From c8aa98316412e8ce4dabbfc0bb1f7c90d348e38a Mon Sep 17 00:00:00 2001
From: shixuan zhang <shixuan.zhang@pnnl.gov>
Date: Thu, 30 Apr 2026 17:22:26 -0700
Subject: [PATCH 01/21] Claude-Augment enhancement on zppy-pcmdi

zppy/pcmdi_diags.py:
- Replace print() with logger.debug() for prefix logging
- Fix break -> continue in commented-out enso skip block
- Add missing else branch with ValueError in add_pcmdi_dependencies
  to prevent UnboundLocalError on invalid run_type

zppy/templates/pcmdi_diags.bash:
- Move $? check before rm in create_links_acyc_climo so ncap2
  failures are caught instead of silently swallowed
- Fix .nc file filter from regex =~ ".nc" to glob != *.nc in
  create_links_acyc_climo_obs and create_links_ts_obs
- Remove unused dofm variable from create_links_acyc_climo and
  create_links_acyc_climo_obs
- Fix double space before --enso_groups in zi-pcmdi-enso command
- Fix Jinja2 spacing: {{var}} -> {{ var }} for model_tableID,
  save_all_data, enso_viewer, enso_vars, enso_years

zppy/defaults/default.ini:
- Fix enso_vars default: hflx -> hfls (correct CMIP variable name)
---
 zppy/defaults/default.ini       |  2 +-
 zppy/pcmdi_diags.py             | 14 ++++++++------
 zppy/templates/pcmdi_diags.bash | 18 ++++++++----------
 3 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/zppy/defaults/default.ini b/zppy/defaults/default.ini
index 948fadbb..d434f1d7 100755
--- a/zppy/defaults/default.ini
+++ b/zppy/defaults/default.ini
@@ -647,7 +647,7 @@ enso_groups = string(default="ENSO_perf,ENSO_proc,ENSO_tel")
 # Specify these for the enso subtask AND the synthetic_plots subtask
 ###########################################################################################
 # enso: vars = "psl,pr,prsn,ts,tas,tauu,tauv,hflx,hfss,rlds,rsds,rlus,rlut,rsdt"
-enso_vars = string(default="psl,pr,prsn,ts,tas,tauu,tauv,hflx,hfss,rlds,rsds,rlus,rlut,rsdt")
+enso_vars = string(default="psl,pr,prsn,ts,tas,tauu,tauv,hfls,hfss,rlds,rsds,rlus,rlut,rsdt")
 ###########################################################################################
 # Specify these for the synthetic_plots subtask
 ###########################################################################################
diff --git a/zppy/pcmdi_diags.py b/zppy/pcmdi_diags.py
index 4d109bee..ece99ab9 100644
--- a/zppy/pcmdi_diags.py
+++ b/zppy/pcmdi_diags.py
@@ -52,11 +52,11 @@ def pcmdi_diags(config, script_dir, existing_bundles, job_ids_file):
     for c in tasks:
         dependencies: List[str] = []
         define_current_set(c)
-        if c["current_set"] == "enso":
-            logger.warning(
-                "The 'enso' set is not yet supported in PCMDI Diags. Skipping launching of associated jobs."
-            )
-            break  # Skip this task
+        #if c["current_set"] == "enso":
+        #    logger.warning(
+        #        "The 'enso' set is not yet supported in PCMDI Diags. Skipping launching of associated jobs."
+        #    )
+        #    continue  # Skip this task
         c["sub"] = get_value_from_parameter(
             c, "subsection", "sub", ParameterInferenceType.SECTION_INFERENCE
         )
@@ -89,7 +89,7 @@ def pcmdi_diags(config, script_dir, existing_bundles, job_ids_file):
 
             if c["current_set"] != "synthetic_plots":
                 check_and_define_parameters(c)
-                print(c["prefix"])
+                logger.debug(c["prefix"])
                 define_relevant_years(c)
             else:
                 prefix = f"pcmdi_diags_{c['sub']}_{c['run_type']}"
@@ -370,6 +370,8 @@ def add_pcmdi_dependencies(
         status_suffix = f"_{c['year1']:04d}-{c['year2']:04d}"
     elif c["run_type"] == "model_vs_model":
         status_suffix = f"_{c['year1']:04d}-{c['year2']:04d}_vs_{c['ref_year1']:04d}-{c['ref_year2']:04d}"
+    else:
+        raise ValueError(f"Invalid run_type={c['run_type']}")
 
     if c["clim_viewer"]:
         status_file = os.path.join(
diff --git a/zppy/templates/pcmdi_diags.bash b/zppy/templates/pcmdi_diags.bash
index a049b5e9..e2678ee1 100755
--- a/zppy/templates/pcmdi_diags.bash
+++ b/zppy/templates/pcmdi_diags.bash
@@ -160,7 +160,6 @@ create_links_acyc_climo() {
   local script_dir="{{ scriptDir }}"
   local prefix="{{ prefix }}"
   local ts_step="{{ ts_num_years }}"
-  local dofm=(15.5 45 74.5 105 125.5 166 196.5 227.5 258 288.5 319 349.5)
 
   for v in ${variables//,/ }; do
     > "${v}_files.txt"  # Start fresh
@@ -194,13 +193,13 @@ create_links_acyc_climo() {
     local cmdfix5='time@bounds="time_bnds"'
     run_nco ncap2 -O -h -s "${cmdfix1};${cmdfix2};${cmdfix3};${cmdfix4};${cmdfix5}" "${combined_name}" "${combined_name}"
 
-    rm -vf "${v}_clm_"*.nc
-
     if [[ $? -ne 0 ]]; then
       cd "${script_dir}" || exit
       echo "ERROR (${error_num})" > "${prefix}.status"
       exit "${error_num}"
     fi
+
+    rm -vf "${v}_clm_"*.nc
   done
 
   if [ -z "$( ls . )" ]; then
@@ -220,7 +219,6 @@ create_links_acyc_climo_obs() {
 
   local script_dir="{{ scriptDir }}"
   local prefix="{{ prefix }}"
-  local dofm=(15.5 45 74.5 105 125.5 166 196.5 227.5 258 288.5 319 349.5)
 
   echo "create_links_acyc_climo_obs: linking from ${ts_dir_source} to ${ts_dir_destination}"
 
@@ -234,7 +232,7 @@ create_links_acyc_climo_obs() {
     local ttag tmp_file MM combined_name
 
     fname=$(basename "${file}")
-    if [[ ! ${fname} =~ ".nc" ]]; then
+    if [[ ${fname} != *.nc ]]; then
       # Skip non-.nc files
       continue
     fi
@@ -412,7 +410,7 @@ create_links_ts_obs() {
   for file in ${ts_dir_source}/*; do
     fname=$(basename "$file")
     echo "create_links_ts_obs: checking if nc file: ${fname}"
-    if [[ ! ${fname} =~ ".nc" ]]; then
+    if [[ ${fname} != *.nc ]]; then
       # Skip non-.nc files
       continue
     fi
@@ -876,7 +874,7 @@ source_dirs="--climo_ts_dir_primary ${ts_dir_primary} --climo_ts_dir_ref ${ts_di
 # So, it's a good idea to make sure they can't be (or at least are unlikely to be) empty.
 # run_type == "model_vs_obs" only: obs_sets (default value is NOT "")
 # run_type == "model_vs_model" only: model_name_ref, tableID_ref (default values are NOT "")
-core_parameters="--num_workers {{ num_workers }} --multiprocessing {{ multiprocessing }} --subsection {{ subsection }} ${source_dirs} --model_name ${model_name} --model_tableID {{model_tableID }} --figure_format {{ figure_format }}  --run_type {{ run_type }} --obs_sets {{ obs_sets }} --model_name_ref ${model_name_ref} --vars ${source_vars} --tableID_ref ${tableID_ref} --generate_sftlf {{ generate_sftlf }} --case_id ${case_id} --results_dir ${results_dir} --debug ${debug,,}"
+core_parameters="--num_workers {{ num_workers }} --multiprocessing {{ multiprocessing }} --subsection {{ subsection }} ${source_dirs} --model_name ${model_name} --model_tableID {{ model_tableID }} --figure_format {{ figure_format }} --run_type {{ run_type }} --obs_sets {{ obs_sets }} --model_name_ref ${model_name_ref} --vars ${source_vars} --tableID_ref ${tableID_ref} --generate_sftlf {{ generate_sftlf }} --case_id ${case_id} --results_dir ${results_dir} --debug ${debug,,}"
 {% endif %}
 
 {% if current_set == "mean_climate" %}
@@ -891,7 +889,7 @@ var_modes={{ movc_modes }}
 command="zi-pcmdi-variability-modes ${core_parameters} --var_modes ${var_modes}"
 {% endif %}
 {% if current_set == "enso" %}
-command="zi-pcmdi-enso ${core_parameters}  --enso_groups {{ enso_groups }}"
+command="zi-pcmdi-enso ${core_parameters} --enso_groups {{ enso_groups }}"
 {% endif %}
 {% if current_set == "synthetic_plots" %}
 
@@ -914,7 +912,7 @@ echo "Done checking. There should be a list of files above, if they exist."
 {% endif %}
 
 #add command for enso viewer
-enso_keys="--enso_viewer {{enso_viewer}} --cmip_enso_dir {{ cmip_enso_dir }} --cmip_enso_set {{ cmip_enso_set }} --enso_vars {{enso_vars}} --enso_years {{enso_years}}"
+enso_keys="--enso_viewer {{ enso_viewer }} --cmip_enso_dir {{ cmip_enso_dir }} --cmip_enso_set {{ cmip_enso_set }} --enso_vars {{ enso_vars }} --enso_years {{ enso_years }}"
 {% if enso_viewer %}
 echo "Checking if var_mode_*.json files exist in variability_modes_dir:"
 enso_dir=${web_dir}/model_vs_obs/metrics_data/enso_metric/*
@@ -922,7 +920,7 @@ find ${enso_dir} -name "*.${case_id}*.json"
 echo "Done checking. There should be a list of files above, if they exist."
 {% endif %}
 
-command="zi-pcmdi-synthetic-plots --synthetic_sets {{ synthetic_sets }} --figure_format {{ figure_format }} --www ${www} --results_dir ${results_dir} --case {{ case }} --model_name {{ model_name }} --model_tableID {{model_tableID }} --web_dir=${web_dir} --pcmdi_webtitle {{ pcmdi_webtitle }} --pcmdi_version {{ pcmdi_version }} --run_type ${run_type} --pcmdi_external_prefix {{ diagnostics_base_path }} --pcmdi_viewer_template {{ pcmdi_viewer_template }} --save_all_data {{save_all_data}} ${clim_keys} ${movs_keys} ${enso_keys} --debug ${debug,,}"
+command="zi-pcmdi-synthetic-plots --synthetic_sets {{ synthetic_sets }} --figure_format {{ figure_format }} --www ${www} --results_dir ${results_dir} --case {{ case }} --model_name {{ model_name }} --model_tableID {{ model_tableID }} --web_dir=${web_dir} --pcmdi_webtitle {{ pcmdi_webtitle }} --pcmdi_version {{ pcmdi_version }} --run_type ${run_type} --pcmdi_external_prefix {{ diagnostics_base_path }} --pcmdi_viewer_template {{ pcmdi_viewer_template }} --save_all_data {{ save_all_data }} ${clim_keys} ${movs_keys} ${enso_keys} --debug ${debug,,}"
 
 {% endif %}
 

From 4220184f6e254b022132446a08abd888c2f43d94 Mon Sep 17 00:00:00 2001
From: shixuan zhang <shixuan.zhang@pnnl.gov>
Date: Thu, 30 Apr 2026 18:24:10 -0700
Subject: [PATCH 02/21] Claude-augument enhancement: fix time precision and
 bnds dimension warnings

zppy/templates/pcmdi_diags.bash:
- Normalize time and time_bnds to the nearest second after ncrcat
  subsetting in create_links_ts and create_links_ts_obs to prevent
  floating-point precision artifacts causing cftime to decode boundary
  values as second=60 (e.g. 2015-12-31 23:59:60 instead of 2016-01-01)
- Guard defdim("bnds",2) with if(!exists("bnds")) in all three ncap2
  call sites to suppress spurious warnings when the bnds dimension is
  already present in the input file
---
 zppy/templates/pcmdi_diags.bash | 30 +++++++++++++++++++++++++-----
 1 file changed, 25 insertions(+), 5 deletions(-)

diff --git a/zppy/templates/pcmdi_diags.bash b/zppy/templates/pcmdi_diags.bash
index e2678ee1..1bad9fbc 100755
--- a/zppy/templates/pcmdi_diags.bash
+++ b/zppy/templates/pcmdi_diags.bash
@@ -297,7 +297,7 @@ create_links_acyc_climo_obs() {
       exit "$((error_num + 1))"
     fi
 
-    local cmdfix4='defdim("bnds",2)'
+    local cmdfix4='if(!exists("bnds")) defdim("bnds",2)'
     local cmdfix5='time_bnds=make_bounds(time,$bnds,"time_bnds")'
     local cmdfix6='time_bnds@units=time@units'
     local cmdfix7='time_bnds@calendar=time@calendar'
@@ -365,12 +365,19 @@ create_links_ts() {
         run_nco ncatted -a calendar,time,o,c,"standard" "${combined_name}"
       fi
 
+      # Normalize time to the nearest second to prevent floating-point precision
+      # artifacts (e.g., cftime decoding a value as second=60 instead of
+      # second=0 of the next day) that arise from ncrcat time subsetting.
+      local cmdfix_t='time=double(round(time*86400.0)/86400.0)'
+      run_nco ncap2 -O -h -s "${cmdfix_t}" "${combined_name}" "${combined_name}"
+
       # Add time bounds
-      local cmdfix1='defdim("bnds",2)'
+      local cmdfix1='if(!exists("bnds")) defdim("bnds",2)'
       local cmdfix2='time_bnds=make_bounds(time,$bnds,"time_bnds")'
       local cmdfix3='time_bnds@units=time@units'
       local cmdfix4='time_bnds@calendar=time@calendar'
-      run_nco ncap2 -O -h -s "${cmdfix1};${cmdfix2};${cmdfix3};${cmdfix4}" "${combined_name}" "${combined_name}"
+      local cmdfix5='time_bnds=double(round(time_bnds*86400.0)/86400.0)'
+      run_nco ncap2 -O -h -s "${cmdfix1};${cmdfix2};${cmdfix3};${cmdfix4};${cmdfix5}" "${combined_name}" "${combined_name}"
 
       if [[ $? -ne 0 ]]; then
         cd "${script_dir}" || exit
@@ -459,12 +466,25 @@ create_links_ts_obs() {
       echo "ncatted successful"
     fi
 
+    # Normalize time to the nearest second to prevent floating-point precision
+    # artifacts (e.g., cftime decoding a value as second=60 instead of
+    # second=0 of the next day) that arise from ncrcat time subsetting.
+    local cmdfix_t='time=double(round(time*86400.0)/86400.0)'
+    run_nco ncap2 -O -h -s "${cmdfix_t}" "${combined_name}" "${combined_name}"
+    if [[ $? -ne 0 ]]; then
+      cd "${script_dir}" || exit
+      echo "ERROR (${error_num})" > "${prefix}.status"
+      exit "${error_num}"
+    fi
+    echo "time normalization successful"
+
     # Add time bounds
-    local cmdfix1='defdim("bnds",2)'
+    local cmdfix1='if(!exists("bnds")) defdim("bnds",2)'
     local cmdfix2='time_bnds=make_bounds(time,$bnds,"time_bnds")'
     local cmdfix3='time_bnds@units=time@units'
     local cmdfix4='time_bnds@calendar=time@calendar'
-    run_nco ncap2 -O -h -s "${cmdfix1};${cmdfix2};${cmdfix3};${cmdfix4}" "${combined_name}" "${combined_name}"
+    local cmdfix5='time_bnds=double(round(time_bnds*86400.0)/86400.0)'
+    run_nco ncap2 -O -h -s "${cmdfix1};${cmdfix2};${cmdfix3};${cmdfix4};${cmdfix5}" "${combined_name}" "${combined_name}"
     if [[ $? -ne 0 ]]; then
       cd "${script_dir}" || exit
       echo "ERROR (${error_num})" > "${prefix}.status"

From 7c0e1cf84274f675a3cda753242c72cc0fa43ddd Mon Sep 17 00:00:00 2001
From: shixuan zhang <shixuan.zhang@pnnl.gov>
Date: Sat, 2 May 2026 13:08:34 -0700
Subject: [PATCH 03/21] Rebase to latest main

---
 zppy/templates/pcmdi_diags.bash | 401 +++++++++++++++++++++++---------
 1 file changed, 289 insertions(+), 112 deletions(-)

diff --git a/zppy/templates/pcmdi_diags.bash b/zppy/templates/pcmdi_diags.bash
index 1bad9fbc..1bd053d6 100755
--- a/zppy/templates/pcmdi_diags.bash
+++ b/zppy/templates/pcmdi_diags.bash
@@ -18,11 +18,22 @@ export UCX_SHM_DEVICES=all # or not set UCX_NET_DEVICES at all
 # Make sure UVCDAT doesn't prompt us about anonymous logging
 export UVCDAT_ANONYMOUS_LOG=False
 
+# Script dir
+cd {{ scriptDir }}
+
+# Get jobid
+id=${SLURM_JOBID}
+
+# Update status file
+STARTTIME=$(date +%s)
+echo "RUNNING ${id}" > {{ prefix }}.status
+
 # Basic definitions
 case="{{ case }}"
 www="{{ www }}"
 run_type="{{ run_type }}"
 results_dir="{{ run_type }}"
+error_key=0
 
 {% if current_set != "synthetic_plots" %}
 
@@ -34,14 +45,9 @@ ref_y2={{ ref_year2 }}
 ref_start_yr={{ ref_start_yr }}
 ref_final_yr={{ ref_final_yr }}
 
-# Formatted versions
+# Formatted versions (analysis window only; ref formatted after refinement below)
 Y1="$(printf "%04d" ${y1})"
 Y2="$(printf "%04d" ${y2})"
-ref_Y1="$(printf "%04d" ${ref_y1})"
-ref_Y2="$(printf "%04d" ${ref_y2})"
-
-num_years=$((y2 - y1 + 1))
-ref_end_yr=$((ref_y1 + num_years - 1))
 
 # Keep originals for fallback
 orig_ref_y1=${ref_y1}
@@ -80,6 +86,10 @@ else
    fi
 fi
 
+# Format reference years after refinement
+ref_Y1="$(printf "%04d" ${ref_y1})"
+ref_Y2="$(printf "%04d" ${ref_y2})"
+
 {% if current_set == "mean_climate"%}
 source_vars="{{ clim_vars }}"
 {% elif current_set == "variability_modes_cpl"%}
@@ -124,7 +134,7 @@ case_id=v$(date '+%Y%m%d')
 {% endif %}
 
 # Create temporary workdir
-workdir=`mktemp -d tmp.{{ prefix }}.${id}.XXXX`
+workdir=$(mktemp -d tmp.{{ prefix }}.${id}.XXXX)
 cd ${workdir}
 
 # files for definition of regions for regional mean
@@ -149,7 +159,7 @@ create_links_acyc_climo() {
   local begin_year="$3"
   local end_year="$4"
   local name_key="$5"
-  local error_num="$6"
+  local error_num="$6" # Will use error_num +0,+1,+2
 
   echo "create_links_acyc_climo: linking from ${ts_dir_source} to ${ts_dir_destination}"
 
@@ -174,16 +184,51 @@ create_links_acyc_climo() {
     done
     shopt -u nullglob
 
+    if [[ ! -s "${v}_files.txt" ]]; then
+      echo "WARNING: No input files found for variable ${v}, skipping climatology. \
+            This variable may not have been processed or output by e3sm_to_cmip."
+      continue
+    fi
+
+    first_file=$(head -n 1 "${v}_files.txt")
+    if ! run_nco ncks -m "${first_file}" >/dev/null 2>&1; then
+      echo "WARNING: First file is not a valid NetCDF for ${v}: ${first_file}, skipping climatology. \
+            This variable may not have been processed or output by e3sm_to_cmip."
+      continue
+    fi
+
     # Derive monthly climatology files
     for month in $(seq 1 12); do
       local MM
       MM=$(printf "%02d" "${month}")
       run_nco ncra -O -h -F -d time,"${month}",,12 $(< "${v}_files.txt") "${v}_clm_${MM}.nc"
+      if [[ $? -ne 0 ]]; then
+        cd "${script_dir}" || exit
+        echo "ERROR ($((error_num + 1)))" > "${prefix}.status"
+        exit "$((error_num + 1))"
+      fi
     done
 
     # Combine to form full annual cycle file
     local combined_name="${name_key}.${v}.${begin_year}01-${end_year}12.AC.${case_id}.nc"
-    run_nco ncrcat -O -d time,0, "${v}_clm_"*.nc "${combined_name}"
+    run_nco ncrcat -O -h -d time,0, "${v}_clm_"*.nc "${combined_name}"
+    if [[ $? -ne 0 ]]; then
+      cd "${script_dir}" || exit
+      echo "ERROR ($((error_num + 2)))" > "${prefix}.status"
+      exit "$((error_num + 2))"
+    fi
+
+    # Add bnds dimension if missing
+    if ! run_nco ncks -m "${combined_name}" | grep -q "bnds = 2"; then
+      echo "Adding missing bnds dimension..."
+      run_nco ncap2 -O -h -s 'defdim("bnds",2)' \
+        "${combined_name}" "${combined_name}"
+      if [[ $? -ne 0 ]]; then
+        cd "${script_dir}" || exit
+	echo "ERROR ($((error_num + 3)))" > "${prefix}.status"
+        exit "$((error_num + 3))"
+      fi
+    fi
 
     # Adjust time metadata for PCMDI diagnostics
     local cmdfix1='time[time]={15.5, 45, 74.5, 105, 125.5, 166, 196.5, 227.5, 258, 288.5,319, 349.5}'
@@ -191,19 +236,25 @@ create_links_acyc_climo() {
     local cmdfix3='time@units="days since 1850-01-01 00:00:00"'
     local cmdfix4='time@calendar="noleap"'
     local cmdfix5='time@bounds="time_bnds"'
-    run_nco ncap2 -O -h -s "${cmdfix1};${cmdfix2};${cmdfix3};${cmdfix4};${cmdfix5}" "${combined_name}" "${combined_name}"
+    local cmdfix6='time_bnds@units=time@units'
+    local cmdfix7='time_bnds@calendar=time@calendar'
+    run_nco ncap2 -O -h -s "${cmdfix1};${cmdfix2};${cmdfix3};${cmdfix4};${cmdfix5};${cmdfix6};${cmdfix7}" \
+      "${combined_name}" "${combined_name}"
 
     if [[ $? -ne 0 ]]; then
       cd "${script_dir}" || exit
-      echo "ERROR (${error_num})" > "${prefix}.status"
-      exit "${error_num}"
+      echo "ERROR ($((error_num + 4)))" > "${prefix}.status"
+      exit "$((error_num + 4))"
     fi
 
     rm -vf "${v}_clm_"*.nc
   done
 
-  if [ -z "$( ls . )" ]; then
+  if [ -z "$(ls ./*.nc 2>/dev/null)" ]; then
     echo "create_links_acyc_climo: ${ts_dir_destination} was not updated!"
+    cd "${script_dir}" || exit
+    echo "ERROR (${error_num})" > "${prefix}.status"
+    exit "${error_num}"
   fi
 
   cd ..
@@ -225,7 +276,7 @@ create_links_acyc_climo_obs() {
   mkdir -p "${ts_dir_destination}"
   cd "${ts_dir_destination}" || exit
 
-  for file in ${ts_dir_source}/*; do
+  for file in "${ts_dir_source}"/*; do
     local fname
     local YYYYS YYYYE
     local SUBSTR
@@ -246,31 +297,47 @@ create_links_acyc_climo_obs() {
       continue
     fi
 
-    # Clip to specified year range
-    if [[ ${YYYYS} -lt ${begin_year} ]]; then YYYYS=${begin_year}; fi
-    if [[ ${YYYYE} -gt ${end_year} ]]; then YYYYE=${end_year}; fi
+    # Clip to specified year range if no overlap use full range covered by file
+    orig_YYYYS="${YYYYS}"
+    file_start_year=${YYYYS:0:4}
+    file_end_year=${YYYYE:0:4}
+
+    if (( file_end_year < begin_year || file_start_year > end_year )); then
+      echo "WARNING: ${fname} does not overlap requested range ${begin_year}-${end_year}; using file range ${file_start_year}-${file_end_year}."
+      YYYYS="${file_start_year}"
+      YYYYE="${file_end_year}"
+    else
+      # Clip to specified year range
+      (( file_start_year < begin_year )) && YYYYS="${begin_year}" || YYYYS="${file_start_year}"
+      (( file_end_year > end_year )) && YYYYE="${end_year}" || YYYYE="${file_end_year}"
+    fi
 
     # Extract prefix before the date range (removes from .${YYYYS} or -${YYYYS})
-    SUBSTR="${fname%%[._-]${YYYYS}*}"
+    SUBSTR="${fname%%[._-]${orig_YYYYS}*}"
 
     ttag="$(printf "%04d" "${YYYYS}")01-$(printf "%04d" "${YYYYE}")12"
     tmp_file="tmp_combine_${ttag}.nc"
 
-    run_nco ncrcat -O -d time,"${YYYYS}-01-01","${YYYYE}-12-31" "${file}" "${tmp_file}"
+    run_nco ncrcat -O -h -d time,"${YYYYS}-01-01","${YYYYE}-12-31" "${file}" "${tmp_file}"
     if [[ $? -ne 0 ]]; then
-      echo "WARNING: ncrcat failed for ${fname} (date range ${YYYYS}-${YYYYE}), skipping."
+      echo "ERROR: ncrcat failed for ${fname} (date range ${YYYYS}-${YYYYE})"
       rm -f "${tmp_file}"
-      continue
+      cd "${script_dir}" || exit
+      echo "ERROR ($((error_num + 1)))" > "${prefix}.status"
+      exit "$((error_num + 1))"
     fi
 
     # Derive monthly climatology
     for month in $(seq 1 12); do
+      local MM
       MM=$(printf "%02d" ${month})
       run_nco ncra -O -h -F -d time,"${month}",,12 "${tmp_file}" "tmp_clm_${MM}.nc"
       if [[ $? -ne 0 ]]; then
-        echo "WARNING: ncra failed for ${fname} month ${MM}, skipping file."
+        echo "ERROR: ncra failed for ${fname} month ${MM}."
         rm -f tmp_clm_*.nc "${tmp_file}"
-        break  # exit the month loop
+        cd "${script_dir}" || exit
+        echo "ERROR ($((error_num + 2)))" > "${prefix}.status"
+        exit "$((error_num + 2))"
       fi
     done
     # If any month failed, the tmp_clm files were cleaned up — skip to next file
@@ -279,11 +346,11 @@ create_links_acyc_climo_obs() {
     fi
 
     combined_name="${SUBSTR}.${ttag}.AC.${case_id}.nc"
-    run_nco ncrcat -O tmp_clm_*.nc "${combined_name}"
+    run_nco ncrcat -O -h tmp_clm_*.nc "${combined_name}"
     if [[ $? -ne 0 ]]; then
       cd "${script_dir}" || exit
-      echo "ERROR (${error_num})" > "${prefix}.status"
-      exit "${error_num}"
+      echo "ERROR ($((error_num + 3)))" > "${prefix}.status"
+      exit "$((error_num + 3))"
     fi
 
     # Adjust time metadata
@@ -293,19 +360,31 @@ create_links_acyc_climo_obs() {
     run_nco ncap2 -O -h -s "${cmdfix1};${cmdfix2};${cmdfix3}" "${combined_name}" "${combined_name}"
     if [[ $? -ne 0 ]]; then
       cd "${script_dir}" || exit
-      echo "ERROR (${error_num})" > "${prefix}.status"
-      exit "$((error_num + 1))"
+      echo "ERROR ($((error_num + 4)))" > "${prefix}.status"
+      exit "$((error_num + 4))"
     fi
 
-    local cmdfix4='if(!exists("bnds")) defdim("bnds",2)'
-    local cmdfix5='time_bnds=make_bounds(time,$bnds,"time_bnds")'
-    local cmdfix6='time_bnds@units=time@units'
-    local cmdfix7='time_bnds@calendar=time@calendar'
+    # Add bnds dimension if missing
+    if ! run_nco ncks -m "${combined_name}" | grep -q "bnds = 2"; then
+      echo "Adding missing bnds dimension..."
+      run_nco ncap2 -O -h -s 'defdim("bnds",2)' \
+        "${combined_name}" "${combined_name}"
+      if [[ $? -ne 0 ]]; then
+        cd "${script_dir}" || exit
+        echo "ERROR ($((error_num + 5)))" > "${prefix}.status"
+        exit "$((error_num + 5))"
+      fi
+    fi
+
+    local cmdfix4='time_bnds=make_bounds(time,$bnds,"time_bnds")'
+    local cmdfix5='time_bnds@units=time@units'
+    local cmdfix6='time_bnds@calendar=time@calendar'
+    local cmdfix7='time@bounds="time_bnds"'
     run_nco ncap2 -O -h -s "${cmdfix4};${cmdfix5};${cmdfix6};${cmdfix7}" "${combined_name}" "${combined_name}"
     if [[ $? -ne 0 ]]; then
       cd "${script_dir}" || exit
-      echo "ERROR (${error_num})" > "${prefix}.status"
-      exit "$((error_num + 2))"
+      echo "ERROR ($((error_num + 6)))" > "${prefix}.status"
+      exit "$((error_num + 6))"
     fi
 
     rm -vf tmp_*.nc
@@ -313,6 +392,9 @@ create_links_acyc_climo_obs() {
 
   if [ -z "$( ls . )" ]; then
     echo "create_links_acyc_climo_obs: ${ts_dir_destination} was not updated!"
+    cd "${script_dir}" || exit
+    echo "ERROR (${error_num})" > "${prefix}.status"
+    exit "${error_num}"
   fi
 
   cd ..
@@ -357,40 +439,80 @@ create_links_ts() {
 
     combined_name="${subname}.${v}.${begin_year}01-${end_year}12.nc"
     if [[ -s "${v}_files.txt" ]]; then
-      run_nco ncrcat -O -v "${v}" -d time,"${begin_year}-01-01","${end_year}-12-31" $(< "${v}_files.txt") "${combined_name}"
+      # Ensure input files have time calendar before string-based subsetting
+      while IFS= read -r file; do
+        [[ -z "${file}" ]] && continue
+
+        if ! run_nco ncks -m "${file}" | grep -q "time:calendar"; then
+          echo "Adding missing calendar attribute to input time: ${file}"
+          run_nco ncatted -O -h -a calendar,time,o,c,"standard" "${file}"
+          if [[ $? -ne 0 ]]; then
+            cd "${script_dir}" || exit
+	    echo "ERROR ($((error_num + 1)))" > "${prefix}.status"
+	    exit "$((error_num + 1))"
+          fi
+        fi
+      done < "${v}_files.txt"
+
+      # Extract subset of time series
+      run_nco ncrcat -O -h \
+        -v "${v},time" \
+        -d time,"${begin_year}-01-01","${end_year}-12-31" $(< "${v}_files.txt") "${combined_name}"
 
-      # Add calendar attribute if missing
-      if ! run_nco ncks -m "${combined_name}" | grep -q "calendar"; then
-        echo "Adding missing calendar attribute to time..."
-        run_nco ncatted -a calendar,time,o,c,"standard" "${combined_name}"
+      if [[ $? -ne 0 ]]; then
+        cd "${script_dir}" || exit
+        echo "ERROR ($((error_num + 2)))" > "${prefix}.status"
+	exit "$((error_num + 2))"
+      fi
+      echo "ncrcat subset successful"
+
+      # Add bnds dimension if missing
+      if ! run_nco ncks -m "${combined_name}" | grep -q "bnds = 2"; then
+        echo "Adding missing bnds dimension..."
+        run_nco ncap2 -O -h -s 'defdim("bnds",2)' "${combined_name}" "${combined_name}"
+        if [[ $? -ne 0 ]]; then
+          cd "${script_dir}" || exit
+          echo "ERROR ($((error_num + 3)))" > "${prefix}.status"
+	  exit "$((error_num + 3))"
+        fi
+        echo "ncap2 defdim successful"
       fi
 
-      # Normalize time to the nearest second to prevent floating-point precision
-      # artifacts (e.g., cftime decoding a value as second=60 instead of
-      # second=0 of the next day) that arise from ncrcat time subsetting.
-      local cmdfix_t='time=double(round(time*86400.0)/86400.0)'
-      run_nco ncap2 -O -h -s "${cmdfix_t}" "${combined_name}" "${combined_name}"
-
-      # Add time bounds
-      local cmdfix1='if(!exists("bnds")) defdim("bnds",2)'
-      local cmdfix2='time_bnds=make_bounds(time,$bnds,"time_bnds")'
-      local cmdfix3='time_bnds@units=time@units'
-      local cmdfix4='time_bnds@calendar=time@calendar'
-      local cmdfix5='time_bnds=double(round(time_bnds*86400.0)/86400.0)'
-      run_nco ncap2 -O -h -s "${cmdfix1};${cmdfix2};${cmdfix3};${cmdfix4};${cmdfix5}" "${combined_name}" "${combined_name}"
+      # Always overwrite time bounds
+      local cmdfix1='time_bnds=make_bounds(time,$bnds,"time_bnds")'
+      local cmdfix2='time_bnds@units=time@units'
+      local cmdfix3='time_bnds@calendar=time@calendar'
+      local cmdfix4='time@bounds="time_bnds"'
+      run_nco ncap2 -O -h -s "${cmdfix1};${cmdfix2};${cmdfix3};${cmdfix4}" \
+        "${combined_name}" "${combined_name}"
+      if [[ $? -ne 0 ]]; then
+        cd "${script_dir}" || exit
+        echo "ERROR ($((error_num + 4)))" > "${prefix}.status"
+        exit "$((error_num + 4))"
+      fi
+      echo "ncap2 time_bnds successful"
 
+      # Add CF metadata
+      run_nco ncatted -O \
+        -a axis,time,o,c,"T" \
+        -a standard_name,time,o,c,"time" \
+        "${combined_name}" "${combined_name}"
       if [[ $? -ne 0 ]]; then
         cd "${script_dir}" || exit
         echo "ERROR (${error_num})" > "${prefix}.status"
         exit "${error_num}"
       fi
+      echo "ncatted CF metadata successful"
     else
       echo "Warning: No input files found for variable ${v} in ${ts_dir_source}. Skipping."
     fi
   done
 
-  if [ -z "$( ls . )" ]; then
+  if [ -z "$(ls ./*.nc 2>/dev/null)" ]; then
     echo "create_links_ts: ${ts_dir_destination} was not updated!"
+    cd "${script_dir}" || exit
+    echo "ERROR (${error_num})" > "${prefix}.status"
+    exit "${error_num}"
   fi
 
   cd ..
@@ -414,7 +536,7 @@ create_links_ts_obs() {
 
   local file fname SUBSTR YYYYS YYYYE ttag combined_name
 
-  for file in ${ts_dir_source}/*; do
+  for file in "${ts_dir_source}"/*; do
     fname=$(basename "$file")
     echo "create_links_ts_obs: checking if nc file: ${fname}"
     if [[ ${fname} != *.nc ]]; then
@@ -422,82 +544,94 @@ create_links_ts_obs() {
       continue
     fi
     echo "create_links_ts_obs: processing ${file}"
+
     # Match two time patterns (YYYYMM or YYYYMMDD) separated by _ or -
     if [[ $fname =~ ^(.+)\.([0-9]{4})([0-9]{2}){1,2}[-_]([0-9]{4})([0-9]{2}){1,2}\.nc$ ]]; then
       SUBSTR="${BASH_REMATCH[1]}"   # everything before the .YYYY...
-      YYYYS="${BASH_REMATCH[2]}"    # start year
-      YYYYE="${BASH_REMATCH[4]}"    # end year
+      file_start_year="${BASH_REMATCH[2]}"  # file start year
+      file_end_year="${BASH_REMATCH[4]}"    # file end year
     else
-
       echo "Warning: Could not extract dates from ${fname}, basename of ${file}"
       continue
     fi
 
-    # Optional: clip years if needed
-    if [[ ${YYYYS} -lt ${begin_year} ]]; then
-      YYYYS="${begin_year}"
-    fi
-
-    if [[ ${YYYYE} -gt ${end_year} ]]; then
-      YYYYE="${end_year}"
+    # Clip years to be in the selected range
+    if (( file_end_year < begin_year || file_start_year > end_year )); then
+      echo "WARNING: ${fname} does not overlap requested range ${begin_year}-${end_year}; using file range ${file_start_year}-${file_end_year}."
+      YYYYS="${file_start_year}"
+      YYYYE="${file_end_year}"
+    else
+      (( file_start_year < begin_year )) && YYYYS="${begin_year}" || YYYYS="${file_start_year}"
+      (( file_end_year > end_year )) && YYYYE="${end_year}" || YYYYE="${file_end_year}"
     fi
 
     ttag="$(printf "%04d" "${YYYYS}")01-$(printf "%04d" "${YYYYE}")12"
     combined_name="${SUBSTR}.${ttag}.nc"
 
+    # Ensure input time has calendar attribute before string-based time subsetting
+    if ! run_nco ncks -m "${file}" | grep -q "time:calendar"; then
+      echo "Adding missing calendar attribute to input time..."
+      run_nco ncatted -O -h -a calendar,time,o,c,"standard" "${file}"
+      if [[ $? -ne 0 ]]; then
+        cd "${script_dir}" || exit
+	echo "ERROR ($((error_num + 1)))" > "${prefix}.status"
+        exit "$((error_num + 1))"
+      fi
+      echo "ncatted successful"
+    fi
+
     # Extract subset of time series
-    run_nco ncrcat -O -d time,"${YYYYS}-01-01","${YYYYE}-12-31" "${file}" "${combined_name}"
+    run_nco ncrcat -O -h -d time,"${YYYYS}-01-01","${YYYYE}-12-31" "${file}" "${combined_name}"
     if [[ $? -ne 0 ]]; then
       cd "${script_dir}" || exit
-      echo "ERROR (${error_num})" > "${prefix}.status"
-      exit "${error_num}"
+      echo "ERROR ($((error_num + 2)))" > "${prefix}.status"
+      exit "$((error_num + 2))"
     fi
-    echo "ncrcat successful"
+    echo "ncrcat subset successful"
 
-    # Ensure time has calendar attribute
-    if ! run_nco ncks -m "${combined_name}" | grep -q "calendar"; then
-      echo "Adding missing calendar attribute to time..."
-      run_nco ncatted -a calendar,time,o,c,"standard" "${combined_name}"
+    # Add bnds dimension if missing
+    if ! run_nco ncks -m "${combined_name}" | grep -q "bnds = 2"; then
+      echo "Adding missing bnds dimension..."
+      run_nco ncap2 -O -h -s 'defdim("bnds",2)' "${combined_name}" "${combined_name}"
       if [[ $? -ne 0 ]]; then
         cd "${script_dir}" || exit
-        echo "ERROR (${error_num})" > "${prefix}.status"
-        exit "$((error_num + 1))"
+        echo "ERROR ($((error_num + 3)))" > "${prefix}.status"
+        exit "$((error_num + 3))"
       fi
-      echo "ncatted successful"
+      echo "ncap2 defdim successful"
     fi
 
-    # Normalize time to the nearest second to prevent floating-point precision
-    # artifacts (e.g., cftime decoding a value as second=60 instead of
-    # second=0 of the next day) that arise from ncrcat time subsetting.
-    local cmdfix_t='time=double(round(time*86400.0)/86400.0)'
-    run_nco ncap2 -O -h -s "${cmdfix_t}" "${combined_name}" "${combined_name}"
+    # Add time bounds
+    local cmdfix1='time_bnds=make_bounds(time,$bnds,"time_bnds")'
+    local cmdfix2='time_bnds@units=time@units'
+    local cmdfix3='time_bnds@calendar=time@calendar'
+    local cmdfix4='time@bounds="time_bnds"'
+    run_nco ncap2 -O -h -s "${cmdfix1};${cmdfix2};${cmdfix3};${cmdfix4}" "${combined_name}" "${combined_name}"
     if [[ $? -ne 0 ]]; then
       cd "${script_dir}" || exit
-      echo "ERROR (${error_num})" > "${prefix}.status"
-      exit "${error_num}"
+      echo "ERROR ($((error_num + 4)))" > "${prefix}.status"
+      exit "$((error_num + 4))"
     fi
-    echo "time normalization successful"
+    echo "ncap2 successful"
 
-    # Add time bounds
-    local cmdfix1='if(!exists("bnds")) defdim("bnds",2)'
-    local cmdfix2='time_bnds=make_bounds(time,$bnds,"time_bnds")'
-    local cmdfix3='time_bnds@units=time@units'
-    local cmdfix4='time_bnds@calendar=time@calendar'
-    local cmdfix5='time_bnds=double(round(time_bnds*86400.0)/86400.0)'
-    run_nco ncap2 -O -h -s "${cmdfix1};${cmdfix2};${cmdfix3};${cmdfix4};${cmdfix5}" "${combined_name}" "${combined_name}"
+    # Add CF metadata
+    run_nco ncatted -O \
+      -a axis,time,o,c,"T" \
+      -a standard_name,time,o,c,"time" \
+      "${combined_name}" "${combined_name}"
     if [[ $? -ne 0 ]]; then
       cd "${script_dir}" || exit
       echo "ERROR (${error_num})" > "${prefix}.status"
-      exit "$((error_num + 2))"
+      exit "${error_num}"
     fi
-    echo "ncap2 successful"
+    echo "ncatted CF metadata successful"
   done
 
   if [ -z "$( ls . )" ]; then
     echo "create_links_ts_obs: ${ts_dir_destination} was not updated!"
     cd "${script_dir}" || exit
-    echo "ERROR (${error_num})" > "${prefix}.status"
-    exit "${error_num}"
+    echo "ERROR ($((error_num + 5)))" > "${prefix}.status"
+    exit "$((error_num + 5))"
   fi
 
   cd ..
@@ -515,13 +649,13 @@ climo_dir_primary="climo"
 # This cmip_ts path is created via zppy/templates/e3sm_to_cmip.bash
 climo_dir_source="{{ output }}/post/atm/{{ grid }}/cmip_ts/monthly"
 # Link and process primary model climo data
-create_links_acyc_climo "${climo_dir_source}" "${climo_dir_primary}" "${Y1}" "${Y2}" "${model_name}.${tableID}" 1
+create_links_acyc_climo "${climo_dir_source}" "${climo_dir_primary}" "${Y1}" "${Y2}" "${model_name}.${tableID}" 10
 {% if run_type == "model_vs_model" %}
 # Path to reference model's climatology files
 climo_dir_source_ref="{{ reference_data_path_ts }}"
 climo_dir_ref="climo_ref"
 # Link and process reference model climo data
-create_links_acyc_climo "${climo_dir_source_ref}" "${climo_dir_ref}" "${ref_Y1}" "${ref_Y2}" "${model_name_ref}.${tableID_ref}" 2
+create_links_acyc_climo "${climo_dir_source_ref}" "${climo_dir_ref}" "${ref_Y1}" "${ref_Y2}" "${model_name_ref}.${tableID_ref}" 20
 {% endif %}
 {% endif %}
 
@@ -531,13 +665,13 @@ create_links_acyc_climo "${climo_dir_source_ref}" "${climo_dir_ref}" "${ref_Y1}"
 ts_dir_primary="ts"
 ts_dir_source="{{ output }}/post/atm/{{ ts_grid }}/cmip_ts/monthly"
 # Create local links and combine time series NetCDF files for the primary model
-create_links_ts "${ts_dir_source}" "${ts_dir_primary}" "${Y1}" "${Y2}" "${model_name}.${tableID}" 3
+create_links_ts "${ts_dir_source}" "${ts_dir_primary}" "${Y1}" "${Y2}" "${model_name}.${tableID}" 30
 {% if run_type == "model_vs_model" %}
 # Define time series path for reference model (adjust for different year spans)
 ts_dir_source_ref="{{ reference_data_path_ts }}"
 ts_dir_ref="ts_ref"
 # Create local links and combine ts files for the reference model
-create_links_ts "${ts_dir_source_ref}" "${ts_dir_ref}" "${ref_Y1}" "${ref_Y2}" "${model_name_ref}.${tableID_ref}" 4
+create_links_ts "${ts_dir_source_ref}" "${ts_dir_ref}" "${ref_Y1}" "${ref_Y2}" "${model_name_ref}.${tableID_ref}" 40
 {% endif %}
 {% endif %}
 
@@ -563,12 +697,12 @@ set -e
 {{ environment_commands_secondary }}
 set +e
 
-time eval "${command}"
+time ${command}
 
 if [ $? -ne 0 ]; then
   cd {{ scriptDir }}
-  echo "ERROR (5)" > {{ prefix }}.status
-  exit 5
+  echo "ERROR (50)" > {{ prefix }}.status
+  exit 50
 fi
 
 set -e
@@ -583,12 +717,12 @@ ts_dir_ref_source="{{ scriptDir }}/${workdir}/${obstmp_dir}"
 
 {% if current_set == "mean_climate" %}
 climo_dir_ref=climo_ref
-# This will use errors code 6,7,8:
-create_links_acyc_climo_obs "${ts_dir_ref_source}" "${climo_dir_ref}" ${ref_Y1} ${ref_Y2} 6
+# This will use errors code 61,62,63...:
+create_links_acyc_climo_obs "${ts_dir_ref_source}" "${climo_dir_ref}" ${ref_Y1} ${ref_Y2} 60
 {% elif current_set in ["variability_modes_cpl", "variability_modes_atm", "enso"] %}
 ts_dir_ref=ts_ref
-# This will use error codes 9,10,11:
-create_links_ts_obs "${ts_dir_ref_source}" "${ts_dir_ref}" ${ref_Y1} ${ref_Y2} 9
+# This will use error codes 71,72,73...:
+create_links_ts_obs "${ts_dir_ref_source}" "${ts_dir_ref}" ${ref_Y1} ${ref_Y2} 70
 {% endif %}
 
 {% endif %}
@@ -890,11 +1024,54 @@ source_dirs="--climo_ts_dir_primary ${climo_dir_primary} --climo_ts_dir_ref ${cl
 {% elif current_set in ["variability_modes_cpl", "variability_modes_atm", "enso"] %}
 source_dirs="--climo_ts_dir_primary ${ts_dir_primary} --climo_ts_dir_ref ${ts_dir_ref}"
 {% endif %}
+
+# -------------------------------------------------------
+# Adaptive safeguard for resource-intensive diagnostics
+# -------------------------------------------------------
+requested_workers={{ num_workers }}
+effective_workers=${requested_workers}
+subsection="{{ subsection }}"
+
+# Each zppy subset is a separate SLURM job, so num_workers spans the entire
+# job allocation.  The relevant CPU budget is the total across all nodes.
+# {{ nodes }} is the compile-time node count (same value as --nodes={{ nodes }}),
+# so multiplying by it is simpler and more portable than relying on the
+# runtime variable SLURM_JOB_NUM_NODES.
+if [[ -n "${SLURM_CPUS_ON_NODE}" ]]; then
+  allocated_cpus=$(( SLURM_CPUS_ON_NODE * {{ nodes }} ))
+elif command -v nproc >/dev/null 2>&1; then
+  allocated_cpus=$(nproc)
+else
+  allocated_cpus=1
+fi
+
+# Guard against zero or empty (should not happen, but be safe)
+if [[ -z "${allocated_cpus}" || "${allocated_cpus}" -lt 1 ]]; then
+  allocated_cpus=1
+fi
+
+# EOF / variability modes are heavy because each subprocess may call
+# threaded LAPACK/BLAS routines and allocate large arrays.
+if [[ "${subsection}" == "variability_modes_atm" || "${subsection}" == "variability_modes_cpl" ]]; then
+  safe_cap=$(( allocated_cpus / 4 ))
+
+  if [[ ${safe_cap} -lt 1 ]]; then
+    safe_cap=1
+  fi
+
+  if [[ ${requested_workers} -gt ${safe_cap} ]]; then
+    echo "WARNING: Reducing num_workers from ${requested_workers} to ${safe_cap} for ${subsection} because EOF diagnostics are resource-intensive."
+    effective_workers=${safe_cap}
+  fi
+fi
+
+echo "PCMDI worker policy: requested_workers=${requested_workers}, allocated_cpus=${allocated_cpus}, effective_workers=${effective_workers}, subsection=${subsection}"
+
 # Parameter passing can encounter errors if parameters are empty.
 # So, it's a good idea to make sure they can't be (or at least are unlikely to be) empty.
 # run_type == "model_vs_obs" only: obs_sets (default value is NOT "")
 # run_type == "model_vs_model" only: model_name_ref, tableID_ref (default values are NOT "")
-core_parameters="--num_workers {{ num_workers }} --multiprocessing {{ multiprocessing }} --subsection {{ subsection }} ${source_dirs} --model_name ${model_name} --model_tableID {{ model_tableID }} --figure_format {{ figure_format }} --run_type {{ run_type }} --obs_sets {{ obs_sets }} --model_name_ref ${model_name_ref} --vars ${source_vars} --tableID_ref ${tableID_ref} --generate_sftlf {{ generate_sftlf }} --case_id ${case_id} --results_dir ${results_dir} --debug ${debug,,}"
+core_parameters="--num_workers ${effective_workers} --multiprocessing {{ multiprocessing }} --subsection {{ subsection }} ${source_dirs} --model_name ${model_name} --model_tableID {{ model_tableID }} --figure_format {{ figure_format }} --run_type {{ run_type }} --obs_sets {{ obs_sets }} --model_name_ref ${model_name_ref} --vars ${source_vars} --tableID_ref ${tableID_ref} --generate_sftlf {{ generate_sftlf }} --case_id ${case_id} --results_dir ${results_dir} --debug ${debug,,}"
 {% endif %}
 
 {% if current_set == "mean_climate" %}
@@ -954,8 +1131,8 @@ echo "The current directory is: $PWD" # This will be of the form .../post/script
 time ${command}
 if [ $? != 0 ]; then
   cd {{ scriptDir }}
-  echo 'ERROR (12)' > {{ prefix }}.status
-  exit 12
+  echo 'ERROR (80)' > {{ prefix }}.status
+  exit 80
 fi
 
 set -e
@@ -972,8 +1149,8 @@ echo
 mkdir -p ${web_dir}
 if [ $? != 0 ]; then
   cd {{ scriptDir }}
-  echo 'ERROR (13)' > {{ prefix }}.status
-  exit 13
+  echo 'ERROR (90)' > {{ prefix }}.status
+  exit 90
 fi
 
 {% if machine in ['pm-cpu', 'pm-gpu'] %}
@@ -997,8 +1174,8 @@ done
 rsync -a ${results_dir} ${web_dir}/
 if [ $? != 0 ]; then
   cd {{ scriptDir }}
-  echo 'ERROR (14)' > {{ prefix }}.status
-  exit 14
+  echo 'ERROR (100)' > {{ prefix }}.status
+  exit 100
 fi
 {% endif %}
 

From 5040692cf2b2c8190162f392b70f5cd405d61456 Mon Sep 17 00:00:00 2001
From: shixuan zhang <shixuan.zhang@pnnl.gov>
Date: Sat, 2 May 2026 22:03:53 -0700
Subject: [PATCH 04/21] Rebase to latest main

---
 zppy/templates/pcmdi_diags.bash | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/zppy/templates/pcmdi_diags.bash b/zppy/templates/pcmdi_diags.bash
index 1bd053d6..7ca285d5 100755
--- a/zppy/templates/pcmdi_diags.bash
+++ b/zppy/templates/pcmdi_diags.bash
@@ -248,6 +248,7 @@ create_links_acyc_climo() {
     fi
 
     rm -vf "${v}_clm_"*.nc
+    rm -f "${v}_files.txt"
   done
 
   if [ -z "$(ls ./*.nc 2>/dev/null)" ]; then
@@ -506,6 +507,7 @@ create_links_ts() {
     else
       echo "Warning: No input files found for variable ${v} in ${ts_dir_source}. Skipping."
     fi
+    rm -f "${v}_files.txt"
   done
 
   if [ -z "$(ls ./*.nc 2>/dev/null)" ]; then

From e4e3b17192a085797269cc852d557d4aa1425ab4 Mon Sep 17 00:00:00 2001
From: shixuan zhang <shixuan.zhang@pnnl.gov>
Date: Sat, 2 May 2026 22:08:51 -0700
Subject: [PATCH 05/21] Claude-Augment Enhancement for robustness

---
 zppy/templates/pcmdi_diags.bash | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/zppy/templates/pcmdi_diags.bash b/zppy/templates/pcmdi_diags.bash
index 7ca285d5..82bf44a1 100755
--- a/zppy/templates/pcmdi_diags.bash
+++ b/zppy/templates/pcmdi_diags.bash
@@ -187,6 +187,7 @@ create_links_acyc_climo() {
     if [[ ! -s "${v}_files.txt" ]]; then
       echo "WARNING: No input files found for variable ${v}, skipping climatology. \
             This variable may not have been processed or output by e3sm_to_cmip."
+      rm -f "${v}_files.txt"
       continue
     fi
 
@@ -194,6 +195,7 @@ create_links_acyc_climo() {
     if ! run_nco ncks -m "${first_file}" >/dev/null 2>&1; then
       echo "WARNING: First file is not a valid NetCDF for ${v}: ${first_file}, skipping climatology. \
             This variable may not have been processed or output by e3sm_to_cmip."
+      rm -f "${v}_files.txt"
       continue
     fi
 

From a550cb611490da316d4b9bfa5b9ba1601ebd5ccb Mon Sep 17 00:00:00 2001
From: shixuan zhang <shixuan.zhang@pnnl.gov>
Date: Sun, 3 May 2026 00:35:23 -0700
Subject: [PATCH 06/21] bug fix

---
 zppy/templates/pcmdi_diags.bash | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/zppy/templates/pcmdi_diags.bash b/zppy/templates/pcmdi_diags.bash
index 82bf44a1..1bd053d6 100755
--- a/zppy/templates/pcmdi_diags.bash
+++ b/zppy/templates/pcmdi_diags.bash
@@ -187,7 +187,6 @@ create_links_acyc_climo() {
     if [[ ! -s "${v}_files.txt" ]]; then
       echo "WARNING: No input files found for variable ${v}, skipping climatology. \
             This variable may not have been processed or output by e3sm_to_cmip."
-      rm -f "${v}_files.txt"
       continue
     fi
 
@@ -195,7 +194,6 @@ create_links_acyc_climo() {
     if ! run_nco ncks -m "${first_file}" >/dev/null 2>&1; then
       echo "WARNING: First file is not a valid NetCDF for ${v}: ${first_file}, skipping climatology. \
             This variable may not have been processed or output by e3sm_to_cmip."
-      rm -f "${v}_files.txt"
       continue
     fi
 
@@ -250,7 +248,6 @@ create_links_acyc_climo() {
     fi
 
     rm -vf "${v}_clm_"*.nc
-    rm -f "${v}_files.txt"
   done
 
   if [ -z "$(ls ./*.nc 2>/dev/null)" ]; then
@@ -509,7 +506,6 @@ create_links_ts() {
     else
       echo "Warning: No input files found for variable ${v} in ${ts_dir_source}. Skipping."
     fi
-    rm -f "${v}_files.txt"
   done
 
   if [ -z "$(ls ./*.nc 2>/dev/null)" ]; then

From 5e38c525550e46337fcf0078a568827fd349063a Mon Sep 17 00:00:00 2001
From: shixuan zhang <shixuan.zhang@pnnl.gov>
Date: Tue, 5 May 2026 16:06:28 -0700
Subject: [PATCH 07/21] precommit refromat

---
 zppy/pcmdi_diags.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/zppy/pcmdi_diags.py b/zppy/pcmdi_diags.py
index ece99ab9..872965ce 100644
--- a/zppy/pcmdi_diags.py
+++ b/zppy/pcmdi_diags.py
@@ -52,11 +52,11 @@ def pcmdi_diags(config, script_dir, existing_bundles, job_ids_file):
     for c in tasks:
         dependencies: List[str] = []
         define_current_set(c)
-        #if c["current_set"] == "enso":
-        #    logger.warning(
-        #        "The 'enso' set is not yet supported in PCMDI Diags. Skipping launching of associated jobs."
-        #    )
-        #    continue  # Skip this task
+        if c["current_set"] == "enso":
+            logger.warning(
+                "The 'enso' set is not yet supported in PCMDI Diags. Skipping launching of associated jobs."
+            )
+            continue  # Skip this task
         c["sub"] = get_value_from_parameter(
             c, "subsection", "sub", ParameterInferenceType.SECTION_INFERENCE
         )

From bede594baa28f7859dc93895bcc1425ab643c55d Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Sun, 10 May 2026 22:24:13 -0700
Subject: [PATCH 08/21] rebase to latest main

---
 zppy/templates/pcmdi_diags.bash | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/zppy/templates/pcmdi_diags.bash b/zppy/templates/pcmdi_diags.bash
index 1bd053d6..6315e52a 100755
--- a/zppy/templates/pcmdi_diags.bash
+++ b/zppy/templates/pcmdi_diags.bash
@@ -253,8 +253,8 @@ create_links_acyc_climo() {
   if [ -z "$(ls ./*.nc 2>/dev/null)" ]; then
     echo "create_links_acyc_climo: ${ts_dir_destination} was not updated!"
     cd "${script_dir}" || exit
-    echo "ERROR (${error_num})" > "${prefix}.status"
-    exit "${error_num}"
+    echo "ERROR ($((error_num + 5)))" > "${prefix}.status"
+    exit "$((error_num + 5))"
   fi
 
   cd ..
@@ -499,8 +499,8 @@ create_links_ts() {
         "${combined_name}" "${combined_name}"
       if [[ $? -ne 0 ]]; then
         cd "${script_dir}" || exit
-        echo "ERROR (${error_num})" > "${prefix}.status"
-        exit "${error_num}"
+        echo "ERROR ($((error_num + 5)))" > "${prefix}.status"
+        exit "$((error_num + 5))"
       fi
       echo "ncatted CF metadata successful"
     else
@@ -511,8 +511,8 @@ create_links_ts() {
   if [ -z "$(ls ./*.nc 2>/dev/null)" ]; then
     echo "create_links_ts: ${ts_dir_destination} was not updated!"
     cd "${script_dir}" || exit
-    echo "ERROR (${error_num})" > "${prefix}.status"
-    exit "${error_num}"
+    echo "ERROR ($((error_num + 6)))" > "${prefix}.status"
+    exit "$((error_num + 6))"
   fi
 
   cd ..
@@ -621,8 +621,8 @@ create_links_ts_obs() {
       "${combined_name}" "${combined_name}"
     if [[ $? -ne 0 ]]; then
       cd "${script_dir}" || exit
-      echo "ERROR (${error_num})" > "${prefix}.status"
-      exit "${error_num}"
+      echo "ERROR ($((error_num + 5)))" > "${prefix}.status"
+      exit "$((error_num + 5))"
     fi
     echo "ncatted CF metadata successful"
   done
@@ -630,8 +630,8 @@ create_links_ts_obs() {
   if [ -z "$( ls . )" ]; then
     echo "create_links_ts_obs: ${ts_dir_destination} was not updated!"
     cd "${script_dir}" || exit
-    echo "ERROR ($((error_num + 5)))" > "${prefix}.status"
-    exit "$((error_num + 5))"
+    echo "ERROR ($((error_num + 6)))" > "${prefix}.status"
+    exit "$((error_num + 6))"
   fi
 
   cd ..

From 7767d8815f9b24583f9bfadd0d5ea004b5ab89fe Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Mon, 11 May 2026 14:27:54 -0700
Subject: [PATCH 09/21] Ajust to allow enso metrics and revise enso vars to be
 identified by workflow

---
 zppy/defaults/default.ini | 2 +-
 zppy/pcmdi_diags.py       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/zppy/defaults/default.ini b/zppy/defaults/default.ini
index d434f1d7..1c6e2d8c 100755
--- a/zppy/defaults/default.ini
+++ b/zppy/defaults/default.ini
@@ -647,7 +647,7 @@ enso_groups = string(default="ENSO_perf,ENSO_proc,ENSO_tel")
 # Specify these for the enso subtask AND the synthetic_plots subtask
 ###########################################################################################
 # enso: vars = "psl,pr,prsn,ts,tas,tauu,tauv,hflx,hfss,rlds,rsds,rlus,rlut,rsdt"
-enso_vars = string(default="psl,pr,prsn,ts,tas,tauu,tauv,hfls,hfss,rlds,rsds,rlus,rlut,rsdt")
+enso_vars = string(default="psl,pr,ts,tas,taux,tauy,hfls,hfss,rlds,rsds,rlus,rlut,rsdt")
 ###########################################################################################
 # Specify these for the synthetic_plots subtask
 ###########################################################################################
diff --git a/zppy/pcmdi_diags.py b/zppy/pcmdi_diags.py
index 872965ce..8dfe42c9 100644
--- a/zppy/pcmdi_diags.py
+++ b/zppy/pcmdi_diags.py
@@ -54,9 +54,9 @@ def pcmdi_diags(config, script_dir, existing_bundles, job_ids_file):
         define_current_set(c)
         if c["current_set"] == "enso":
             logger.warning(
-                "The 'enso' set is not yet supported in PCMDI Diags. Skipping launching of associated jobs."
+                "The 'enso' set is currently a testing mode in PCMDI Diags. Turn on it with care."
             )
-            continue  # Skip this task
+        #    continue  # Skip this task
         c["sub"] = get_value_from_parameter(
             c, "subsection", "sub", ParameterInferenceType.SECTION_INFERENCE
         )

From faf9999c4611d02b7f37b13ac83e22a368cb1486 Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Tue, 12 May 2026 17:26:43 -0700
Subject: [PATCH 10/21] Modify the job dependency workflow for the pcmdi

This commit contains the changes made to the pcmdi.py so that it will
allow users to pass the dependencies of the pcmdi section on the
subsection of ts and e3sm_to_cmip
---
 zppy/pcmdi_diags.py | 86 +++++++++++++++++++++++++++++++++------------
 1 file changed, 64 insertions(+), 22 deletions(-)

diff --git a/zppy/pcmdi_diags.py b/zppy/pcmdi_diags.py
index 8dfe42c9..b8cc1380 100644
--- a/zppy/pcmdi_diags.py
+++ b/zppy/pcmdi_diags.py
@@ -119,21 +119,8 @@ def pcmdi_diags(config, script_dir, existing_bundles, job_ids_file):
             if c["current_set"] != "synthetic_plots":
                 for yr in range(c["year1"], c["year2"], c["ts_num_years"]):
                     add_ts_dependencies(c, dependencies, script_dir, yr)
-                    set_value_of_parameter_if_undefined(
-                        c,
-                        "e3sm_to_cmip_atm_subsection",
-                        "atm_monthly_180x360_aave",
-                        ParameterInferenceType.SECTION_INFERENCE,
-                    )
-                add_dependencies(
-                    dependencies,
-                    script_dir,
-                    "e3sm_to_cmip",
-                    c["e3sm_to_cmip_atm_subsection"],
-                    c["year1"],
-                    c["year2"],
-                    c["ts_num_years"],
-                )
+                for yr in range(c["year1"], c["year2"], c["ts_num_years"]):
+                    add_e3sm_to_cmip_dependencies(c, dependencies, script_dir, yr)
             else:
                 if i < len(year_sets) - 1:
                     continue
@@ -344,23 +331,78 @@ def define_relevant_years_for_synthetic_plots(c: Dict[str, Any]) -> None:
     if c["enso_years"] == "":
         c["enso_years"] = year_str
 
+def _as_subsection_list(subsection: str) -> List[str]:
+    return [item.strip() for item in subsection.split(",") if item.strip()]
 
 def add_ts_dependencies(
     c: Dict[str, Any], dependencies: List[str], script_dir: str, yr: int
 ):
     start_yr = yr
     end_yr = yr + c["ts_num_years"] - 1
+
     if c["current_set"] in BASE_PCMDI_SETS:
-        add_dependencies(
-            dependencies,
-            script_dir,
-            "ts",
+        # Ensure the key exists because set_value_of_parameter_if_undefined()
+        # only fills values for existing keys with an empty string.
+        if "ts_subsection" not in c:
+            c["ts_subsection"] = ""
+
+        set_value_of_parameter_if_undefined(
+            c,
+            "ts_subsection",
+            "atm_monthly_180x360_aave",
+            ParameterInferenceType.SECTION_INFERENCE,
+        )
+
+        ts_subsections = [
+            item.strip()
+            for item in c["ts_subsection"].split(",")
+            if item.strip()
+        ]
+
+        for ts_subsection in ts_subsections:
+            add_dependencies(
+                dependencies,
+                script_dir,
+                "ts",
+                ts_subsection,
+                start_yr,
+                end_yr,
+                c["ts_num_years"],
+            )
+
+def add_e3sm_to_cmip_dependencies(
+    c: Dict[str, Any], dependencies: List[str], script_dir: str, yr: int
+):
+    start_yr = yr
+    end_yr = yr + c["ts_num_years"] - 1
+
+    if c["current_set"] in BASE_PCMDI_SETS:
+        if "e3sm_to_cmip_atm_subsection" not in c:
+            c["e3sm_to_cmip_atm_subsection"] = ""
+
+        set_value_of_parameter_if_undefined(
+            c,
+            "e3sm_to_cmip_atm_subsection",
             "atm_monthly_180x360_aave",
-            start_yr,
-            end_yr,
-            c["ts_num_years"],
+            ParameterInferenceType.SECTION_INFERENCE,
         )
 
+        e3sm_to_cmip_atm_subsections = [
+            item.strip()
+            for item in c["e3sm_to_cmip_atm_subsection"].split(",")
+            if item.strip()
+        ]
+
+        for e3sm_to_cmip_atm_subsection in e3sm_to_cmip_atm_subsections:
+            add_dependencies(
+                dependencies,
+                script_dir,
+                "e3sm_to_cmip",
+                e3sm_to_cmip_atm_subsection,
+                start_yr,
+                end_yr,
+                c["ts_num_years"],
+            )
 
 def add_pcmdi_dependencies(
     c: Dict[str, Any], dependencies: List[str], script_dir: str

From aa1a3f4a11246a81d45242bd58746e92c4e791e3 Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Tue, 12 May 2026 17:28:10 -0700
Subject: [PATCH 11/21] Enanble ts processing on mpaso and mpassi model output

---
 zppy/utils.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/zppy/utils.py b/zppy/utils.py
index 4afff338..2ac18b9d 100644
--- a/zppy/utils.py
+++ b/zppy/utils.py
@@ -227,6 +227,12 @@ def set_component_and_prc_typ(c: Dict[str, Any]) -> None:
     elif tmp in ("mosart",):
         component = "rof"
         prc_typ = tmp
+    elif tmp in ("mpaso",):
+        component = "ocn"
+        prc_typ = tmp
+    elif tmp in ("mpassi",):
+        component = "ice"
+        prc_typ = tmp
     else:
         raise ValueError(
             f"Cannot extract output component name from {c['input_component']} or {c['input_files']}."

From 4b0370d74d33a0539bd78b7bd4315f9a074ec6db Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Wed, 13 May 2026 13:05:13 -0700
Subject: [PATCH 12/21] Correct the variable name for default setup for enso

---
 zppy/defaults/default.ini | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/zppy/defaults/default.ini b/zppy/defaults/default.ini
index 1c6e2d8c..00802bc3 100755
--- a/zppy/defaults/default.ini
+++ b/zppy/defaults/default.ini
@@ -131,6 +131,8 @@ climo_jobs = integer(default=0)
 vars = string(default="")
 # Model component having generated input files (eam, eamxx, elm, mosart, ...)
 input_component = string(default="")
+# MPAS model restart file template to guide the time series processing 
+mpas_rst_template = string(default="")
 
   [[__many__]]
   exclude = boolean(default=None)
@@ -138,6 +140,7 @@ input_component = string(default="")
   climo_jobs = integer(default=0)
   vars = string(default=None)
   input_component = string(default=None)
+  mpas_rst_template = string(default=None)
 
 [ts]
 area_nm = string(default="area")
@@ -647,7 +650,7 @@ enso_groups = string(default="ENSO_perf,ENSO_proc,ENSO_tel")
 # Specify these for the enso subtask AND the synthetic_plots subtask
 ###########################################################################################
 # enso: vars = "psl,pr,prsn,ts,tas,tauu,tauv,hflx,hfss,rlds,rsds,rlus,rlut,rsdt"
-enso_vars = string(default="psl,pr,ts,tas,taux,tauy,hfls,hfss,rlds,rsds,rlus,rlut,rsdt")
+enso_vars = string(default="psl,pr,ts,tas,tauu,tauv,hfls,hfss,rlds,rsds,rlus,rlut,rsdt")
 ###########################################################################################
 # Specify these for the synthetic_plots subtask
 ###########################################################################################

From 44fce794ffc6104adb10920440dc39313d360029 Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Thu, 14 May 2026 08:49:08 -0700
Subject: [PATCH 13/21] Bug fix in zppy/templates/ts.bash for variable
 filtering in global average section

---
 zppy/templates/ts.bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/zppy/templates/ts.bash b/zppy/templates/ts.bash
index e49b9a99..e8103568 100644
--- a/zppy/templates/ts.bash
+++ b/zppy/templates/ts.bash
@@ -54,7 +54,7 @@ vars={{ vars }}
 # https://unix.stackexchange.com/questions/237297/the-fastest-way-to-remove-a-string-in-a-variable
 # https://stackoverflow.com/questions/26457052/remove-a-substring-from-a-bash-variable
 # Remove U, since it is a 3D variable and thus will not work with rgn_avg
-vars=${vars//,U}
+# vars=${vars//,U}
 {%- else %}
 vars={{ vars }}
 {%- endif %}

From 3d24cdee9fa26d2e39ae9ba80b176606dcf996f8 Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Thu, 14 May 2026 16:05:00 -0700
Subject: [PATCH 14/21] Fix the ocean and seaice data processing typ setup

---
 zppy/utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/zppy/utils.py b/zppy/utils.py
index 2ac18b9d..ed9c0272 100644
--- a/zppy/utils.py
+++ b/zppy/utils.py
@@ -229,10 +229,10 @@ def set_component_and_prc_typ(c: Dict[str, Any]) -> None:
         prc_typ = tmp
     elif tmp in ("mpaso",):
         component = "ocn"
-        prc_typ = tmp
+        prc_typ = "mpasocean"
     elif tmp in ("mpassi",):
         component = "ice"
-        prc_typ = tmp
+        prc_typ = "mpasseaice"
     else:
         raise ValueError(
             f"Cannot extract output component name from {c['input_component']} or {c['input_files']}."

From 6345cfd682aeaf9b9e7fca4e55f9ff778391b665 Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Thu, 14 May 2026 18:19:12 -0700
Subject: [PATCH 15/21] Add export MPLBACKEND=Agg to the pcmdi workflow

Use a non-interactive Matplotlib backend for batch diagnostics.
Safe for workflows that save figures to files and avoids GUI/Tkinter errors
on systems without a display.
---
 zppy/templates/pcmdi_diags.bash | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/zppy/templates/pcmdi_diags.bash b/zppy/templates/pcmdi_diags.bash
index 6315e52a..d61f1c4f 100755
--- a/zppy/templates/pcmdi_diags.bash
+++ b/zppy/templates/pcmdi_diags.bash
@@ -18,6 +18,12 @@ export UCX_SHM_DEVICES=all # or not set UCX_NET_DEVICES at all
 # Make sure UVCDAT doesn't prompt us about anonymous logging
 export UVCDAT_ANONYMOUS_LOG=False
 
+
+# Use a non-interactive Matplotlib backend for batch diagnostics.
+# Safe for workflows that save figures to files and avoids GUI/Tkinter errors
+# on systems without a display.
+export MPLBACKEND=Agg
+
 # Script dir
 cd {{ scriptDir }}
 

From 1595ef6a419421fe5182b247c32b4ce8fefb6111 Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Thu, 14 May 2026 22:49:37 -0700
Subject: [PATCH 16/21] Enable MPAS ocean/sea-ice time-series processing to
 support pcmdi

Split MPAS-Ocean and MPAS-Seaice time-series processing into native
ncclimo generation followed by explicit ncremap regridding. This allows
the workflow to restore MPAS-native time metadata, construct a CF-style
numeric time coordinate from timeMonthly_avg_daysSinceStartOfSim, and
preserve missing_value metadata after regridding.

For MPAS-Seaice, construct spatial-only SGS helper variables from
timeMonthly_avg_iceAreaCell before regridding. This avoids failures when
ncremap attempts to use the time-dependent timeMonthly_avg_iceAreaCell
field directly as the SGS fraction. Temporary helper variables are removed
from final output, and timeMonthly_avg_iceAreaCell is retained only when it
is the requested output variable.
---
 zppy/templates/ts.bash | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/zppy/templates/ts.bash b/zppy/templates/ts.bash
index e8103568..21197dec 100644
--- a/zppy/templates/ts.bash
+++ b/zppy/templates/ts.bash
@@ -66,7 +66,7 @@ if grep -q "*" input.txt; then
   echo 'ERROR (1)' > {{ prefix }}.status
   exit 1
 fi
-# Generate time series files
+# Generate time series files.
 # If the user-defined parameter "vars" is "", then ${vars}, defined above, will be too.
 cat input.txt | run_nco ncclimo \
 -c {{ case }} \
@@ -86,17 +86,21 @@ cat input.txt | run_nco ncclimo \
 --yr_srt={{ yr_start }} \
 --yr_end={{ yr_end }} \
 --ypf={{ ypf }} \
-{% if mapping_file == '' -%}
+{%- if mapping_file == '' %}
 -o output \
-{%- elif mapping_file == 'glb' -%}
+{%- elif mapping_file == 'glb' %}
 -o output \
 --rgn_avg \
 --area={{ area_nm }} \
-{%- else -%}
+{%- else %}
+{%- if prc_typ in ['mpasocean', 'mpasseaice'] %}
+-o trash \
+{%- else %}
 --map={{ mapping_file }} \
 -o trash \
 -O output \
 {%- endif %}
+{%- endif %}
 {%- if frequency != 'monthly' %}
 --clm_md=hfs \
 --dpf={{ dpf }} \
@@ -104,8 +108,7 @@ cat input.txt | run_nco ncclimo \
 {%- endif %}
 --prc_typ={{ prc_typ }}
 
-
-
+# Check ncclimo status before any optional separate regridding.
 if [ $? != 0 ]; then
   cd {{ scriptDir }}
   echo 'ERROR (2)' > {{ prefix }}.status
@@ -156,8 +159,8 @@ done
 }
 if [ $? != 0 ]; then
   cd {{ scriptDir }}
-  echo 'ERROR (3)' > {{ prefix }}.status
-  exit 3
+  echo 'ERROR (5)' > {{ prefix }}.status
+  exit 5
 fi
 
 {%- if vrt_remap_vars != '' %}

From 740f2317c08b80066d9d49764ef3675e7b478301 Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Fri, 15 May 2026 10:57:48 -0700
Subject: [PATCH 17/21] Fix by pre-commit check

---
 zppy/defaults/default.ini | 2 +-
 zppy/pcmdi_diags.py       | 8 +++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/zppy/defaults/default.ini b/zppy/defaults/default.ini
index 00802bc3..268ee426 100755
--- a/zppy/defaults/default.ini
+++ b/zppy/defaults/default.ini
@@ -131,7 +131,7 @@ climo_jobs = integer(default=0)
 vars = string(default="")
 # Model component having generated input files (eam, eamxx, elm, mosart, ...)
 input_component = string(default="")
-# MPAS model restart file template to guide the time series processing 
+# MPAS model restart file template to guide the time series processing
 mpas_rst_template = string(default="")
 
   [[__many__]]
diff --git a/zppy/pcmdi_diags.py b/zppy/pcmdi_diags.py
index b8cc1380..a4ccfe4b 100644
--- a/zppy/pcmdi_diags.py
+++ b/zppy/pcmdi_diags.py
@@ -331,9 +331,11 @@ def define_relevant_years_for_synthetic_plots(c: Dict[str, Any]) -> None:
     if c["enso_years"] == "":
         c["enso_years"] = year_str
 
+
 def _as_subsection_list(subsection: str) -> List[str]:
     return [item.strip() for item in subsection.split(",") if item.strip()]
 
+
 def add_ts_dependencies(
     c: Dict[str, Any], dependencies: List[str], script_dir: str, yr: int
 ):
@@ -354,9 +356,7 @@ def add_ts_dependencies(
         )
 
         ts_subsections = [
-            item.strip()
-            for item in c["ts_subsection"].split(",")
-            if item.strip()
+            item.strip() for item in c["ts_subsection"].split(",") if item.strip()
         ]
 
         for ts_subsection in ts_subsections:
@@ -370,6 +370,7 @@ def add_ts_dependencies(
                 c["ts_num_years"],
             )
 
+
 def add_e3sm_to_cmip_dependencies(
     c: Dict[str, Any], dependencies: List[str], script_dir: str, yr: int
 ):
@@ -404,6 +405,7 @@ def add_e3sm_to_cmip_dependencies(
                 c["ts_num_years"],
             )
 
+
 def add_pcmdi_dependencies(
     c: Dict[str, Any], dependencies: List[str], script_dir: str
 ) -> None:

From d2c8d7f39f281d4f5a9f1a362d9a936fa3da7d09 Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Sun, 28 Jun 2026 20:16:08 -0700
Subject: [PATCH 18/21] Rebase code to the main branch and refactor MPAS regrid
 handling

Keep existing vertical regridding behavior intact while adding MPAS
ocean/sea-ice post-ncclimo regridding and defaults for MPAS time metadata.
---
 zppy/defaults/default.ini |  11 ++
 zppy/templates/ts.bash    | 249 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 260 insertions(+)

diff --git a/zppy/defaults/default.ini b/zppy/defaults/default.ini
index 268ee426..07b93b60 100755
--- a/zppy/defaults/default.ini
+++ b/zppy/defaults/default.ini
@@ -154,6 +154,15 @@ job_nbr = integer(default=0)
 tpd = integer(default=1)
 # Model component having generated input files (eam, eamxx, elm, mosart, ...)
 input_component = string(default="")
+# MPAS calendar used to construct a CF-style numeric time coordinate
+# from timeMonthly_avg_daysSinceStartOfSim when native MPAS time-series
+# files do not contain a standard time variable.
+mpas_calendar = string(default="noleap")
+# MPAS simulation start time used as the reference time for constructing
+# a CF-style numeric time coordinate:
+# time:units = "days since <mpas_start_time>"
+# This should match the MPAS/E3SM config_start_time when possible.
+mpas_start_time = string(default="0001-01-01 00:00:00")
 # Vertical regrid (model levels → pressure levels) — applied after ncclimo splits
 # files into per-var time-series. Vars listed here will additionally be regridded
 # and written to a sibling directory `ts_vrt_remap/` parallel to `ts/`, so users
@@ -174,6 +183,8 @@ vrt_in_file = string(default="")
   job_nbr = integer(default=None)
   tpd = integer(default=None)
   input_component = string(default=None)
+  mpas_calendar = string(default=None)
+  mpas_start_time = string(default=None)
   vrt_remap_vars = string(default=None)
   vrt_remap_file = string(default=None)
   vrt_in_file = string(default=None)
diff --git a/zppy/templates/ts.bash b/zppy/templates/ts.bash
index 21197dec..9bba3434 100644
--- a/zppy/templates/ts.bash
+++ b/zppy/templates/ts.bash
@@ -115,6 +115,255 @@ if [ $? != 0 ]; then
   exit 2
 fi
 
+{%- if mapping_file != '' and mapping_file != 'glb' and prc_typ in ['mpasocean', 'mpasseaice'] %}
+
+# Regrid MPAS-Ocean and MPAS-Seaice files separately.
+#
+# For MPAS components, generate native-grid time-series files first, then
+# regrid them with ncremap. This lets us restore MPAS-native time metadata,
+# construct a CF-style numeric time coordinate, and repair missing_value
+# attributes after regridding if needed.
+#
+# For MPAS-Seaice, also provide valid spatial-only SGS helper variables for
+# regridding. MPAS-Seaice monthly files may include time-dependent SGS
+# diagnostics such as:
+#
+#   timeMonthly_avg_iceAreaCell(Time,nCells)
+#
+# This variable should remain in the final time-series output. However,
+# NCO's regridder requires sgs_frc_nm and sgs_msk_nm to be spatial-only
+# fields matching the horizontal source grid size, i.e., nCells. Therefore,
+# create temporary spatial-only helper variables with separate names and use
+# them only for regridding.
+mkdir -p output
+
+mpas_calendar="{{ mpas_calendar }}"
+mpas_start_time="{{ mpas_start_time }}"
+mpas_start_time="${mpas_start_time/_/ }"
+
+for f in trash/*.nc ; do
+  bname=$(basename "${f}")
+  tmp_f="tmp_regrid_${bname}"
+  tmp_frc="tmp_sgs_frc_${bname}"
+  tmp_msk="tmp_sgs_msk_${bname}"
+  out_f="output/${bname}"
+
+  cp "${f}" "${tmp_f}"
+
+  # Detect whether the time dimension is named Time or time.
+  # MPAS native ncclimo files often have a Time dimension but no
+  # coordinate variable named Time/time.
+  if run_nco ncks -m "${tmp_f}" | grep -qE "^[[:space:]]*Time[[:space:]]*=|\(Time[,)]|, Time[,)]"; then
+    time_dim="Time"
+  elif run_nco ncks -m "${tmp_f}" | grep -qE "^[[:space:]]*time[[:space:]]*=|\(time[,)]|, time[,)]"; then
+    time_dim="time"
+  else
+    echo "ERROR: Cannot find Time/time dimension in ${tmp_f}"
+    cd {{ scriptDir }}
+    echo 'ERROR (3)' > {{ prefix }}.status
+    exit 3
+  fi
+
+  # Infer the main variable name from the output filename.
+  # Example:
+  #   timeMonthly_avg_seaSurfaceTemperature_000101_000512.nc
+  # becomes:
+  #   timeMonthly_avg_seaSurfaceTemperature
+  main_var=$(echo "${bname}" | sed -E 's/_[0-9]{6}_[0-9]{6}\.nc$//')
+
+  use_sgs_helpers="false"
+
+  {%- if prc_typ == 'mpasseaice' %}
+
+  # Construct explicit static SGS helpers for MPAS-Seaice.
+  #
+  # ncremap -P mpasseaice automatically tries to use
+  # timeMonthly_avg_iceAreaCell as sgs_frc_nm. However, that variable is
+  # time-dependent, with shape Time x nCells, while NCO requires sgs_frc_nm
+  # to be spatial-only, with shape nCells.
+  #
+  # Therefore, whenever timeMonthly_avg_iceAreaCell is available, construct:
+  #
+  #   sgs_frc_static(nCells) = time mean of timeMonthly_avg_iceAreaCell
+  #   sgs_msk_static(nCells) = 1 where sgs_frc_static > 0, else 0
+  #
+  # Do not fall back to implicit ncremap SGS handling when this helper can be
+  # constructed, because the implicit path may reuse the time-dependent field.
+  if run_nco ncks -m "${tmp_f}" | grep -q "timeMonthly_avg_iceAreaCell"; then
+
+    # Construct spatial-only SGS fraction helper.
+    run_nco ncwa -O -a "${time_dim}" -y avg \
+      -v timeMonthly_avg_iceAreaCell \
+      "${tmp_f}" "${tmp_frc}"
+
+    run_nco ncrename -O \
+      -v timeMonthly_avg_iceAreaCell,sgs_frc_static \
+      "${tmp_frc}"
+
+    # Construct a spatial-only binary SGS mask from the static fraction.
+    # This avoids relying on timeMonthly_avg_icePresentIntMask, which may
+    # not be present in every split file.
+    run_nco ncap2 -O \
+      -s 'sgs_msk_static=(sgs_frc_static > 0.0)' \
+      "${tmp_frc}" "${tmp_msk}"
+
+    run_nco ncks -O -x -v sgs_frc_static "${tmp_msk}" "${tmp_msk}.only_msk"
+    mv "${tmp_msk}.only_msk" "${tmp_msk}"
+
+    # Append helper variables to the temporary file.
+    # This does not remove or overwrite the original time-dependent variables.
+    run_nco ncks -A "${tmp_frc}" "${tmp_f}"
+    run_nco ncks -A "${tmp_msk}" "${tmp_f}"
+
+    use_sgs_helpers="true"
+  else
+    echo "ERROR: timeMonthly_avg_iceAreaCell is missing in ${tmp_f}; cannot construct static SGS helpers for MPAS-Seaice."
+    cd {{ scriptDir }}
+    echo 'ERROR (3)' > {{ prefix }}.status
+    exit 3
+  fi
+
+  {%- endif %}
+
+  if [ "${use_sgs_helpers}" == "true" ]; then
+    run_nco ncremap \
+      -P {{ prc_typ }} \
+      --d2f \
+      --no_stagger \
+      -t 1 \
+      --nco_opt='--no_tmp_fl --hdr_pad=10000' \
+      --map={{ mapping_file }} \
+      --sgs_frc=sgs_frc_static \
+      --sgs_msk=sgs_msk_static \
+      --sgs_nrm=1.0 \
+      "${tmp_f}" \
+      "${out_f}"
+  else
+    run_nco ncremap \
+      -P {{ prc_typ }} \
+      --d2f \
+      --no_stagger \
+      -t 1 \
+      --nco_opt='--no_tmp_fl --hdr_pad=10000' \
+      --map={{ mapping_file }} \
+      "${tmp_f}" \
+      "${out_f}"
+  fi
+
+  rc=$?
+
+  # Remove temporary/helper variables from the final regridded output.
+  # Keep timeMonthly_avg_iceAreaCell only when it is the requested main variable.
+  if [ ${rc} == 0 ] && [ "{{ prc_typ }}" == "mpasseaice" ]; then
+    vars_to_remove="sgs_frc_static,sgs_msk_static"
+
+    if [ "${main_var}" != "timeMonthly_avg_iceAreaCell" ]; then
+      vars_to_remove="${vars_to_remove},timeMonthly_avg_iceAreaCell"
+    fi
+
+    # Remove helper variables only if at least one is present in the output.
+    remove_present="false"
+    for rm_var in $(echo "${vars_to_remove}" | tr ',' ' '); do
+      if run_nco ncks -m "${out_f}" | grep -qE "^[[:space:]]*[^:]+[[:space:]]+${rm_var}(\(|\[)"; then
+        remove_present="true"
+        break
+      fi
+    done
+
+    if [ "${remove_present}" == "true" ]; then
+      run_nco ncks -O -x -v "${vars_to_remove}" "${out_f}" "${out_f}.clean"
+      mv "${out_f}.clean" "${out_f}"
+      rc=$?
+    fi
+  fi
+
+  # Restore MPAS-native time metadata variables if needed.
+  # MPAS files often have a Time dimension and xtime_* variables, but no
+  # standard numeric coordinate variable named Time/time.
+  if [ ${rc} == 0 ]; then
+    for tvar in xtime_startMonthly xtime_endMonthly timeMonthly_avg_daysSinceStartOfSim; do
+      if run_nco ncks -m "${tmp_f}" | grep -q "${tvar}"; then
+        if ! run_nco ncks -m "${out_f}" | grep -q "${tvar}"; then
+          run_nco ncks -A -v "${tvar}" "${tmp_f}" "${out_f}"
+          rc=$?
+          if [ ${rc} != 0 ]; then
+            break
+          fi
+        fi
+      fi
+    done
+  fi
+
+  # Construct a CF-style numeric time coordinate if it is missing.
+  # Use MPAS days-since-start metadata:
+  #
+  #   timeMonthly_avg_daysSinceStartOfSim(Time)
+  #
+  # to create:
+  #
+  #   time(Time)
+  #     units    = "days since ${mpas_start_time}"
+  #     calendar = "${mpas_calendar}"
+  #
+  # This improves compatibility with downstream tools that expect a
+  # standard numeric time coordinate.
+  if [ ${rc} == 0 ]; then
+    if ! run_nco ncks -m "${out_f}" | grep -qE "^[[:space:]]*(float|double)[[:space:]]+time(\(|\[)"; then
+      if run_nco ncks -m "${tmp_f}" | grep -q "timeMonthly_avg_daysSinceStartOfSim"; then
+        tmp_time="tmp_time_${bname}"
+
+        run_nco ncks -O \
+          -v timeMonthly_avg_daysSinceStartOfSim \
+          "${tmp_f}" "${tmp_time}"
+
+        run_nco ncrename -O \
+          -v timeMonthly_avg_daysSinceStartOfSim,time \
+          "${tmp_time}"
+
+        run_nco ncatted -O \
+          -a units,time,o,c,"days since ${mpas_start_time}" \
+          -a calendar,time,o,c,"${mpas_calendar}" \
+          -a long_name,time,o,c,time \
+          -a standard_name,time,o,c,time \
+          "${tmp_time}"
+
+        run_nco ncks -A -v time "${tmp_time}" "${out_f}"
+        rc=$?
+
+        rm -f "${tmp_time}"
+      fi
+    fi
+  fi
+
+  # Add missing_value metadata only for the main floating-point data variable
+  # if it is missing. Avoid modifying coordinate or integer mask variables.
+  # Do not force-create _FillValue here, because some NetCDF workflows are
+  # sensitive to adding _FillValue after variable creation. Existing _FillValue
+  # attributes are preserved.
+  if [ ${rc} == 0 ]; then
+    if run_nco ncks -m "${out_f}" | grep -qE "^[[:space:]]*(float|double)[[:space:]]+${main_var}(\(|\[)"; then
+      if ! run_nco ncks -m "${out_f}" | grep -A8 -E "^[[:space:]]*(float|double)[[:space:]]+${main_var}(\(|\[)" | grep -q "missing_value"; then
+        run_nco ncatted -O \
+          -a missing_value,"${main_var}",o,f,1.0e36 \
+          "${out_f}"
+        rc=$?
+      fi
+    fi
+  fi
+
+  rm -f "${tmp_f}" "${tmp_frc}" "${tmp_msk}" "${tmp_msk}.only_msk" "${out_f}.clean"
+
+  if [ ${rc} != 0 ]; then
+    echo "ERROR: MPAS component regridding failed for ${bname}"
+    cd {{ scriptDir }}
+    echo 'ERROR (4)' > {{ prefix }}.status
+    exit 4
+  fi
+
+done
+
+{%- endif %}
+
 {%- if vrt_remap_vars != '' %}
 
 # Vertical regrid (model levels → pressure levels)

From f17a7e11cb454cd498c199befa68c24f5ac4bb97 Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Sun, 28 Jun 2026 20:22:31 -0700
Subject: [PATCH 19/21] Update tests for MPAS TS defaults

Include mpas_calendar and mpas_start_time in expected TS config
dictionaries, and provide infer_section_parameters for the PCMDI
dependency unit test.
---
 tests/test_sections.py         | 14 ++++++++++++++
 tests/test_zppy_pcmdi_diags.py |  1 +
 2 files changed, 15 insertions(+)

diff --git a/tests/test_sections.py b/tests/test_sections.py
index 8b34fd42..c3e6364b 100644
--- a/tests/test_sections.py
+++ b/tests/test_sections.py
@@ -118,6 +118,8 @@ def test_sections():
         "input_component": "",
         "job_nbr": 0,
         "mapping_file": "MAPPING_FILE_TS",
+        "mpas_calendar": "noleap",
+        "mpas_start_time": "0001-01-01 00:00:00",
         "tpd": 1,
         "vars": "FSNTOA,FLUT,FSNT,FLNT,FSNS,FLNS,SHFLX,QFLX,PRECC,PRECL,PRECSC,PRECSL,TS,TREFHT",
         "vrt_remap_vars": "",
@@ -155,6 +157,8 @@ def test_sections():
         "input_subdir": "INPUT_SUBDIR",
         "job_nbr": 0,
         "mapping_file": "MAPPING_FILE_TS",
+        "mpas_calendar": "noleap",
+        "mpas_start_time": "0001-01-01 00:00:00",
         "ncclimo_cmd": "ncclimo",
         "nco_path": "",
         "nodes": 1,
@@ -333,6 +337,8 @@ def test_subsections():
             "input_component": None,
             "job_nbr": None,
             "mapping_file": "MAPPING_FILE_TS_GRID1",
+            "mpas_calendar": None,
+            "mpas_start_time": None,
             "tpd": None,
             "vrt_remap_vars": None,
             "vrt_in_file": None,
@@ -346,6 +352,8 @@ def test_subsections():
             "input_component": None,
             "job_nbr": None,
             "mapping_file": "MAPPING_FILE_TS_GRID2",
+            "mpas_calendar": None,
+            "mpas_start_time": None,
             "tpd": None,
             "vrt_remap_vars": None,
             "vrt_in_file": None,
@@ -353,6 +361,8 @@ def test_subsections():
             "years": ["0001:0020:10"],
         },
         "vars": "FSNTOA,FLUT,FSNT,FLNT,FSNS,FLNS,SHFLX,QFLX,PRECC,PRECL,PRECSC,PRECSL,TS,TREFHT",
+        "mpas_calendar": "noleap",
+        "mpas_start_time": "0001-01-01 00:00:00",
         "vrt_remap_vars": "",
         "vrt_in_file": "",
         "vrt_remap_file": "",
@@ -387,6 +397,8 @@ def test_subsections():
         "input_subdir": "INPUT_SUBDIR",
         "job_nbr": 0,
         "mapping_file": "MAPPING_FILE_TS_GRID1",
+        "mpas_calendar": "noleap",
+        "mpas_start_time": "0001-01-01 00:00:00",
         "ncclimo_cmd": "ncclimo",
         "nco_path": "",
         "nodes": 1,
@@ -442,6 +454,8 @@ def test_subsections():
         "input_subdir": "INPUT_SUBDIR",
         "job_nbr": 0,
         "mapping_file": "MAPPING_FILE_TS_GRID2",
+        "mpas_calendar": "noleap",
+        "mpas_start_time": "0001-01-01 00:00:00",
         "ncclimo_cmd": "ncclimo",
         "nco_path": "",
         "nodes": 1,
diff --git a/tests/test_zppy_pcmdi_diags.py b/tests/test_zppy_pcmdi_diags.py
index ef8656b9..74e5f878 100644
--- a/tests/test_zppy_pcmdi_diags.py
+++ b/tests/test_zppy_pcmdi_diags.py
@@ -542,6 +542,7 @@ def test_add_ts_dependencies():
     dependencies: List[str] = []
     c = {
         "current_set": "mean_climate",
+        "infer_section_parameters": True,
         "ts_num_years": 5,
     }
     script_dir = "/scripts"

From 9b02629f0cf25ad50f03e9d6bf49e26047d5f75e Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Sun, 28 Jun 2026 20:46:21 -0700
Subject: [PATCH 20/21] Remove obsolete mpas_rst_template default

---
 zppy/defaults/default.ini | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/zppy/defaults/default.ini b/zppy/defaults/default.ini
index 07b93b60..290a9429 100755
--- a/zppy/defaults/default.ini
+++ b/zppy/defaults/default.ini
@@ -131,8 +131,6 @@ climo_jobs = integer(default=0)
 vars = string(default="")
 # Model component having generated input files (eam, eamxx, elm, mosart, ...)
 input_component = string(default="")
-# MPAS model restart file template to guide the time series processing
-mpas_rst_template = string(default="")
 
   [[__many__]]
   exclude = boolean(default=None)
@@ -140,7 +138,6 @@ mpas_rst_template = string(default="")
   climo_jobs = integer(default=0)
   vars = string(default=None)
   input_component = string(default=None)
-  mpas_rst_template = string(default=None)
 
 [ts]
 area_nm = string(default="area")

From 984e77e47f779e6dc365ed22fcdccece1bcd0acb Mon Sep 17 00:00:00 2001
From: ShixuanZhang <shixuan.zhang@pnnl.gov>
Date: Mon, 29 Jun 2026 09:12:07 -0700
Subject: [PATCH 21/21] Save PCMDI mean climate data

---
 zppy/templates/pcmdi_diags.bash | 34 ++++++++++++++++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

diff --git a/zppy/templates/pcmdi_diags.bash b/zppy/templates/pcmdi_diags.bash
index d61f1c4f..e45e2527 100755
--- a/zppy/templates/pcmdi_diags.bash
+++ b/zppy/templates/pcmdi_diags.bash
@@ -18,7 +18,6 @@ export UCX_SHM_DEVICES=all # or not set UCX_NET_DEVICES at all
 # Make sure UVCDAT doesn't prompt us about anonymous logging
 export UVCDAT_ANONYMOUS_LOG=False
 
-
 # Use a non-interactive Matplotlib backend for batch diagnostics.
 # Safe for workflows that save figures to files and avoids GUI/Tkinter errors
 # on systems without a display.
@@ -1185,11 +1184,39 @@ if [ $? != 0 ]; then
 fi
 {% endif %}
 
+{% if current_set == "mean_climate" %}
+# optional, when save_all_data = True, also copy the mean climate nc data
+{% if save_all_data|lower == "true" %}
+cd ${workdir}
+
+clim_dir=${web_dir}/${run_type}/metrics_data/mean_climate/
+mkdir -p ${clim_dir}
+
+rsync -a climo ${clim_dir}/
+rc1=$?
+
+rsync -a climo_ref ${clim_dir}/
+rc2=$?
+
+if [ ${rc1} != 0 ] || [ ${rc2} != 0 ]; then
+  cd {{ scriptDir }}
+  echo 'ERROR (110)' > {{ prefix }}.status
+  exit 110
+fi
+{% endif %}
+{% endif %}
+
 {% if machine in ['pm-cpu', 'pm-gpu'] %}
 # For NERSC, change permissions of new files
 pushd ${web_dir}/
 chgrp -R e3sm ${results_dir}
 chmod -R go+rX,go-w ${results_dir}
+{% if current_set == "mean_climate" %}
+{% if save_all_data|lower == "true" %}
+chgrp -R e3sm ${run_type}/metrics_data/mean_climate
+chmod -R go+rX,go-w ${run_type}/metrics_data/mean_climate
+{% endif %}
+{% endif %}
 popd
 {% endif %}
 
@@ -1197,6 +1224,11 @@ popd
 # For LCRC, change permissions of new files
 pushd ${web_dir}/
 chmod -R go+rX,go-w ${results_dir}
+{% if current_set == "mean_climate" %}
+{% if save_all_data|lower == "true" %}
+chmod -R go+rX,go-w ${run_type}/metrics_data/mean_climate
+{% endif %}
+{% endif %}
 popd
 {% endif %}