Retire getic.sh and init.sh jobs from global-workflow (#1578)

This PR removes:
- `getic.sh` - job used to get initial conditions from HPSS from a past experiment/ops
- `init.sh` - job used to create experiment resolution specific initial conditions from the ones fetched by `getic.sh`.

Both these jobs were primarily used by the atmosphere model component developers in the past.
They have since been staging pre-generated ICs making these jobs obsolete.

Documentation will point to ufs-utils to generate the initial conditions.  The utilities from ufs-utils were used to identify the appropriate HPSS tarball as well as performing interpolation for the atmospheric model component.
There is no such utility available for the other model components making these scripts only partially useful.

In a future PR, an update to the definition of `BASE_CPLIC` and `coupled_ic` jobs will be made to make use of `--icsdir` to point to pre-staged locations of initial conditions.

Fixes #1569

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                     |               |             |                                                   |
 +----------------+------------------------------+---------------+-------------+---------------------------------------------------+

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
 

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"

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"

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"

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"

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

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}"