[develop] Add plotting scripts to the workflow. (#482)

* Add level for data: section indicating ics_lbcs.

* Add the NaturalEarth shape files.

* Add plotting to the workflow.

* Fix some deprecation warnings.

* Don't plot 500mb vars if it is not available.

* Add modulefiles for plot_allvars task.

* Add a test case for plotting graphics.

* Add diff plotting.

* Remove ush/Python folder.

* Turn off plotting by default.

* Bug fix plot_diff call.

* Add missing diff plot script.

* Make plotting work in NCO mode.

* Avoid positional arguments in the plotting scripts.
Some bug fixes.

* Make COMOUT_REF a template to compare multiple dates and cycles correctly.

* Use logging to capture output from plot scripts in log files.

* Turn off debug level, too much information.

* Ignore warnings in plotting.

* Bug fix diff plotter: mismatch in number of ticks, and ticklabels.

* Increase wallclock time, bugfix orion FIXshp.

* Add some default values to config.community/nco for convenience.

jobs/JREGIONAL_PLOT_ALLVARS

@@ -0,0 +1,112 @@
+#!/bin/bash
+
+#
+#-----------------------------------------------------------------------
+#
+# Source the variable definitions file and the bash utility functions.
+#
+#-----------------------------------------------------------------------
+#
+. $USHdir/source_util_funcs.sh
+source_config_for_task "task_plot_allvars|task_run_fcst" ${GLOBAL_VAR_DEFNS_FP}
+. $USHdir/job_preamble.sh
+#
+#-----------------------------------------------------------------------
+#
+# Save current shell options (in a global array).  Then set new options
+# for this script/function.
+#
+#-----------------------------------------------------------------------
+#
+{ save_shell_opts; . $USHdir/preamble.sh; } > /dev/null 2>&1
+#
+#-----------------------------------------------------------------------
+#
+# Get the full path to the file in which this script/function is located 
+# (scrfunc_fp), the name of that file (scrfunc_fn), and the directory in
+# which the file is located (scrfunc_dir).
+#
+#-----------------------------------------------------------------------
+#
+scrfunc_fp=$( $READLINK -f "${BASH_SOURCE[0]}" )
+scrfunc_fn=$( basename "${scrfunc_fp}" )
+scrfunc_dir=$( dirname "${scrfunc_fp}" )
+#
+#-----------------------------------------------------------------------
+#
+# Print message indicating entry into script.
+#
+#-----------------------------------------------------------------------
+#
+print_info_msg "
+========================================================================
+Entering script:  \"${scrfunc_fn}\"
+In directory:     \"${scrfunc_dir}\"
+
+This is the J-job script for the plotting task
+========================================================================"
+#
+#-----------------------------------------------------------------------
+#
+# Set grid name and COMOUT locations.
+#
+#-----------------------------------------------------------------------
+#
+GRID_NAME=${PREDEF_GRID_NAME:-$EXPT_SUBDIR}
+if [ "${RUN_ENVIR}" != "nco" ]; then
+  export COMOUT="${COMOUT}${SLASH_ENSMEM_SUBDIR}/postprd"
+fi
+# if COMOUT_REF is templatized with $PDY and $cyc, evaluate it
+# This is necessary to compare multiple cycles correctly
+COMOUT_REF=$(eval echo ${COMOUT_REF})
+#
+#-----------------------------------------------------------------------
+#
+# Call the ex-script for this J-job and pass to it the necessary variables.
+#
+#-----------------------------------------------------------------------
+#
+
+# plot all variables
+$SCRIPTSdir/exregional_plot_allvars.py \
+           --cycle ${CDATE} \
+           --start ${PLOT_FCST_START} \
+           --end ${PLOT_FCST_END:-$FCST_LEN_HRS} \
+           --inc ${PLOT_FCST_INC:-1} \
+           --comout ${COMOUT} \
+           --cartopy-dir ${FIXshp} \
+           --domain ${GRID_NAME} || \
+print_err_msg_exit "\
+Call to ex-script corresponding to J-job \"${scrfunc_fn}\" failed."
+
+# plot all variables diff with baseline
+if [ ! -z $COMOUT_REF ]; then
+  $SCRIPTSdir/exregional_plot_allvars_diff.py \
+           --cycle ${CDATE} \
+           --start ${PLOT_FCST_START} \
+           --end ${PLOT_FCST_END:-$FCST_LEN_HRS} \
+           --inc ${PLOT_FCST_INC:-1} \
+           --comout-1 ${COMOUT} \
+           --comout-2 ${COMOUT_REF} \
+           --cartopy-dir ${FIXshp} \
+           --domain ${GRID_NAME} || \
+  print_err_msg_exit "\
+  Call to ex-script corresponding to J-job \"${scrfunc_fn}\" failed."
+fi
+#
+#-----------------------------------------------------------------------
+#
+# Run job postamble.
+#
+#-----------------------------------------------------------------------
+#
+job_postamble
+#
+#-----------------------------------------------------------------------
+#
+# Restore the shell options saved at the beginning of this script/function.
+#
+#-----------------------------------------------------------------------
+#
+{ restore_shell_opts; } > /dev/null 2>&1
+

modulefiles/tasks/cheyenne/plot_allvars.local.lua

@@ -0,0 +1 @@
+load("miniconda_regional_workflow")

modulefiles/tasks/gaea/plot_allvars.local.lua

@@ -0,0 +1 @@
+load("miniconda_regional_workflow")

modulefiles/tasks/hera/plot_allvars.local.lua

@@ -0,0 +1 @@
+load("miniconda_regional_workflow")

modulefiles/tasks/jet/plot_allvars.local.lua

@@ -0,0 +1 @@
+load("miniconda_regional_workflow")

modulefiles/tasks/noaacloud/plot_allvars.local.lua

@@ -0,0 +1 @@
+load("miniconda_regional_workflow")

modulefiles/tasks/orion/plot_allvars.local.lua

@@ -0,0 +1 @@
+load("miniconda_regional_workflow")

modulefiles/tasks/wcoss2/plot_allvars.local.lua

@@ -0,0 +1 @@
+load("python_regional_workflow")

parm/FV3LAM_wflow.xml

@@ -67,6 +67,7 @@ Workflow task names.
 <!ENTITY VX_ENSPOINT_TN            "{{ vx_enspoint_tn }}">
 <!ENTITY VX_ENSPOINT_MEAN_TN       "{{ vx_enspoint_mean_tn }}">
 <!ENTITY VX_ENSPOINT_PROB_TN       "{{ vx_enspoint_prob_tn }}">
+<!ENTITY PLOT_ALLVARS_TN           "{{ plot_allvars_tn }}">
 
 <!--
 Flags that specify whether to run the preprocessing and/or verification tasks.
@@ -755,6 +756,44 @@ the <task> tag to be identical to the ones above for other output times.
   {%- endif %}
 {%- endif %}
 
+{%- if run_task_plot_allvars %}
+<!--
+************************************************************************
+************************************************************************
+-->
+  <task name="&PLOT_ALLVARS_TN;" cycledefs="forecast" maxtries="{{ maxtries_plot_allvars }}">
+
+    &RSRV_DEFAULT;
+    <command>&LOAD_MODULES_RUN_TASK_FP; "&PLOT_ALLVARS_TN;" "&JOBSdir;/JREGIONAL_PLOT_ALLVARS"</command>
+    <nodes>{{ nnodes_plot_allvars }}:ppn={{ ppn_plot_allvars }}</nodes>
+    <walltime>{{ wtime_plot_allvars }}</walltime>
+    <nodesize>&NCORES_PER_NODE;</nodesize>
+  {%- if machine not in ["WCOSS2"] %}
+    <native>&SCHED_NATIVE_CMD;</native>
+  {%- endif %}
+    <jobname>&PLOT_ALLVARS_TN;</jobname>
+    <join>&LOGDIR;/&PLOT_ALLVARS_TN;<cyclestr>_@Y@m@d@H</cyclestr>&LOGEXT;</join>
+
+    <envar><name>GLOBAL_VAR_DEFNS_FP</name><value>&GLOBAL_VAR_DEFNS_FP;</value></envar>
+    <envar><name>USHdir</name><value>&USHdir;</value></envar>
+    <envar><name>PDY</name><value><cyclestr>@Y@m@d</cyclestr></value></envar>
+    <envar><name>cyc</name><value><cyclestr>@H</cyclestr></value></envar>
+    <envar><name>subcyc</name><value><cyclestr>@M</cyclestr></value></envar>
+    <envar><name>LOGDIR</name><value>&LOGDIR;</value></envar>
+    <envar><name>SLASH_ENSMEM_SUBDIR</name><value><cyclestr>{{ slash_ensmem_subdir }}</cyclestr></value></envar>
+    <envar><name>ENSMEM_INDX</name><value><cyclestr>#{{ ensmem_indx_name }}#</cyclestr></value></envar>
+
+    <dependency>
+        {%- if write_dopost %}
+      <taskdep task="&RUN_FCST_TN;{{ uscore_ensmem_name }}"/>
+        {%- else %}
+      <metataskdep metatask="&RUN_POST_TN;{{ uscore_ensmem_name }}"/>
+        {%- endif %}
+    </dependency>
+
+  </task>
+{%- endif %}
+
 {%- if run_task_get_obs_ccpa %}
 <!--
 ************************************************************************