GFSv16.2.0 - WCOSS2 transition (#892)

The GFSv16 is ported to the new WCOSS2 system (Cactus/Dogwood).

Refs #398, #399

.gitignore

@@ -1,16 +1,194 @@
 # Ignore all compiled files
+#--------------------------
+__pycache__
 *.pyc
-*.o
+*.[aox]
 *.mod
+*.sw[a-p]
 
-# Ignore exec folder
+# Ignore folders
+#-------------------
 exec/
+build*/
+install*/
 
-# Ignore sorc folders from externals
-sorc/logs/
-sorc/fv3gfs.fd/
-sorc/gfs_post.fd/
-sorc/gsi.fd/
-sorc/ufs_utils.fd/
-sorc/gfs_wafs.fd/
-sorc/verif-global.fd/
+# Ignore fix directory symlinks
+#------------------------------
+fix/0readme
+fix/fix_*
+fix/gdas/
+fix/wafs
+
+# Ignore parm file symlinks
+#--------------------------
+parm/config/config.base
+parm/config/config.fv3
+parm/config/config.resources
+parm/gldas
+parm/mon
+parm/post
+parm/wafs
+
+# Ignore sorc and logs folders from externals
+#--------------------------------------------
+sorc/*log
+sorc/logs
+sorc/fv3gfs.fd
+sorc/gfs_post.fd
+sorc/gfs_wafs.fd
+sorc/gsi.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/filter_topo.fd
+sorc/fregrid.fd
+sorc/gdas2gldas.fd
+sorc/getsfcensmeanp.fd
+sorc/getsigensmeanp_smooth.fd
+sorc/getsigensstatp.fd
+sorc/gfs_ncep_post.fd
+sorc/gldas.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/mkgfsnemsioctl.fd
+sorc/ncdiag_cat.fd
+sorc/nemsio_chgdate.fd
+sorc/nemsio_get.fd
+sorc/nemsio_read.fd
+sorc/nst_tf_chg.fd
+sorc/orog.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/shave.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
+
+# Ignore scripts from externals
+#------------------------------
+# jobs symlinks
+jobs/JGDAS_ATMOS_ANALYSIS_DIAG
+jobs/JGDAS_ATMOS_CHGRES_FORENKF
+jobs/JGDAS_ATMOS_GLDAS
+jobs/JGDAS_ATMOS_VERFOZN
+jobs/JGDAS_ATMOS_VERFRAD
+jobs/JGDAS_ATMOS_VMINMON
+jobs/JGDAS_ENKF_DIAG
+jobs/JGDAS_ENKF_ECEN
+jobs/JGDAS_ENKF_FCST
+jobs/JGDAS_ENKF_POST
+jobs/JGDAS_ENKF_SELECT_OBS
+jobs/JGDAS_ENKF_SFC
+jobs/JGDAS_ENKF_UPDATE
+jobs/JGFS_ATMOS_VMINMON
+jobs/JGFS_ATMOS_WAFS
+jobs/JGFS_ATMOS_WAFS_BLENDING
+jobs/JGFS_ATMOS_WAFS_BLENDING_0P25
+jobs/JGFS_ATMOS_WAFS_GCIP
+jobs/JGFS_ATMOS_WAFS_GRIB2
+jobs/JGFS_ATMOS_WAFS_GRIB2_0P25
+jobs/JGLOBAL_ATMOS_ANALYSIS
+jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
+jobs/JGLOBAL_ATMOS_NCEPPOST
+jobs/JGLOBAL_ATMOS_POST_MANAGER
+# scripts symlinks
+scripts/exemcsfc_global_sfc_prep.sh
+scripts/exgdas_atmos_chgres_forenkf.sh
+scripts/exgdas_atmos_gldas.sh
+scripts/exgdas_atmos_nceppost.sh
+scripts/exgdas_atmos_verfozn.sh
+scripts/exgdas_atmos_verfrad.sh
+scripts/exgdas_atmos_vminmon.sh
+scripts/exgdas_enkf_ecen.sh
+scripts/exgdas_enkf_fcst.sh
+scripts/exgdas_enkf_post.sh
+scripts/exgdas_enkf_select_obs.sh
+scripts/exgdas_enkf_sfc.sh
+scripts/exgdas_enkf_update.sh
+scripts/exgfs_atmos_nceppost.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
+scripts/exgfs_atmos_wafs_grib.sh
+scripts/exgfs_atmos_wafs_grib2.sh
+scripts/exgfs_atmos_wafs_grib2_0p25.sh
+scripts/exglobal_atmos_analysis.sh
+scripts/exglobal_atmos_analysis_calc.sh
+scripts/exglobal_atmos_pmgr.sh
+scripts/exglobal_diag.sh
+# ush symlinks
+ush/calcanl_gfs.py
+ush/calcinc_gfs.py
+ush/emcsfc_ice_blend.sh
+ush/emcsfc_snow.sh
+ush/fix_precip.sh
+ush/fv3gfs_chgres.sh
+ush/fv3gfs_downstream_nems.sh
+ush/fv3gfs_driver_grid.sh
+ush/fv3gfs_dwn_nems.sh
+ush/fv3gfs_filter_topo.sh
+ush/fv3gfs_make_grid.sh
+ush/fv3gfs_make_orog.sh
+ush/getncdimlen
+ush/gfs_nceppost.sh
+ush/gfs_transfer.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/gsi_utils.py
+ush/link_crtm_fix.sh
+ush/minmon_xtrct_costs.pl
+ush/minmon_xtrct_gnorms.pl
+ush/minmon_xtrct_reduct.pl
+ush/mkwfsgbl.sh
+ush/mod_icec.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/trim_rh.sh
+ush/wafs_blending.sh
+ush/wafs_grib2.regrid.sh
+ush/wafs_intdsk.sh
+# util symlinks
+util/sub_slurm
+util/sub_wcoss_c
+util/sub_wcoss_d

Externals.cfg

@@ -1,37 +1,37 @@
 # External sub-modules of global-workflow
 
 [FV3GFS]
-tag = GFS.v16.0.17
+tag = GFS.v16.2.0
 local_path = sorc/fv3gfs.fd
 repo_url = https://github.com/ufs-community/ufs-weather-model.git
 protocol = git
 required = True
 
 [GSI]
-tag = gfsda.v16.1.8
+tag = gfsda.v16.2.0
 local_path = sorc/gsi.fd
 repo_url = https://github.com/NOAA-EMC/GSI.git
 protocol = git
 required = True
 
 [GLDAS]
-tag = gldas_gfsv16_release.v1.12.0
+tag = gldas_gfsv16_release.v.2.0.0
 local_path = sorc/gldas.fd
 repo_url = https://github.com/NOAA-EMC/GLDAS.git
 protocol = git
 required = True
 
 [UPP]
-tag = upp_gfsv16_release.v1.1.4
+tag = upp_v8.1.2
 local_path = sorc/gfs_post.fd
 repo_url = https://github.com/NOAA-EMC/UPP.git
 protocol = git
 required = True
 
 [UFS_UTILS]
-tag = ops-gfsv16.0.0
+tag = ops-gfsv16.2.0
 local_path = sorc/ufs_utils.fd
-repo_url = https://github.com/NOAA-EMC/UFS_UTILS.git
+repo_url = https://github.com/ufs-community/UFS_UTILS.git
 protocol = git
 required = True
 
@@ -43,7 +43,7 @@ protocol = git
 required = True
 
 [EMC_gfs_wafs]
-tag = gfs_wafs.v6.0.22
+tag = gfs_wafs.v6.2.8
 local_path = sorc/gfs_wafs.fd
 repo_url = https://github.com/NOAA-EMC/EMC_gfs_wafs.git
 protocol = git

docs/Release_Notes.gfs.v16.1.4.txt

@@ -2,31 +2,31 @@ GFS V16.1.4 RELEASE NOTES
 
 
 PRELUDE
- 
+
   NOAA awarded Delivery Order 3 (DO-3) of its commercial radio occultation
-  (RO) data purchase to Spire Global on August 12, 2021.  This purchase 
-  covers 3000 occultations per day over a six month period with the data 
-  flow starting on September 16, 2021.  On the same date, the GeoOptics 
+  (RO) data purchase to Spire Global on August 12, 2021.  This purchase
+  covers 3000 occultations per day over a six month period with the data
+  flow starting on September 16, 2021.  On the same date, the GeoOptics
   data from Delivery Order 2 (DO-2) will be discontinued.
 
-  GNSSRO bending angle observations from GeoOptics and Spire were initially 
-  evaluated as part of Delivery Order 1 (DO-1), covering a 30-day period 
-  starting on December 15, 2020.  The data from both vendors were found to 
-  be of similar quality to other operationally assimilated RO data.  Low 
-  resolution experiments informed the configuration of the quality control 
-  and observation errors for the following DO-2, which was awarded to 
-  GeoOptics only, covering an average of 1300 occultations per day over a 
-  six month period starting on March 17, 2021.  These data began to be 
-  assimilated operationally with the implementation of GFSv16.1.1 on 
+  GNSSRO bending angle observations from GeoOptics and Spire were initially
+  evaluated as part of Delivery Order 1 (DO-1), covering a 30-day period
+  starting on December 15, 2020.  The data from both vendors were found to
+  be of similar quality to other operationally assimilated RO data.  Low
+  resolution experiments informed the configuration of the quality control
+  and observation errors for the following DO-2, which was awarded to
+  GeoOptics only, covering an average of 1300 occultations per day over a
+  six month period starting on March 17, 2021.  These data began to be
+  assimilated operationally with the implementation of GFSv16.1.1 on
   May 22, 2021 after two months of parallel testing at full resolution.
 
-  Following the v16.1.1 implementation, the observation errors for 
-  commercial RO were tuned to better utilize the new data.  Additionally, 
-  two fixes related to the handling of super-refractivity in the RO bending 
-  angle observation operator were added.  These fixes resolve minimization 
-  issues that were related to the increased vertical resolution in v16. 
-  Therefore, the stricter gross check quality control measures originally 
-  put in place to mitigate minimization problems will now be relaxed.  
+  Following the v16.1.1 implementation, the observation errors for
+  commercial RO were tuned to better utilize the new data.  Additionally,
+  two fixes related to the handling of super-refractivity in the RO bending
+  angle observation operator were added.  These fixes resolve minimization
+  issues that were related to the increased vertical resolution in v16.
+  Therefore, the stricter gross check quality control measures originally
+  put in place to mitigate minimization problems will now be relaxed.
 
   This implementation plans to:
     * Turn off the active assimilation of GeoOptics data
@@ -43,11 +43,11 @@ PRELUDE
 
 IMPLEMENTATION INSTRUCTIONS
 
-  The NOAA VLab and both the NOAA-EMC and NCAR organization spaces on GitHub.com 
-  are used to manage the GFS.v16.1.4 code. The SPA(s) handling the GFS.v16.1.4 
-  implementation need to have permissions to clone VLab gerrit repositories and 
-  the private NCAR UPP_GTG repository. All NOAA-EMC organization repositories are 
-  publicly readable and do not require access permissions.  Please follow the 
+  The NOAA VLab and both the NOAA-EMC and NCAR organization spaces on GitHub.com
+  are used to manage the GFS.v16.1.4 code. The SPA(s) handling the GFS.v16.1.4
+  implementation need to have permissions to clone VLab gerrit repositories and
+  the private NCAR UPP_GTG repository. All NOAA-EMC organization repositories are
+  publicly readable and do not require access permissions.  Please follow the
   following steps to install the package on WCOSS-Dell:
 
   1) cd $NWROOTp3
@@ -70,30 +70,30 @@ IMPLEMENTATION INSTRUCTIONS
          WAFS      tag gfs_wafs.v6.0.22              Yali.Mao@noaa.gov
 
   7) ./build_all.sh
-     * This script compiles all GFS components. Runtime output from the build for 
-       each package is written to log files in directory logs. To build an 
+     * This script compiles all GFS components. Runtime output from the build for
+       each package is written to log files in directory logs. To build an
        individual program, for instance, gsi, use build_gsi.sh.
 
-  8) ./link_fv3gfs.sh nco dell	
+  8) ./link_fv3gfs.sh nco dell
 
 
 SORC CHANGES
 
 * sorc/
   * checkout.sh will checkout the following changed model tags:
     * GSI; tag gfsda.v16.1.4
-      * src/gsi/setupbend.f90:  Add two fixes for handling of 
+      * src/gsi/setupbend.f90:  Add two fixes for handling of
         super-refractivity layer, change the observation errors
-        of the commercial data, relax stricter gross check back to 
-        original values 
+        of the commercial data, relax stricter gross check back to
+        original values
       * src/read_nsstbufr.f90: Changes to handle NC001013, NC001101
         and NC001113 marine bufr subsets.
 
 
 FIX CHANGES
 
 * fix/fix_gsi:
-  * global_convinfo.txt: Discontinue assimilating GeoOptics and 
+  * global_convinfo.txt: Discontinue assimilating GeoOptics and
     begin assimilating Spire, relax stricter gross check back to
     original values.
   * gfsv16_historical/: Add fix files for retrospective parallels.
@@ -125,7 +125,7 @@ CHANGES TO RESOURCES AND FILE SIZES
 PRE-IMPLEMENTATION TESTING REQUIREMENTS
 
 * Which production jobs should be tested as part of this implementation?
-  * The entire GFS v16.1.4 package needs to be installed and tested. 
+  * The entire GFS v16.1.4 package needs to be installed and tested.
 
 * Does this change require a 30-day evaluation?
   * No.