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

* origin/develop: Code Updates for New Wave Fix Files (NOAA-EMC#1605) Make JEDI cycling toggle switches YAML configurable and their names more explicit (NOAA-EMC#1607) Update gfs-utils hash to 8965258 (NOAA-EMC#1586) Allow YAML input to override config.base and make HPSS_PROJECT configurable (NOAA-EMC#1603) Fix RTD python requirements path Clean up RTD python install settings Use RTD python system packages Fix python RTD parameter name Update RTD python install Restore RTD python version and add requirements Revert python version for RTD (NOAA-EMC#1598) Move RTD config to root of repo (NOAA-EMC#1597) Add RTD config (NOAA-EMC#1596) Add `schema` library to manage schema for variety of input configurations. (NOAA-EMC#1567) Add S2SA to the allowed app list in setup expt (NOAA-EMC#1591) Avoid parsing group name when checking RadMon diagnostic files (NOAA-EMC#1559) Remove gldas from global-workflow (NOAA-EMC#1590) Add GEFS capability to setup_expt (NOAA-EMC#1582)
KateFriedman-NOAA · May 16, 2023 · dbdd150 · dbdd150
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,21 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+  system_packages: true
diff --git a/Externals.cfg b/Externals.cfg
@@ -8,7 +8,7 @@ protocol = git
 required = True
 
 [gfs-utils]
-hash = 0b8ff56
+hash = 8965258
 local_path = sorc/gfs_utils.fd
 repo_url = https://github.com/NOAA-EMC/gfs-utils
 protocol = git
@@ -56,13 +56,6 @@ repo_url = https://github.com/NOAA-EMC/GDASApp.git
 protocol = git
 required = False
 
-[GLDAS]
-tag = fd8ba62
-local_path = sorc/gldas.fd
-repo_url = https://github.com/NOAA-EMC/GLDAS.git
-protocol = git
-required = False
-
 [EMC-gfs_wafs]
 hash = 014a0b8
 local_path = sorc/gfs_wafs.fd

diff --git a/docs/source/components.rst b/docs/source/components.rst
@@ -1,5 +1,5 @@
 ###########################
-Global Workflow Components 
+Global Workflow Components
 ###########################
 
 The global-workflow is a combination of several components working together to prepare, analyze, produce, and post-process forecast data.
@@ -13,20 +13,19 @@ The major components of the system are:
 * Post-processing
 * Verification
 
-The Global Workflow repository contains the workflow and script layers. After running the checkout script, the code and additional offline scripts for the analysis, forecast, and post-processing components will be present. Any non-workflow component is known as a sub-module. All of the sub-modules of the system reside in their respective repositories on GitHub. The global-workflow sub-modules are obtained by running the checkout script found under the /sorc folder. 
+The Global Workflow repository contains the workflow and script layers. After running the checkout script, the code and additional offline scripts for the analysis, forecast, and post-processing components will be present. Any non-workflow component is known as a sub-module. All of the sub-modules of the system reside in their respective repositories on GitHub. The global-workflow sub-modules are obtained by running the checkout script found under the /sorc folder.
 
 ======================
 Component repositories
 ======================
 
 Components checked out via sorc/checkout.sh:
 
-* **GFS UTILS** (https://github.com/ufs-community/gfs_utils): Utility codes needed by Global Workflow to run the GFS configuration 
-* **UFS-Weather-Model** (https://github.com/ufs-community/ufs-weather-model): This is the core model used by the Global-Workflow to provide forecasts. The UFS-weather-model repository is an umbrella repository consisting of cooupled component earth systeme that are all checked out when we check out the code at the top level of the repoitory 
+* **GFS UTILS** (https://github.com/ufs-community/gfs_utils): Utility codes needed by Global Workflow to run the GFS configuration
+* **UFS-Weather-Model** (https://github.com/ufs-community/ufs-weather-model): This is the core model used by the Global-Workflow to provide forecasts. The UFS-weather-model repository is an umbrella repository consisting of cooupled component earth systeme that are all checked out when we check out the code at the top level of the repoitory
 * **GSI** (https://github.com/NOAA-EMC/GSI): This is the core code base for atmospheric Data Assimilation
-* **GSI UTILS** (https://github.com/NOAA-EMC/GSI-Utils): Utility codes needed by GSI to create analysis 
-* **GSI Monitor** (https://github.com/NOAA-EMC/GSI-Monitor): These tools monitor the GSI package's data assimilation, detecting and reporting missing data sources, low observation counts, and high penalty values 
-* **GLDAS** (https://github.com/NOAA-EMC/GLDAS): Code base for Land Data Assimiation
+* **GSI UTILS** (https://github.com/NOAA-EMC/GSI-Utils): Utility codes needed by GSI to create analysis
+* **GSI Monitor** (https://github.com/NOAA-EMC/GSI-Monitor): These tools monitor the GSI package's data assimilation, detecting and reporting missing data sources, low observation counts, and high penalty values
 * **GDAS** (https://github.com/NOAA-EMC/GDASApp): Jedi based Data Assimilation system. This system is currently being developed for marine Data Assimilation and in time will replace GSI for atmospheric data assimilation as well
 * **UFS UTILS** (https://github.com/ufs-community/UFS_UTILS): Utility codes needed for UFS-weather-model
 * **Verif global** (https://github.com/NOAA-EMC/EMC_verif-global): Verification package to evaluate GFS parallels. It uses MET and METplus. At this moment the verification package is limited to providing atmospheric metrics only
@@ -43,7 +42,7 @@ External dependencies
 Libraries
 ^^^^^^^^^
 
-All the libraries that are needed to run the end to end Global Workflow are built using a package manager. Currently these are served via HPC-STACK but will soon be available via SPACK-STACK. These libraries are already available on supported NOAA HPC platforms 
+All the libraries that are needed to run the end to end Global Workflow are built using a package manager. Currently these are served via HPC-STACK but will soon be available via SPACK-STACK. These libraries are already available on supported NOAA HPC platforms
 
 Find information on official installations of HPC-STACK here:
 

diff --git a/docs/source/configure.rst b/docs/source/configure.rst
@@ -10,7 +10,7 @@ The global-workflow configs contain switches that change how the system runs. Ma
 | APP            | Model application            | ATM           | YES         | See case block in config.base for options         |
 +----------------+------------------------------+---------------+-------------+---------------------------------------------------+
 | DOIAU          | Enable 4DIAU for control     | YES           | NO          | Turned off for cold-start first half cycle        |
-|                | with 3 increments            |               |             |                                                   | 
+|                | with 3 increments            |               |             |                                                   |
 +----------------+------------------------------+---------------+-------------+---------------------------------------------------+
 | DOHYBVAR       | Run EnKF                     | YES           | YES         | Don't recommend turning off                       |
 +----------------+------------------------------+---------------+-------------+---------------------------------------------------+
@@ -26,9 +26,6 @@ The global-workflow configs contain switches that change how the system runs. Ma
 | DO_GEMPAK      | Run job to produce GEMPAK    | NO            | YES         | downstream processing, ops only                   |
 |                | products                     |               |             |                                                   |
 +----------------+------------------------------+---------------+-------------+---------------------------------------------------+
-| DO_GLDAS       | Run GLDAS to spin up land    | YES           | YES         | Spins up for 84hrs if sflux files not available   |
-|                | ICs                          |               |             |                                                   |
-+----------------+------------------------------+---------------+-------------+---------------------------------------------------+
 | DO_VRFY        | Run vrfy job                 | NO            | YES         | Whether to include vrfy job (GSI monitoring,      |
 |                |                              |               |             | tracker, VSDB, fit2obs)                           |
 +----------------+------------------------------+---------------+-------------+---------------------------------------------------+

diff --git a/docs/source/jobs.rst b/docs/source/jobs.rst
@@ -3,7 +3,7 @@ GFS Configuration
 #################
 
 .. figure:: _static/GFS_v16_flowchart.png
- 
+
    Schematic flow chart for GFS v16 in operations
 
 The sequence of jobs that are run for an end-to-end (analysis+forecast+post processing+verification) GFS configuration using the Global Workflow is shown above. The system utilizes a collection of scripts that perform the tasks for each step.
@@ -12,7 +12,7 @@ For any cycle the system consists of two suites -- the "gdas" suite which provid
 
 An experimental run is different from operations in the following ways:
 
-* Workflow manager: operations utilizes `ecFlow <https://www.ecmwf.int/en/learning/training/introduction-ecmwf-job-scheduler-ecflow>`__, while development currently utilizes `ROCOTO <https://github.com/christopherwharrop/rocoto/wiki/documentation>`__. Note, experiments can also be run using ecFlow on platforms with ecFlow servers established. 
+* Workflow manager: operations utilizes `ecFlow <https://www.ecmwf.int/en/learning/training/introduction-ecmwf-job-scheduler-ecflow>`__, while development currently utilizes `ROCOTO <https://github.com/christopherwharrop/rocoto/wiki/documentation>`__. Note, experiments can also be run using ecFlow on platforms with ecFlow servers established.
 
 * Dump step is not run as it has already been completed during the real-time production runs and dump data is available in the global dump archive on supported machines.
 
@@ -25,7 +25,7 @@ An experimental run is different from operations in the following ways:
 Downstream jobs (e.g. awips, gempak, etc.) are not included in the diagram. Those jobs are not normally run in developmental tests.
 
 =============================
-Jobs in the GFS Configuration 
+Jobs in the GFS Configuration
 =============================
 +-------------------+-----------------------------------------------------------------------------------------------------------------------+
 | JOB NAME          | PURPOSE                                                                                                               |
@@ -65,8 +65,6 @@ Jobs in the GFS Configuration
 +-------------------+-----------------------------------------------------------------------------------------------------------------------+
 | fcst              | Runs the forecast (with or without one-way waves).                                                                    |
 +-------------------+-----------------------------------------------------------------------------------------------------------------------+
-| gldas             | Runs the Global Land Data Assimilation System (GLDAS).                                                                |
-+-------------------+-----------------------------------------------------------------------------------------------------------------------+
 | metpN             | Runs MET/METplus verification via EMC_verif-global.                                                                   |
 +-------------------+-----------------------------------------------------------------------------------------------------------------------+
 | prep              | Runs the data preprocessing prior to the analysis (storm relocation if needed and generation of prepbufr file).       |

diff --git a/docs/source/setup.rst b/docs/source/setup.rst
@@ -84,18 +84,20 @@ The following command examples include variables for reference but users should
 ::
 
    cd workflow
-   ./setup_expt.py forecast-only --idate $IDATE --edate $EDATE [--app $APP] [--start $START] [--gfs_cyc $GFS_CYC] [--resdet $RESDET]
+   ./setup_expt.py gfs forecast-only --idate $IDATE --edate $EDATE [--app $APP] [--start $START] [--gfs_cyc $GFS_CYC] [--resdet $RESDET]
      [--pslot $PSLOT] [--configdir $CONFIGDIR] [--comrot $COMROT] [--expdir $EXPDIR]
 
 where:
 
-   * ``forecast-only`` is the first positional argument that instructs the setup script to produce an experiment directory for forecast only experiments.
+   * ``gfs`` is the first positional argument that instructs the setup script to produce a GFS experiment directory
+   * ``forecast-only`` is the second positional argument that instructs the setup script to produce an experiment directory for forecast only experiments.
    * ``$APP`` is the target application, one of:
 
      - ATM: atmosphere-only [default]
      - ATMW: atm-wave
      - ATMA: atm-aerosols
      - S2S: atm-ocean-ice
+     - S2SA: atm-ocean-ice-aerosols
      - S2SW: atm-ocean-ice-wave
      - S2SWA: atm-ocean-ice-wave-aerosols
 
@@ -116,21 +118,21 @@ Atm-only:
 ::
 
    cd workflow
-   ./setup_expt.py forecast-only --pslot test --idate 2020010100 --edate 2020010118 --resdet 384 --gfs_cyc 4 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir
+   ./setup_expt.py gfs forecast-only --pslot test --idate 2020010100 --edate 2020010118 --resdet 384 --gfs_cyc 4 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir
 
 Coupled:
 
 ::
 
    cd workflow
-   ./setup_expt.py forecast-only --app S2SW --pslot coupled_test --idate 2013040100 --edate 2013040100 --resdet 384 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir
+   ./setup_expt.py gfs forecast-only --app S2SW --pslot coupled_test --idate 2013040100 --edate 2013040100 --resdet 384 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir
 
 Coupled with aerosols:
 
 ::
 
    cd workflow
-   ./setup_expt.py forecast-only --app S2SWA --pslot coupled_test --idate 2013040100 --edate 2013040100 --resdet 384 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir
+   ./setup_expt.py gfs forecast-only --app S2SWA --pslot coupled_test --idate 2013040100 --edate 2013040100 --resdet 384 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir
 
 ****************************************
 Step 2: Set user and experiment settings
@@ -193,13 +195,14 @@ The following command examples include variables for reference but users should
 ::
 
    cd workflow
-   ./setup_expt.py cycled --idate $IDATE --edate $EDATE [--app $APP] [--start $START] [--gfs_cyc $GFS_CYC]
+   ./setup_expt.py gfs cycled --idate $IDATE --edate $EDATE [--app $APP] [--start $START] [--gfs_cyc $GFS_CYC]
      [--resdet $RESDET] [--resens $RESENS] [--nens $NENS] [--cdump $CDUMP]
      [--pslot $PSLOT] [--configdir $CONFIGDIR] [--comrot $COMROT] [--expdir $EXPDIR] [--icsdir $ICSDIR]
 
 where:
 
-   * ``cycled`` is the first positional argument that instructs the setup script to produce an experiment directory for cycled experiments.
+   * ``gfs`` is the first positional argument that instructs the setup script to produce a GFS experiment directory
+   * ``cycled`` is the second positional argument that instructs the setup script to produce an experiment directory for cycled experiments.
    * ``$APP`` is the target application, one of:
 
      - ATM: atmosphere-only [default]
@@ -226,13 +229,13 @@ Example:
 ::
 
    cd workflow
-   ./setup_expt.py cycled --pslot test --configdir /home/Joe.Schmo/git/global-workflow/parm/config --idate 2020010100 --edate 2020010118 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir --resdet 384 --resens 192 --nens 80 --gfs_cyc 4
+   ./setup_expt.py gfs cycled --pslot test --configdir /home/Joe.Schmo/git/global-workflow/parm/config --idate 2020010100 --edate 2020010118 --comrot /some_large_disk_area/Joe.Schmo/comrot --expdir /some_safe_disk_area/Joe.Schmo/expdir --resdet 384 --resens 192 --nens 80 --gfs_cyc 4
 
 Example ``setup_expt.py`` on Orion:
 
 ::
 
-   Orion-login-3$ ./setup_expt.py cycled --pslot test --idate 2022010118 --edate 2022010200 --resdet 192 --resens 96 --nens 80 --comrot /work/noaa/stmp/jschmo/comrot --expdir /work/noaa/global/jschmo/expdir
+   Orion-login-3$ ./setup_expt.py gfs cycled --pslot test --idate 2022010118 --edate 2022010200 --resdet 192 --resens 96 --nens 80 --comrot /work/noaa/stmp/jschmo/comrot --expdir /work/noaa/global/jschmo/expdir
    EDITED:  /work/noaa/global/jschmo/expdir/test/config.base as per user input.
    EDITED:  /work/noaa/global/jschmo/expdir/test/config.aeroanl as per user input.
    EDITED:  /work/noaa/global/jschmo/expdir/test/config.ocnanal as per user input.
@@ -243,7 +246,7 @@ What happens if I run ``setup_expt.py`` again for an experiment that already exi
 
 ::
 
-   Orion-login-3$ ./setup_expt.py cycled --pslot test --idate 2022010118 --edate 2022010200 --resdet 192 --resens 96 --nens 80 --comrot /work/noaa/stmp/jschmo/comrot --expdir /work/noaa/global/jschmo/expdir
+   Orion-login-3$ ./setup_expt.py gfs cycled --pslot test --idate 2022010118 --edate 2022010200 --resdet 192 --resens 96 --nens 80 --comrot /work/noaa/stmp/jschmo/comrot --expdir /work/noaa/global/jschmo/expdir
 
    directory already exists in /work/noaa/stmp/jschmo/comrot/test
 

diff --git a/ecf/defs/gfs_00.def b/ecf/defs/gfs_00.def
@@ -2224,10 +2224,6 @@
               trigger /prod/primary/00/obsproc/v1.0/gdas/atmos/dump/jobsproc_gdas_atmos_dump:release_sfcprep
           endfamily
         endfamily
-        family init
-          task jgdas_atmos_gldas
-            trigger ../analysis/jgdas_atmos_analysis == complete
-        endfamily
         family analysis
           task jgdas_atmos_analysis
             trigger /prod/primary/00/obsproc/v1.0/gdas/atmos/prep/jobsproc_gdas_atmos_prep == complete and ../obsproc/prep/jgdas_atmos_emcsfc_sfc_prep == complete
@@ -2354,7 +2350,7 @@
         endfamily
       endfamily
       task jgdas_forecast
-        trigger ./atmos/analysis/jgdas_atmos_analysis:release_fcst and ./wave/prep/jgdas_wave_prep == complete and ./atmos/init/jgdas_atmos_gldas == complete
+        trigger ./atmos/analysis/jgdas_atmos_analysis:release_fcst and ./wave/prep/jgdas_wave_prep == complete
     endfamily
     family enkfgdas
       edit RUN 'gdas'

diff --git a/ecf/defs/gfs_06.def b/ecf/defs/gfs_06.def
@@ -2224,10 +2224,6 @@
               trigger /prod/primary/06/obsproc/v1.0/gdas/atmos/dump/jobsproc_gdas_atmos_dump:release_sfcprep
           endfamily
         endfamily
-        family init
-          task jgdas_atmos_gldas
-            trigger ../analysis/jgdas_atmos_analysis == complete
-        endfamily
         family analysis
           task jgdas_atmos_analysis
             trigger /prod/primary/06/obsproc/v1.0/gdas/atmos/prep/jobsproc_gdas_atmos_prep == complete and ../obsproc/prep/jgdas_atmos_emcsfc_sfc_prep == complete
@@ -2354,7 +2350,7 @@
         endfamily
       endfamily
       task jgdas_forecast
-        trigger ./atmos/analysis/jgdas_atmos_analysis:release_fcst and ./wave/prep/jgdas_wave_prep == complete and ./atmos/init/jgdas_atmos_gldas == complete
+        trigger ./atmos/analysis/jgdas_atmos_analysis:release_fcst and ./wave/prep/jgdas_wave_prep == complete
     endfamily
     family enkfgdas
       edit RUN 'gdas'

diff --git a/ecf/defs/gfs_12.def b/ecf/defs/gfs_12.def
@@ -2225,10 +2225,6 @@
               trigger /prod/primary/12/obsproc/v1.0/gdas/atmos/dump/jobsproc_gdas_atmos_dump:release_sfcprep
           endfamily
         endfamily
-        family init
-          task jgdas_atmos_gldas
-            trigger ../analysis/jgdas_atmos_analysis == complete
-        endfamily
         family analysis
           task jgdas_atmos_analysis
             trigger /prod/primary/12/obsproc/v1.0/gdas/atmos/prep/jobsproc_gdas_atmos_prep == complete and ../obsproc/prep/jgdas_atmos_emcsfc_sfc_prep == complete
@@ -2355,7 +2351,7 @@
         endfamily
       endfamily
       task jgdas_forecast
-        trigger ./atmos/analysis/jgdas_atmos_analysis:release_fcst and ./wave/prep/jgdas_wave_prep == complete and ./atmos/init/jgdas_atmos_gldas == complete
+        trigger ./atmos/analysis/jgdas_atmos_analysis:release_fcst and ./wave/prep/jgdas_wave_prep == complete
     endfamily
     family enkfgdas
       edit RUN 'gdas'