresses #516
        Fixes #403

    commit a0e23e254c7c881b20d66c1c53cd36de509e6d69
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Tue Mar 1 10:50:39 2022 -0500

        Specify memory for init job (#669)

        The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed.

        Fixes #631

    commit 6874e8939211fdc07143450bfd1b6a2863172e10
    Author: arun chawla <[email protected]>
    Date:   Fri Feb 25 16:39:45 2022 -0500

        Cleanup of utils directory (#660)

        Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo.

        Fixes #618

    commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Thu Feb 24 22:49:45 2022 -0500

        Fix bug with partition_batch on WCOSS (#668)

        partition_batch was not being defined for WCOSS machines, but was
        being used in a substitution for config.base.

        Fixes #667

    commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Mon Feb 21 02:10:00 2022 -0500

        Split output filetype variable into atm and sfc (#602)

        The determination of the FV3 output filetype was a bit unwieldy as it
        contained two different settings (one for the atmosphere and one for
        the surface) that were not necessarily changed at the same time. They
        were also being determined in a different location than other settings
        based on the model resolution.

        Now the old OUTPUT_FILETYPES variable has been split into two different
        variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi-
        nation was also moved into the config.fv3 file, where other resolution-
        dependent computational settings are set.

        This has resulted in some functional change on WCOSS Dell, as the EnKF
        was using different chunking settings and never used parallel output
        for the surface likely because wasn't being run at a low enough resolu-
        tion to consider it. However, there is no reason to believe the two
        forecast modes should have different chunk or output settings. So, I've
        used the EnKF chunking settings and the free forecast switchover point
        for the surface output mode.

        The new filetype settings are now also divorced from the OUTPUT_FILE
        setting. However, that setting will soon be unnecessary as nemsio
        is removed from the code as an option (see Issue #601).

        Fixes #600
        Refs #601

    commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Thu Feb 17 15:55:24 2022 -0500

        Correct MODE comparisons for forecast only (#658)

        When the setup_expt scripts were combined, the forecast mode became a mandatory
        argument. The value of this option is then directly used for the MODE variable,
        but the argument name (forecast-only) does not match what was previously used
        for MODE in the forecast-only script (free) and some scripts were still testing
        against the old value instead of the new one. Those comparisons have now been
        updated to use the new MODE name.

        Fixes #657

    commit f8867d3f0b1f3b5d238dced412996c56e30d31a1
    Author: David Huber <[email protected]>
    Date:   Thu Feb 10 20:23:54 2022 -0500

        Add LOCALARCH option (#628)

        Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR.

        Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO).

        Fixes #624.

    commit 2950c7b97f99341caa738526138022987f665627
    Author: Jessica Meixner <[email protected]>
    Date:   Thu Feb 10 18:07:43 2022 -0500

        Turn on fractional grid by default for uncoupled forecasts (#638)

        Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true.

        Fixes #571

    commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4
    Author: David Huber <[email protected]>
    Date:   Wed Feb 9 17:02:39 2022 -0500

        Specify warm start as .true. or .false. (#644)

        Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`.

        Fixes #643

    commit e537f0cecabc8e16e26b14e606558de906b19e3f
    Author: David Huber <[email protected]>
    Date:   Tue Feb 8 23:33:21 2022 -0500

        Archive TC tracking logs if produced (#627)

        The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track.

        Fixes #625.

    commit 32f93becde5ffa07c162252b95417845f2ab5159
    Author: David Huber <[email protected]>
    Date:   Tue Feb 8 20:59:37 2022 -0500

        Fix separate threading for GFS and GDAS forecasts. (#621)

        Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs.

        Fixes #610

    commit 9bb09a92c55d4534feca5d521fbbd1c664730317
    Author: David Huber <[email protected]>
    Date:   Tue Feb 8 20:58:05 2022 -0500

        Updated the RadMon and OznMon links. #596 (#597)

    commit 97ebc4d4e6483b135468d85cd9ed974f88955914
    Author: Rahul Mahajan <[email protected]>
    Date:   Thu Feb 3 02:56:34 2022 -0500

        Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537)

        `setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name.

        The user is now required to provide a `mode` as the first positional argument to `setup.py`.  Valid options are `cycled` and `forecast-only`.

        ```
        ❯ python3 setup_expt.py -h
        usage: setup_expt.py [-h] {cycled,forecast-only} ...

        Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link
        initial condition files from $ICSDIR to $COMROT

        positional arguments:
          {cycled,forecast-only}
            cycled              arguments for cycled mode
            forecast-only       arguments for forecast-only mode

        optional arguments:
          -h, --help            show this help message and exit
        ```

        Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively.

        ```
        ❯ python3 setup_expt.py forecast-only -h                                                                  feature/unify-setups
        usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE
                                           [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}]
                                           [--app {ATM,ATMW,S2S,S2SW}]

        optional arguments:
          -h, --help            show this help message and exit
          --pslot PSLOT         parallel experiment name
          --resdet RESDET       resolution of the deterministic model forecast
          --comrot COMROT       full path to COMROT
          --expdir EXPDIR       full path to EXPDIR
          --idate IDATE         starting date of experiment, initial conditions must exist!
          --edate EDATE         end date experiment
          --icsdir ICSDIR       full path to initial condition directory
          --configdir CONFIGDIR
                                full path to directory containing the config files
          --cdump CDUMP         CDUMP to start the experiment
          --gfs_cyc {0,1,2,4}   GFS cycles to run
          --start {warm,cold}   restart mode: warm or cold
          --app {ATM,ATMW,S2S,S2SW}
                                UFS application
        ```

        ```
        ❯ python3 setup_expt.py cycled -h                                                                         feature/unify-setups
        usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE
                                    [--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}]
                                    [--resens RESENS] [--nens NENS] [--app {ATM,ATMW}]

        optional arguments:
          -h, --help            show this help message and exit
          --pslot PSLOT         parallel experiment name
          --resdet RESDET       resolution of the deterministic model forecast
          --comrot COMROT       full path to COMROT
          --expdir EXPDIR       full path to EXPDIR
          --idate IDATE         starting date of experiment, initial conditions must exist!
          --edate EDATE         end date experiment
          --icsdir ICSDIR       full path to initial condition directory
          --configdir CONFIGDIR
                                full path to directory containing the config files
          --cdump CDUMP         CDUMP to start the experiment
          --gfs_cyc {0,1,2,4}   GFS cycles to run
          --start {warm,cold}   restart mode: warm or cold
          --resens RESENS       resolution of the ensemble model forecast
          --nens NENS           number of ensemble members
          --app {ATM,ATMW}      UFS application
        ```

        Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications.

        The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing.

        The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source.

        The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation.

        There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR.   It will be cleaned up in subsequent PR's.

        Another unnecessary complication is the argument of `--start`.  The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot.  It is left unchanged.

    commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Feb 2 11:19:43 2022 -0500

        Stop archiving gfsarch.log as it is being written (#581)

        The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group.

        Fixes: #558

    commit 1b300dbf98eccdf03117b3795a2d8da3310a6126
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Feb 2 11:18:55 2022 -0500

        Fix build on non-WCOSS2 machines (#612)

        The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions.

        Also updates the UFS_UTILS repository to its new location under UFS instead of EMC.

        Fixes #476, #561

    commit d3028b9d8268028226f9c27800fcd6655e9e4bb8
    Author: David Huber <[email protected]>
    Date:   Wed Jan 19 14:29:51 2022 -0500

        Fix setting of OUTPUT_FILETYPES (#589)

        The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine.

        Fixes #588

    commit 13421b01a07e5d1cca32ee7579a4094d8209b072
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jan 19 12:16:29 2022 -0500

        Update PR template

    commit 322a61a61238e8486cb42d7d26282b2728d0c32f
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jan 19 12:13:33 2022 -0500

        Move PR template MD file. Update issue templates

    commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jan 19 11:32:51 2022 -0500

        rename pull_request_template.md

    commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c
    Author: Rahul Mahajan <[email protected]>
    Date:   Wed Jan 19 10:34:54 2022 -0500

        make changes to the templates

    commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Jan 19 10:08:45 2022 -0500

        Fix lfrac entry in diag table (#570)

        Land fraction was listed in the wrong module, keeping it from being
        written to output.

        Refs: #562

    commit e2657adbdadaac7089591390428324c6aec260a9
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jan 18 17:04:04 2022 -0500

        Update NCO_bug_report.md

    commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jan 18 16:59:18 2022 -0500

        Update bug report issue template

    commit 2fab8b4213645b79b3fea8127e7d4ab21044188e
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Jan 18 15:13:53 2022 -0500

        Add templates for Github (#560)

        Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included.

    commit 03be05309b184421c473f1b43082b766b114fd46
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Tue Jan 18 10:02:02 2022 -0500

        Fix toggle for building workflow_utils (#580)

        The fv3gfs_build.cfg did not have a space between the periods and
        the setting for workflow_utils, which means the setting was ignored
        and the default of yes was always used.

        Fixes: #577

    commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Tue Jan 18 10:01:24 2022 -0500

        Remove redundant toggle for gldas build (#579)

        The build cfg files controlling which components are built and the
        partial_build.sh script all have two instances trying to set the
        value for gldas. This means one of the settings did nothing when
        changed.

        Fixes: #578

    commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Jan 14 01:05:59 2022 -0500

        Update config missed in last GSI update (#569)

        When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489).

        Refs: PR #530

    commit 33308ea3b477db17a5db455a4c4887e3d5cbc711
    Author: Jessica Meixner <[email protected]>
    Date:   Thu Jan 6 00:44:43 2022 -0500

        Updates for P8a (#538)

        Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype.

        Updates include:

        Turn on ice-albedo feedback in atm (Requires changing input.nml to set use_cice_alb=true in &gfs_physics_nml )
        Updates to CA namelists
        Updates for NOAH-MP which require input.nml update for to export iopt_sfc="3" and modifying parm_fv3diag to include pahi, pah_ave, ecan_acc, etran_acc,edir_acc,wa_acc, lfrac to the grib outputs "gfs_phys", "pahi", "pahi", "fv3_history2d", "all", .false., "none", 2

        Closes #525

    commit ae7092405e7552f76674b33fc81cb3973a68ad4e
    Author: David Huber <[email protected]>
    Date:   Mon Jan 3 17:28:47 2022 -0500

        Reordered CDUMP_LIST Refs #541 (#542)

    commit 033b1d8ef29b7c829e8131758135b372ae61de26
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Sun Dec 19 22:18:48 2021 -0500

        Update GSI version to 2021 Dec 14 (#530)

    commit b187e2aa15bfd7600c49627fd4c2d02915b50abe
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Thu Dec 16 22:15:45 2021 -0500

        Replace all backticks for command substitution (#526)

        All instances where backticks are used for command substitution are
        replaced with $( ). This standardizes usage around $( ), which can
        be nested and does not be confused with single quotation marks.

        Refs: #397

    commit dd03ed0953bfc65f5a9c85529dd2c95ac0625189
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Fri Dec 10 15:35:00 2021 -0500

        Add coupled support and update UFS (#500)

        Adds support for full coupled model except aerosols (FV3-WW3-MOM6-CICE) following the prototype settings. Support for aerosols will be added soon.

        This also updates the UFS version to develop as of Oct 7. There are associated additions or changes to settings, but we've tried to have defaults maintain the same behavior as previously.

        Issues related to memory in prep and ocnpost on Hera and Orion due to changes in the slurm configuration have been addressed.

        Due to a change in the dycore that uses the checksum in the NetCDF files to check for data integrity, warm start ICs may need an additional offline step before use to update the checksum:
        ```
        ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_core.res.tile1.nc ./fv_core.res.tile1.nc
        ncatted -a checksum,,d,, ${RESTARTinp}/${PDY}.${cyc}0000.fv_tracer.res.tile1.nc ./fv_tracer.res.tile1.nc
        ```

        A new setting APP controls what components (and their respective jobs) are turned on. The setting can be found in config.base, but can be set at experiment setup time using the new --app option. Recognized values are ATM (atm-only), ATMW (atm and waves), S2S (atm-ocn-ice), S2SW (atm-ocn-ice-wav). If no value is given, the default is ATM, so there is no change in behavior if you omit the option. For now, these values follow their UFS equivalents, but they may diverge in the future based on the needs of global workflow. ATMW is known to not quite work; S2S is so far untested.

        When run using the S2SW app, the workflow will automatically substitute the coupled IC copying job in place of the normal gfsprep jobs and use roughly the settings from prototype 7.2 (except aerosols). The alternate settings for the coupled configuration (compared to ATM) are taken from the config.defaults.s2sw file.

        Coupled prototype ICs are currently being maintained on Hera, Orion, and WCOSS-Dell. The locations are set in the config.coupled_ic. There is a base location (BASE_CPLIC) and a setting for each component specifying a subdirectory within the base location.

        There are new options available for the checkout.sh, build_all, and link_fv3 scripts:
        - checkout.sh has a new -m option that allows you to override the UFS hash that is checked out.
        - build_all.sh has two new options: -c to build UFS as the coupled model, and -a to build UFS as ATM-GOCART (but aerosols are not fully supported yet). These options are then passed to build_ufs.sh. The options are temporary, as all configurations will be available from a single executable soon. When building for coupled, the subcomponents built is controlled by cpl_build.cfg.
        - link_fv3.sh is renamed to link_workflow.sh and adds an optional third argument, "coupled". When provided, the files necessary for coupled are linked. This option is also temporary, as the link script will be updated to always link these files.

        ### To run in coupled mode with prototype settings/inputs
        1. Clone as usual
        2. Run checkout.sh
        3. Run build_all.sh with the -c option `./build_all.sh -c` (the -c option is temporary)
        4. Run link using the coupled argument: `./link_workflow.sh emc <machine> coupled`
        5. Run setup_expt_fcstonly.py using the --app option S2SW
        6. Modify config files as necessary. config.defaults.s2sw will automatically override some settings when app is S2SW
        7. Run setup_workflow_fcstonly.py as usual
        8. Setup rocoto to run your experiment

        ### Technical udpates
        Converts global forecast into a set of modular scripts. The scripts define a bunch of functions to be called, with separate functions for each component in each classification. For instance, there is an FV3_GFS_predet, MOM6_predet, CICE_predet, etc. that are conditionally run if the associated component is on.

        The diag table for AOD 550 (diag_table_aod) is reduced to just the portion needed in addition to the normal diag table so it can be appended. Ideally, in the future, we extend this treatment so diag tables can be built based on settings instead of having separate ones for each combination.

        Wave input file templates that were formerly kept in the fix directory are now more appropriately moved inside the global-workflow in parm.

        The group labels for the post jobs now indicates the forecast hours included instead of just an index. This required minor updates to check for 'anl' instead of 0 for analysis jobs.

        The checkout script now writes its logs to the logs/ directory the same way as build does, instead of leaving them in sorc/

        The UFS model source has been moved to a ufs_model.fd directory, and the build script has been renamed build_ufs.sh.

        Error checking was added to the build_ww3prepost.sh script.

        The archive script has been streamlined and the section that saves gaussian grid files was fixed, but turned off by default (see PR #517).

        rocoto_viewer has been updated to python3 and the dependency on prod_utils was removed, which makes the script more portable. Be sure to load a sufficient version of python to use.

        For those coming from coupled-crow: ice and ocean output files are now linked to COM from the forecast run directory instead of being copied at the end of the forecast. This allows post to run as files are produced instead of after the forecast is complete. Ocean post jobs are handled the same as atmosphere post: forecast hours are grouped into a number of tasks determined by NPOSTGRP in config.ocnpost. The ocean and ice output are now also located in their own component directories in COM (the joint ocean-ice files are located in the ocean directory for now). The atmosphere latitudes are reversed from coupled-crow (see c59260b0).

        Co-authored-by: jikuang <[email protected]>
        Co-authored-by: Kate.Friedman <[email protected]>
        Co-authored-by: Rahul Mahajan <[email protected]>
        Co-authored-by: JessicaMeixner-NOAA <[email protected]>
        Co-authored-by: JianKuang-UMD <[email protected]>
        Co-authored-by: lgannoaa <[email protected]>

    commit 8abe1dfa8d613f9398cd86564046b53235f62749
    Author: lgannoaa <[email protected]>
    Date:   Wed Dec 8 16:36:52 2021 -0500

        Fix resource assignment issue found in analysis job running global_cycle (#467)

        Correct settings for nth_anal on WCOSS-Dell and nth_cycle everywhere.

    commit fdffeaaf013f638ac43ad421981e48fabf7a7070
    Author: malloryprow <[email protected]>
    Date:   Thu Nov 18 14:17:02 2021 -0500

        Update gfsmetp, gfsarch dependencies (related update of EMC_verif-global tag) (#508)

        * Update gfsmetp and gfsarch dependencies
        * Update EMC_verif-global tag to verif_global_v2.8.0

        Refs: #437, #472

    commit 108abc589b746b2ba585d18a6b6587e5a0d89f39
    Merge: f6f1bb702 e5cd63693
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Tue Nov 16 10:11:39 2021 -0500

        Merge pull request #497 from NOAA-EMC/feature/shebang

        Update ush/ script files with "python3" in shebang

    commit e5cd636930b0e36ae9b2b25697cda317a2df996d
    Author: jikuang <[email protected]>
    Date:   Fri Nov 12 11:50:53 2021 -0600

        update the following files with "python3" in shebang

    commit f6f1bb7026bcb4983b0f9e921a6332b6722fe724
    Author: lgannoaa <[email protected]>
    Date:   Wed Nov 10 10:08:42 2021 -0500

        Add flag to launcher command to prepend task number to lines in stdout/err (#493)

        Modified env file settings for launcher variable to prepend task number label with "-l" flag.

    commit 096fc1fb76ee01aff7908b91adc9851da9235cad
    Author: Rahul Mahajan <[email protected]>
    Date:   Tue Nov 9 08:47:22 2021 -0500

        Update NSSTBUFR file logic in prep job (#469)

        Add switch in config.prep to toggle NSSTBUFR file creation in prep.sh.  Add logic in prep.sh to copy NSSTBUFR from DMPDIR if not creating as part of the workflow.  NSSTBUFR is created with different DTYPS_nsst before 2020102200.

    commit 84194a735b46c907656fe2b2cca3ca97799396f0
    Merge: a39cb11ef 0740b5b6c
    Author: Walter Kolczynski - NOAA <[email protected]>
    Date:   Wed Oct 27 11:52:55 2021 -0400

        Merge pull request #474 from NOAA-EMC/feature/setx2

        Hide module load commands

    commit 0740b5b6c622d64b770c73aa47d9789494d94a99
    Author: jikuang <[email protected]>
    Date:   Tue Oct 26 13:19:07 2021 -0500

        wrap module load commands with set +x

    commit a39cb11ef9e72b2913d81521d6f9e51da3a8bc22
    Author: Kate Friedman <[email protected]>
    Date:   Wed Sep 29 09:36:31 2021 -0400

        Update EMC_verif-global tag to verif_global_v2.5.2 (#450)

        New tag provides the following updates since the verif_global_v2.2.1 tag:
        - Added capability to produce a scorecard (no need to use METviewer AWS to produce scorecards)
        - Added capability to produce fit-to-obs plots
        - Added support for Jet
        - Updated DA ensemble plots graphics to support when models ensemble mean and spread output is on different grids
        - Hot fix for new METviewer AWS host name
        - Hot fix for reorganizing precipitation verification input files

        Refs: #438

    commit 6f74cacdffe22f67e99aed1ac0e75720dac27c30
    Author: JianKuang-UMD <[email protected]>
    Date:   Tue Sep 28 09:53:16 2021 -0400

        Remove firstcyc job (#440)

        The need for the firstcyc job has gone away, removing redundant job.

    commit 1ca27148d776eedf96636a845feb95881cfaa138
    Author: Kate Friedman <[email protected]>
    Date:   Thu Sep 9 11:53:11 2021 -0400

        Update repository name for EMC_post component to UPP (#441)

        - the "EMC_post" repository was renamed to "UPP" on September 6th 2021
        - update repository url in checkout script and Externals.cfg

        Refs: #433

    commit 7233d0c46cc9d24b01bee0ef6be12d775d2523a4
    Author: Kate Friedman <[email protected]>
    Date:   Mon Aug 23 11:22:26 2021 -0400

        Add rstprod support to Orion (#421)

        - Update EMC_verif-global tag to verif_global_v2.2.1
        - Turn on rstprod support by default on Orion
        - Change default DMPDIR path on Orion to new rstprod-supported GDA

        Refs: #347

    commit 20c331dd9678834b980ccc932b6235a8266d4a88
    Author: Kate Friedman <[email protected]>
    Date:   Thu Aug 19 13:01:07 2021 -0400

        Update obsproc package versions for TAC2BUFR implementation (#423)

        Update obsproc package versions for TAC2BUFR implementation:

        - obsproc_prep v5.5.0
        - obsproc_global v3.4.2
        - new packages installed on WCOSS-Dell, Hera, Jet, Orion

        Refs: #341

    commit 7f0f7400520b031e2428238a9741d4d8bfb8207a
    Author: Kate Friedman <[email protected]>
    Date:   Wed Aug 18 12:41:09 2021 -0400

        Update vrfy/metp jobs to use jobid in their DATAROOT folders (#414)

        Update vrfy/metp jobs to use jobid in their respective DATAROOT folder names; fixes race condition between vrfy and metp jobs

        Refs: #401

    commit 9233d965cd19a94ee649b4ee8c117bb587b78923
    Author: Kate Friedman <[email protected]>
    Date:   Tue Aug 17 12:48:12 2021 -0400

        Update workflow_utils build modules and remove ncio module hack (#412)

        Add ncio/1.0.0 module load to workflow_utils and remove hack that builds this library inline.
        Refs: #407

    commit df26e953792913669698ba64b414b3be5184f43d
    Author: Kate Friedman <[email protected]>
    Date:   Tue Aug 17 11:15:38 2021 -0400

        UFS_UTILS tag update - gdas_init support on Jet and HPSS path update for GFSv16 real-time parallel (#410)

        * Update UFS_UTILS tag to ufs_utils_1_6_0
        * Update HPSS path for real-time GFSv16 pre-implementation parallels

        Refs: #400

    commit 34427f560c729ee3b7cc91ff357b3ad908a7486a
    Author: lgannoaa <[email protected]>
    Date:   Mon Aug 9 15:47:27 2021 -0400

        Free-forecast mode support on Jet (#394)

        Support for free-forecast mode on Jet is added. Setup support for multiple partitions included (xjet, kjet, sjet, vjet) but tested/recommend to use xjet (default). Verification pieces and cycled mode not yet supported.

    commit 8c777ad04bce0555bed9f6666b808515b0a3766d
    Merge: ce66c74bb fc48af56d
    Author: Kate Friedman <[email protected]>
    Date:   Tue Jul 20 15:53:45 2021 -0400

        Merge pull request #370 from BrianCurtis-NOAA/feature/rocoto-py3

        Convert setup scripts to python3

    commit fc48af56d3a0ccbd3e142d22452b9b5e34173b7b
    Author: Brian Curtis <[email protected]>
    Date:   Mon Jul 19 20:48:05 2021 +0000

        Missed a set of raw_input(), in py3 they are just input()

    commit 44dc907a2ea3b8a29334b2416183ca8775ff4c82
    Author: Brian Curtis <[email protected]>
    Date:   Mon Jul 19 19:59:54 2021 +0000

        revert rocoto_viewer as its being worked on elsewhere

    commit 37f25384c29f6697be5c851868ce98d8b6c31207
    Author: Brian Curtis <[email protected]>
    Date:   Mon Jul 19 19:27:32 2021 +0000

        Fixes from testing

    commit c0716f41f2446fec9a441b285d9033f73345c5d4
    Author: Brian Curtis <[email protected]>
    Date:   Mon Jul 19 10:28:06 2021 -0400

        Merge w/upstream and update those changes to py3

    commit cf8758f84418c236fb45913912491a1c27b2829f
    Merge: f9013decd ce66c74bb
    Author: Brian Curtis <[email protected]>
    Date:   Mon Jul 19 09:21:25 2021 -0400

        fix merge conflict in workflow_fcstonly

    commit ce66c74bbc43e997bae66a2c2035f2412d3f602b
    Merge: 96347ea52 7a166da9f
    Author: Kate Friedman <[email protected]>
    Date:   Wed Jul 14 16:18:55 2021 -0400

        Merge pull request #362 from KateFriedman-NOAA/bugfix/ffhighres

        Correct wrong settings for high-res warm-start free-forecast

    commit 7a166da9f20a59729be39fff953bfe367987f046
    Author: Kate.Friedman <[email protected]>
    Date:   Wed Jul 14 19:19:45 2021 +0000

        Reduce C768 npe_wav_gfs from ops 440 to dev 140

        Refs: #353

    commit b34c581c3b19ecdcdb4eff463e855597e5c08d80
    Author: Kate.Friedman <[email protected]>
    Date:   Wed Jul 14 19:15:31 2021 +0000

        Adjust how EXP_WARM_START is set from setup_expt_fcstonly.py step

        - remove default value for start (EXP_WARM_START)
        - if user provides start flag then use it for EXP_WARM_START
        - if user doesn't provide start flag then make a decision for them based on resolution
        - if start=None and res=768 then start=warm
        - if start=None and res!=768 then start=cold

        Refs: #353

    commit 69cf53412a61e7fe0fb49e8c688bc2cbb4ded572
    Author: Kate.Friedman <[email protected]>
    Date:   Thu Jun 24 16:38:25 2021 +0000

        Set EXP_WARM_START=true in config.base via setup_expt_fcsonly.py if resolution is C768

        - have free-forecast setup_expt script check if resolution is operational resolution (C768)
          and if so, set EXP_WARM_START=.true.
        - forcing EXP_WARM_START=.true. when C768 covers most C768 scenarios regarding cold vs warm starting
        - the --start argument still works but new check will override if res=768
        - users can still change config.base setting as needed for special scenarios

        Refs: #353

    commit 08f62e45319c9772ef33cdb3c7aa3ec165fede09
    Author: Kate.Friedman <[email protected]>
    Date:   Wed Jun 23 21:21:51 2021 +0000

        Revert EXP_WARM_START if-block addition in config.getic

        - need to determine better way to set EXP_WARM_START

        Refs: #353

    commit 1c03067ca570295b65f967467ef2329fb7999578
    Author: Kate.Friedman <[email protected]>
    Date:   Wed Jun 23 19:33:18 2021 +0000

        Revert config.base EXP_WARM_START check change

        Refs: #353

    commit 0f1cea6662695cad9ecf7df8317a36e1ab5c57e1
    Author: Kate.Friedman <[email protected]>
    Date:   Wed Jun 23 19:12:27 2021 +0000

        Add checks for EXP_WARM_START in config.base and config.getic

        - add OPS_RES variable to both config.base.emc.dyn and config.getic
        - add if-block in both configs to force EXP_WARM_START=true if CASE=OPS_RES and gfs_ver=v16 (current ops)
        - check in config.base helps with later IAU checks
        - help catch when user doesn't set EXP_WARM_START=true when running v16 C768

        Refs: #353

    commit 7ed96c34f3dd6e4c4251e87d9abf62a0dbb413a2
    Author: Kate.Friedman <[email protected]>
    Date:   Wed Jun 23 19:10:17 2021 +0000

        Add cd to ROTDIR when pulling ops warm starts

        - pull v16 warm starts directly into ROTDIR; don't need temporary location to handle subfolder diffs
        - resolves issue with GDATE gdas restart files being left in EXTRACT_DIR

        Refs: #353

    commit 06c5e3cb7bd9d82d4e51a63168465118a34e5882
    Author: Kate.Friedman <[email protected]>
    Date:   Wed Jun 23 19:06:42 2021 +0000

        Reduce C768 resource settings to fit node limits

        - default C768 resources on Hera were 218 nodes which is higher than the 210 node limit per job
        - bring C768 settings in config.fv3 down to 148 nodes (on Hera)
        - tested new settings in free-forecast mode on Hera

        Refs: #353

    commit 96347ea527f7b0ab61a1aae6576e2709fb387c7c
    Merge: cfca8bb2c 5c042e087
    Author: Kate Friedman <[email protected]>
    Date:   Wed Jun 23 11:13:06 2021 -0400

        Merge pull request #316 from NOAA-EMC/feature/hpc-stack

        GFS components update for hpc-stack support

    commit 5c042e087c02cb82fe24ce666e477791f5e2417e
    Merge: b36414e4c cfca8bb2c
    Author: kate.friedman <[email protected]>
    Date:   Thu Jun 17 19:33:03 2021 +0000

        Merge remote-tracking branch 'origin/develop' into feature/hpc-stack

    commit cfca8bb2ca0dc0105b905c536f346002408db771
    Merge: e08f55583 fba8cef5b
    Author: Kate Friedman <[email protected]>
    Date:   Thu Jun 17 14:40:18 2021 -0400

        Merge pull request #342 from KateFriedman-NOAA/issue178

        Free-forecast integration with chgres_cube and resolve know mode bugs

    commit fba8cef5b870d46df1c665d3e9cabb23904ad3cf
    Author: Kate.Friedman <[email protected]>
    Date:   Wed Jun 16 13:57:14 2021 +0000

        Remove wave restart pull in getic script

        Refs: #178

    commit 921838feb9f6fd3fc3c69579c677ffdd7175a103
    Author: Kate.Friedman <[email protected]>
    Date:   Wed Jun 16 13:18:35 20…
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Convert module files from Tcl to Lua WalterKolczynski-NOAA/global-workflow
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