NOAA-GSL · christinaholtNOAA · Feb 17, 2021 · Feb 1, 2021 · Feb 6, 2021 · Feb 10, 2021
diff --git a/jobs/JREGIONAL_GET_EXTRN_MDL_FILES b/jobs/JREGIONAL_GET_EXTRN_MDL_FILES
@@ -57,7 +57,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #

diff --git a/jobs/JREGIONAL_MAKE_GRID b/jobs/JREGIONAL_MAKE_GRID
@@ -125,7 +125,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #

diff --git a/jobs/JREGIONAL_MAKE_ICS b/jobs/JREGIONAL_MAKE_ICS
@@ -27,7 +27,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #

diff --git a/jobs/JREGIONAL_MAKE_LBCS b/jobs/JREGIONAL_MAKE_LBCS
@@ -27,7 +27,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #

diff --git a/jobs/JREGIONAL_MAKE_OROG b/jobs/JREGIONAL_MAKE_OROG
@@ -27,7 +27,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #

diff --git a/jobs/JREGIONAL_MAKE_SFC_CLIMO b/jobs/JREGIONAL_MAKE_SFC_CLIMO
@@ -27,7 +27,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #

diff --git a/jobs/JREGIONAL_RUN_FCST b/jobs/JREGIONAL_RUN_FCST
@@ -37,7 +37,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #

diff --git a/jobs/JREGIONAL_RUN_POST b/jobs/JREGIONAL_RUN_POST
@@ -36,7 +36,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #
@@ -100,7 +100,7 @@ cd_vrfy "${fhr_dir}"
 #
 #-----------------------------------------------------------------------
 #
-fhr=$( printf "%s" "${fhr}" | sed -n -r -e "s/^([0-9]+)$/\1/p" )
+fhr=$( printf "%s" "${fhr}" | $SED -n -r -e "s/^([0-9]+)$/\1/p" )
 if [ -z "$fhr" ]; then
   print_err_msg_exit "\
 The forecast hour (fhr) must be a non-empty string consisting of only 

diff --git a/modulefiles/tasks/linux/make_grid.local b/modulefiles/tasks/linux/make_grid.local
@@ -0,0 +1,6 @@
+#%Module
+module use -a /contrib/miniconda3/modulefiles
+module load miniconda3
+if [module-info mode load] {
+  system "conda activate regional_workflow"
+}
diff --git a/modulefiles/tasks/linux/make_ics.local b/modulefiles/tasks/linux/make_ics.local
@@ -0,0 +1,6 @@
+#%Module
+module use -a /contrib/miniconda3/modulefiles
+module load miniconda3
+if [module-info mode load] {
+  system "conda activate regional_workflow"
+}
diff --git a/modulefiles/tasks/linux/make_lbcs.local b/modulefiles/tasks/linux/make_lbcs.local
@@ -0,0 +1,6 @@
+#%Module
+module use -a /contrib/miniconda3/modulefiles
+module load miniconda3
+if [module-info mode load] {
+  system "conda activate regional_workflow"
+}
diff --git a/modulefiles/tasks/linux/run_fcst.local b/modulefiles/tasks/linux/run_fcst.local
@@ -0,0 +1,6 @@
+#%Module
+module use -a /contrib/miniconda3/modulefiles
+module load miniconda3
+if [module-info mode load] {
+  system "conda activate regional_workflow"
+}
diff --git a/scripts/exregional_get_extrn_mdl_files.sh b/scripts/exregional_get_extrn_mdl_files.sh
@@ -27,7 +27,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #
@@ -524,7 +524,7 @@ not happen."
 # to the current directory.  Then move the files.
 #
         rel_dir=$( printf "%s" "${extrn_mdl_arcvrel_dir}" | \
-                   sed -r 's%^(\/|\.\/)([^/]*)(.*)%\2\3%' ) 
+                   $SED -r 's%^(\/|\.\/)([^/]*)(.*)%\2\3%' ) 
         mv_vrfy ${rel_dir}/* .
 #
 # Get the first subdirectory in rel_dir, i.e. the subdirectory before the 
@@ -533,7 +533,7 @@ not happen."
 # it.
 #
         subdir_to_remove=$( printf "%s" "${rel_dir}" | \
-                            sed -r 's%^([^/]*)(.*)%\1%' ) 
+                            $SED -r 's%^([^/]*)(.*)%\1%' ) 
         rm_vrfy -rf ./${subdir_to_remove}
 #
 # If extrn_mdl_arcvrel_dir does not start with a "/" (and it is not 

diff --git a/scripts/exregional_make_grid.sh b/scripts/exregional_make_grid.sh
@@ -20,7 +20,7 @@
 . $USHDIR/link_fix.sh
 . $USHDIR/set_FV3nml_sfc_climo_filenames.sh
 . $USHDIR/set_FV3nml_stoch_params.sh
-. $USHDIR/create_diag_table_files.sh
+. $USHDIR/create_diag_table_file.sh
 #
 #-----------------------------------------------------------------------
 #
@@ -39,7 +39,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #
@@ -147,6 +147,14 @@ case $MACHINE in
     ulimit -a
     ;;
 
+  "MACOS")
+    APRUN=time
+    ;;
+
+  "LINUX")
+    APRUN=time
+    ;;
+
   *)
     print_err_msg_exit "\
 Run command has not been specified for this machine:
@@ -433,11 +441,19 @@ uniform cubed-sphere grid equivalent resolution returned with nonzero exit
 code:
   exec_fp = \"${exec_fp}\""
 
+# Make sure 'ncdump' is available before we try to use it
+if ! command -v ncdump &> /dev/null
+then
+  print_err_msg_exit "\
+The utility 'ncdump' was not found in the environment. Be sure to add the
+netCDF 'bin/' directory to your PATH."
+fi
+
 # Make the following (reading of res_equiv) a function in another file
 # so that it can be used both here and in the exregional_make_orog.sh
 # script.
 res_equiv=$( ncdump -h "${grid_fp}" | \
-             grep -o ":RES_equiv = [0-9]\+" | grep -o "[0-9]" ) || \
+             grep -o ":RES_equiv = [0-9]\+" | $SED 's/[^0-9]*//g' ) || \
 print_err_msg_exit "\
 Attempt to extract the equivalent global uniform cubed-sphere grid reso-
 lution from the grid file (grid_fp) failed:
@@ -683,9 +699,6 @@ Call to function to set stochastic parameters in the FV3 namelist files
 for the various ensemble members failed."
 fi
 
-create_diag_table_files || print_err_msg_exit "\
-Call to function to create a diagnostics table file under each cycle
-directory failed."
 #
 #-----------------------------------------------------------------------
 #

diff --git a/scripts/exregional_make_ics.sh b/scripts/exregional_make_ics.sh
@@ -27,7 +27,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #
@@ -116,6 +116,21 @@ case "$MACHINE" in
     APRUN="ibrun"
     ;;
 
+  "MACOS")
+    APRUN=$RUN_CMD_UTILS
+    ;;
+
+  "LINUX")
+    APRUN=$RUN_CMD_UTILS
+    ;;
+
+  *)
+    print_err_msg_exit "\
+Run command has not been specified for this machine:
+  MACHINE = \"$MACHINE\"
+  APRUN = \"$APRUN\""
+    ;;
+
 esac
 #
 #-----------------------------------------------------------------------

diff --git a/scripts/exregional_make_lbcs.sh b/scripts/exregional_make_lbcs.sh
@@ -27,7 +27,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #
@@ -116,6 +116,21 @@ case "$MACHINE" in
     APRUN="ibrun"
     ;;
 
+  "MACOS")
+    APRUN=$RUN_CMD_UTILS
+    ;;
+
+  "LINUX")
+    APRUN=$RUN_CMD_UTILS
+    ;;
+
+  *)
+    print_err_msg_exit "\
+Run command has not been specified for this machine:
+  MACHINE = \"$MACHINE\"
+  APRUN = \"$APRUN\""
+    ;;
+
 esac
 #
 #-----------------------------------------------------------------------
@@ -409,7 +424,7 @@ list file has not specified for this external LBC model (EXTRN_MDL_NAME_LBCS):
   dd="${EXTRN_MDL_CDATE:6:2}"
   hh="${EXTRN_MDL_CDATE:8:2}"
 
-  cdate_crnt_fhr=$( date --utc --date "${yyyymmdd} ${hh} UTC + ${fhr} hours" "+%Y%m%d%H" )
+  cdate_crnt_fhr=$( $DATE_UTIL --utc --date "${yyyymmdd} ${hh} UTC + ${fhr} hours" "+%Y%m%d%H" )
 #
 # Get the month, day, and hour corresponding to the current forecast time
 # of the the external model.

diff --git a/scripts/exregional_make_orog.sh b/scripts/exregional_make_orog.sh
@@ -35,7 +35,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #
@@ -147,6 +147,14 @@ case $MACHINE in
     export APRUN="time"
     ;;
 
+  "MACOS")
+    APRUN=time
+    ;;
+
+  "LINUX")
+    APRUN=time
+    ;;
+
   *)
     print_err_msg_exit "\
 Run command has not been specified for this machine:

diff --git a/scripts/exregional_make_sfc_climo.sh b/scripts/exregional_make_sfc_climo.sh
@@ -35,7 +35,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #
@@ -170,6 +170,14 @@ case $MACHINE in
     APRUN="ibrun -np ${nprocs}"
     ;;
 
+  "MACOS")
+    APRUN=$RUN_CMD_UTILS
+    ;;
+
+  "LINUX")
+    APRUN=$RUN_CMD_UTILS
+    ;;
+
   *)
     print_err_msg_exit "\
 Run command has not been specified for this machine:

diff --git a/scripts/exregional_run_fcst.sh b/scripts/exregional_run_fcst.sh
@@ -9,6 +9,7 @@
 #
 . ${GLOBAL_VAR_DEFNS_FP}
 . $USHDIR/source_util_funcs.sh
+. $USHDIR/create_diag_table_file.sh
 #
 #-----------------------------------------------------------------------
 #
@@ -35,7 +36,7 @@
 #
 #-----------------------------------------------------------------------
 #
-scrfunc_fp=$( readlink -f "${BASH_SOURCE[0]}" )
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
 scrfunc_fn=$( basename "${scrfunc_fp}" )
 scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #
@@ -144,6 +145,14 @@ case $MACHINE in
     APRUN="ibrun -np ${PE_MEMBER01}"
     ;;
 
+  "MACOS")
+    APRUN=$RUN_CMD_FCST
+    ;;
+
+  "LINUX")
+    APRUN=$RUN_CMD_FCST
+    ;;
+
   *)
     print_err_msg_exit "\
 Run command has not been specified for this machine:
@@ -360,9 +369,9 @@ for (( i=0; i<${num_symlinks}; i++ )); do
 
   mapping="${CYCLEDIR_LINKS_TO_FIXam_FILES_MAPPING[$i]}"
   symlink=$( printf "%s\n" "$mapping" | \
-             sed -n -r -e "s/${regex_search}/\1/p" )
+             $SED -n -r -e "s/${regex_search}/\1/p" )
   target=$( printf "%s\n" "$mapping" | \
-            sed -n -r -e "s/${regex_search}/\2/p" )
+            $SED -n -r -e "s/${regex_search}/\2/p" )
 
   symlink="${run_dir}/$symlink"
   target="$FIXam/$target"
@@ -432,6 +441,19 @@ cycle's (cdate) run directory (run_dir) failed:
 #
 #-----------------------------------------------------------------------
 #
+# Call the function that creates the model configuration file within each
+# cycle directory.
+#
+#-----------------------------------------------------------------------
+#
+create_diag_table_file \
+    run_dir="${run_dir}" || print_err_msg_exit "\
+      Call to function to create a diag table file for the current
+      cycle's (cdate) run directory (run_dir) failed:
+         run_dir = \"${run_dir}\""
+#
+#-----------------------------------------------------------------------
+#
 # If running ensemble forecasts, create a link to the cycle-specific
 # diagnostic tables file in the cycle directory.  Note that this link
 # should not be made if not running ensemble forecasts because in that