From aff6ca7ae559e424dae128d6cfd5da4a4e3049e7 Mon Sep 17 00:00:00 2001
From: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com>
Date: Fri, 27 Oct 2023 14:11:55 -0400
Subject: [PATCH] GEFS Staging in exglobal_stage_ic  (#1892)

Adjusts source paths for forecast-only ICs in support of extension to ensembles.
New paths omit the resolution (that is captured by the IC id name) and allow for
a member level.

Directories with the reorganized ICs have been added to the three tier-1 machines
under glopara space.

Building on this, also adds capability to stage GEFS ICs.

Resolves #911
---
 parm/config/gefs/config.base.emc.dyn |   1 +
 parm/config/gefs/config.coupled_ic   |  43 --------
 parm/config/gefs/config.resources    |  12 +--
 parm/config/gefs/config.stage_ic     |  23 +++++
 parm/config/gfs/config.stage_ic      |  24 ++---
 scripts/exglobal_stage_ic.sh         | 148 +++++++++++++--------------
 workflow/applications/gefs.py        |   4 +-
 workflow/hosts/hera.yaml             |   2 +-
 workflow/hosts/wcoss2.yaml           |   2 +-
 workflow/rocoto/gefs_tasks.py        |  58 ++++++++++-
 workflow/rocoto/gfs_tasks.py         |  19 ++--
 workflow/setup_expt.py               |  11 +-
 12 files changed, 181 insertions(+), 166 deletions(-)
 delete mode 100644 parm/config/gefs/config.coupled_ic
 create mode 100644 parm/config/gefs/config.stage_ic

diff --git a/parm/config/gefs/config.base.emc.dyn b/parm/config/gefs/config.base.emc.dyn
index 3d17421408..b62c921ed0 100644
--- a/parm/config/gefs/config.base.emc.dyn
+++ b/parm/config/gefs/config.base.emc.dyn
@@ -40,6 +40,7 @@ export FIXreg2grb2=${HOMEgfs}/fix/reg2grb2
 export PACKAGEROOT="@PACKAGEROOT@"    # TODO: set via prod_envir in Ops
 export COMROOT="@COMROOT@"    # TODO: set via prod_envir in Ops
 export COMINsyn="@COMINsyn@"
+export BASE_CPLIC="@BASE_CPLIC@"
 
 # USER specific paths
 export HOMEDIR="@HOMEDIR@"
diff --git a/parm/config/gefs/config.coupled_ic b/parm/config/gefs/config.coupled_ic
deleted file mode 100644
index 50fab283b5..0000000000
--- a/parm/config/gefs/config.coupled_ic
+++ /dev/null
@@ -1,43 +0,0 @@
-#! /usr/bin/env bash
-
-########## config.coupled_ic ##########
-
-echo "BEGIN: config.coupled_ic"
-
-# Get task specific resources
-source ${EXPDIR}/config.resources coupled_ic
-
-if [[ "${machine}" == "WCOSS2" ]]; then
-  export BASE_CPLIC="/lfs/h2/emc/couple/noscrub/Jiande.Wang/IC"
-elif [[ "${machine}" == "HERA" ]]; then
-  export BASE_CPLIC="/scratch1/NCEPDEV/climate/role.ufscpara/IC"
-elif [[ "${machine}" == "ORION" ]]; then
-  export BASE_CPLIC="/work/noaa/global/glopara/data/ICSDIR/prototype_ICs"
-elif [[ "${machine}" == "S4" ]]; then
-  export BASE_CPLIC="/data/prod/glopara/coupled_ICs"
-elif [[ "${machine}" == "JET" ]]; then
-  export BASE_CPLIC="/mnt/lfs4/HFIP/hfv3gfs/glopara/data/ICSDIR/prototype_ICs"
-fi
-
-
-case "${CASE}" in
-  "C384")
-    #C384 and P8 ICs
-    export CPL_ATMIC=GEFS-NoahMP-aerosols-p8c
-    export CPL_ICEIC=CPC
-    export CPL_OCNIC=CPC3Dvar
-    export CPL_WAVIC=GEFSwave20210528v2
-    ;;
-  "C768")
-    export CPL_ATMIC=HR1
-    export CPL_ICEIC=HR1
-    export CPL_OCNIC=HR1
-    export CPL_WAVIC=HR1
-    ;;
-  *)
-    echo "Unrecognized case: ${1}"
-    exit 1
-    ;;
-esac
-
-echo "END: config.coupled_ic"
diff --git a/parm/config/gefs/config.resources b/parm/config/gefs/config.resources
index 33156a768a..74e9854084 100644
--- a/parm/config/gefs/config.resources
+++ b/parm/config/gefs/config.resources
@@ -8,7 +8,7 @@ if [[ $# -ne 1 ]]; then
 
     echo "Must specify an input task argument to set resource variables!"
     echo "argument can be any one of the following:"
-    echo "coupled_ic aerosol_init"
+    echo "stage_ic aerosol_init"
     echo "sfcanl analcalc analdiag fcst post vrfy fit2obs metp arch echgres"
     echo "ecen esfc efcs epos earc"
     echo "init_chem mom6ic ocnpost"
@@ -416,12 +416,12 @@ elif [[ ${step} = "arch" || ${step} = "earc" ]]; then
       eval "export memory_${step}=50GB"
     fi
 
-elif [[ ${step} = "coupled_ic" ]]; then
+elif [[ ${step} = "stage_ic" ]]; then
 
-    export wtime_coupled_ic="00:15:00"
-    export npe_coupled_ic=1
-    export npe_node_coupled_ic=1
-    export nth_coupled_ic=1
+    export wtime_stage_ic="00:15:00"
+    export npe_stage_ic=1
+    export npe_node_stage_ic=1
+    export nth_stage_ic=1
     export is_exclusive=True
 
 elif [[ ${step} = "ecen" ]]; then
diff --git a/parm/config/gefs/config.stage_ic b/parm/config/gefs/config.stage_ic
new file mode 100644
index 0000000000..e2bb0af2b8
--- /dev/null
+++ b/parm/config/gefs/config.stage_ic
@@ -0,0 +1,23 @@
+#! /usr/bin/env bash
+
+########## config.stage_ic ##########
+
+echo "BEGIN: config.stage_ic"
+
+# Get task specific resources
+source "${EXPDIR}/config.resources" stage_ic
+
+case "${CASE}" in
+  "C48")
+    export CPL_ATMIC="gefs_test"
+    export CPL_ICEIC="gefs_test"
+    export CPL_OCNIC="gefs_test"
+    export CPL_WAVIC="gefs_test"
+    ;;
+  *)
+    echo "FATAL ERROR Unrecognized resolution: ${CASE}"
+    exit 1
+    ;;
+esac
+
+echo "END: config.stage_ic"
diff --git a/parm/config/gfs/config.stage_ic b/parm/config/gfs/config.stage_ic
index 4e29c3306e..6d081b3fe0 100644
--- a/parm/config/gfs/config.stage_ic
+++ b/parm/config/gfs/config.stage_ic
@@ -9,22 +9,22 @@ source "${EXPDIR}/config.resources" stage_ic
 
 case "${CASE}" in
   "C48" | "C96")
-    export CPL_ATMIC=workflowtest
-    export CPL_ICEIC=workflowtest
-    export CPL_OCNIC=workflowtest
-    export CPL_WAVIC=workflowtest
+    export CPL_ATMIC="workflow_${CASE}_refactored"
+    export CPL_ICEIC="workflow_${CASE}_refactored"
+    export CPL_OCNIC="workflow_${CASE}_refactored"
+    export CPL_WAVIC="workflow_${CASE}_refactored"
     ;;
   "C384")
-    export CPL_ATMIC=GEFS-NoahMP-aerosols-p8c
-    export CPL_ICEIC=CPC
-    export CPL_OCNIC=CPC3Dvar
-    export CPL_WAVIC=GEFSwave20210528v2
+    export CPL_ATMIC=GEFS-NoahMP-aerosols-p8c_refactored
+    export CPL_ICEIC=CPC_refactored
+    export CPL_OCNIC=CPC3Dvar_refactored
+    export CPL_WAVIC=GEFSwave20210528v2_refactored
     ;;
   "C768")
-    export CPL_ATMIC=HR2
-    export CPL_ICEIC=HR1
-    export CPL_OCNIC=HR1
-    export CPL_WAVIC=HR1
+    export CPL_ATMIC=HR2_refactored
+    export CPL_ICEIC=HR1_refactored
+    export CPL_OCNIC=HR1_refactored
+    export CPL_WAVIC=HR1_refactored
     ;;
   *)
     echo "FATAL ERROR Unrecognized resolution: ${CASE}"
diff --git a/scripts/exglobal_stage_ic.sh b/scripts/exglobal_stage_ic.sh
index e42a4943d4..fc95fa6654 100755
--- a/scripts/exglobal_stage_ic.sh
+++ b/scripts/exglobal_stage_ic.sh
@@ -1,4 +1,4 @@
-#! /usr/bin/env bash
+#!/usr/bin/env bash
 
 source "${HOMEgfs}/ush/preamble.sh"
 
@@ -8,99 +8,89 @@ GDATE=$(date --utc -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)
 gPDY="${GDATE:0:8}"
 gcyc="${GDATE:8:2}"
 
+MEMDIR_ARRAY=()
+if [[ "${RUN}" == "gefs" ]]; then
+  # Populate the member_dirs array based on the value of NMEM_ENS
+  for ((ii = 0; ii <= "${NMEM_ENS}"; ii++)); do
+    MEMDIR_ARRAY+=("mem$(printf "%03d" "${ii}")")
+  done
+else
+  MEMDIR_ARRAY+=("")
+fi
+
 # Initialize return code
 err=0
 
-error_message(){
-    echo "FATAL ERROR: Unable to copy ${1} to ${2} (Error code ${3})"
+error_message() {
+  echo "FATAL ERROR: Unable to copy ${1} to ${2} (Error code ${3})"
 }
 
 ###############################################################
-# Start staging
-
-# Stage the FV3 initial conditions to ROTDIR (cold start)
-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="${COM_ATMOS_INPUT}/gfs_ctrl.nc"
-${NCP} "${source}" "${target}"
-rc=$?
-(( rc != 0 )) && error_message "${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${tt}.nc"
-    target="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
-    ${NCP} "${source}" "${target}"
-    rc=$?
-    (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
-    err=$((err + rc))
-  done
-done
-
-# Stage ocean initial conditions to ROTDIR (warm start)
-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}" "${target}"
+for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
+  # Stage the FV3 initial conditions to ROTDIR (cold start)
+  YMD=${PDY} HH=${cyc} generate_com COM_ATMOS_INPUT
+  [[ ! -d "${COM_ATMOS_INPUT}" ]] && mkdir -p "${COM_ATMOS_INPUT}"
+  src="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${MEMDIR}/atmos/gfs_ctrl.nc"
+  tgt="${COM_ATMOS_INPUT}/gfs_ctrl.nc"
+  ${NCP} "${src}" "${tgt}"
   rc=$?
-  (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
+  ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
   err=$((err + rc))
-  case "${OCNRES}" in
-    "500" | "100")  # Only 5 degree or 1 degree ocean does not have MOM.res_[1-4].nc files
-    ;;
-    "025")  # Only 1/4 degree ocean has MOM.res_[1-4].nc files
-      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 != 0 )) && error_message "${source}" "${target}" "${rc}"
-          err=$((err + rc))
-        fi
-      done
-    ;;
-    *)
-      echo "FATAL ERROR: Unsupported ocean resolution ${OCNRES}"
-      rc=1
+  for ftype in gfs_data sfc_data; do
+    for ((tt = 1; tt <= 6; tt++)); do
+      src="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${MEMDIR}/atmos/${ftype}.tile${tt}.nc"
+      tgt="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
+      ${NCP} "${src}" "${tgt}"
+      rc=$?
+      tgt="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
+      ${NCP} "${src}" "${tgt}"
+      rc=$?
+      ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
       err=$((err + rc))
-    ;;
-  esac
-fi
-
-# Stage ice initial conditions to ROTDIR (warm start)
-if [[ "${DO_ICE:-}" = "YES" ]]; then
-  YMD=${gPDY} HH=${gcyc} generate_com -r COM_ICE_RESTART
-  [[ ! -d "${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 != 0 )) && error_message "${source}" "${target}" "${rc}"
-  err=$((err + rc))
-fi
+    done
+  done
 
-# Stage the WW3 initial conditions to ROTDIR (warm start; TODO: these should be placed in $RUN.$gPDY/$gcyc)
-if [[ "${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.${grdID}"
-    target="${COM_WAVE_RESTART}/${PDY}.${cyc}0000.restart.${grdID}"
-    ${NCP} "${source}" "${target}"
+  # Stage ocean initial conditions to ROTDIR (warm start)
+  if [[ "${DO_OCN:-}" = "YES" ]]; then
+    YMD=${gPDY} HH=${gcyc} generate_com COM_OCEAN_RESTART
+    [[ ! -d "${COM_OCEAN_RESTART}" ]] && mkdir -p "${COM_OCEAN_RESTART}"
+    src="${BASE_CPLIC}/${CPL_OCNIC}/${PDY}${cyc}/${MEMDIR}/ocean/${PDY}.${cyc}0000.MOM.res.nc"
+    tgt="${COM_OCEAN_RESTART}/${PDY}.${cyc}0000.MOM.res.nc"
+    ${NCP} "${src}" "${tgt}"
     rc=$?
-    (( rc != 0 )) && error_message "${source}" "${target}" "${rc}"
+    ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
     err=$((err + rc))
-  done
-fi
+  fi
+  # Stage ice initial conditions to ROTDIR (warm start)
+  if [[ "${DO_ICE:-}" = "YES" ]]; then
+    YMD=${gPDY} HH=${gcyc} generate_com COM_ICE_RESTART
+    [[ ! -d "${COM_ICE_RESTART}" ]] && mkdir -p "${COM_ICE_RESTART}"
+    src="${BASE_CPLIC}/${CPL_ICEIC}/${PDY}${cyc}/${MEMDIR}/ice/${PDY}.${cyc}0000.cice_model.res.nc"
+    tgt="${COM_ICE_RESTART}/${PDY}.${cyc}0000.cice_model.res.nc"
+    ${NCP} "${src}" "${tgt}"
+    rc=$?
+    ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
+    err=$((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
+    YMD=${PDY} HH=${cyc} generate_com COM_WAVE_RESTART
+    [[ ! -d "${COM_WAVE_RESTART}" ]] && mkdir -p "${COM_WAVE_RESTART}"
+    for grdID in ${waveGRD}; do # TODO: check if this is a bash array; if so adjust
+      src="${BASE_CPLIC}/${CPL_WAVIC}/${PDY}${cyc}/${MEMDIR}/wave/${PDY}.${cyc}0000.restart.${grdID}"
+      tgt="${COM_WAVE_RESTART}/${PDY}.${cyc}0000.restart.${grdID}"
+      ${NCP} "${src}" "${tgt}"
+      rc=$?
+      ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
+      err=$((err + rc))
+    done
+  fi
 
+done # for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
 ###############################################################
 # Check for errors and exit if any of the above failed
-if  [[ "${err}" -ne 0 ]] ; then
+if [[ "${err}" -ne 0 ]]; then
   echo "FATAL ERROR: Unable to copy ICs from ${BASE_CPLIC} to ${ROTDIR}; ABORT!"
   exit "${err}"
 fi
diff --git a/workflow/applications/gefs.py b/workflow/applications/gefs.py
index a46451bd3e..8ac4cdc18e 100644
--- a/workflow/applications/gefs.py
+++ b/workflow/applications/gefs.py
@@ -14,7 +14,7 @@ def _get_app_configs(self):
         """
         Returns the config_files that are involved in gefs
         """
-        configs = ['fcst']
+        configs = ['stage_ic', 'fcst']
 
         if self.nens > 0:
             configs += ['efcs']
@@ -32,7 +32,7 @@ def _update_base(base_in):
 
     def get_task_names(self):
 
-        tasks = ['fcst']
+        tasks = ['stage_ic', 'fcst']
 
         if self.nens > 0:
             tasks += ['efcs']
diff --git a/workflow/hosts/hera.yaml b/workflow/hosts/hera.yaml
index 61270b7b27..31911f2d21 100644
--- a/workflow/hosts/hera.yaml
+++ b/workflow/hosts/hera.yaml
@@ -1,6 +1,6 @@
 BASE_GIT: '/scratch1/NCEPDEV/global/glopara/git'
 DMPDIR: '/scratch1/NCEPDEV/global/glopara/dump'
-BASE_CPLIC: '/scratch1/NCEPDEV/climate/role.ufscpara/IC'
+BASE_CPLIC: '/scratch1/NCEPDEV/global/glopara/data/ICSDIR/prototype_ICs'
 PACKAGEROOT: '/scratch1/NCEPDEV/global/glopara/nwpara'
 COMROOT: '/scratch1/NCEPDEV/global/glopara/com'
 COMINsyn: '${COMROOT}/gfs/prod/syndat'
diff --git a/workflow/hosts/wcoss2.yaml b/workflow/hosts/wcoss2.yaml
index 2a301064db..41e1044eff 100644
--- a/workflow/hosts/wcoss2.yaml
+++ b/workflow/hosts/wcoss2.yaml
@@ -1,6 +1,6 @@
 BASE_GIT: '/lfs/h2/emc/global/save/emc.global/git'
 DMPDIR: '/lfs/h2/emc/dump/noscrub/dump'
-BASE_CPLIC: '/lfs/h2/emc/couple/noscrub/Jiande.Wang/IC'
+BASE_CPLIC: '/lfs/h2/emc/global/noscrub/emc.global/data/ICSDIR/prototype_ICs'
 PACKAGEROOT: '${PACKAGEROOT:-"/lfs/h1/ops/prod/packages"}'
 COMROOT: '${COMROOT:-"/lfs/h1/ops/prod/com"}'
 COMINsyn: '${COMROOT}/gfs/v16.3/syndat'
diff --git a/workflow/rocoto/gefs_tasks.py b/workflow/rocoto/gefs_tasks.py
index b0c56bdb66..c5dae3a13d 100644
--- a/workflow/rocoto/gefs_tasks.py
+++ b/workflow/rocoto/gefs_tasks.py
@@ -8,9 +8,64 @@ class GEFSTasks(Tasks):
     def __init__(self, app_config: AppConfig, cdump: str) -> None:
         super().__init__(app_config, cdump)
 
+    def stage_ic(self):
+
+        cpl_ic = self._configs['stage_ic']
+
+        deps = []
+
+        # Atm ICs
+        if self.app_config.do_atm:
+            prefix = f"{cpl_ic['BASE_CPLIC']}/{cpl_ic['CPL_ATMIC']}/@Y@m@d@H/mem000/atmos"
+            for file in ['gfs_ctrl.nc'] + \
+                        [f'{datatype}_data.tile{tile}.nc'
+                         for datatype in ['gfs', 'sfc']
+                         for tile in range(1, self.n_tiles + 1)]:
+                data = f"{prefix}/{file}"
+                dep_dict = {'type': 'data', 'data': data}
+                deps.append(rocoto.add_dependency(dep_dict))
+
+        # Ocean ICs
+        if self.app_config.do_ocean:
+            ocn_res = f"{self._base.get('OCNRES', '025'):03d}"
+            prefix = f"{cpl_ic['BASE_CPLIC']}/{cpl_ic['CPL_OCNIC']}/@Y@m@d@H/mem000/ocean"
+            data = f"{prefix}/@Y@m@d.@H0000.MOM.res.nc"
+            dep_dict = {'type': 'data', 'data': data}
+            deps.append(rocoto.add_dependency(dep_dict))
+            if ocn_res in ['025']:
+                # 0.25 degree ocean model also has these additional restarts
+                for res in [f'res_{res_index}' for res_index in range(1, 4)]:
+                    data = f"{prefix}/@Y@m@d.@H0000.MOM.{res}.nc"
+                    dep_dict = {'type': 'data', 'data': data}
+                    deps.append(rocoto.add_dependency(dep_dict))
+
+        # Ice ICs
+        if self.app_config.do_ice:
+            prefix = f"{cpl_ic['BASE_CPLIC']}/{cpl_ic['CPL_ICEIC']}/@Y@m@d@H/mem000/ice"
+            data = f"{prefix}/@Y@m@d.@H0000.cice_model.res.nc"
+            dep_dict = {'type': 'data', 'data': data}
+            deps.append(rocoto.add_dependency(dep_dict))
+
+        # Wave ICs
+        if self.app_config.do_wave:
+            prefix = f"{cpl_ic['BASE_CPLIC']}/{cpl_ic['CPL_WAVIC']}/@Y@m@d@H/mem000/wave"
+            for wave_grid in self._configs['waveinit']['waveGRD'].split():
+                data = f"{prefix}/{wave_grid}/@Y@m@d.@H0000.restart.{wave_grid}"
+                dep_dict = {'type': 'data', 'data': data}
+                deps.append(rocoto.add_dependency(dep_dict))
+
+        dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
+
+        resources = self.get_resource('stage_ic')
+        task = create_wf_task('stage_ic', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
+
+        return task
+
     def fcst(self):
         # TODO: Add real dependencies
         dependencies = []
+        dep_dict = {'type': 'task', 'name': f'{self.cdump}stage_ic'}
+        dependencies.append(rocoto.add_dependency(dep_dict))
 
         resources = self.get_resource('fcst')
         task = create_wf_task('fcst', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)
@@ -18,8 +73,9 @@ def fcst(self):
         return task
 
     def efcs(self):
-        # TODO: Add real dependencies
         dependencies = []
+        dep_dict = {'type': 'task', 'name': f'{self.cdump}stage_ic'}
+        dependencies.append(rocoto.add_dependency(dep_dict))
 
         efcsenvars = self.envars.copy()
         efcsenvars.append(rocoto.create_envar(name='ENSGRP', value='#grp#'))
diff --git a/workflow/rocoto/gfs_tasks.py b/workflow/rocoto/gfs_tasks.py
index 56449cb9d5..d5c5ba2ed1 100644
--- a/workflow/rocoto/gfs_tasks.py
+++ b/workflow/rocoto/gfs_tasks.py
@@ -23,13 +23,12 @@ def stage_ic(self):
 
         # Atm ICs
         if self.app_config.do_atm:
-            atm_res = self._base.get('CASE', 'C384')
-            prefix = f"{cpl_ic['BASE_CPLIC']}/{cpl_ic['CPL_ATMIC']}/@Y@m@d@H/{self.cdump}"
+            prefix = f"{cpl_ic['BASE_CPLIC']}/{cpl_ic['CPL_ATMIC']}/@Y@m@d@H/atmos"
             for file in ['gfs_ctrl.nc'] + \
                         [f'{datatype}_data.tile{tile}.nc'
                          for datatype in ['gfs', 'sfc']
                          for tile in range(1, self.n_tiles + 1)]:
-                data = f"{prefix}/{atm_res}/INPUT/{file}"
+                data = f"{prefix}/{file}"
                 dep_dict = {'type': 'data', 'data': data}
                 deps.append(rocoto.add_dependency(dep_dict))
         else:  # data-atmosphere
@@ -42,31 +41,29 @@ def stage_ic(self):
         # Ocean ICs
         if self.app_config.do_ocean:
             ocn_res = f"{self._base.get('OCNRES', '025'):03d}"
-            prefix = f"{cpl_ic['BASE_CPLIC']}/{cpl_ic['CPL_OCNIC']}/@Y@m@d@H/ocn"
-            data = f"{prefix}/{ocn_res}/MOM.res.nc"
+            prefix = f"{cpl_ic['BASE_CPLIC']}/{cpl_ic['CPL_OCNIC']}/@Y@m@d@H/ocean"
+            data = f"{prefix}/@Y@m@d.@H0000.MOM.res.nc"
             dep_dict = {'type': 'data', 'data': data}
             deps.append(rocoto.add_dependency(dep_dict))
             if ocn_res in ['025']:
                 # 0.25 degree ocean model also has these additional restarts
                 for res in [f'res_{res_index}' for res_index in range(1, 4)]:
-                    data = f"{prefix}/{ocn_res}/MOM.{res}.nc"
+                    data = f"{prefix}/@Y@m@d.@H0000.MOM.{res}.nc"
                     dep_dict = {'type': 'data', 'data': data}
                     deps.append(rocoto.add_dependency(dep_dict))
 
         # Ice ICs
         if self.app_config.do_ice:
-            ice_res = f"{self._base.get('ICERES', '025'):03d}"
-            ice_res_dec = f'{float(ice_res) / 100:.2f}'
             prefix = f"{cpl_ic['BASE_CPLIC']}/{cpl_ic['CPL_ICEIC']}/@Y@m@d@H/ice"
-            data = f"{prefix}/{ice_res}/cice5_model_{ice_res_dec}.res_@Y@m@d@H.nc"
+            data = f"{prefix}/@Y@m@d.@H0000.cice_model.res.nc"
             dep_dict = {'type': 'data', 'data': data}
             deps.append(rocoto.add_dependency(dep_dict))
 
         # Wave ICs
         if self.app_config.do_wave:
-            prefix = f"{cpl_ic['BASE_CPLIC']}/{cpl_ic['CPL_WAVIC']}/@Y@m@d@H/wav"
+            prefix = f"{cpl_ic['BASE_CPLIC']}/{cpl_ic['CPL_WAVIC']}/@Y@m@d@H/wave"
             for wave_grid in self._configs['waveinit']['waveGRD'].split():
-                data = f"{prefix}/{wave_grid}/@Y@m@d.@H0000.restart.{wave_grid}"
+                data = f"{prefix}/@Y@m@d.@H0000.restart.{wave_grid}"
                 dep_dict = {'type': 'data', 'data': data}
                 deps.append(rocoto.add_dependency(dep_dict))
 
diff --git a/workflow/setup_expt.py b/workflow/setup_expt.py
index a9810ec3f2..a808cafd91 100755
--- a/workflow/setup_expt.py
+++ b/workflow/setup_expt.py
@@ -232,16 +232,7 @@ def fill_COMROT_forecasts(host, inputs):
     """
     Implementation of 'fill_COMROT' for forecast-only mode
     """
-    if inputs.system in ['gfs']:
-        print('forecast-only mode treats ICs differently and cannot be staged here')
-    elif inputs.system in ['gefs']:  # Temporarily copy ICs from icsdir into COM for      testing
-        print('temporary hack to stage gefs ICs for testing')
-        comrot = os.path.join(inputs.comrot, inputs.pslot)
-        idatestr = datetime_to_YMDH(inputs.idate)
-        current_cycle_dir = f"gefs.{idatestr[:8]}"
-        cmd = f"cp -as {inputs.icsdir}/{current_cycle_dir} {comrot}/{current_cycle_dir}"
-        os.system(cmd)
-    return
+    print('forecast-only mode treats ICs differently and cannot be staged here')
 
 
 def fill_EXPDIR(inputs):