Merge branch 'NOAA-EMC:develop' into feature/gmi_on

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+exclude = .git,.github,venv,__pycache__,old,build,dist
+max-line-length = 160

.github/workflows/orion.yaml → .github/workflows/hercules.yaml

@@ -1,4 +1,4 @@
-name: Orion
+name: Hercules
 
 on:
   pull_request_target:
@@ -26,7 +26,7 @@ jobs:
           echo "labels=$LABELS" >> $GITHUB_OUTPUT
 
   passed:
-    if: contains( needs.getlabels.outputs.labels, 'CI-Orion-Passed') && github.event.pull_request.merged
+    if: contains( needs.getlabels.outputs.labels, 'CI-Hercules-Passed') && github.event.pull_request.merged
     runs-on: ubuntu-22.04
     needs:
      - getlabels
@@ -38,13 +38,13 @@ jobs:
         forceUpdate: true
         auth: ${{ secrets.CLI_DYNAMIC_BADGES }}
         gistID: e35aa2904a54deae6bbb1fdc2d960c71
-        filename: orion.json
-        label: orion
+        filename: hercules.json
+        label: hercules
         message: passing
         color: green
 
   failed:
-    if: contains( needs.getlabels.outputs.labels, 'CI-Orion-Failed') && github.event.pull_request.merged
+    if: contains( needs.getlabels.outputs.labels, 'CI-Hercules-Failed') && github.event.pull_request.merged
     runs-on: ubuntu-latest
     needs:
      - getlabels
@@ -56,14 +56,14 @@ jobs:
         forceUpdate: true
         auth: ${{ secrets.CLI_DYNAMIC_BADGES }}
         gistID: e35aa2904a54deae6bbb1fdc2d960c71
-        filename: orion.json
-        label: orion
+        filename: hercules.json
+        label: hercules
         message: failing
         color: red
 
 
   pending:
-    if: "!contains( needs.getlabels.outputs.labels, 'CI-Orion-Passed') && !contains( needs.getlabels.outputs.labels, 'CI-Orion-Failed')"
+    if: "!contains( needs.getlabels.outputs.labels, 'CI-Hercules-Passed') && !contains( needs.getlabels.outputs.labels, 'CI-Hercules-Failed')"
     runs-on: ubuntu-latest
     needs:
      - getlabels
@@ -75,7 +75,7 @@ jobs:
         forceUpdate: true
         auth: ${{ secrets.CLI_DYNAMIC_BADGES }}
         gistID: e35aa2904a54deae6bbb1fdc2d960c71
-        filename: orion.json
-        label: orion
+        filename: hercules.json
+        label: hercules
         message: pending
         color: orange

.github/workflows/wcoss2.yaml

@@ -0,0 +1,81 @@
+name: WCOSS2
+
+on:
+  pull_request_target:
+    branches:
+      - develop
+    types: [closed]
+
+jobs:
+
+  getlabels:
+    runs-on: ubuntu-22.04
+    outputs:
+      labels: ${{ steps.id.outputs.labels }}
+    steps:
+      - name: Get Label Steps
+        id: id
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          OWNER: ${{ github.repository_owner }}
+          REPO_NAME: ${{ github.event.repository.name }}
+          PULL_REQUEST_NUMBER: ${{ github.event.pull_request.number }}
+        run: |
+          LABELS1="$(gh api repos/$OWNER/$REPO_NAME/pulls/$PULL_REQUEST_NUMBER --jq '.labels.[].name')"
+          LABELS=$(echo "$LABELS1" | tr '\n' ' ')
+          echo "labels=$LABELS" >> $GITHUB_OUTPUT
+
+  passed:
+    if: contains( needs.getlabels.outputs.labels, 'CI-Wcoss2-Passed') && github.event.pull_request.merged
+    runs-on: ubuntu-latest
+    needs:
+     - getlabels
+
+    steps:
+    - name: Passed
+      uses: schneegans/[email protected]
+      with:
+        forceUpdate: true
+        auth: ${{ secrets.CLI_DYNAMIC_BADGES }}
+        gistID: e35aa2904a54deae6bbb1fdc2d960c71
+        filename: wcoss2.json
+        label: wcoss2
+        message: passing
+        color: green
+
+  failed:
+    if: contains( needs.getlabels.outputs.labels, 'CI-Wcoss2-Failed') && github.event.pull_request.merged
+    runs-on: ubuntu-latest
+    needs:
+     - getlabels
+
+    steps:
+    - name: Failed
+      uses: schneegans/[email protected]
+      with:
+        forceUpdate: true
+        auth: ${{ secrets.CLI_DYNAMIC_BADGES }}
+        gistID: e35aa2904a54deae6bbb1fdc2d960c71
+        filename: wcoss2.json
+        label: wcoss2
+        message: failing
+        color: red
+
+
+  pending:
+    if: "!contains( needs.getlabels.outputs.labels, 'CI-Wcoss2-Passed') && !contains( needs.getlabels.outputs.labels, 'CI-Wcoss2-Failed')"
+    runs-on: ubuntu-latest
+    needs:
+     - getlabels
+
+    steps:
+    - name: Pending
+      uses: schneegans/[email protected]
+      with:
+        forceUpdate: true
+        auth: ${{ secrets.CLI_DYNAMIC_BADGES }}
+        gistID: e35aa2904a54deae6bbb1fdc2d960c71
+        filename: wcoss2.json
+        label: wcoss2
+        message: pending
+        color: orange

README.md

@@ -3,28 +3,42 @@
 [![pynorms](https://github.com/NOAA-EMC/global-workflow/actions/workflows/pynorms.yaml/badge.svg)](https://github.com/NOAA-EMC/global-workflow/actions/workflows/pynorms.yaml)
 
 ![Custom badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/emcbot/e35aa2904a54deae6bbb1fdc2d960c71/raw/hera.json)
-![Custom badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/emcbot/e35aa2904a54deae6bbb1fdc2d960c71/raw/orion.json)
+![Custom badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/emcbot/e35aa2904a54deae6bbb1fdc2d960c71/raw/hercules.json)
+![Custom badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/emcbot/e35aa2904a54deae6bbb1fdc2d960c71/raw/wcoss2.json)
 
-# global-workflow
-Global Workflow currently supporting the Global Forecast System (GFS) with the [UFS-weather-model](https://github.com/ufs-community/ufs-weather-model) and [GSI](https://github.com/NOAA-EMC/GSI)-based Data Assimilation System.
+The Global Workflow supporting the Global Forecast System (GFS), the Global Ensemble Forecasting System (GEFS), and the Seasonal Forecast System (SFS) with the [UFS-weather-model](https://github.com/ufs-community/ufs-weather-model).  Data assimilation, currently only available for the GFS, is provides by both the [GSI](https://github.com/NOAA-EMC/GSI)- and [GDASApp (JEDI)](https://github.com/NOAA-EMC/GDASApp)-based Data Assimilation systems.
 
-The `global-workflow` depends on the following prerequisities to be available on the system:
+In progress [documentation](https://global-workflow.readthedocs.io/en/latest/) is available.
 
-* Workflow Engine - [Rocoto](https://github.com/christopherwharrop/rocoto) and [ecFlow](https://github.com/ecmwf/ecflow) (for NWS Operations)
-* Compiler - Intel Compiler Suite
-* Software - NCEPLIBS (various), ESMF, HDF5, NetCDF, and a host of other softwares (see module files under /modulefiles for additional details)
+# Prerequisites
 
-The `global-workflow` current supports the following tier-1 machines:
+The Global Workflow depends on the following prerequisities to be available on the system:
 
-* NOAA RDHPCS - Hera
-* MSU HPC - Orion
-* MSU HPC - Hercules
-* NOAA's operational HPC - WCOSS2
+* Workflow Engines - [Rocoto](https://github.com/christopherwharrop/rocoto) and [ecFlow](https://github.com/ecmwf/ecflow) (for NWS Operations)
+* Compiler - Intel classic compiler suite version 2021.x
+* Software - NCEPLIBS (various), ESMF, HDF5, NetCDF, and a host of other softwares (see module files under /modulefiles for additional details).
+    - [Spack-stack](https://github.com/JCSDA/spack-stack) is recommended for the installation of dependent libraries.
 
-Additionally, the following tier-2 machine is supported:
-* SSEC at Univ. of Wisconsin - S4 (Note that S2S+ experiments are not fully supported)
+## Supported platforms
 
-Documentation (in progress) is available [here](https://global-workflow.readthedocs.io/en/latest/).
+The Global Workflow currently supports the following machines at the indicated tier.
+
+| HPC                                     | Tier | Notes                                                                      |
+| --------------------------------------- |:----:|:--------------------------------------------------------------------------:|
+| WCOSS2<br>NCO                           | 1    | GEFS testing is not regularly performed.                                   |
+| Hera<br>NOAA RDHPCS                     | 1    |                                                                            |
+| Hercules<br>MSU                         | 1    | Currently does not support the TC Tracker.                                 |
+| Orion<br>MSU                            | 2    | The GSI runs very slowly on Orion and the TC tracker is not supported.     |
+| Gaea C5/C6<br>RDHPCS                    | 3    | Currently non-operational following an OS upgrade.<br>Supported by EPIC.   |
+| AWS, GCP, Azure <br>NOAA Parallel Works | 3    | Supported by EPIC.                                                         |
+| Jet<br>RDHPCS                           | 3    | Supported by NESDIS.                                                       |
+| S4<br>SSEC                              | 3    | Currently non-operational following an OS upgrade.<br>Supported by NESDIS. |
+
+<ins>**Tier Definitions**</ins>
+
+1. Fully supported by the EMC global workflow team.  CI testing is regularly performed on these systems, the majority of the global workflow features are supported, and the team will address any platform-specific features, bugs, upgrades, and requests for data.
+2. Supported by the global workflow team on an ad-hoc basis.  CI tests are supported on these systems, but not regularly performed.
+3. No official support by the global workflow team, but may be supported by other entities (e.g. EPIC).
 
 # Disclaimer
 

ci/cases/gfsv17/C384mx025_3DVarAOWCDA.yaml

@@ -9,10 +9,11 @@ arguments:
   resdetocean: 0.25
   nens: 0
   interval: 6
-  start: cold
+  start: warm
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  idate: 2021063000
+  idate: 2021063018
   edate: 2021070306
-  icsdir: /scratch1/NCEPDEV/climate/Jessica.Meixner/cycling/IC_2021063000_V2
-  yaml: {{ HOMEgfs }}/ci/cases/gfsv17/ocnanal.yaml
+  #icsdir: /scratch1/NCEPDEV/climate/Jessica.Meixner/cycling/IC_2021063000_V2
+  icsdir: /work/noaa/da/gvernier/ensda/ictest/1440x1080x75/
+  yaml: {{ HOMEgfs }}/ci/cases/gfsv17/marine3dvar.yaml

ci/cases/gfsv17/C384mx025_hybAOWCDA.yaml

@@ -0,0 +1,19 @@
+experiment:
+  system: gfs
+  mode: cycled
+
+arguments:
+  pslot: {{ 'pslot' | getenv }}
+  app: S2S
+  resdetatmos: 384
+  resensatmos: 192
+  resdetocean: 0.25
+  nens: 30
+  interval: 0
+  start: warm
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  idate: 2021063018
+  edate: 2021070306
+  icsdir: /work/noaa/da/gvernier/ensda/ictest/1440x1080x75/
+  yaml: {{ HOMEgfs }}/ci/cases/gfsv17/marinehyb.yaml

ci/cases/gfsv17/ocnanal.yaml → ci/cases/gfsv17/marine3dvar.yaml

@@ -21,8 +21,3 @@ marineanl:
   SOCA_INPUT_FIX_DIR: {{ HOMEgfs }}/fix/gdas/soca/1440x1080x75/soca
   SOCA_OBS_LIST: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
   SOCA_NINNER: 100
-
-prepoceanobs:
-  SOCA_OBS_LIST: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
-  OBSPREP_YAML: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obsprep/obsprep_config.yaml
-  DMPDIR: /scratch1/NCEPDEV/da/common/

ci/cases/gfsv17/marinehyb.yaml

@@ -0,0 +1,21 @@
+defaults:
+  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+
+base:
+  DOIAU: "YES"
+  DO_JEDIATMVAR: "NO"
+  DO_JEDIATMENS: "NO"
+  DO_JEDIOCNVAR: "YES"
+  DO_JEDISNOWDA: "NO"
+  DO_MERGENSST: "NO"
+  DOHYBVAR_OCN: "YES"
+  DO_FIT2OBS: "YES"
+  DO_VERFOZN: "YES"
+  DO_VERFRAD: "YES"
+  DO_VRFY_OCEANDA: "NO"
+  FHMAX_GFS: 240
+  ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+
+marineanl:
+  SOCA_INPUT_FIX_DIR: {{ HOMEgfs }}/fix/gdas/soca/1440x1080x75/soca
+  SOCA_NINNER: 20  # revert to ~100 after the memory leak is fixed

ci/cases/pr/C48mx500_3DVarAOWCDA.yaml

@@ -10,8 +10,8 @@ arguments:
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48mx500/20241120
-  idate: 2021032412
-  edate: 2021032418
+  idate: 2021032418
+  edate: 2021032500
   nens: 0
   interval: 0
   start: warm
@@ -21,4 +21,3 @@ skip_ci_on_hosts:
   - wcoss2
   - gaea
   - orion
-  - hercules

ci/cases/pr/C48mx500_hybAOWCDA.yaml

@@ -6,21 +6,19 @@ arguments:
   pslot: {{ 'pslot' | getenv }}
   app: S2S
   resdetatmos: 48
-  resdetocean: 5.0
   resensatmos: 48
+  resdetocean: 5.0
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48mx500/20241120
-  idate: 2021032412
-  edate: 2021032418
-  nens: 3
+  idate: 2021032418
+  edate: 2021032500
+  nens: 2
   interval: 0
   start: warm
-  yaml: {{ HOMEgfs }}/ci/cases/yamls/soca_gfs_defaults_ci.yaml
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/soca_hyb_gfs_defaults_ci.yaml
 
 skip_ci_on_hosts:
   - wcoss2
-  - orion
-  - hercules
-  - hera
   - gaea
+  - orion

ci/cases/yamls/soca_gfs_defaults_ci.yaml

@@ -3,4 +3,7 @@ defaults:
 base:
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
   DO_JEDIOCNVAR: "YES"
+
+marineanl:
+  SOCA_NINNER: 1
   DO_TEST_MODE: "YES"

ci/cases/yamls/soca_hyb_gfs_defaults_ci.yaml

@@ -0,0 +1,8 @@
+defaults:
+  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+base:
+  ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  DO_JEDIOCNVAR: "YES"
+  DOHYBVAR_OCN: "YES"
+marineanl:
+  SOCA_NINNER: 1

docs/source/components.rst

@@ -12,6 +12,7 @@ The major components of the system are:
 * Forecast
 * Post-processing
 * Verification
+* Archiving
 
 The Global Workflow repository contains the workflow and script layers. External components will be checked out as git submodules. All of the submodules of the system reside in their respective repositories on GitHub.
 

docs/source/configure.rst

@@ -48,12 +48,15 @@ The global-workflow configs contain switches that change how the system runs. Ma
 |                  | (.true.) or cold (.false)?       |               |             | be set when running ``setup_expt.py`` script with |
 |                  |                                  |               |             | the ``--start`` flag (e.g. ``--start warm``)      |
 +------------------+----------------------------------+---------------+-------------+---------------------------------------------------+
-| HPSSARCH         | Archive to HPPS                  | NO            | Possibly    | Whether to save output to tarballs on HPPS        |
+| HPSSARCH         | Archive to HPPS                  | NO            | NO          | Whether to save output to tarballs on HPPS.       |
 +------------------+----------------------------------+---------------+-------------+---------------------------------------------------+
-| LOCALARCH        | Archive to a local directory     | NO            | Possibly    | Instead of archiving data to HPSS, archive to a   |
-|                  |                                  |               |             | local directory, specified by ATARDIR. If         |
-|                  |                                  |               |             | LOCALARCH=YES, then HPSSARCH must =NO. Changing   |
-|                  |                                  |               |             | HPSSARCH from YES to NO will adjust the XML.      |
+| LOCALARCH        | Archive to a local directory     | NO            | NO          | Whether to save output to tarballs locally. For   |
+|                  |                                  |               |             | HPSSARCH and LOCALARCH, ARCDIR specifies the      |
+|                  |                                  |               |             | directory. These options are mutually exclusive.  |
++------------------+----------------------------------+---------------+-------------+---------------------------------------------------+
+| ARCH_EXPDIR      | Archive the EXPDIR               | NO            | NO          | Whether to create a tarball of the EXPDIR.        |
+|                  |                                  |               |             | ARCH_HASHES and ARCH_DIFFS generate text files    |
+|                  |                                  |               |             | of git output that are archived with the EXPDIR.  |
 +------------------+----------------------------------+---------------+-------------+---------------------------------------------------+
 | QUILTING         | Use I/O quilting                 | .true.        | NO          | If .true. choose OUTPUT_GRID as cubed_sphere_grid |
 |                  |                                  |               |             | in netcdf or gaussian_grid                        |