Merge branch 'NOAA-EMC:develop' into develop

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -40,6 +40,7 @@ body:
         - WCOSS2
         - Hera
         - Orion
+        - Hercules
         - Jet
         - Cloud
     validations:

.gitignore

@@ -31,6 +31,7 @@ fix/cice
 fix/cpl
 fix/datm
 fix/gldas
+fix/gdas
 fix/gsi
 fix/lut
 fix/mom6
@@ -40,7 +41,6 @@ fix/sfc_climo
 fix/ugwd
 fix/verif
 fix/wave
-fix/wafs
 
 # Ignore parm file symlinks
 #--------------------------
@@ -97,8 +97,42 @@ parm/wafs
 #--------------------------------------------
 sorc/*log
 sorc/logs
-sorc/*.cd
-sorc/*.fd
+sorc/calc_analysis.fd
+sorc/calc_increment_ens.fd
+sorc/calc_increment_ens_ncio.fd
+sorc/emcsfc_ice_blend.fd
+sorc/emcsfc_snow2mdl.fd
+sorc/enkf.fd
+sorc/enkf_chgres_recenter_nc.fd
+sorc/fbwndgfs.fd
+sorc/gaussian_sfcanl.fd
+sorc/getsfcensmeanp.fd
+sorc/getsigensmeanp_smooth.fd
+sorc/getsigensstatp.fd
+sorc/gfs_bufr.fd
+sorc/global_cycle.fd
+sorc/gsi.fd
+sorc/interp_inc.fd
+sorc/mkgfsawps.fd
+sorc/overgridid.fd
+sorc/oznmon_horiz.fd
+sorc/oznmon_time.fd
+sorc/radmon_angle.fd
+sorc/radmon_bcoef.fd
+sorc/radmon_bcor.fd
+sorc/radmon_time.fd
+sorc/rdbfmsua.fd
+sorc/recentersigp.fd
+sorc/reg2grb2.fd
+sorc/supvit.fd
+sorc/syndat_getjtbul.fd
+sorc/syndat_maksynrc.fd
+sorc/syndat_qctropcy.fd
+sorc/tave.fd
+sorc/tocsbufr.fd
+sorc/upp.fd
+sorc/vint.fd
+sorc/webtitle.fd
 
 # Ignore scripts from externals
 #------------------------------
@@ -121,6 +155,7 @@ scripts/exgfs_atmos_wafs_grib2_0p25.sh
 ush/chgres_cube.sh
 ush/emcsfc_ice_blend.sh
 ush/emcsfc_snow.sh
+ush/exglobal_prep_ocean_obs.py
 ush/fix_precip.sh
 ush/fv3gfs_driver_grid.sh
 ush/fv3gfs_filter_topo.sh
@@ -150,7 +185,6 @@ versions/build.ver
 versions/run.ver
 
 # wxflow checkout and symlinks
-sorc/wxflow
 ush/python/wxflow
 workflow/wxflow
 ci/scripts/wxflow

.gitmodules

@@ -0,0 +1,28 @@
+[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
+[submodule "sorc/gfs_utils.fd"]
+	path = sorc/gfs_utils.fd
+	url = https://github.com/NOAA-EMC/gfs-utils
+[submodule "sorc/ufs_utils.fd"]
+	path = sorc/ufs_utils.fd
+	url = https://github.com/ufs-community/UFS_UTILS.git
+[submodule "sorc/verif-global.fd"]
+	path = sorc/verif-global.fd
+	url = https://github.com/NOAA-EMC/EMC_verif-global.git
+[submodule "sorc/gsi_enkf.fd"]
+	path = sorc/gsi_enkf.fd
+	url = https://github.com/NOAA-EMC/GSI.git
+[submodule "sorc/gdas.cd"]
+	path = sorc/gdas.cd
+	url = https://github.com/NOAA-EMC/GDASApp.git
+[submodule "sorc/gsi_utils.fd"]
+	path = sorc/gsi_utils.fd
+	url = https://github.com/NOAA-EMC/GSI-Utils.git
+[submodule "sorc/gsi_monitor.fd"]
+	path = sorc/gsi_monitor.fd
+	url = https://github.com/NOAA-EMC/GSI-Monitor.git

ci/cases/pr/C96C48_hybatmDA.yaml

@@ -16,3 +16,6 @@ arguments:
   gfs_cyc: 1
   start: cold
   yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
+
+skip_ci_on_hosts:
+  - hercules

ci/cases/pr/C96_atm3DVar.yaml

@@ -15,3 +15,6 @@ arguments:
   gfs_cyc: 1
   start: cold
   yaml: {{ HOMEgfs }}/ci/platforms/gfs_defaults_ci.yaml
+
+skip_ci_on_hosts:
+  - hercules

ci/platforms/config.hercules

@@ -0,0 +1,8 @@
+#!/usr/bin/bash
+
+export GFS_CI_ROOT=/work2/noaa/stmp/GFS_CI_ROOT/HERCULES
+export ICSDIR_ROOT=/work/noaa/global/glopara/data/ICSDIR
+export STMP="/work2/noaa/stmp/${USER}"
+export SLURM_ACCOUNT=nems
+export max_concurrent_cases=5
+export max_concurrent_pr=4

ci/platforms/config.orion

@@ -1,6 +1,6 @@
 #!/usr/bin/bash
 
-export GFS_CI_ROOT=/work2/noaa/stmp/GFS_CI_ROOT
+export GFS_CI_ROOT=/work2/noaa/stmp/GFS_CI_ROOT/ORION
 export ICSDIR_ROOT=/work/noaa/global/glopara/data/ICSDIR
 export STMP="/work2/noaa/stmp/${USER}"
 export SLURM_ACCOUNT=nems

ci/scripts/clone-build_ci.sh

@@ -48,7 +48,7 @@ git clone "${REPO_URL}"
 cd global-workflow || exit 1
 
 # checkout pull request
-"${GH}" pr checkout "${PR}" --repo "${REPO_URL}"
+"${GH}" pr checkout "${PR}" --repo "${REPO_URL}" --recurse-submodules
 HOMEgfs="${PWD}"
 source "${HOMEgfs}/ush/detect_machine.sh"
 
@@ -67,30 +67,14 @@ source "${HOMEgfs}/ush/detect_machine.sh"
 commit=$(git log --pretty=format:'%h' -n 1)
 echo "${commit}" > "../commit"
 
-# run checkout script
+# build full cycle
 cd sorc || exit 1
 set +e
-./checkout.sh -c -g -u >> log.checkout 2>&1
-checkout_status=$?
-DATE=$(date +'%D %r')
-if [[ ${checkout_status} != 0 ]]; then
-  {
-    echo "Checkout: *** FAILED ***"
-    echo "Checkout: Failed at ${DATE}"
-    echo "Checkout: see output at ${PWD}/log.checkout"
-  } >> "${outfile}"
-  exit "${checkout_status}"
-else
-  {
-    echo "Checkout: Completed at ${DATE}"
-  } >> "${outfile}"
-fi
 
-# build full cycle
 source "${HOMEgfs}/ush/module-setup.sh"
 export BUILD_JOBS=8
 rm -rf log.build
-./build_all.sh  >> log.build 2>&1
+./build_all.sh -gu  >> log.build 2>&1
 build_status=$?
 
 DATE=$(date +'%D %r')

ci/scripts/driver_weekly.sh

@@ -66,7 +66,7 @@ echo "Creating new branch ${branch} from develop on ${MACHINE_ID} in ${develop_d
 rm -Rf "${develop_dir}"
 mkdir -p "${develop_dir}"
 cd "${develop_dir}" || exit 1
-git clone "${REPO_URL}"
+git clone --recursive "${REPO_URL}"
 cd global-workflow || exit 1
 git checkout -b "${branch}"