From 5e739610bbd15886004b804e290305e484cd934a Mon Sep 17 00:00:00 2001
From: Ryan Forsyth <forsyth2@llnl.gov>
Date: Tue, 5 Sep 2023 13:18:54 -0500
Subject: [PATCH] Make e3sm_to_cmip task

---
 zppy/templates/e3sm_to_cmip.bash | 96 ++++++++++++++++++++++++++++++++
 zppy/templates/ts.bash           | 60 --------------------
 2 files changed, 96 insertions(+), 60 deletions(-)
 create mode 100644 zppy/templates/e3sm_to_cmip.bash

diff --git a/zppy/templates/e3sm_to_cmip.bash b/zppy/templates/e3sm_to_cmip.bash
new file mode 100644
index 00000000..73838dbc
--- /dev/null
+++ b/zppy/templates/e3sm_to_cmip.bash
@@ -0,0 +1,96 @@
+#!/bin/bash
+{% include 'slurm_header.sh' %}
+{{ environment_commands }}
+
+# Turn on debug output if needed
+debug={{ debug }}
+if [[ "${debug,,}" == "true" ]]; then
+  set -x
+fi
+
+# Script dir
+cd {{ scriptDir }}
+
+# Get jobid
+id=${SLURM_JOBID}
+
+# Update status file
+STARTTIME=$(date +%s)
+echo "RUNNING ${id}" > {{ prefix }}.status
+
+# Create temporary workdir
+workdir=`mktemp -d tmp.${id}.XXXX`
+cd ${workdir}
+
+# Create symbolic links to input files
+input={{ input }}/{{ input_subdir }}
+for (( year={{ yr_start }}; year<={{ yr_end }}; year++ ))
+do
+  YYYY=`printf "%04d" ${year}`
+  for file in ${input}/{{ case }}.{{ input_files }}.${YYYY}-*.nc
+  do
+    ln -s ${file} .
+  done
+done
+
+
+
+
+
+tmp_dir=tmp_{{ prefix }}
+
+# Generate CMIP ts
+cat > default_metadata.json << EOF
+{% include cmip_metadata %}
+EOF
+{
+  export cmortables_dir={{ cmor_tables_prefix }}/cmip6-cmor-tables/Tables
+  input_dir={{ output }}/post/{{ component }}/{{ grid }}/ts/{{ frequency }}/{{ '%dyr' % (ypf) }}
+  dest_cmip={{ output }}/post/{{ component }}/{{ grid }}/cmip_ts/{{ frequency }}
+  mkdir -p ${dest_cmip}
+  srun -N 1 e3sm_to_cmip \
+  --output-path \
+  ${dest_cmip}/${tmp_dir} \
+  {% if input_files.split(".")[0] == 'clm2' or input_files.split(".")[0] == 'elm' -%}
+  --var-list \
+  'mrsos, mrso, mrfso, mrros, mrro, prveg, evspsblveg, evspsblsoi, tran, tsl, lai, cLitter, cProduct, cSoilFast, cSoilMedium, cSoilSlow, fFire, fHarvest, cVeg, nbp, gpp, ra, rh' \
+  --realm \
+  lnd \
+  {% endif -%}
+  {% if input_files.split(".")[0] == 'cam' or input_files.split(".")[0] == 'eam' -%}
+  --var-list \
+  'pr, tas, rsds, rlds, rsus' \
+  --realm \
+  atm \
+  {% endif -%}
+  --input-path \
+  ${input_dir}\
+  --user-metadata \
+  {{ scriptDir }}/${workdir}/default_metadata.json \
+  --num-proc \
+  12 \
+  --tables-path \
+  ${cmortables_dir}
+
+  if [ $? != 0 ]; then
+    cd {{ scriptDir }}
+    echo 'ERROR (1)' > {{ prefix }}.status
+    exit 1
+  fi
+
+  # Move output ts files to final destination
+  mv ${dest_cmip}/${tmp_dir}/CMIP6/CMIP/*/*/*/*/*/*/*/*/*.nc ${dest_cmip}
+  if [ $? != 0 ]; then
+    cd {{ scriptDir }}
+    echo 'ERROR (2)' > {{ prefix }}.status
+    exit 2
+  fi
+
+      rm -r ${dest_cmip}/${tmp_dir}
+
+}
+if [ $? != 0 ]; then
+  cd {{ scriptDir }}
+  echo 'ERROR (3)' > {{ prefix }}.status
+  exit 3
+fi
diff --git a/zppy/templates/ts.bash b/zppy/templates/ts.bash
index ee9f82dc..f9d0d9e7 100644
--- a/zppy/templates/ts.bash
+++ b/zppy/templates/ts.bash
@@ -136,66 +136,6 @@ if [ $? != 0 ]; then
   exit 3
 fi
 
-{%- if ts_fmt != 'ts_only' %}
-tmp_dir=tmp_{{ prefix }}
-
-# Generate CMIP ts
-cat > default_metadata.json << EOF
-{% include cmip_metadata %}
-EOF
-{
-  export cmortables_dir={{ cmor_tables_prefix }}/cmip6-cmor-tables/Tables
-  input_dir={{ output }}/post/{{ component }}/{{ grid }}/ts/{{ frequency }}/{{ '%dyr' % (ypf) }}
-  dest_cmip={{ output }}/post/{{ component }}/{{ grid }}/cmip_ts/{{ frequency }}
-  mkdir -p ${dest_cmip}
-  srun -N 1 e3sm_to_cmip \
-  --output-path \
-  ${dest_cmip}/${tmp_dir} \
-  {% if input_files.split(".")[0] == 'clm2' or input_files.split(".")[0] == 'elm' -%}
-  --var-list \
-  'mrsos, mrso, mrfso, mrros, mrro, prveg, evspsblveg, evspsblsoi, tran, tsl, lai, cLitter, cProduct, cSoilFast, cSoilMedium, cSoilSlow, fFire, fHarvest, cVeg, nbp, gpp, ra, rh' \
-  --realm \
-  lnd \
-  {% endif -%}
-  {% if input_files.split(".")[0] == 'cam' or input_files.split(".")[0] == 'eam' -%}
-  --var-list \
-  'pr, tas, rsds, rlds, rsus' \
-  --realm \
-  atm \
-  {% endif -%}
-  --input-path \
-  ${input_dir}\
-  --user-metadata \
-  {{ scriptDir }}/${workdir}/default_metadata.json \
-  --num-proc \
-  12 \
-  --tables-path \
-  ${cmortables_dir}
-
-  if [ $? != 0 ]; then
-    cd {{ scriptDir }}
-    echo 'ERROR (4)' > {{ prefix }}.status
-    exit 4
-  fi
-
-  # Move output ts files to final destination
-  mv ${dest_cmip}/${tmp_dir}/CMIP6/CMIP/*/*/*/*/*/*/*/*/*.nc ${dest_cmip}
-  if [ $? != 0 ]; then
-    cd {{ scriptDir }}
-    echo 'ERROR (5)' > {{ prefix }}.status
-    exit 5
-  fi
-
-      rm -r ${dest_cmip}/${tmp_dir}
-
-}
-if [ $? != 0 ]; then
-  cd {{ scriptDir }}
-  echo 'ERROR (6)' > {{ prefix }}.status
-  exit 6
-fi
-{%- endif %}
-
 # Delete temporary workdir
 cd ..
 if [[ "${debug,,}" != "true" ]]; then