Merge pull request #273 from christinaholtNOAA/merge_dev

rrfs_ci: Merge authoritative develop

jobs/JREGIONAL_GET_EXTRN_MDL_FILES

@@ -167,28 +167,29 @@ check_var_valid_value "ICS_OR_LBCS" "valid_vals_ICS_OR_LBCS"
 #
 #-----------------------------------------------------------------------
 #
-# Set the parameter anl_or_fcst that determines whether we want to get 
-# analysis or forecast files.  This depends on whether we want these files 
-# to generate initial condition and surface field files or lateral boundary 
-# condition files.  Also, set time_offset_hrs, which is the offset in 
-# hours between the current cycle's starting time and the starting time 
-# of the external model providing the LBCs.
+# Set parameters for grabbing either the initial conditions from analysis or
+# forecast files of external models, or the lateral boundary conditions
+# from external models. The script has been called to do the work for
+# one or the other.
 #
 #-----------------------------------------------------------------------
 #
 if [ "${ICS_OR_LBCS}" = "ICS" ]; then
-  anl_or_fcst="ANL"
-  time_offset_hrs="0"
+  if [ ${EXTRN_MDL_ICS_OFFSET_HRS} -eq 0 ] ; then
+    anl_or_fcst="ANL"
+    time_offset_hrs=0
+  else
+    anl_or_fcst="FCST"
+    time_offset_hrs=${EXTRN_MDL_ICS_OFFSET_HRS:-0}
+  fi
 elif [ "${ICS_OR_LBCS}" = "LBCS" ]; then
   anl_or_fcst="FCST"
-  time_offset_hrs="${EXTRN_MDL_LBCS_OFFSET_HRS}"
+  time_offset_hrs=${EXTRN_MDL_LBCS_OFFSET_HRS:-0}
 fi
 #
 #-----------------------------------------------------------------------
 #
-# Set the name of and then create the directory in which to stage the 
-# external model files for the current cycle (if it doesn't already exist).  
-# Then change location to that directory.
+# Create the directory where the exetrnal model files should be stored
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_GET_OBS_CCPA

@@ -29,7 +29,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_GET_OBS_MRMS

@@ -25,7 +25,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_GET_OBS_NDAS

@@ -25,7 +25,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_MAKE_ICS

@@ -17,7 +17,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_RUN_POST

@@ -26,7 +26,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_RUN_VX_ENSGRID

@@ -26,7 +26,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_RUN_VX_ENSGRID_MEAN

@@ -26,7 +26,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_RUN_VX_ENSGRID_PROB

@@ -26,7 +26,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_RUN_VX_ENSPOINT

@@ -24,7 +24,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_RUN_VX_ENSPOINT_MEAN

@@ -24,7 +24,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_RUN_VX_ENSPOINT_PROB

@@ -24,7 +24,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_RUN_VX_GRIDSTAT

@@ -26,7 +26,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

jobs/JREGIONAL_RUN_VX_POINTSTAT

@@ -24,7 +24,7 @@
 #
 #-----------------------------------------------------------------------
 #
-{ save_shell_opts; set -u -x; } > /dev/null 2>&1
+{ save_shell_opts; set -u +x; } > /dev/null 2>&1
 #
 #-----------------------------------------------------------------------
 #

scripts/exregional_make_ics.sh

@@ -187,6 +187,7 @@ case "${CCPP_PHYS_SUITE}" in
   "FV3_GSD_SAR" | \
   "FV3_RRFS_v1alpha" | \
   "FV3_RRFS_v1beta" | \
+  "FV3_GFS_v15_thompson_mynn_lam3km" | \
   "FV3_HRRR" )
     if [ "${EXTRN_MDL_NAME_ICS}" = "RAP" ] || \
        [ "${EXTRN_MDL_NAME_ICS}" = "HRRR" ]; then

scripts/exregional_make_lbcs.sh

@@ -186,6 +186,7 @@ case "${CCPP_PHYS_SUITE}" in
   "FV3_GSD_SAR" | \
   "FV3_RRFS_v1alpha" | \
   "FV3_RRFS_v1beta" | \
+  "FV3_GFS_v15_thompson_mynn_lam3km" | \
   "FV3_HRRR" )
     if [ "${EXTRN_MDL_NAME_LBCS}" = "RAP" ] || \
        [ "${EXTRN_MDL_NAME_LBCS}" = "HRRR" ]; then

scripts/exregional_run_fcst.sh

@@ -108,7 +108,7 @@ case "$MACHINE" in
     if [ ${PE_MEMBER01} -gt 24 ];then
       APRUN="aprun -b -j1 -n${PE_MEMBER01} -N24 -d1 -cc depth"
     else
-      APRUN="aprun -b -j1 -n24 -N24 -d1 -cc depth"
+      APRUN="aprun -b -j1 -n${PE_MEMBER01} -N${PE_MEMBER01} -d1 -cc depth"
     fi
     ;;
 
@@ -127,7 +127,7 @@ case "$MACHINE" in
   "ORION")
     ulimit -s unlimited
     ulimit -a
-    APRUN="srun"
+    APRUN="srun -n ${PE_MEMBER01}"
     ;;
 
   "JET")
@@ -405,6 +405,30 @@ done
 #
 #-----------------------------------------------------------------------
 #
+# Create links in the current run directory to the MERRA2 aerosol 
+# climatology data files and lookup table for optics properties.
+#
+#-----------------------------------------------------------------------
+#
+if [ "${USE_MERRA_CLIMO}" = "TRUE" ]; then
+  for f_nm_path in ${FIXclim}/*; do
+    f_nm=$( basename "${f_nm_path}" )
+    pre_f="${f_nm%%.*}"
+
+    if [ "${pre_f}" = "merra2" ]; then
+      mnth=$( printf "%s\n" "${f_nm}" | grep -o -P '(?<=2014.m).*(?=.nc)' )
+      symlink="${run_dir}/aeroclim.m${mnth}.nc"
+    else
+      symlink="${run_dir}/${pre_f}.dat"
+    fi
+    target="${f_nm_path}"
+    create_symlink_to_file target="$target" symlink="$symlink" \
+                         relative="${relative_link_flag}"
+  done
+fi
+#
+#-----------------------------------------------------------------------
+#
 # If running this cycle/ensemble member combination more than once (e.g.
 # using rocotoboot), remove any time stamp file that may exist from the
 # previous attempt.

scripts/exregional_run_post.sh

@@ -234,8 +234,8 @@ tmmark="tm00"
 # minutes and seconds of the corresponding output forecast time.
 #
 # Note that if the forecast model is instructed to output at some hourly
-# interval (via the nfhout and nfhout_hf parameters in the MODEL_CONFIG_FN
-# file, with nsout set to a non-positive value), then the write-component
+# interval (via the output_fh parameter in the MODEL_CONFIG_FN file, 
+# with nsout set to a non-positive value), then the write-component
 # output file names will not contain any suffix for the minutes and seconds.
 # For this reason, when SUB_HOURLY_POST is not set to "TRUE", mnts_sec_str
 # must be set to a null string.

tests/WE2E/get_WE2Etest_names_subdirs_descs.sh

@@ -759,7 +759,7 @@ This is probably because it is a directory.  Please correct and rerun."
   test_names=("${prim_test_names[@]}")
   test_subdirs=("${prim_test_subdirs[@]}")
   if [ "${num_alt_tests}" -gt "0" ]; then
-    test_names+=("${alt_test_subdirs[@]:-}")
+    test_names+=("${alt_test_names[@]:-}")
     test_subdirs+=("${alt_test_subdirs[@]:-}")
   fi
 #
@@ -1025,7 +1025,7 @@ Please correct and rerun."
 # listed first.  
 #
 # Finally, we extract from test_ids_and_inds_sorted the second number 
-# in each element (the one afte the first number, which is the test ID,
+# in each element (the one after the first number, which is the test ID,
 # and the test type, which we no longer need), which is the original 
 # array index before sorting, and save the results in the array sort_inds.  
 # This array will contain the original indices in sorted order that we 

tests/WE2E/get_expts_status.sh

@@ -50,7 +50,7 @@ scrfunc_dir=$( dirname "${scrfunc_fp}" )
 #
 #-----------------------------------------------------------------------
 #
-homerrfs=${scrfunc_dir%/*}
+homerrfs=${scrfunc_dir%/*/*}
 #
 #-----------------------------------------------------------------------
 #

tests/WE2E/run_WE2E_tests.sh

@@ -538,8 +538,8 @@ accordingly and rerun."
   if [ "${match_found}" = "FALSE" ]; then
     avail_WE2E_test_names_str=$( printf "  \"%s\"\n" "${avail_WE2E_test_names[@]}" )
     print_err_msg_exit "\
-The name current user-specified test to run (user_spec_test) does not 
-match any of the names (either primary or alternate) of the available
+The name of the current user-specified test to run (user_spec_test) does 
+not match any of the names (either primary or alternate) of the available
 WE2E tests:
   user_spec_test = \"${user_spec_test}\"
 Valid values for user_spec_test consist of the names (primary or alternate)
@@ -938,7 +938,7 @@ PTMP=\"${PTMP}\""
     elif [ "$MACHINE" = "HERA" ]; then
       extrn_mdl_source_basedir="/scratch2/BMC/det/Gerard.Ketefian/UFS_CAM/staged_extrn_mdl_files"
     elif [ "$MACHINE" = "JET" ]; then
-      extrn_mdl_source_basedir="/mnt/lfs1/BMC/fim/Gerard.Ketefian/UFS_CAM/staged_extrn_mdl_files"
+      extrn_mdl_source_basedir="/mnt/lfs1/BMC/gsd-fv3/Gerard.Ketefian/UFS_CAM/staged_extrn_mdl_files"
     elif [ "$MACHINE" = "CHEYENNE" ]; then
       extrn_mdl_source_basedir="/glade/p/ral/jntp/UFS_SRW_app/staged_extrn_mdl_files"
     elif [ "$MACHINE" = "ORION" ]; then

tests/WE2E/test_configs/grids_extrn_mdls_suites_community/config.grid_RRFS_CONUS_3km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v15_thompson_mynn_lam3km.sh

@@ -0,0 +1,27 @@
+#
+# TEST PURPOSE/DESCRIPTION:
+# ------------------------
+#
+# This test is to ensure that the workflow running in community mode 
+# completes successfully on the RRFS_CONUS_3km grid using the GFS_v15_
+# thompson_mynn_lam3km physics suite with ICs and LBCs derived from FV3GFS.
+#
+
+RUN_ENVIR="community"
+PREEXISTING_DIR_METHOD="rename"
+
+PREDEF_GRID_NAME="RRFS_CONUS_3km"
+CCPP_PHYS_SUITE="FV3_GFS_v15_thompson_mynn_lam3km"
+
+USE_MERRA_CLIMO="TRUE"
+
+EXTRN_MDL_NAME_ICS="FV3GFS"
+EXTRN_MDL_NAME_LBCS="FV3GFS"
+USE_USER_STAGED_EXTRN_FILES="TRUE"
+
+DATE_FIRST_CYCL="20190701"
+DATE_LAST_CYCL="20190701"
+CYCL_HRS=( "00" )
+
+FCST_LEN_HRS="6"
+LBC_SPEC_INTVL_HRS="3"

tests/WE2E/test_configs/wflow_features/config.deactivate_tasks.sh

@@ -0,0 +1,60 @@
+#
+# TEST PURPOSE/DESCRIPTION:
+# ------------------------
+#
+# This test has two purposes:
+#
+# 1) It checks that the various workflow tasks can be deactivated, i.e. 
+#    removed from the Rocoto XML.
+# 2) It checks the capability of the workflow to use "template" experiment 
+#    variables, i.e. variables whose definitions include references to 
+#    other variables, e.g.
+#
+#      MY_VAR='\${ANOTHER_VAR}'
+#
+# Note that we do not deactivate all tasks in the workflow; we leave the 
+# MAKE_GRID_TN, MAKE_OROG_TN, and MAKE_SFC_CLIMO_TN activated because:
+#
+# 1) There is already a WE2E test that runs with these three tasks
+#    deactivated (that test is to ensure that pre-generated grid, 
+#    orography, and surface climatology files can be used).
+# 2) In checking the template variable capability, we want to make sure
+#    that the variable defintions file (GLOBAL_VAR_DEFNS_FN) generated
+#    does not have syntax or other errors in it by sourcing it in these 
+#    three tasks.
+#
+
+RUN_ENVIR="community"
+PREEXISTING_DIR_METHOD="rename"
+
+PREDEF_GRID_NAME="RRFS_CONUS_25km"
+CCPP_PHYS_SUITE="FV3_GFS_v15p2"
+
+EXTRN_MDL_NAME_ICS="FV3GFS"
+EXTRN_MDL_NAME_LBCS="FV3GFS"
+USE_USER_STAGED_EXTRN_FILES="TRUE"
+
+DATE_FIRST_CYCL="20190701"
+DATE_LAST_CYCL="20190701"
+CYCL_HRS=( "00" )
+
+FCST_LEN_HRS="6"
+LBC_SPEC_INTVL_HRS="3"
+
+RUN_TASK_GET_EXTRN_ICS="FALSE"
+RUN_TASK_GET_EXTRN_LBCS="FALSE"
+RUN_TASK_MAKE_ICS="FALSE"
+RUN_TASK_MAKE_LBCS="FALSE"
+RUN_TASK_RUN_FCST="FALSE"
+RUN_TASK_RUN_POST="FALSE"
+#
+# The following shows examples of how to define template variables.  Here,
+# we define RUN_CMD_UTILS, RUN_CMD_FCST, and RUN_CMD_POST as template 
+# variables.  Note that during this test, these templates aren't actually 
+# expanded/used (something that would be done using bash's "eval" built-in 
+# command) anywhere in the scripts.  They are included here only to verify
+# that the test completes with some variables defined as templates.
+#
+RUN_CMD_UTILS='cd $yyyymmdd'
+RUN_CMD_FCST='mpirun -np ${PE_MEMBER01}'
+RUN_CMD_POST='echo hello $yyyymmdd'

tests/WE2E/test_configs/wflow_features/config.template_vars.sh

@@ -0,0 +1 @@
+config.deactivate_tasks.sh