Merge branch 'develop' into feature/gefs_v13_822_add_atm_fcst

 Conflicts:
	ush/forecast_predet.sh

Refs: NOAA-EMC#822

.github/workflows/linters.yaml

@@ -0,0 +1,30 @@
+#
+name: linters
+on:
+  pull_request:
+
+permissions:
+  contents: read
+
+defaults:
+  run:
+    shell: bash -o pipefail {0}
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    permissions:
+      security-events: write
+      pull-requests: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v1
+        with:
+          fetch-depth: 0
+
+      - name: Lint shell scripts
+        uses: redhat-plumbers-in-action/differential-shellcheck@latest
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -17,8 +17,23 @@ install*/
 # Ignore fix directory symlinks
 #------------------------------
 fix/0readme
-fix/fix_*
-fix/gdas/
+fix/aer
+fix/am
+fix/chem
+fix/cice
+fix/cpl
+fix/datm
+fix/gdas
+fix/gldas
+fix/gsi
+fix/lut
+fix/mom6
+fix/orog
+fix/reg2grb2
+fix/sfc_climo
+fix/ugwd
+fix/verif
+fix/wave
 fix/wafs
 
 # Ignore parm file symlinks
@@ -75,71 +90,12 @@ parm/wafs
 #--------------------------------------------
 sorc/*log
 sorc/logs
-sorc/ufs_model.fd
-sorc/gfs_post.fd
-sorc/gfs_wafs.fd
-sorc/gldas.fd
-sorc/gsi_enkf.fd
-sorc/gsi.fd
-sorc/enkf.fd
-sorc/gdas.cd
-sorc/gsi_utils.fd
-sorc/gsi_monitor.fd
-sorc/ufs_utils.fd
-sorc/verif-global.fd
-
-# Ignore sorc symlinks
-#---------------------
-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/fregrid.fd
-sorc/gdas2gldas.fd
-sorc/getsfcensmeanp.fd
-sorc/getsigensmeanp_smooth.fd
-sorc/getsigensstatp.fd
-sorc/gfs_ncep_post.fd
-sorc/gldas2gdas.fd
-sorc/gldas_forcing.fd
-sorc/gldas_model.fd
-sorc/gldas_post.fd
-sorc/gldas_rst.fd
-sorc/global_chgres.fd
-sorc/global_cycle.fd
-sorc/global_enkf.fd
-sorc/global_gsi.fd
-sorc/interp_inc.fd
-sorc/make_hgrid.fd
-sorc/make_solo_mosaic.fd
-sorc/ncdiag_cat.fd
-sorc/nst_tf_chg.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/recentersigp.fd
-sorc/upp.fd
-sorc/wafs_awc_wafavn.fd
-sorc/wafs_blending.fd
-sorc/wafs_blending_0p25.fd
-sorc/wafs_cnvgrib2.fd
-sorc/wafs_gcip.fd
-sorc/wafs_grib2_0p25.fd
-sorc/wafs_makewafs.fd
-sorc/wafs_setmissing.fd
+sorc/*.cd
+sorc/*.fd
 
 # Ignore scripts from externals
 #------------------------------
 # jobs symlinks
-jobs/JGDAS_ATMOS_GLDAS
-jobs/JGDAS_ATMOS_VERFOZN
-jobs/JGDAS_ATMOS_VERFRAD
-jobs/JGDAS_ATMOS_VMINMON
-jobs/JGFS_ATMOS_VMINMON
 jobs/JGFS_ATMOS_WAFS
 jobs/JGFS_ATMOS_WAFS_BLENDING
 jobs/JGFS_ATMOS_WAFS_BLENDING_0P25
@@ -148,11 +104,6 @@ jobs/JGFS_ATMOS_WAFS_GRIB2
 jobs/JGFS_ATMOS_WAFS_GRIB2_0P25
 # scripts symlinks
 scripts/exemcsfc_global_sfc_prep.sh
-scripts/exgdas_atmos_gldas.sh
-scripts/exgdas_atmos_verfozn.sh
-scripts/exgdas_atmos_verfrad.sh
-scripts/exgdas_atmos_vminmon.sh
-scripts/exgfs_atmos_vminmon.sh
 scripts/exgfs_atmos_wafs_blending.sh
 scripts/exgfs_atmos_wafs_blending_0p25.sh
 scripts/exgfs_atmos_wafs_gcip.sh
@@ -168,29 +119,17 @@ ush/fv3gfs_driver_grid.sh
 ush/fv3gfs_filter_topo.sh
 ush/fv3gfs_make_grid.sh
 ush/fv3gfs_make_orog.sh
-ush/gldas_archive.sh
-ush/gldas_forcing.sh
-ush/gldas_get_data.sh
-ush/gldas_liscrd.sh
-ush/gldas_post.sh
-ush/gldas_process_data.sh
 ush/global_chgres.sh
 ush/global_chgres_driver.sh
 ush/global_cycle.sh
 ush/global_cycle_driver.sh
-ush/minmon_xtrct_costs.pl
-ush/minmon_xtrct_gnorms.pl
-ush/minmon_xtrct_reduct.pl
 ush/mkwfsgbl.sh
-ush/ozn_xtrct.sh
-ush/radmon_ck_stdout.sh
-ush/radmon_err_rpt.sh
-ush/radmon_verf_angle.sh
-ush/radmon_verf_bcoef.sh
-ush/radmon_verf_bcor.sh
-ush/radmon_verf_time.sh
 ush/ufsda
-ush/rstprod.sh
 ush/wafs_blending.sh
 ush/wafs_grib2.regrid.sh
 ush/wafs_intdsk.sh
+ush/finddate.sh
+ush/make_NTC_file.pl
+ush/make_ntc_bull.pl
+ush/make_tif.sh
+ush/month_name.sh

.shellcheckrc

@@ -0,0 +1,13 @@
+# Global settings for Spellcheck (https://github.com/koalaman/shellcheck)
+enable=all
+
+external-sources=false
+
+# Disable variable referenced but not assigned
+disable=SC2154
+
+# Disable following non-constant source
+disable=SC1090
+
+# Disable non-existent binary
+disable=SC1091

Externals.cfg

@@ -1,50 +1,70 @@
 # External sub-modules of global-workflow
 
-[FV3GFS]
-hash = 9350745855aebe0790813e0ed2ba5ad680e3f75c
-local_path = sorc/fv3gfs.fd
+[UFS]
+tag = 6b73f5d
+local_path = sorc/ufs_model.fd
 repo_url = https://github.com/ufs-community/ufs-weather-model.git
 protocol = git
 required = True
 
-[GSI]
-hash = 9c1fc15d42573b398037319bbf8d5143ad126fb6
-local_path = sorc/gsi.fd
-repo_url = https://github.com/NOAA-EMC/GSI.git
-protocol = git
-required = True
-
-[GLDAS]
-tag = gldas_gfsv16_release.v1.15.0
-local_path = sorc/gldas.fd
-repo_url = https://github.com/NOAA-EMC/GLDAS.git
+[gfs-utils]
+hash = 0b8ff56
+local_path = sorc/gfs_utils.fd
+repo_url = https://github.com/NOAA-EMC/gfs-utils
 protocol = git
 required = True
 
-[UPP]
-#No externals setting = .gitmodules will be invoked for CMakeModules and comupp/src/lib/crtm2 submodules
-hash = ff42e0227d6100285d4179a2572b700fd5a959cb
-local_path = sorc/gfs_post.fd
-repo_url = https://github.com/NOAA-EMC/UPP.git
-protocol = git
-required = True
-
-[UFS_UTILS]
-tag = ufs_utils_1_6_0
+[UFS-Utils]
+hash = 8b990c0
 local_path = sorc/ufs_utils.fd
 repo_url = https://github.com/NOAA-EMC/UFS_UTILS.git
 protocol = git
 required = True
 
 [EMC_verif-global]
-tag = verif_global_v2.5.2
+tag = c267780
 local_path = sorc/verif-global.fd
 repo_url = https://github.com/NOAA-EMC/EMC_verif-global.git
 protocol = git
 required = True
 
-[EMC_gfs_wafs]
-hash = c2a29a67d9432b4d6fba99eac7797b81d05202b6
+[GSI-EnKF]
+hash = 48d8676
+local_path = sorc/gsi_enkf.fd
+repo_url = https://github.com/NOAA-EMC/GSI.git
+protocol = git
+required = False
+
+[GSI-Utils]
+hash = 322cc7b
+local_path = sorc/gsi_utils.fd
+repo_url = https://github.com/NOAA-EMC/GSI-utils.git
+protocol = git
+required = False
+
+[GSI-Monitor]
+hash = c64cc47
+local_path = sorc/gsi_monitor.fd
+repo_url = https://github.com/NOAA-EMC/GSI-monitor.git
+protocol = git
+required = False
+
+[GDASApp]
+hash = 843d3a9
+local_path = sorc/gdas.cd
+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
 repo_url = https://github.com/NOAA-EMC/EMC_gfs_wafs.git
 protocol = git

README.md

@@ -7,13 +7,14 @@ The global-workflow depends on the following prerequisities to be available on t
 * workflow manager - ROCOTO (https://github.com/christopherwharrop/rocoto)
 * modules - NCEPLIBS (various), esmf v8.0.0bs48, hdf5, intel/ips v18, impi v18, wgrib2, netcdf v4.7.0, hpss, gempak (see module files under /modulefiles for additional details)
 
-The global-workflow current supports the following machines:
+The global-workflow current supports the following tier-1 machines:
 
-* WCOSS-Dell
-* WCOSS-Cray
 * Hera
 * Orion
 
+Additionally, the following tier-2 machine is supported:
+* S4 (Note that S2S+ experiments are not fully supported)
+
 Quick-start instructions are below. Full instructions are available in the [wiki](https://github.com/NOAA-EMC/global-workflow/wiki/Run-Global-Workflow)
 
 ## Build global-workflow:

ecf/scripts/enkfgdas/analysis/recenter/jenkfgdas_sfc.ecf

@@ -4,7 +4,7 @@
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
 #PBS -l walltime=00:06:00
-#PBS -l select=1:mpiprocs=80:ompthreads=1:ncpus=80:mem=60GB
+#PBS -l select=1:mpiprocs=80:ompthreads=1:ncpus=80:mem=80GB
 #PBS -l place=vscatter
 #PBS -l debug=true
 

ecf/scripts/gfs/atmos/post_processing/grib2_wafs/jgfs_atmos_wafs_blending_0p25.ecf

@@ -4,7 +4,7 @@
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
 #PBS -l walltime=00:30:00
-#PBS -l select=1:mpiprocs=1:ompthreads=1:ncpus=1:mem=1GB
+#PBS -l select=1:mpiprocs=1:ompthreads=1:ncpus=1:mem=15GB
 #PBS -l place=vscatter
 #PBS -l debug=true
 
@@ -35,6 +35,7 @@ module list
 #############################################################
 export cyc=%CYC%
 export cycle=t%CYC%z
+export ICAO2023=no
 
 ############################################################
 # CALL executable job script here

ecf/scripts/gfs/atmos/post_processing/grib2_wafs/jgfs_atmos_wafs_grib2.ecf

@@ -4,7 +4,7 @@
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
 #PBS -l walltime=00:30:00
-#PBS -l select=1:mpiprocs=1:ompthreads=1:ncpus=1:mem=5GB
+#PBS -l select=1:mpiprocs=18:ompthreads=1:ncpus=18:mem=80GB
 #PBS -l place=vscatter
 #PBS -l debug=true
 
@@ -28,6 +28,7 @@ module load cray-pals/${cray_pals_ver}
 module load libjpeg/${libjpeg_ver}
 module load grib_util/${grib_util_ver}
 module load wgrib2/${wgrib2_ver}
+module load cfp/${cfp_ver}
 
 module list
 
@@ -36,6 +37,8 @@ module list
 #############################################################
 export cyc=%CYC%
 export cycle=t%CYC%z
+export USE_CFP=YES
+export ICAO2023=no
 
 ############################################################
 # CALL executable job script here

ecf/scripts/gfs/atmos/post_processing/grib2_wafs/jgfs_atmos_wafs_grib2_0p25.ecf

@@ -4,7 +4,7 @@
 #PBS -q %QUEUE%
 #PBS -A %PROJ%-%PROJENVIR%
 #PBS -l walltime=00:30:00
-#PBS -l select=1:mpiprocs=1:ompthreads=1:ncpus=1:mem=1GB
+#PBS -l select=1:mpiprocs=11:ompthreads=1:ncpus=11:mem=80GB
 #PBS -l place=vscatter
 #PBS -l debug=true
 
@@ -28,6 +28,7 @@ module load cray-pals/${cray_pals_ver}
 module load libjpeg/${libjpeg_ver}
 module load grib_util/${grib_util_ver}
 module load wgrib2/${wgrib2_ver}
+module load cfp/${cfp_ver}
 
 module list
 
@@ -36,6 +37,8 @@ module list
 #############################################################
 export cyc=%CYC%
 export cycle=t%CYC%z
+export USE_CFP=YES
+export ICAO2023=no
 
 ############################################################
 # CALL executable job script here

ecf/scripts/gfs/atmos/post_processing/jgfs_atmos_wafs_gcip.ecf

@@ -40,6 +40,7 @@ module list
 export cyc=%CYC%
 export cycle=t%CYC%z
 export USE_CFP=YES
+export ICAO2023=no
 
 ############################################################
 # CALL executable job script here