Templating diag_tables with Jinja (#211)

* Templating diag table with jinja. * Cleaning modulefiles, and adding run_fcst.local. * Small mods needed at run time. * Jet modulefile should be same as Hera. * Adding missing files back. * Addressing Gerard's comments. * Applying this PR's mods to recent additions. * Updating modulefiles. * Cheyenne modulefile needs "system" command to call ncar_pylib Co-authored-by: Michael Kavulich, Jr <[email protected]>
ufs-community · Jun 22, 2020 · 2bfa034 · 2bfa034
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commit 2bfa034
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diff --git a/modulefiles/tasks/.gitignore b/modulefiles/tasks/.gitignore
@@ -0,0 +1,6 @@
+make_orog
+make_ics
+make_lbcs
+make_sfc_climo
+run_fcst
+run_post
diff --git a/modulefiles/tasks/cheyenne/run_fcst.local b/modulefiles/tasks/cheyenne/run_fcst.local
@@ -0,0 +1,2 @@
+
+system "ncar_pylib /glade/p/ral/jntp/UFS_CAM/ncar_pylib_20200427"
diff --git a/modulefiles/tasks/hera/make_ics.local b/modulefiles/tasks/hera/make_ics.local
@@ -1,3 +1,4 @@
+module load wgrib2
 
 module use -a /contrib/miniconda3/modulefiles
 module load miniconda3

diff --git a/modulefiles/tasks/hera/make_lbcs.local b/modulefiles/tasks/hera/make_lbcs.local
@@ -1,3 +1,4 @@
+module load wgrib2
 
 module use -a /contrib/miniconda3/modulefiles
 module load miniconda3

diff --git a/modulefiles/tasks/hera/run_fcst.local b/modulefiles/tasks/hera/run_fcst.local
@@ -0,0 +1,5 @@
+module use -a /contrib/miniconda3/modulefiles
+module load miniconda3
+if [module-info mode load] {
+  system "conda activate regional_workflow"
+}
diff --git a/modulefiles/tasks/jet/make_grid b/modulefiles/tasks/jet/make_grid
@@ -10,4 +10,6 @@ module load hdf5/1.10.5
 
 module use -a /contrib/miniconda3/modulefiles
 module load miniconda3
-system "conda activate regional_workflow"
+if [module-info mode load] {
+  system "conda activate regional_workflow"
+}
diff --git a/modulefiles/tasks/jet/make_ics.local b/modulefiles/tasks/jet/make_ics.local
@@ -1,3 +1,4 @@
+module load wgrib2/2.0.8 
 
 module use -a /contrib/miniconda3/modulefiles
 module load miniconda3

diff --git a/modulefiles/tasks/jet/make_lbcs.local b/modulefiles/tasks/jet/make_lbcs.local
@@ -1,3 +1,4 @@
+module load wgrib2/2.0.8 
 
 module use -a /contrib/miniconda3/modulefiles
 module load miniconda3

diff --git a/modulefiles/tasks/jet/run_fcst.local b/modulefiles/tasks/jet/run_fcst.local
@@ -0,0 +1,5 @@
+module use -a /contrib/miniconda3/modulefiles
+module load miniconda3
+if [module-info mode load] {
+  system "conda activate regional_workflow"
+}
diff --git a/scripts/exregional_run_fcst.sh b/scripts/exregional_run_fcst.sh
@@ -391,12 +391,6 @@ print_info_msg "$VERBOSE" "
 Copying cycle-dependent model input files from the templates directory 
 to the current cycle's run directory..." 
 
-print_info_msg "$VERBOSE" "
-  Copying the template diagnostics table file to the current cycle's run
-  directory..."
-diag_table_fp="${CYCLE_DIR}/${DIAG_TABLE_FN}"
-cp_vrfy "${DIAG_TABLE_TMPL_FP}" "${diag_table_fp}"
-
 print_info_msg "$VERBOSE" "
   Copying the template model configuration file to the current cycle's
   run directory..."
@@ -414,24 +408,45 @@ YYYY=${CDATE:0:4}
 MM=${CDATE:4:2}
 DD=${CDATE:6:2}
 HH=${CDATE:8:2}
-YYYYMMDD=${CDATE:0:8}
 #
 #-----------------------------------------------------------------------
 #
 # Set parameters in the diagnostics table file.
 #
 #-----------------------------------------------------------------------
 #
+
+diag_table_fp="${CYCLE_DIR}/${DIAG_TABLE_FN}"
+
 print_info_msg "$VERBOSE" "
-Setting parameters in file:
-  diag_table_fp = \"${diag_table_fp}\""
-
-set_file_param "${diag_table_fp}" "CRES" "$CRES"
-set_file_param "${diag_table_fp}" "YYYY" "$YYYY"
-set_file_param "${diag_table_fp}" "MM" "$MM"
-set_file_param "${diag_table_fp}" "DD" "$DD"
-set_file_param "${diag_table_fp}" "HH" "$HH"
-set_file_param "${diag_table_fp}" "YYYYMMDD" "$YYYYMMDD"
+  Using the template diagnostics table file:
+
+      diag_table_tmpl_fp = ${DIAG_TABLE_TMPL_FP}
+
+  to create:
+
+      diag_table_fp = \"${diag_table_fp}\""
+
+settings="
+  starttime: !datetime ${CDATE}
+  cres: ${CRES}
+"
+
+$USHDIR/fill_jinja_template.py -q -u "${settings}" -t "${DIAG_TABLE_TMPL_FP}" -o "${diag_table_fp}"
+
+if [[ $? -ne 0 ]] ; then
+  echo "
+  !!!!!!!!!!!!!!!!!
+
+  fill_jinja_template.py failed!
+
+  !!!!!!!!!!!!!!!!!
+  "
+
+  exit 1
+fi
+
+
 #
 #-----------------------------------------------------------------------
 #

diff --git a/ush/create_xml.py → ush/fill_jinja_template.py b/ush/create_xml.py → ush/fill_jinja_template.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 '''
 This utility fills in a user-supplied Jinja template from either a YAML file, or

diff --git a/ush/generate_FV3SAR_wflow.sh b/ush/generate_FV3SAR_wflow.sh
@@ -184,35 +184,36 @@ settings="\
 # Forecast length (same for all cycles).
 #
   'fcst_len_hrs': ${FCST_LEN_HRS}"
-#
-# For debugging purposes, print out what "settings" has been set to.
-#
+
 print_info_msg $VERBOSE "
 The variable \"settings\" specifying values of the rococo XML variables
 has been set as follows:
-
+#-----------------------------------------------------------------------
 settings =
 $settings"
+
 #
 # Set the full path to the template rocoto XML file.  Then call a python
 # script to generate the experiment's actual XML file from this template
 # file.
 #
 template_xml_fp="${TEMPLATE_DIR}/${WFLOW_XML_FN}"
-$USHDIR/create_xml.py -q \
-                      -t ${template_xml_fp} \
-                      -u "$settings" \
-                      -o ${WFLOW_XML_FP} || \
+$USHDIR/fill_jinja_template.py -q \
+                               -u "${settings}" \
+                               -t ${template_xml_fp} \
+                               -o ${WFLOW_XML_FP} || \
   print_err_msg_exit "\
-Call to python script create_xml.py to create a rocoto workflow XML file
-from a template file failed.  Parameters passed to this script are:
+Call to python script fill_jinja_template.py to create a rocoto workflow
+XML file from a template file failed.  Parameters passed to this script
+are:
   Full path to template rocoto XML file:
     template_xml_fp = \"${template_xml_fp}\"
   Full path to output rocoto XML file:
     WFLOW_XML_FP = \"${WFLOW_XML_FP}\"
   Namelist settings specified on command line:
     settings =
 $settings"
+
 #
 #-----------------------------------------------------------------------
 #
@@ -269,6 +270,7 @@ fi
 #
 # Only some platforms build EMC_post using modules.
 #
+
 case $MACHINE in
 
   "CHEYENNE")

diff --git a/ush/load_modules_run_task.sh b/ush/load_modules_run_task.sh
@@ -160,40 +160,9 @@ jjob_fp="$2"
 #
 # where HOMErrfs is the base directory of the workflow, machine is the
 # name of the machine that we're running on (in lowercase), and task_-
-# name is the name of the current task (an input to this script).  For
-# all tasks in the rocoto XML except run_fcst, these are actual files
-# (as opposed to symlinks).  For the run_fcst task, there are two possi-
-# ble module files.  The first one is named "run_fcst_no_ccpp" and is
-# used to run FV3 without CCPP (i.e. it is used if USE_CCPP is set to
-# "FALSE" in the experiment/workflow configuration file).  This is also
-# an actual file.  The second one is named "run_fcst_ccpp" and is used
-# to run FV3 with CCPP (i.e. it is used if USE_CCPP is set to "TRUE").
-# This second file is a symlink (and is a part of the regional_workflow
-# repo), and its target is
-#
-#   ${UFS_WTHR_MDL_DIR}/NEMS/src/conf/modules.fv3
-#
-# Here, UFS_WTHR_MDL_DIR is the directory in which the ufs_weather_model
-# repository containing the FV3 model is cloned (normally "$HOMErrfs/
-# sorc/ufs_weather_model"), and modules.fv3 is a module file that is ge-
-# nerated by the forecast model's build process.  It contains the appro-
-# priate modules to use when running the FV3 model.  Thus, we just point
-# to it via the symlink "run_fcst_ccpp" in the modulefiles/$machine di-
-# rectory.
-#
-# QUESTION:
-# Why don't we do this for the non-CCPP version of FV3?
-#
-# ANSWER:
-# Because for that case, we load different versions of intel and impi
-# (compare modules.nems to the modules loaded for the case of USE_CCPP
-# set to "FALSE" in run_FV3SAR.sh).  Maybe these can be combined at some
-# point.  Note that a modules.nems file is generated in the same rela-
-# tive location in the non-CCPP-enabled version of the FV3 forecast mo-
-# del, so maybe that can be used and the run_FV3SAR.sh script modified
-# to accomodate such a change.  That way the below can be performed for
-# both the CCPP-enabled and non-CCPP-enabled versions of the forecast
-# model.
+# name is the name of the current task (an input to this script). The
+# collection of modulefiles is staged by the generate_workflow.sh
+# script. Please see that script for information on their creation.
 #
 #-----------------------------------------------------------------------
 #
@@ -217,6 +186,7 @@ use_default_modulefile=0
 #  fi
 #fi
 #
+
 #-----------------------------------------------------------------------
 #
 # This comment needs to be updated:
@@ -310,45 +280,48 @@ Loading modules for task \"${task_name}\" ..."
   module use "${modules_dir}" || print_err_msg_exit "\
 Call to \"module use\" command failed."
 
-#
-# If NOT using the default modulefile...
-#
+  #
+  # If NOT using the default modulefile...
+  #
   if [ ${use_default_modulefile} -eq 0 ]; then
-#
-# Some of the task module files that are symlinks to module files in the
-# external repositories are in fact shell scripts (they shouldn't be;
-# such cases should be fixed in the external repositories).  For such
-# files, we source the "module" file.  For true module files, we use the
-# "module load" command.
-#
+
+    #
+    # Some of the task module files that are symlinks to module files in the
+    # external repositories are in fact shell scripts (they shouldn't be;
+    # such cases should be fixed in the external repositories).  For such
+    # files, we source the "module" file.  For true module files, we use the
+    # "module load" command.
+    #
     case "${task_name}" in
-#
-     "${MAKE_ICS_TN}" | "${MAKE_LBCS_TN}" | "${MAKE_SFC_CLIMO_TN}")
-       . ${modulefile_path} || print_err_msg_exit "\
-Sourcing of \"module\" file (modulefile_path; really a shell script) for
-the specified task (task_name) failed:
-  task_name = \"${task_name}\"
-  modulefile_path = \"${modulefile_path}\""
-       ;;
-#
-     *)
-       module load ${modulefile_name} || print_err_msg_exit "\
-Loading of module file (modulefile_name; in directory specified by 
-modules_dir) for the specified task (task_name) failed:
-  task_name = \"${task_name}\"
-  modulefile_name = \"${modulefile_name}\"
-  modules_dir = \"${modules_dir}\""
-       ;;
-#
+
+      "${MAKE_ICS_TN}" | "${MAKE_LBCS_TN}" | "${MAKE_SFC_CLIMO_TN}")
+        . ${modulefile_path} || print_err_msg_exit "\
+        Sourcing of \"module\" file (modulefile_path; really a shell script) for
+        the specified task (task_name) failed:
+          task_name = \"${task_name}\"
+          modulefile_path = \"${modulefile_path}\""
+
+        ;;
+      *)
+        module use "${modules_dir}" || print_err_msg_exit "\
+        Call to \"module use\" command failed."
+
+        module load ${modulefile_name} || print_err_msg_exit "\
+        Loading of module file (modulefile_name; in directory specified by mod-
+        ules_dir) for the specified task (task_name) failed:
+           task_name = \"${task_name}\"
+           modulefile_name = \"${modulefile_name}\"
+           modules_dir = \"${modules_dir}\""
+        ;;
     esac
 
   else # using default modulefile
 
     module load ${default_modulefile_name} || print_err_msg_exit "\
-Loading of default module file failed:
-  task_name = \"${task_name}\"
-  default_modulefile_name = \"${default_modulefile_name}\"
-  default_modules_dir = \"${default_modules_dir}\""
+    Loading of default module file failed:
+      task_name = \"${task_name}\"
+      default_modulefile_name = \"${default_modulefile_name}\"
+      default_modules_dir = \"${default_modules_dir}\""
 
   fi
 

diff --git a/ush/templates/diag_table.FV3_CPT_v0 b/ush/templates/diag_table.FV3_CPT_v0
@@ -1,5 +1,5 @@
-<YYYYMMDD>.<HH>Z.<CRES>.32bit.non-hydro.regional
-<YYYY> <MM> <DD> <HH> 0 0
+{{ starttime.strftime("%Y%m%d.%H") }}Z.{{ cres }}.32bit.non-hydro.regional
+{{ starttime.strftime("%Y %m %d %H %M %S") }}
 
 "grid_spec",              -1,  "months",  1, "days",  "time"
 "atmos_4xdaily",           6,  "hours",   1, "days",  "time"

diff --git a/ush/templates/diag_table.FV3_GFS_2017_gfdlmp b/ush/templates/diag_table.FV3_GFS_2017_gfdlmp
@@ -1,5 +1,5 @@
-<YYYYMMDD>.<HH>Z.<CRES>.32bit.non-hydro.regional
-<YYYY> <MM> <DD> <HH> 0 0
+{{ starttime.strftime("%Y%m%d.%H") }}Z.{{ cres }}.32bit.non-hydro.regional
+{{ starttime.strftime("%Y %m %d %H %M %S") }}
 
 "grid_spec",              -1,  "months",  1, "days",  "time"
 "atmos_static",           -1,  "hours",   1, "hours", "time"

diff --git a/ush/templates/diag_table.FV3_GFS_v15p2 b/ush/templates/diag_table.FV3_GFS_v15p2
@@ -1,5 +1,5 @@
-<YYYYMMDD>.<HH>Z.<CRES>.32bit.non-hydro.regional
-<YYYY> <MM> <DD> <HH> 0 0
+{{ starttime.strftime("%Y%m%d.%H") }}Z.{{ cres }}.32bit.non-hydro.regional
+{{ starttime.strftime("%Y %m %d %H %M %S") }}
 
 "grid_spec",              -1,  "months",  1, "days",  "time"
 "atmos_4xdaily",           6,  "hours",   1, "days",  "time"

diff --git a/ush/templates/diag_table.FV3_GFS_v16beta b/ush/templates/diag_table.FV3_GFS_v16beta
@@ -1,5 +1,5 @@
-<YYYYMMDD>.<HH>Z.<CRES>.32bit.non-hydro.regional
-<YYYY> <MM> <DD> <HH> 0 0
+{{ starttime.strftime("%Y%m%d.%H") }}Z.{{ cres }}.32bit.non-hydro.regional
+{{ starttime.strftime("%Y %m %d %H %M %S") }}
 
 "grid_spec",              -1,  "months",  1, "days",  "time"
 "atmos_4xdaily",           6,  "hours",   1, "days",  "time"

diff --git a/ush/templates/diag_table.FV3_GSD_SAR b/ush/templates/diag_table.FV3_GSD_SAR
@@ -1,5 +1,5 @@
-<YYYYMMDD>.<HH>Z.<CRES>.32bit.non-hydro.regional
-<YYYY> <MM> <DD> <HH> 0 0
+{{ starttime.strftime("%Y%m%d.%H") }}Z.{{ cres }}.32bit.non-hydro.regional
+{{ starttime.strftime("%Y %m %d %H %M %S") }}
 
 "grid_spec",              -1,  "months",  1, "days",  "time"
 "atmos_static",           -1,  "hours",   1, "hours", "time"

diff --git a/ush/templates/diag_table.FV3_GSD_SAR_v1 b/ush/templates/diag_table.FV3_GSD_SAR_v1
@@ -1,5 +1,5 @@
-<YYYYMMDD>.<HH>Z.<CRES>.32bit.non-hydro.regional
-<YYYY> <MM> <DD> <HH> 0 0
+{{ starttime.strftime("%Y%m%d.%H") }}Z.{{ cres }}.32bit.non-hydro.regional
+{{ starttime.strftime("%Y %m %d %H %M %S") }}
 
 "grid_spec",              -1,  "months",   1, "days",  "time"
 "atmos_static",           -1,  "hours",    1, "hours", "time"

diff --git a/ush/templates/diag_table.FV3_GSD_v0 b/ush/templates/diag_table.FV3_GSD_v0
@@ -1,5 +1,5 @@
-<YYYYMMDD>.<HH>Z.<CRES>.32bit.non-hydro.regional
-<YYYY> <MM> <DD> <HH> 0 0
+{{ starttime.strftime("%Y%m%d.%H") }}Z.{{ cres }}.32bit.non-hydro.regional
+{{ starttime.strftime("%Y %m %d %H %M %S") }}
 
 "grid_spec",              -1,  "months",  1, "days",  "time"
 "atmos_static",           -1,  "hours",   1, "hours", "time"

diff --git a/ush/templates/diag_table.FV3_RRFS_v0 b/ush/templates/diag_table.FV3_RRFS_v0
@@ -1,5 +1,5 @@
-<YYYYMMDD>.<HH>Z.<CRES>.32bit.non-hydro.regional
-<YYYY> <MM> <DD> <HH> 0 0
+{{ starttime.strftime("%Y%m%d.%H") }}Z.{{ cres }}.32bit.non-hydro.regional
+{{ starttime.strftime("%Y %m %d %H %M %S") }}
 
 "grid_spec",              -1,  "months",   1, "days",  "time"
 "atmos_static",           -1,  "hours",    1, "hours", "time"
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@

		system "ncar_pylib /glade/p/ral/jntp/UFS_CAM/ncar_pylib_20200427"