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"
diff --git a/zppy/defaults/default.ini b/zppy/defaults/default.ini
index 948fadbb..290a9429 100755
--- a/zppy/defaults/default.ini
+++ b/zppy/defaults/default.ini
@@ -151,6 +151,15 @@ 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
@@ -171,6 +180,8 @@ 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)
@@ -647,7 +658,7 @@ 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,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..a4ccfe4b 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."
             )
-            break  # Skip this task
+        #    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']}"
@@ -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
@@ -345,22 +332,79 @@ def define_relevant_years_for_synthetic_plots(c: Dict[str, Any]) -> None:
         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
@@ -370,6 +414,8 @@ 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..e45e2527 100755
--- a/zppy/templates/pcmdi_diags.bash
+++ b/zppy/templates/pcmdi_diags.bash
@@ -18,11 +18,27 @@ 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 }}
+
+# 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 +50,9 @@ 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 +91,10 @@ else
    fi
 fi
 
+# Format reference years after refinement
+ref_Y1="$(printf "%04d" ${ref_y1})"
+ref_Y2="$(printf "%04d" ${ref_y2})"
+
 {% if current_set == "mean_climate"%}
 source_vars="{{ clim_vars }}"
 {% elif current_set == "variability_modes_cpl"%}
@@ -124,7 +139,7 @@ case_id=v$(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 +164,7 @@ 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}"
 
@@ -160,7 +175,6 @@ 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
@@ -175,16 +189,51 @@ 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}'
@@ -192,19 +241,25 @@ 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}" "${combined_name}"
-
-    rm -vf "${v}_clm_"*.nc
+    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 ($((error_num + 5)))" > "${prefix}.status"
+    exit "$((error_num + 5))"
   fi
 
   cd ..
@@ -220,21 +275,20 @@ 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}"
 
   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
     local ttag tmp_file MM combined_name
 
     fname=$(basename "${file}")
-    if [[ ! ${fname} =~ ".nc" ]]; then
+    if [[ ${fname} != *.nc ]]; then
       # Skip non-.nc files
       continue
     fi
@@ -248,31 +302,47 @@ 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
@@ -281,11 +351,11 @@ 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
@@ -295,19 +365,31 @@ 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='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
@@ -315,6 +397,9 @@ 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 ..
@@ -359,33 +444,80 @@ 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
 
-      # Add time bounds
-      local cmdfix1='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}" "${combined_name}"
+      # Always overwrite time bounds
+      local cmdfix1='time_bnds=make_bounds(time,$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 "${error_num}"
+        echo "ERROR ($((error_num + 5)))" > "${prefix}.status"
+        exit "$((error_num + 5))"
       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 ($((error_num + 6)))" > "${prefix}.status"
+    exit "$((error_num + 6))"
   fi
 
   cd ..
@@ -409,77 +541,102 @@ 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
+    if [[ ${fname} != *.nc ]]; then
       # Skip non-.nc files
       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
 
     # Add time bounds
-    local cmdfix1='defdim("bnds",2)'
-    local cmdfix2='time_bnds=make_bounds(time,$bnds,"time_bnds")'
-    local cmdfix3='time_bnds@units=time@units'
-    local cmdfix4='time_bnds@calendar=time@calendar'
+    local cmdfix1='time_bnds=make_bounds(time,$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 "$((error_num + 2))"
+      echo "ERROR ($((error_num + 4)))" > "${prefix}.status"
+      exit "$((error_num + 4))"
     fi
     echo "ncap2 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 ($((error_num + 5)))" > "${prefix}.status"
+      exit "$((error_num + 5))"
+    fi
+    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 + 6)))" > "${prefix}.status"
+    exit "$((error_num + 6))"
   fi
 
   cd ..
@@ -497,13 +654,13 @@ 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 %}
 
@@ -513,13 +670,13 @@ 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 %}
 
@@ -545,12 +702,12 @@ 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
@@ -565,12 +722,12 @@ 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 %}
@@ -872,11 +1029,54 @@ 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" %}
@@ -891,7 +1091,7 @@ 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 +1114,7 @@ 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 +1122,7 @@ 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 %}
 
@@ -936,8 +1136,8 @@ 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
@@ -954,8 +1154,8 @@ 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'] %}
@@ -979,16 +1179,44 @@ 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 %}
 
+{% 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 %}
 
@@ -996,6 +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 %}
 
diff --git a/zppy/templates/ts.bash b/zppy/templates/ts.bash
index e49b9a99..9bba3434 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 %}
@@ -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 }} \
@@ -104,14 +108,262 @@ 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
   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)
@@ -156,8 +408,8 @@ 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 != '' %}
diff --git a/zppy/utils.py b/zppy/utils.py
index 4afff338..ed9c0272 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 = "mpasocean"
+    elif tmp in ("mpassi",):
+        component = "ice"
+        prc_typ = "mpasseaice"
     else:
         raise ValueError(
             f"Cannot extract output component name from {c['input_component']} or {c['input_files']}."