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

.github/workflows/pw_aws_ci.yaml

@@ -72,9 +72,9 @@ jobs:
       id: get-branch
       run: |
         pr_number=${{ github.event.inputs.pr_number }}
+        repo=${{ github.repository }}
         if [ "$pr_number" -eq "0" ]; then
           branch=${{ github.event.inputs.ref }}
-          repo=${{ github.repository }}
         else
           branch=$(gh pr view $pr_number --repo $repo --json headRefName --jq '.headRefName')
           repo_owner=$(gh pr view $pr_number --repo $repo --json headRepositoryOwner --jq '.headRepositoryOwner.login')

.gitignore

@@ -69,6 +69,7 @@ parm/post/params_grib2_tbl_new
 parm/post/post_tag_gfs128
 parm/post/gfs
 parm/post/gefs
+parm/post/sfs
 parm/post/ocean.csv
 parm/post/ice.csv
 parm/post/ocnicepost.nml.jinja2

.gitmodules

@@ -1,7 +1,6 @@
 [submodule "sorc/ufs_model.fd"]
   path = sorc/ufs_model.fd
   url = https://github.com/ufs-community/ufs-weather-model
-  ignore = dirty
 [submodule "sorc/wxflow"]
   path = sorc/wxflow
   url = https://github.com/NOAA-EMC/wxflow

ci/Jenkinsfile

@@ -222,6 +222,7 @@ pipeline {
                                                 def build_system = yaml_case.experiment.system
                                                 try {
                                                     sh(script: "${HOMEgfs}/ci/scripts/run-check_ci.sh ${CUSTOM_WORKSPACE} ${pslot} ${build_system}")
+                                                    sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh cleanup_experiment ${CUSTOM_WORKSPACE}/RUNTESTS/EXPDIR/${pslot}")
                                                 } catch (Exception error_experment) {
                                                     sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh cancel_batch_jobs ${pslot}")
                                                     ws(CUSTOM_WORKSPACE) {

ci/cases/gfsv17/ocnanal.yaml

@@ -15,6 +15,7 @@ base:
   DO_VRFY_OCEANDA: "NO"
   FHMAX_GFS: 240
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  DO_TEST_MODE: "YES"
 
 marineanl:
   SOCA_INPUT_FIX_DIR: {{ HOMEgfs }}/fix/gdas/soca/1440x1080x75/soca

ci/cases/pr/C48mx500_3DVarAOWCDA.yaml

@@ -9,7 +9,7 @@ arguments:
   resdetocean: 5.0
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48mx500/20240610
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48mx500/20241120
   idate: 2021032412
   edate: 2021032418
   nens: 0

ci/cases/pr/C48mx500_hybAOWCDA.yaml

@@ -10,7 +10,7 @@ arguments:
   resensatmos: 48
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48mx500/20240610
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48mx500/20241120
   idate: 2021032412
   edate: 2021032418
   nens: 3

ci/cases/pr/C96C48_hybatmDA.yaml

@@ -10,7 +10,7 @@ arguments:
   resensatmos: 48
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20240610
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20241120
   idate: 2021122018
   edate: 2021122106
   nens: 2

ci/cases/pr/C96C48_hybatmaerosnowDA.yaml

@@ -9,7 +9,7 @@ arguments:
   resensatmos: 48
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20240610
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20241120
   idate: 2021122012
   edate: 2021122100
   nens: 2

ci/cases/pr/C96C48_ufs_hybatmDA.yaml

@@ -9,7 +9,7 @@ arguments:
   resensatmos: 48
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20240610
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20241120
   idate: 2024022318
   edate: 2024022406
   nens: 2
@@ -21,4 +21,4 @@ skip_ci_on_hosts:
   - gaea
   - orion
   - hercules
-
+  - wcoss2

ci/cases/pr/C96_atm3DVar.yaml

@@ -8,7 +8,7 @@ arguments:
   resdetatmos: 96
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20240610
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20241120
   idate: 2021122018
   edate: 2021122106
   nens: 0

ci/cases/pr/C96_atm3DVar_extended.yaml

@@ -8,7 +8,7 @@ arguments:
   resdetatmos: 96
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20240610
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20241120
   idate: 2021122018
   edate: 2021122118
   nens: 0

ci/cases/sfs/C96mx100_S2S.yaml

@@ -0,0 +1,19 @@
+experiment:
+  system: gefs
+  mode: forecast-only
+
+arguments:
+  idate: 1994050100 
+  edate: 1994050100
+  pslot: {{ 'pslot' | getenv }}
+  app: S2S
+  resdetatmos: 96
+  resensatmos: 96
+  resdetocean: 1
+  start: 'cold'
+  nens: 10
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  icsdir: {{ 'TOPICDIR' | getenv }}/HR4/C96mx100
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/sfs_defaults.yaml
+

ci/cases/weekly/C384C192_hybatmda.yaml

@@ -10,7 +10,7 @@ arguments:
   resensatmos: 192
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C384C192
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C384C192/20240610
   idate: 2023040118
   edate: 2023040200
   nens: 2

ci/cases/weekly/C384_atm3DVar.yaml

@@ -10,7 +10,7 @@ arguments:
   resensatmos: 192
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C384C192
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C384C192/20240610
   idate: 2023040118
   edate: 2023040200
   nens: 0

ci/cases/yamls/atmaerosnowDA_defaults_ci.yaml

@@ -3,3 +3,4 @@ defaults:
 base:
   DO_JEDISNOWDA: "YES"
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  DO_TEST_MODE: "YES"

ci/cases/yamls/gefs_defaults_ci.yaml

@@ -2,3 +2,11 @@ defaults:
   !INC {{ HOMEgfs }}/parm/config/gefs/yaml/defaults.yaml
 base:
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  SFS_POST: "NO"
+  FHOUT_GFS: 6
+stage_ic:
+  USE_OCN_ENS_PERTURB_FILES: "NO"
+  USE_ATM_ENS_PERTURB_FILES: "NO"
+ocn:
+  MOM6_INTERP_ICS: "NO"
+

ci/cases/yamls/gefs_replay_ci.yaml

@@ -11,4 +11,8 @@ base:
   FHOUT_OCN_GFS: 24
   FHOUT_ICE_GFS: 24
   HOMEDIR: {{ 'RUNTESTS' | getenv }}/GLOBAL
+  SFS_POST: "NO"
+stage_ic:
+  USE_OCN_ENS_PERTURB_FILES: "YES"
+  USE_ATM_ENS_PERTURB_FILES: "YES"
 

ci/cases/yamls/gfs_defaults_ci.yaml

@@ -2,3 +2,4 @@ defaults:
   !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
 base:
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  DO_TEST_MODE: "YES"

ci/cases/yamls/gfs_extended_ci.yaml

@@ -12,3 +12,4 @@ base:
   FCST_BREAKPOINTS: 192
   FHMAX_GFS: 384
   FHMAX_HF_GFS: 120
+  DO_TEST_MODE: "YES"

ci/cases/yamls/sfs_defaults.yaml

@@ -0,0 +1,33 @@
+base:
+  DO_JEDIATMVAR: "NO"
+  DO_JEDIATMENS: "NO"
+  DO_JEDIOCNVAR: "NO"
+  DO_JEDISNOWDA: "NO"
+  DO_MERGENSST: "NO"
+  DO_BUFRSND: "NO"
+  DO_GEMPAK: "NO"
+  DO_AWIPS: "NO"
+  KEEPDATA: "YES"
+  DO_EXTRACTVARS: "NO"
+  FHMAX_GFS: 2976
+  FHMAX_HF_GFS: 0
+  FHOUT_HF_GFS: 1
+  FHOUT_GFS: 24
+  FHOUT_OCN_GFS: 24
+  FHOUT_ICE_GFS: 24
+  FCST_BREAKPOINTS: ""
+  REPLAY_ICS: "NO"
+  HPSSARCH: "NO"
+  LOCALARCH: "NO"
+  SFS_POST: "YES"
+  ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+fcst:
+  TYPE: "hydro"
+  MONO: "mono"
+  reforecast: "YES"
+  FHZER: 24
+stage_ic:
+  USE_OCN_ENS_PERTURB_FILES: "YES"
+  USE_ATM_ENS_PERTURB_FILES: "YES"
+ocn:
+  MOM6_INTERP_ICS: "YES"

ci/cases/yamls/soca_gfs_defaults_ci.yaml

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

ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml

@@ -17,4 +17,3 @@ nsst:
   NST_MODEL: "1"
 sfcanl:
   DONST: "NO"
-

ci/scripts/check_ci.sh

@@ -168,8 +168,7 @@ for pr in ${pr_list}; do
     fi
     if [[ "${rocoto_state}" == "DONE" ]]; then
       #Remove Experment cases that completed successfully
-      rm -Rf "${pslot_dir}"
-      rm -Rf "${pr_dir}/RUNTESTS/COMROOT/${pslot}"
+      "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh" cleanup_experiment "${pslot_dir}"
       rm -f "${output_ci_single}"
       # echo "\`\`\`" > "${output_ci_single}"
       DATE=$(date +'%D %r')

ci/scripts/utils/ci_utils.sh

@@ -122,7 +122,9 @@ function create_experiment () {
   source "${HOMEgfs}/ci/platforms/config.${MACHINE_ID}"
   source "${HOMEgfs}/workflow/gw_setup.sh"
 
-  # Remove RUNDIRS dir incase this is a retry
+  # Remove RUNDIRS dir incase this is a retry (STMP now in host file)
+  STMP=$("${HOMEgfs}/ci/scripts/utils/parse_yaml.py" -y "${HOMEgfs}/workflow/hosts/${MACHINE_ID}.yaml" -k STMP -s)
+  echo "Removing ${STMP}/RUNDIRS/${pslot} directory incase this is a retry"
   rm -Rf "${STMP}/RUNDIRS/${pslot}"
 
   "${HOMEgfs}/${system}/workflow/create_experiment.py" --overwrite --yaml "${yaml_config}"
@@ -137,7 +139,6 @@ function publish_logs() {
     local PR_header="$1"
     local dir_path="$2"
     local file="$3"
-
     local full_paths=""
     while IFS= read -r line; do
         full_path="${dir_path}/${line}"
@@ -155,3 +156,24 @@ function publish_logs() {
     fi
     echo "${URL}"
 }
+
+function cleanup_experiment() {
+
+    local EXPDIR="$1"
+    local pslot
+    local ARCDIR
+    local ATARDIR
+    local COMROOT
+
+    EXPDIR="$1"
+    pslot=$(basename "${EXPDIR}")
+
+    # Use the Python utility to get the required variables
+    read -r ARCDIR ATARDIR STMP COMROOT < <("${HOMEgfs}/ci/scripts/utils/get_config_var.py" ARCDIR ATARDIR STMP COMROOT "${EXPDIR}") || true
+
+    rm -Rf "${ARCDIR:?}"
+    rm -Rf "${ATARDIR:?}"
+    rm -Rf "${COMROOT}/${pslot:?}"
+    rm -Rf "${EXPDIR}/${pslot:?}"
+    rm -Rf "${STMP}/RUNDIRS/${pslot:?}"
+}

ci/scripts/utils/get_config_var.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+
+import os
+import argparse
+from wxflow import Configuration
+
+
+def get_config_vars(var_names, config_path):
+    """
+    GET_CONFIG_VARS Get configuration variables from a config file or directory.
+    Parameters:
+    var_names (list of str): The names of the configuration variables to retrieve.
+    config_path (str): The path to the configuration file or directory.
+    Returns:
+    list of str: The values of the specified configuration variables.
+    """
+    if os.path.isfile(config_path):
+        config_dir = os.path.dirname(config_path)
+        config_file = os.path.basename(config_path)
+    elif os.path.isdir(config_path):
+        config_dir = config_path
+        config_file = 'config.base'
+    config = Configuration(config_dir)
+    config_data = config.parse_config(config_file)
+    return [config_data[var_name] for var_name in var_names]
+
+
+if __name__ == "__main__":
+    """
+    Main entry point for the script.
+    Parses command-line arguments and retrieves the specified configuration variables.
+    """
+    parser = argparse.ArgumentParser(description="Get configuration variables from a config file or directory.")
+    parser.add_argument("var_names", nargs='+', help="The names of the configuration variables to retrieve.")
+    parser.add_argument("config_path", help="The path to the configuration file or directory.")
+
+    args = parser.parse_args()
+
+    var_names = args.var_names
+    config_path = args.config_path
+
+    values = get_config_vars(var_names, config_path)
+    print(" ".join(values))

docs/source/conf.py

@@ -25,6 +25,7 @@
 # The full version, including alpha/beta/rc tags
 release = '0.1'
 
+numfig = True
 
 # -- General configuration ---------------------------------------------------
 
@@ -42,7 +43,7 @@
     'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
     'sphinx.ext.napoleon',
-    'sphinxcontrib.bibtex'
+    'sphinxcontrib.bibtex',
 ]
 
 bibtex_bibfiles = ['references.bib']
@@ -120,3 +121,4 @@ def setup(app):
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'Global-Workflow'
+

docs/source/index.rst

@@ -41,5 +41,6 @@ Table of Contents
    hpc.rst
    output.rst
    run.rst
+   wave.rst
    noaa_csp.rst
    errors_faq.rst