From d81a8b509c8c734ceaf4aa44f120c80452c38706 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon, 15 Aug 2022 16:49:10 -0400
Subject: [PATCH 1/3] use a robust Findwgrib2.cmake to find wgrib2 built w/
 native wgrib2 build (#970)

---
 sorc/cmake/Findwgrib2.cmake     | 98 +++++++++++++++++++++++++++++++++
 sorc/reg2grb2.fd/CMakeLists.txt |  2 +-
 2 files changed, 99 insertions(+), 1 deletion(-)
 create mode 100644 sorc/cmake/Findwgrib2.cmake

diff --git a/sorc/cmake/Findwgrib2.cmake b/sorc/cmake/Findwgrib2.cmake
new file mode 100644
index 0000000000..ecede0d21f
--- /dev/null
+++ b/sorc/cmake/Findwgrib2.cmake
@@ -0,0 +1,98 @@
+# Find the wgrib2 headers, library and executable
+#
+# This module defines:
+#
+#   - wgrib2::wgrib2      - library and include directory, all in a single target.
+#   - WGRIB2_INCLUDE_DIR  - include directory
+#   - WGRIB2_LIBRARIES    - wgrib2 library
+#   - WGRIB2API_LIBRARIES - wgrib2_api library (if using NCEPLibs-wgrib2 cmake build system)
+#   - WGRIB2_EXE          - wgrib2 executable
+#
+# The following paths will be searched in order:
+#
+#   - WGRIB2_INCLUDE_DIRS - folders containing wgrib2.
+#   - WGRIB2_LIBRARY_DIRS - folders containing libwgrib2.a
+#   - wgrib2_ROOT         - root of wgrib2 installation
+#   - wgrib2_PATH         - root of wgrib2 installation
+#
+# TODO
+# Remove all instances of WGRIB2API_LIBRARIES when cmake build of wgrib2 is removed from all systems
+
+find_path(
+  WGRIB2_INCLUDE_DIR
+  NAMES wgrib2.h wgrib2api.mod
+  HINTS ${WGRIB2_INCLUDE_DIRS}
+        ${wgrib2_ROOT} $ENV{wgrib2_ROOT}
+        ${wgrib2_PATH} $ENV{wgrib2_PATH}
+  PATH_SUFFIXES include include/wgrib2
+  DOC "Path to wgrib2.h, wgrib2api.mod"
+  )
+
+find_library(
+  WGRIB2_LIBRARIES
+  NAMES libwgrib2.a
+  HINTS ${WGRIB2_LIBRARY_DIRS}
+        ${wgrib2_ROOT} $ENV{wgrib2_ROOT}
+        ${wgrib2_PATH} $ENV{wgrib2_PATH}
+  PATH_SUFFIXES lib lib64
+  DOC "Path to libwgrib2.a"
+  )
+
+find_library(
+  WGRIB2API_LIBRARIES
+  NAMES libwgrib2_api.a
+  HINTS ${WGRIB2_LIBRARY_DIRS}
+        ${wgrib2_ROOT} $ENV{wgrib2_ROOT}
+        ${wgrib2_PATH} $ENV{wgrib2_PATH}
+  PATH_SUFFIXES lib lib64
+  DOC "Path to libwgrib2_api.a"
+  )
+
+find_program(WGRIB2_EXE
+  NAMES wgrib2
+  HINTS ${wgrib2_ROOT} $ENV{wgrib2_ROOT}
+        ${wgrib2_PATH} $ENV{wgrib2_PATH}
+  PATH_SUFFIXES bin
+  DOC "Path to wgrib2 executable"
+  )
+
+mark_as_advanced(WGRIB2_INCLUDE_DIR WGRIB2_LIBRARIES WGRIB2API_LIBRARIES WGRIB2_EXE)
+
+message(DEBUG "[Findwgrib2.cmake]: creating target wgrib2::wgrib2")
+add_library(wgrib2::wgrib2 UNKNOWN IMPORTED)
+set_target_properties(wgrib2::wgrib2 PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${WGRIB2_INCLUDE_DIR})
+if(WGRIB2API_LIBRARIES)
+  message(DEBUG "[Findwgrib2.cmake]: linking with libwgrib2_api.a and libwgrib2.a")
+  set_target_properties(wgrib2::wgrib2 PROPERTIES IMPORTED_LOCATION ${WGRIB2API_LIBRARIES})
+  set_target_properties(wgrib2::wgrib2 PROPERTIES INTERFACE_LINK_LIBRARIES ${WGRIB2_LIBRARIES})
+else()
+  message(DEBUG "[Findwgrib2.cmake]: linking with libwgrib2.a")
+  set_target_properties(wgrib2::wgrib2 PROPERTIES IMPORTED_LOCATION ${WGRIB2_LIBRARIES})
+endif()
+
+# wgrib2 changed how it outputs --version from "v0.x.y.z" to "vx.y.z" starting in wgrib2 3.0
+execute_process(COMMAND ${WGRIB2_EXE} --version OUTPUT_VARIABLE version)
+if(version MATCHES "^v0.*")
+  string(SUBSTRING "${version}" 3 5 WGRIB2_VERSION)
+else()
+  string(SUBSTRING "${version}" 1 5 WGRIB2_VERSION)
+endif()
+unset(version)
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(wgrib2
+  REQUIRED_VARS WGRIB2_LIBRARIES WGRIB2_INCLUDE_DIR WGRIB2_EXE
+  VERSION_VAR WGRIB2_VERSION
+  )
+
+if(wgrib2_FOUND AND NOT wgrib2_FIND_QUIETLY)
+  message(STATUS "Findwgrib2:")
+  message(STATUS "  - WGRIB2_INCLUDE_DIR: ${WGRIB2_INCLUDE_DIR}")
+  message(STATUS "  - WGRIB2_LIBRARIES: ${WGRIB2_LIBRARIES}")
+  if(WGRIB2API_LIBRARIES)
+    message(STATUS "  - WGRIB2API_LIBRARIES: ${WGRIB2API_LIBRARIES}")
+  endif()
+  message(STATUS "  - WGRIB2_EXE: ${WGRIB2_EXE}")
+  message(STATUS "  - WGRIB2_VERSION: ${WGRIB2_VERSION}")
+endif()
+
diff --git a/sorc/reg2grb2.fd/CMakeLists.txt b/sorc/reg2grb2.fd/CMakeLists.txt
index 4157c315bf..c866ca515f 100644
--- a/sorc/reg2grb2.fd/CMakeLists.txt
+++ b/sorc/reg2grb2.fd/CMakeLists.txt
@@ -18,7 +18,7 @@ target_link_libraries(
   sp::sp_d
   bacio::bacio_4
   w3nco::w3nco_4
-  wgrib2::wgrib2_api
+  wgrib2::wgrib2
   NetCDF::NetCDF_Fortran)
 
 if(OpenMP_Fortran_FOUND)

From cfcc21f9f96106b17bba9fd194cd360dda1fffb8 Mon Sep 17 00:00:00 2001
From: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Thu, 18 Aug 2022 07:10:44 +0000
Subject: [PATCH 2/3] Update diag table to remove wav-ocn coupling fields
 (#979)

Removes the wavocn output which is used to evaluate wav->ocean coupling. These were only needed for prototype diagnostics and when these variables are output without wave coupling, it can lead to failures.

Fixes #977
---
 jobs/rocoto/arch.sh              |  2 +-
 parm/parm_fv3diag/diag_table_cpl | 18 ------------------
 ush/forecast_postdet.sh          |  4 ----
 ush/hpssarch_gen.sh              |  3 ---
 4 files changed, 1 insertion(+), 26 deletions(-)

diff --git a/jobs/rocoto/arch.sh b/jobs/rocoto/arch.sh
index c9441b5a75..05eb34e1ad 100755
--- a/jobs/rocoto/arch.sh
+++ b/jobs/rocoto/arch.sh
@@ -203,7 +203,7 @@ if [ $CDUMP = "gfs" ]; then
     fi
 
     if [ $DO_OCN = "YES" ]; then
-        targrp_list="$targrp_list ocn_ice_grib2_0p5 ocn_ice_grib2_0p25 ocn_2D ocn_3D ocn_xsect ocn_daily wavocn gfs_flux_1p00"
+        targrp_list="$targrp_list ocn_ice_grib2_0p5 ocn_ice_grib2_0p25 ocn_2D ocn_3D ocn_xsect ocn_daily gfs_flux_1p00"
     fi
 
     if [ $DO_ICE = "YES" ]; then
diff --git a/parm/parm_fv3diag/diag_table_cpl b/parm/parm_fv3diag/diag_table_cpl
index 3a5bb4a5bc..6974dafac3 100644
--- a/parm/parm_fv3diag/diag_table_cpl
+++ b/parm/parm_fv3diag/diag_table_cpl
@@ -9,7 +9,6 @@
 ######################
 "ocn%4yr%2mo%2dy%2hr",      6,  "hours", 1, "hours", "time", 6, "hours", "1901 1 1 0 0 0"
 "ocn_daily%4yr%2mo%2dy",      1,  "days",  1, "days",  "time", 1, "days",  "1901 1 1 0 0 0"
-"wavocn%4yr%2mo%2dy%2hr",      6,  "hours", 1, "hours", "time", 6, "hours", "1901 1 1 0 0 0"
 ##############################################
 # static fields
  "ocean_model", "geolon",      "geolon",      "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
@@ -81,23 +80,6 @@
  "ocean_model", "LwLatSens", "LwLatSens",     "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
  "ocean_model", "Heat_PmE",  "Heat_PmE",      "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
 
-#wave_variables
- "ocean_model", "geolon",             "geolon",             "wavocn%4yr%2mo%2dy%2hr","all", .false., "none", 2
- "ocean_model", "geolat",             "geolat",             "wavocn%4yr%2mo%2dy%2hr","all", .false., "none", 2
- "ocean_model", "MSTAR",              "MSTAR",              "wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
- "ocean_model", "LA",                 "LA",                 "wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
- "ocean_model", "LA_MOD",             "LA_MOD",             "wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
- "ocean_model", "MSTAR_LT",           "MSTAR_LT",           "wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
- "ocean_model", "ePBL_h_ML",          "ePBL",               "wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
- "ocean_model", "ustar",              "ustar",              "wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
- "ocean_model", "ePBL_TKE_wind",      "ePBL_TKE_wind",      "wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
- "ocean_model", "ePBL_TKE_MKE",       "ePBL_TKE_MKE",       "wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
- "ocean_model", "ePBL_TKE_conv",      "ePBL_TKE_conv",      "wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
- "ocean_model", "ePBL_TKE_forcing",   "ePBL_TKE_forcing",   "wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
- "ocean_model", "ePBL_TKE_mixing",    "ePBL_TKE_mixing",    "wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
- "ocean_model", "ePBL_TKE_mech_decay","ePBL_TKE_mech_decay","wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
- "ocean_model", "ePBL_TKE_conv_decay","ePBL_TKE_conv_decay","wavocn%4yr%2mo%2dy%2hr","all", .true.,  "none", 2
-
 #=============================================================================================
 "gfs_dyn",     "ucomp",       "ugrd",         "fv3_history",    "all",  .false.,  "none",  2
 "gfs_dyn",     "vcomp",       "vgrd",         "fv3_history",    "all",  .false.,  "none",  2
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 089ff7dd5b..eeae89c11b 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -844,10 +844,6 @@ MOM6_postdet() {
     dest_file="ocn${VDATE}.${ENSMEM}.${IDATE}.nc"
     ${NLN} ${COMOUTocean}/${dest_file} ${DATA}/${source_file}
 
-    source_file="wavocn_${YYYY_MID}_${MM_MID}_${DD_MID}_${HH_MID}.nc"
-    dest_file=${source_file}
-    ${NLN} ${COMOUTocean}/${dest_file} ${DATA}/${source_file}
-
     source_file="ocn_daily_${YYYY}_${MM}_${DD}.nc"
     dest_file=${source_file}
     if [ ! -a "${DATA}/${source_file}" ]; then
diff --git a/ush/hpssarch_gen.sh b/ush/hpssarch_gen.sh
index 9785de98ac..245a402692 100755
--- a/ush/hpssarch_gen.sh
+++ b/ush/hpssarch_gen.sh
@@ -233,7 +233,6 @@ if [ $type = "gfs" ]; then
     rm -f ocn_3D.txt
     rm -f ocn_xsect.txt
     rm -f ocn_daily.txt
-    rm -f wavocn.txt
     touch gfs_flux_1p00.txt
     touch ocn_ice_grib2_0p5.txt
     touch ocn_ice_grib2_0p25.txt
@@ -241,13 +240,11 @@ if [ $type = "gfs" ]; then
     touch ocn_3D.txt
     touch ocn_xsect.txt
     touch ocn_daily.txt
-    touch wavocn.txt
     echo  "${dirname}MOM_input                  " >>ocn_2D.txt
     echo  "${dirname}ocn_2D*                    " >>ocn_2D.txt
     echo  "${dirname}ocn_3D*                    " >>ocn_3D.txt
     echo  "${dirname}ocn*EQ*                    " >>ocn_xsect.txt
     echo  "${dirname}ocn_daily*                 " >>ocn_daily.txt
-    echo  "${dirname}wavocn*                    " >>wavocn.txt
     echo  "${dirname}ocn_ice*0p5x0p5.grb2       " >>ocn_ice_grib2_0p5.txt
     echo  "${dirname}ocn_ice*0p25x0p25.grb2     " >>ocn_ice_grib2_0p25.txt
 

From 8a62c3a9e2dcc5de05ca974be8852736d423de76 Mon Sep 17 00:00:00 2001
From: Cory Martin <cory.r.martin@noaa.gov>
Date: Fri, 19 Aug 2022 14:09:07 -0400
Subject: [PATCH 3/3] Add initial config files for global aerosol DA (#986)

Add new config files for aerosol da
---
 env/HERA.env                    | 11 +++++++++
 env/ORION.env                   | 11 +++++++++
 parm/config/config.aeroanl      | 17 +++++++++++++
 parm/config/config.aeroanlfinal | 10 ++++++++
 parm/config/config.aeroanlinit  | 10 ++++++++
 parm/config/config.aeroanlrun   | 14 +++++++++++
 parm/config/config.resources    | 42 +++++++++++++++++++++++++++++++++
 7 files changed, 115 insertions(+)
 create mode 100755 parm/config/config.aeroanl
 create mode 100755 parm/config/config.aeroanlfinal
 create mode 100755 parm/config/config.aeroanlinit
 create mode 100755 parm/config/config.aeroanlrun

diff --git a/env/HERA.env b/env/HERA.env
index 124b3e8b9a..51a7c85a33 100755
--- a/env/HERA.env
+++ b/env/HERA.env
@@ -5,6 +5,7 @@ if [ $# -ne 1 ]; then
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
     echo "atmanalrun atmensanalrun"
+    echo "aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -75,6 +76,16 @@ elif [ $step = "atmensanalrun" ]; then
     [[ $NTHREADS_ATMENSANAL -gt $nth_max ]] && export NTHREADS_ATMENSANAL=$nth_max
     export APRUN_ATMENSANAL="$launcher -n $npe_atmensanalrun"
 
+elif [ $step = "aeroanlrun" ]; then
+
+    export APRUNCFP="$launcher -n \$ncmd --multi-prog"
+
+    nth_max=$(($npe_node_max / $npe_node_aeroanlrun))
+
+    export NTHREADS_AEROANL=${nth_aeroanlrun:-$nth_max}
+    [[ $NTHREADS_AEROANL -gt $nth_max ]] && export NTHREADS_AEROANL=$nth_max
+    export APRUN_AEROANL="$launcher -n $npe_aeroanlrun"
+
 elif [ $step = "anal" ]; then
 
     export MKL_NUM_THREADS=4
diff --git a/env/ORION.env b/env/ORION.env
index bef0661f47..8dc267631f 100755
--- a/env/ORION.env
+++ b/env/ORION.env
@@ -5,6 +5,7 @@ if [ $# -ne 1 ]; then
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
     echo "atmanalrun atmensanalrun"
+    echo "aeroanlrun"
     echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen efcs epos"
     echo "postsnd awips gempak"
@@ -74,6 +75,16 @@ elif [ $step = "atmensanalrun" ]; then
     [[ $NTHREADS_ATMENSANAL -gt $nth_max ]] && export NTHREADS_ATMENSANAL=$nth_max
     export APRUN_ATMENSANAL="$launcher -n $npe_atmensanalrun"
 
+elif [ $step = "aeroanlrun" ]; then
+
+    export APRUNCFP="$launcher -n \$ncmd --multi-prog"
+
+    nth_max=$(($npe_node_max / $npe_node_aeroanlrun))
+
+    export NTHREADS_AEROANL=${nth_aeroanlrun:-$nth_max}
+    [[ $NTHREADS_AEROANL -gt $nth_max ]] && export NTHREADS_AEROANL=$nth_max
+    export APRUN_AEROANL="$launcher -n $npe_aeroanlrun"
+
 elif [ $step = "anal" ]; then
 
     export MKL_NUM_THREADS=4
diff --git a/parm/config/config.aeroanl b/parm/config/config.aeroanl
new file mode 100755
index 0000000000..d1c28a3e10
--- /dev/null
+++ b/parm/config/config.aeroanl
@@ -0,0 +1,17 @@
+#!/bin/bash -x
+
+########## config.aeroanl ##########
+# configuration common to all aero analysis tasks
+
+echo "BEGIN: config.aeroanl"
+
+export OBS_YAML_DIR=$HOMEgfs/sorc/gdas.cd/parm/aero/obs/config/
+export OBS_LIST=$HOMEgfs/sorc/gdas.cd/parm/aero/obs/lists/aero_prototype.yaml
+export AEROVARYAML=$HOMEgfs/sorc/gdas.cd/parm/aero/variational/3dvar_dripcg.yaml
+export BERROR_YAML=$HOMEgfs/sorc/gdas.cd/parm/aero/berror/static_bump.yaml
+export FV3JEDI_FIX=$HOMEgfs/fix/fix_jedi
+
+export io_layout_x=1
+export io_layout_y=1
+
+echo "END: config.aeroanl"
diff --git a/parm/config/config.aeroanlfinal b/parm/config/config.aeroanlfinal
new file mode 100755
index 0000000000..230ec5205a
--- /dev/null
+++ b/parm/config/config.aeroanlfinal
@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+########## config.aeroanlfinal ##########
+# Post Aero Analysis specific
+
+echo "BEGIN: config.aeroanlfinal"
+
+# Get task specific resources
+. $EXPDIR/config.resources aeroanlfinal
+echo "END: config.aeroanlfinal"
diff --git a/parm/config/config.aeroanlinit b/parm/config/config.aeroanlinit
new file mode 100755
index 0000000000..72175b8d0c
--- /dev/null
+++ b/parm/config/config.aeroanlinit
@@ -0,0 +1,10 @@
+#!/bin/bash -x
+
+########## config.aeroanlinit ##########
+# Pre Aero Analysis specific
+
+echo "BEGIN: config.aeroanlinit"
+
+# Get task specific resources
+. $EXPDIR/config.resources aeroanlinit
+echo "END: config.aeroanlinit"
diff --git a/parm/config/config.aeroanlrun b/parm/config/config.aeroanlrun
new file mode 100755
index 0000000000..537f33081f
--- /dev/null
+++ b/parm/config/config.aeroanlrun
@@ -0,0 +1,14 @@
+#!/bin/bash -x
+
+########## config.aeroanlrun ##########
+# Aerosol Analysis specific
+
+echo "BEGIN: config.aeroanlrun"
+
+# Get task specific resources
+. $EXPDIR/config.resources aeroanlrun
+
+# Task specific variables
+export JEDIVAREXE=$HOMEgfs/exec/fv3jedi_var.x
+
+echo "END: config.aeroanlrun"
diff --git a/parm/config/config.resources b/parm/config/config.resources
index b2390970ae..b69e87b800 100755
--- a/parm/config/config.resources
+++ b/parm/config/config.resources
@@ -11,6 +11,7 @@ if [ $# -ne 1 ]; then
     echo "getic init coupled_ic aerosol_init"
     echo "atmanalprep atmanalrun atmanalpost"
     echo "atmensanalprep atmensanalrun atmensanalpost"
+    echo "aeroanlinit aeroanlrun aeroanlfinal"
     echo "anal sfcanl analcalc analdiag gldas fcst post vrfy metp arch echgres"
     echo "eobs ediag eomg eupd ecen esfc efcs epos earc"
     echo "init_chem mom6ic ocnpost"
@@ -156,6 +157,47 @@ elif [ $step = "atmanalpost" ]; then
     export nth_atmanalpost=1
     export npe_node_atmanalpost=$(echo "$npe_node_max / $nth_atmanalpost" | bc)
 
+elif [ $step = "aeroanlinit" ]; then
+
+    export wtime_aeroanlinit="00:10:00"
+    export npe_aeroanlinit=1
+    export nth_aeroanlinit=1
+    export npe_node_aeroanlinit=$(echo "$npe_node_max / $nth_aeroanlinit" | bc)
+    export memory_aeroanlinit="3072M"
+
+elif [ $step = "aeroanlrun" ]; then
+
+   case $CASE in
+     C768)    
+        layout_x=6
+        layout_y=6
+        ;;
+      C384)    
+        layout_x=5
+        layout_y=5
+        ;;
+     C192 | C96 | C48)    
+        layout_x=3
+        layout_y=3
+        ;;
+    esac
+
+    export wtime_aeroanlrun="00:30:00"
+    export npe_aeroanlrun=$(echo "$layout_x * $layout_y * 6" | bc)
+    export npe_aeroanlrun_gfs=$(echo "$layout_x * $layout_y * 6" | bc)
+    export nth_aeroanlrun=1
+    export nth_aeroanlrun_gfs=1
+    export native_aeroanlrun="--exclusive"
+    export npe_node_aeroanlrun=$(echo "$npe_node_max / $nth_aeroanlrun" | bc)
+
+elif [ $step = "aeroanlfinal" ]; then
+
+    export wtime_aeroanlfinal="00:10:00"
+    export npe_aeroanlfinal=1
+    export nth_aeroanlfinal=1
+    export npe_node_aeroanlfinal=$(echo "$npe_node_max / $nth_aeroanlfinal" | bc)
+    export memory_aeroanlfinal="3072M"
+
 elif [ $step = "anal" ]; then
 
     export wtime_anal="01:00:00"