Merge remote-tracking branch 'origin/develop' into feature/epic-stack

* origin/develop: Redo v16.3 GSI script updates to scripts/exglobal_atmos_analysis.sh (NOAA-EMC#1535) Fix bugs in the COM refactor of marine DA (NOAA-EMC#1566) Retire `getic.sh` and `init.sh` jobs from global-workflow (NOAA-EMC#1578) New UFS_UTILS hash for gdas_init COM reorg updates (NOAA-EMC#1581) Update documentation for PR standards (NOAA-EMC#1573)
KateFriedman-NOAA · May 9, 2023 · a9acca0 · a9acca0
2 parents 1266c36 + 2fd43d1
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diff --git a/Externals.cfg b/Externals.cfg
@@ -15,7 +15,7 @@ protocol = git
 required = True
 
 [UFS-Utils]
-hash = 5b67e4d
+hash = 72a0471
 local_path = sorc/ufs_utils.fd
 repo_url = https://github.com/ufs-community/UFS_UTILS.git
 protocol = git

diff --git a/docs/source/configure.rst b/docs/source/configure.rst
@@ -48,9 +48,6 @@ The global-workflow configs contain switches that change how the system runs. Ma
 | QUILTING       | Use I/O quilting             | .true.        | NO          | If .true. choose OUTPUT_GRID as cubed_sphere_grid |
 |                |                              |               |             | in netcdf or gaussian_grid                        |
 +----------------+------------------------------+---------------+-------------+---------------------------------------------------+
-| RETRO          | Use retrospective parallel   | NO            | NO          | Default of NO will tell getic job to pull from    |
-|                | for ICs                      |               |             | production tapes.                                 |
-+----------------+------------------------------+---------------+-------------+---------------------------------------------------+
 | WAFSF          | Run jobs to produce WAFS     | NO            | YES         | downstream processing, ops only                   |
 |                | products                     |               |             |                                                   |
 +----------------+------------------------------+---------------+-------------+---------------------------------------------------+

diff --git a/docs/source/development.rst b/docs/source/development.rst
@@ -92,21 +92,21 @@ All new code after 2022 Sep 1 will be required to meet these standards. We will
 
 .. _commit-standards:
 
-========================
-Commit message standards
-========================
+======================
+Pull request standards
+======================
 
-**ALL** commits must follow best practices for commit messages: https://chris.beams.io/posts/git-commit/
+Pull requests should follow the pre-filled template provided when you open the PR. PR titles and descriptions become the commit message when the PR is squashed and merged, so we ask that they follow best practices for commit messages:
 
- * Separate subject from body with a blank line
- * Limit the subject line to 50 characters
+ * Limit the subject line (PR title) to 50 characters
  * Capitalize the subject line
  * Do not end the subject line with a period
  * Use the `imperative mood <https://en.wikipedia.org/wiki/Imperative_mood>`_ in the subject line
- * Wrap the body at 72 characters
  * Use the body to explain what and why vs. how
  * The final line of the commit message should include tags to relevant issues (e.g. ``Refs: #217, #300``)
 
+This list is a modified version of the one provided at https://chris.beams.io/posts/git-commit/ with a couple removed that are not relevant to GitHub PRs. That source also provides the motivation for making sure we have good commit messages.
+
 Here is the example commit message from the article linked above; it includes descriptions of what would be in each part of the commit message for guidance:
 
 ::

diff --git a/docs/source/init.rst b/docs/source/init.rst
@@ -261,9 +261,7 @@ Coupled initial conditions are currently only generated offline and copied prior
 Forecast-only mode (atm-only)
 -----------------------------
 
-Forecast-only mode in global workflow includes ``getic`` and ``init`` jobs for the gfs suite. The ``getic`` job pulls inputs for ``chgres_cube`` (init job) or warm start ICs into your ``ROTDIR/COMROT``. The ``init`` job then ingests those files to produce initial conditions for your experiment. 
-
-Users on machines without HPSS access (e.g. Orion) need to perform the ``getic`` step manually and stage inputs for the ``init`` job. The table below lists the needed files for ``init`` and where to place them in your ``ROTDIR``.
+The table below lists the needed initial condition files from past GFS versions to be used by the UFS_UTILS gdas_init utility. The utility will pull these files for you. See the next section (Manual Generation) for how to run the UFS_UTILS gdas_init utility and create initial conditions for your experiment.
 
 Note for table: yyyy=year; mm=month; dd=day; hh=cycle
 

diff --git a/env/HERA.env b/env/HERA.env
@@ -261,10 +261,6 @@ elif [[ "${step}" = "epos" ]]; then
     [[ ${NTHREADS_EPOS} -gt ${nth_max} ]] && export NTHREADS_EPOS=${nth_max}
     export APRUN_EPOS="${launcher} -n ${npe_epos}"
 
-elif [[ "${step}" = "init" ]]; then
-
-    export APRUN="${launcher} -n ${npe_init}"
-
 elif [[ "${step}" = "postsnd" ]]; then
 
     export CFP_MP="YES"

diff --git a/env/JET.env b/env/JET.env
@@ -231,10 +231,6 @@ elif [[ "${step}" = "epos" ]]; then
     [[ ${NTHREADS_EPOS} -gt ${nth_max} ]] && export NTHREADS_EPOS=${nth_max}
     export APRUN_EPOS="${launcher} -n ${npe_epos}"
 
-elif [[ "${step}" = "init" ]]; then
-
-    export APRUN="${launcher} -n ${npe_init}"
-
 elif [[ "${step}" = "postsnd" ]]; then
 
     export CFP_MP="YES"

diff --git a/env/ORION.env b/env/ORION.env
@@ -260,10 +260,6 @@ elif [[ "${step}" = "epos" ]]; then
     [[ ${NTHREADS_EPOS} -gt ${nth_max} ]] && export NTHREADS_EPOS=${nth_max}
     export APRUN_EPOS="${launcher} -n ${npe_epos}"
 
-elif [[ "${step}" = "init" ]]; then
-
-    export APRUN="${launcher} -n ${npe_init}"
-
 elif [[ "${step}" = "postsnd" ]]; then
 
     export CFP_MP="YES"

diff --git a/env/S4.env b/env/S4.env
@@ -234,10 +234,6 @@ elif [[ "${step}" = "epos" ]]; then
     [[ ${NTHREADS_EPOS} -gt ${nth_max} ]] && export NTHREADS_EPOS=${nth_max}
     export APRUN_EPOS="${launcher} -n ${npe_epos}"
 
-elif [[ "${step}" = "init" ]]; then
-
-    export APRUN="${launcher} -n ${npe_init}"
-
 elif [[ "${step}" = "postsnd" ]]; then
 
     export CFP_MP="YES"

diff --git a/env/WCOSS2.env b/env/WCOSS2.env
@@ -249,10 +249,6 @@ elif [[ "${step}" = "epos" ]]; then
     [[ ${NTHREADS_EPOS} -gt ${nth_max} ]] && export NTHREADS_EPOS=${nth_max}
     export APRUN_EPOS="${launcher} -n ${npe_epos} -ppn ${npe_node_epos} --cpu-bind depth --depth ${NTHREADS_EPOS}"
 
-elif [[ "${step}" = "init" ]]; then
-
-    export APRUN="${launcher}"
-
 elif [[ "${step}" = "postsnd" ]]; then
 
     export MPICH_MPIIO_HINTS_DISPLAY=1

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
@@ -23,8 +23,9 @@ export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 
 # Generate COM variables from templates
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_HISTORY:COM_ATMOS_HISTORY_TMPL
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
+YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS
+
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
 
 
 ##############################################

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
@@ -2,7 +2,7 @@
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
 export WIPE_DATA="NO"
-DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
+export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalpost" -c "base ocnanalpost"
 
 
@@ -14,8 +14,7 @@ export CDATE=${CDATE:-${PDY}${cyc}}
 export GDUMP=${GDUMP:-"gdas"}
 
 # Generate COM variables from templates
-RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_OCEAN_ANALYSIS:COM_OCEAN_ANALYSIS_TMPL
-RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_ICE_RESTART
+YMD=${PDY} HH=${cyc} generate_com -rx COM_OCEAN_ANALYSIS COM_ICE_RESTART
 
 mkdir -p "${COM_OCEAN_ANALYSIS}"
 mkdir -p "${COM_ICE_RESTART}"

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
@@ -22,11 +22,12 @@ export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 
 # Generate COM variables from templates
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_OCEAN_HISTORY:COM_OCEAN_HISTORY_TMPL
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ICE_HISTORY:COM_ICE_HISTORY_TMPL
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ICE_RESTART:COM_ICE_RESTART_TMPL
-
+YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
 
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx \
+   COM_OCEAN_HISTORY_PREV:COM_OCEAN_HISTORY_TMPL \
+   COM_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL \
+   COM_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
 
 ##############################################
 # Begin JOB SPECIFIC work

diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
@@ -6,11 +6,14 @@ export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalrun"
 
 
+##############################################
+# Set variables used in the script
+##############################################
+
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
 
-export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
 
 ###############################################################
 # Run relevant script

diff --git a/jobs/rocoto/coupled_ic.sh b/jobs/rocoto/coupled_ic.sh
@@ -44,25 +44,22 @@ error_message(){
     echo "FATAL ERROR: Unable to copy ${1} to ${2} (Error code ${3})"
 }
 
-YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_INPUT COM_ICE_RESTART COM_WAVE_RESTART
-YMD=${gPDY} HH=${gcyc} generate_com -rx COM_OCEAN_RESTART
-
 ###############################################################
 # Start staging
 
 # Stage the FV3 initial conditions to ROTDIR (cold start)
-ATMdir="${COM_ATMOS_INPUT}"
-[[ ! -d "${ATMdir}" ]] && mkdir -p "${ATMdir}"
+YMD=${PDY} HH=${cyc} generate_com -r COM_ATMOS_INPUT
+[[ ! -d "${COM_ATMOS_INPUT}" ]] && mkdir -p "${COM_ATMOS_INPUT}"
 source="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${CDUMP}/${CASE}/INPUT/gfs_ctrl.nc"
-target="${ATMdir}/gfs_ctrl.nc"
+target="${COM_ATMOS_INPUT}/gfs_ctrl.nc"
 ${NCP} "${source}" "${target}"
 rc=$?
 [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
 err=$((err + rc))
 for ftype in gfs_data sfc_data; do
   for tt in $(seq 1 6); do
     source="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${CDUMP}/${CASE}/INPUT/${ftype}.tile${tt}.nc"
-    target="${ATMdir}/${ftype}.tile${tt}.nc"
+    target="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
     ${NCP} "${source}" "${target}"
     rc=$?
     [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
@@ -71,52 +68,56 @@ for ftype in gfs_data sfc_data; do
 done
 
 # Stage ocean initial conditions to ROTDIR (warm start)
-OCNdir="${COM_OCEAN_RESTART}"
-[[ ! -d "${OCNdir}" ]] && mkdir -p "${OCNdir}"
-source="${BASE_CPLIC}/${CPL_OCNIC}/${PDY}${cyc}/ocn/${OCNRES}/MOM.res.nc"
-target="${OCNdir}/${PDY}.${cyc}0000.MOM.res.nc"
-${NCP} "${source}" "${target}"
-rc=$?
-[[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
-err=$((err + rc))
-case $OCNRES in
-  "025")
-    for nn in $(seq 1 4); do
-      source="${BASE_CPLIC}/${CPL_OCNIC}/${PDY}${cyc}/ocn/${OCNRES}/MOM.res_${nn}.nc"
-      if [[ -f "${source}" ]]; then
-        target="${OCNdir}/${PDY}.${cyc}0000.MOM.res_${nn}.nc"
-        ${NCP} "${source}" "${target}"
-        rc=$?
-        [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
-        err=$((err + rc))
-      fi
-    done
-  ;;
-  *)
-    echo "FATAL ERROR: Unsupported ocean resolution ${OCNRES}"
-    rc=1
-    err=$((err + rc))
-  ;;
-esac
+if [[ "${DO_OCN:-}" = "YES" ]]; then
+  YMD=${gPDY} HH=${gcyc} generate_com -r COM_OCEAN_RESTART
+  [[ ! -d "${COM_OCEAN_RESTART}" ]] && mkdir -p "${COM_OCEAN_RESTART}"
+  source="${BASE_CPLIC}/${CPL_OCNIC}/${PDY}${cyc}/ocn/${OCNRES}/MOM.res.nc"
+  target="${COM_OCEAN_RESTART}/${PDY}.${cyc}0000.MOM.res.nc"
+  ${NCP} "${source}" "${target}"
+  rc=$?
+  [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+  err=$((err + rc))
+  case "${OCNRES}" in
+    "025")
+      for nn in $(seq 1 4); do
+        source="${BASE_CPLIC}/${CPL_OCNIC}/${PDY}${cyc}/ocn/${OCNRES}/MOM.res_${nn}.nc"
+        if [[ -f "${source}" ]]; then
+          target="${COM_OCEAN_RESTART}/${PDY}.${cyc}0000.MOM.res_${nn}.nc"
+          ${NCP} "${source}" "${target}"
+          rc=$?
+          [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+          err=$((err + rc))
+        fi
+      done
+    ;;
+    *)
+      echo "FATAL ERROR: Unsupported ocean resolution ${OCNRES}"
+      rc=1
+      err=$((err + rc))
+    ;;
+  esac
+fi
 
 # Stage ice initial conditions to ROTDIR (cold start as these are SIS2 generated)
-ICEdir="${COM_ICE_RESTART}"
-[[ ! -d "${ICEdir}" ]] && mkdir -p "${ICEdir}"
-ICERESdec=$(echo "${ICERES}" | awk '{printf "%0.2f", $1/100}')
-source="${BASE_CPLIC}/${CPL_ICEIC}/${PDY}${cyc}/ice/${ICERES}/cice5_model_${ICERESdec}.res_${PDY}${cyc}.nc"
-target="${ICEdir}/${PDY}.${cyc}0000.cice_model.res.nc"
-${NCP} "${source}" "${target}"
-rc=$?
-[[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
-err=$((err + rc))
+if [[ "${DO_ICE:-}" = "YES" ]]; then
+  YMD=${PDY} HH=${cyc} generate_com -r COM_ICE_RESTART
+  [[ ! -d "${COM_ICE_RESTART}" ]] && mkdir -p "${COM_ICE_RESTART}"
+  ICERESdec=$(echo "${ICERES}" | awk '{printf "%0.2f", $1/100}')
+  source="${BASE_CPLIC}/${CPL_ICEIC}/${PDY}${cyc}/ice/${ICERES}/cice5_model_${ICERESdec}.res_${PDY}${cyc}.nc"
+  target="${COM_ICE_RESTART}/${PDY}.${cyc}0000.cice_model.res.nc"
+  ${NCP} "${source}" "${target}"
+  rc=$?
+  [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+  err=$((err + rc))
+fi
 
 # Stage the WW3 initial conditions to ROTDIR (warm start; TODO: these should be placed in $RUN.$gPDY/$gcyc)
-if [[ "${DO_WAVE}" = "YES" ]]; then
-  WAVdir="${COM_WAVE_RESTART}"
-  [[ ! -d "${WAVdir}" ]] && mkdir -p "${WAVdir}"
+if [[ "${DO_WAVE:-}" = "YES" ]]; then
+  YMD=${PDY} HH=${cyc} generate_com -r COM_WAVE_RESTART
+  [[ ! -d "${COM_WAVE_RESTART}" ]] && mkdir -p "${COM_WAVE_RESTART}"
   for grdID in ${waveGRD}; do  # TODO: check if this is a bash array; if so adjust
     source="${BASE_CPLIC}/${CPL_WAVIC}/${PDY}${cyc}/wav/${grdID}/${PDY}.${cyc}0000.restart.${grdID}"
-    target="${WAVdir}/${PDY}.${cyc}0000.restart.${grdID}"
+    target="${COM_WAVE_RESTART}/${PDY}.${cyc}0000.restart.${grdID}"
     ${NCP} "${source}" "${target}"
     rc=$?
     [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"