Bugfix/coupled crow (#137)

README.md

@@ -56,12 +56,17 @@ generate a 3-day run case (test_3d) starting from 2016040100. From the /workflow
 ```
 mkdir -p $EXPROOT
 (Note that $EXPROOT is the experiment directory that has been set in the user.yaml file.)
-./setup_case.sh -p HERA coupled_free_forecast test_3d
+./setup_case.sh -p HERA $CASE test2d
 
 or
 
-./setup_case.sh -p HERA ../cases/coupled_free_forecast.yaml test_3d
+./setup_case.sh -p HERA ../cases/$CASE.yaml test2d
 
+where $CASE is one of the following:
+- prototype_5: Used for UFS S2S Prototype 5 (Runs 35 day cases with atm-ocn-ice-wav coupling)
+- coupled_free_forecast: 2 day tests for atm-ocn-ice coupling 
+- coupled_free_forecast_wave: 2 day test for atm-ocn-ice-wav coupling (same as p5 except shorter) 
+- atm_free_forecast:  Run the atm only case with same ICs as coupled tests 
 
 For Orion: 
 First make sure you have python loaded: 

jobs/JGLOBAL_FORECAST

@@ -32,6 +32,8 @@ status=$?
 ##############################################
 export pid=${pid:-$$}
 export outid=${outid:-"LL$job"}
+export DATAROOT="$RUNDIR/$CDATE/$CDUMP"
+[[ ! -d $DATAROOT ]] && mkdir -p $DATAROOT
 export DATA=${DATA:-${DATAROOT}/${jobid:?}}
 mkdir -p $DATA
 cd $DATA

jobs/JGLOBAL_FORECAST_MEDCOLD

@@ -32,6 +32,9 @@ status=$?
 ##############################################
 export pid=${pid:-$$}
 export outid=${outid:-"LL$job"}
+
+export DATAROOT="$RUNDIR/$CDATE/$CDUMP"
+[[ ! -d $DATAROOT ]] && mkdir -p $DATAROOT
 export DATA=${DATA:-${DATAROOT}/${jobid:?}}
 mkdir -p $DATA
 cd $DATA

jobs/rocoto/coupled_ic.sh

@@ -20,6 +20,9 @@ set -x
 status=$?
 [[ $status -ne 0 ]] && exit $status
 
+export DATAROOT="$RUNDIR/$CDATE/$CDUMP"
+[[ ! -d $DATAROOT ]] && mkdir -p $DATAROOT
+
 ###############################################################
 # Source relevant configs
 configs="base fv3ic wave"

jobs/rocoto/ocnpost.sh

@@ -40,6 +40,9 @@ export pid=${pid:-$$}
 export outid=${outid:-"LL$job"}
 export jobid=${jobid:-"${outid}.o${pid}"}
 
+export DATAROOT="$RUNDIR/$CDATE/$CDUMP"
+[[ ! -d $DATAROOT ]] && mkdir -p $DATAROOT
+
 export DATA="$DATAROOT/${job}.${pid}"
 # DATA dir not used for now.
 

jobs/rocoto/post.sh

@@ -20,6 +20,8 @@ else
     restart_file=$ROTDIR/${CDUMP}.${PDY}/${cyc}/${CDUMP}.t${cyc}z.logf
 fi
 
+export DATAROOT="$RUNDIR/$CDATE/$CDUMP"
+[[ ! -d $DATAROOT ]] && mkdir -p $DATAROOT
 
 #---------------------------------------------------------------
 for fhr in $fhrlst; do

jobs/rocoto/waveinit.sh

@@ -7,6 +7,9 @@ echo "=============== START TO SOURCE FV3GFS WORKFLOW MODULES ==============="
 status=$?
 [[ $status -ne 0 ]] && exit $status
 
+export DATAROOT="$RUNDIR/$CDATE/$CDUMP"
+[[ ! -d $DATAROOT ]] && mkdir -p $DATAROOT
+
 ###############################################################
 echo
 echo "=============== START TO RUN WAVE INIT ==============="

jobs/rocoto/wavepostsbs.sh

@@ -7,6 +7,9 @@ echo "=============== START TO SOURCE FV3GFS WORKFLOW MODULES ==============="
 status=$?
 [[ $status -ne 0 ]] && exit $status
 
+export DATAROOT="$RUNDIR/$CDATE/$CDUMP"
+[[ ! -d $DATAROOT ]] && mkdir -p $DATAROOT
+
 ###############################################################
 echo
 echo "=============== START TO RUN WAVE POST_SBS ==============="

jobs/rocoto/waveprep.sh

@@ -7,6 +7,9 @@ echo "=============== START TO SOURCE FV3GFS WORKFLOW MODULES ==============="
 status=$?
 [[ $status -ne 0 ]] && exit $status
 
+export DATAROOT="$RUNDIR/$CDATE/$CDUMP"
+[[ ! -d $DATAROOT ]] && mkdir -p $DATAROOT
+
 ###############################################################
 echo
 echo "=============== START TO RUN WAVE PREP ==============="

ush/forecast_postdet.sh

@@ -497,7 +497,7 @@ if [ $SEND = "YES" ]; then
   fi
 fi
 
-$NCP -p $DATA/input.nml $COMOUT/
+$NCP $DATA/input.nml $ROTDIR/${CDUMP}.${PDY}/${cyc}/
 
 echo "SUB ${FUNCNAME[0]}: Output data for FV3 copied"
 }
@@ -570,7 +570,8 @@ WW3_nml()
 WW3_out()
 {
 	echo "SUB ${FUNCNAME[0]}: Copying output data for WW3"
-	# soft link commands insert here
+        $NCP $DATA/ww3_multi.inp $ROTDIR/${COMPONENTwave}.${PDY}/${cyc}/
+        $NCP $DATA/mod_def.* $ROTDIR/${COMPONENTwave}.${PDY}/${cyc}/
 }
 
 MOM6_postdet()

ush/nems.configure.med_atm_ocn_ice.IN

@@ -42,7 +42,10 @@ ICE_attributes::
   DumpFields = @[DumpFields]
   ProfileMemory = false
   OverwriteSlice = true
-  dbug_flag = 0 
+  mesh_ice = @[MESHICE]
+  stop_n = @[FHMAX]
+  stop_option = nhours
+  stop_ymd = -999
 ::
 
 # CMEPS warm run sequence
@@ -95,4 +98,6 @@ ALLCOMP_attributes::
       restart_n = @[restart_interval_hours]
       restart_option = nhours
       restart_ymd = -999
+      dbug_flag = 0
+      use_coldstart = .true.
 ::

ush/nems.configure.medcold_atm_ocn_ice.IN

@@ -42,7 +42,10 @@ ICE_attributes::
   DumpFields = @[DumpFields]
   ProfileMemory = false
   OverwriteSlice = true
-  dbug_flag = 0  
+  mesh_ice = @[MESHICE]
+  stop_n = @[FHMAX]
+  stop_option = nhours
+  stop_ymd = -999
 ::
 
 # CMEPS cold run sequence
@@ -95,4 +98,5 @@ ALLCOMP_attributes::
       restart_n = 1
       restart_option = nhours
       restart_ymd = -999
+      dbug_flag = 0
 ::

ush/parsing_namelists_CICE.sh

@@ -375,17 +375,17 @@ cat > ice_in <<eof
    f_VGRDi         = .false.
    f_VGRDs         = .false.
    f_VGRDb         = .false.
-   f_VGRDa         = .true.
+   f_VGRDa         = .false.
    f_bounds        = .false.
    f_aice          = 'mdhxx' 
    f_hi            = 'mdhxx'
    f_hs            = 'mdhxx' 
    f_Tsfc          = 'mdhxx' 
-   f_sice          = 'mdhxx' 
+   f_sice          = 'x' 
    f_uvel          = 'mdhxx' 
    f_vvel          = 'mdhxx'
-   f_uatm          = 'mdhxx'
-   f_vatm          = 'mdhxx'
+   f_uatm          = 'x'
+   f_vatm          = 'x'
    f_fswdn         = 'mdhxx' 
    f_flwdn         = 'mdhxx'
    f_snowfrac      = 'x'
@@ -395,26 +395,26 @@ cat > ice_in <<eof
    f_rain_ai       = 'x' 
    f_sst           = 'mdhxx' 
    f_sss           = 'mdhxx' 
-   f_uocn          = 'mdhxx' 
-   f_vocn          = 'mdhxx' 
-   f_frzmlt        = 'mdhxx'
+   f_uocn          = 'x' 
+   f_vocn          = 'x' 
+   f_frzmlt        = 'x'
    f_fswfac        = 'mdhxx'
    f_fswint_ai     = 'x'
    f_fswabs        = 'mdhxx' 
    f_fswabs_ai     = 'x' 
    f_albsni        = 'mdhxx' 
-   f_alvdr         = 'mdhxx'
-   f_alidr         = 'mdhxx'
-   f_alvdf         = 'mdhxx'
-   f_alidf         = 'mdhxx'
+   f_alvdr         = 'x'
+   f_alidr         = 'x'
+   f_alvdf         = 'x'
+   f_alidf         = 'x'
    f_alvdr_ai      = 'x'
    f_alidr_ai      = 'x'
    f_alvdf_ai      = 'x'
    f_alidf_ai      = 'x'
-   f_albice        = 'mdhxx'
-   f_albsno        = 'mdhxx'
-   f_albpnd        = 'mdhxx'
-   f_coszen        = 'mdhxx'
+   f_albice        = 'x'
+   f_albsno        = 'x'
+   f_albpnd        = 'x'
+   f_coszen        = 'x'
    f_flat          = 'mdhxx' 
    f_flat_ai       = 'x' 
    f_fsens         = 'mdhxx' 
@@ -428,21 +428,21 @@ cat > ice_in <<eof
    f_Tref          = 'mdhxx' 
    f_Qref          = 'mdhxx'
    f_congel        = 'mdhxx' 
-   f_frazil        = 'mdhxx' 
-   f_snoice        = 'mdhxx' 
-   f_dsnow         = 'mdhxx' 
-   f_melts         = 'mdhxx'
+   f_frazil        = 'x' 
+   f_snoice        = 'x' 
+   f_dsnow         = 'x' 
+   f_melts         = 'x'
    f_meltt         = 'mdhxx'
    f_meltb         = 'mdhxx'
    f_meltl         = 'mdhxx'
-   f_fresh         = 'mdhxx'
+   f_fresh         = 'x'
    f_fresh_ai      = 'x'
-   f_fsalt         = 'mdhxx'
+   f_fsalt         = 'x'
    f_fsalt_ai      = 'x'
-   f_fbot          = 'mdhxx'
-   f_fhocn         = 'mdhxx' 
+   f_fbot          = 'x'
+   f_fhocn         = 'x' 
    f_fhocn_ai      = 'x' 
-   f_fswthru       = 'mdhxx' 
+   f_fswthru       = 'x' 
    f_fswthru_ai    = 'x' 
    f_fsurf_ai      = 'x'
    f_fcondtop_ai   = 'x'
@@ -453,22 +453,22 @@ cat > ice_in <<eof
    f_strtlty       = 'x' 
    f_strcorx       = 'x' 
    f_strcory       = 'x' 
-   f_strocnx       = 'mdhxx' 
-   f_strocny       = 'mdhxx' 
+   f_strocnx       = 'x' 
+   f_strocny       = 'x' 
    f_strintx       = 'x' 
    f_strinty       = 'x'
    f_taubx         = 'x'
    f_tauby         = 'x'
    f_strength      = 'x'
-   f_divu          = 'x'
-   f_shear         = 'x'
+   f_divu          = 'mdhxx'
+   f_shear         = 'mdhxx'
    f_sig1          = 'x' 
    f_sig2          = 'x'
    f_sigP          = 'x' 
-   f_dvidtt        = 'x' 
-   f_dvidtd        = 'x' 
-   f_daidtt        = 'x'
-   f_daidtd        = 'x' 
+   f_dvidtt        = 'mdhxx' 
+   f_dvidtd        = 'mdhxx' 
+   f_daidtt        = 'mdhxx'
+   f_daidtd        = 'mdhxx' 
    f_dagedtt       = 'x'
    f_dagedtd       = 'x'
    f_mlt_onset     = 'mdhxx'

workflow/cases/atm_free_forecast.yaml

@@ -0,0 +1,52 @@
+case:
+  places:
+    workflow_file: layout/free_forecast_gfs.yaml
+    #BASE_CPLIC: /scratch2/NCEPDEV/climate/climpara/S2S/IC
+
+  settings: 
+    SDATE: 2013-04-01t00:00:00
+    EDATE: 2013-04-01t00:00:00
+
+    cplflx: .false.
+    print_esmf: .true.
+    nems_temp: 'atm'
+    nems_temp_cold: 'atm'
+    mom6ic_prepared: .false.
+    KEEPDATA: NO
+    ic_source: coupled_ic
+
+  nsst:
+    NST_MODEL: 0
+
+  output_settings:
+    FHOUT_GFS: 6
+    FHMIN_GFS: 0
+    FHMAX_GFS: 48
+    FHMAX_HF_GFS: 0
+    FHOUT_HF_GFS: -1
+
+  fv3_gfs_settings:
+    CASE: C384
+    LEVS: 65
+    DELTIM: 450
+    SEEDLET: 10
+    CCPP_SUITE: FV3_GFS_v15p2_coupled
+    nst_anl: no
+    DO_SKEB: false
+    DO_SHUM: false
+    DO_SPPT: false
+    layout:
+       x: 6
+       y: 8
+       nth: 2
+       WGRP: 1
+       WGRP_NTASKS: 24
+       WRTIOBUF: "32M"
+    cdmbgwd: "1.0,1.2"
+
+  ice_settings:
+    ICEPETS: 48
+
+  post:
+    downset: 2
+    GOESF: no

workflow/cases/coupled_free_forecast.yaml

@@ -13,6 +13,7 @@ case:
     nems_temp_cold: 'medcold_atm_ocn_ice'
     mom6ic_prepared: .false.
     KEEPDATA: NO
+    ic_source: coupled_ic
 
   nsst:
     NST_MODEL: 0
@@ -37,15 +38,15 @@ case:
     DO_SPPT: false
     layout:
        x: 6
-       y: 8
-       nth: 2
+       y: 12
+       nth: 1
        WGRP: 1
        WGRP_NTASKS: 24
        WRTIOBUF: "32M"
     cdmbgwd: "1.0,1.2"
 
   ocn_settings:
-    OCNPETS: 120
+    OCNPETS: 240
 
   ice_settings:
     ICEPETS: 48

workflow/cases/coupled_free_forecast_wave.yaml

@@ -14,7 +14,7 @@ case:
     nems_temp: 'med_atm_ocn_ice_wav'
     nems_temp_cold: 'medcold_atm_ocn_ice_wav'
     mom6ic_prepared: .false.
-    KEEPDATA: YES
+    KEEPDATA: NO
 
   nsst:
     NST_MODEL: 0
@@ -39,21 +39,21 @@ case:
     DO_SPPT: false
     layout:
        x: 6
-       y: 8
-       nth: 2
+       y: 12
+       nth: 1
        WGRP: 1
        WGRP_NTASKS: 24
        WRTIOBUF: "32M"
     cdmbgwd: "1.0,1.2"
 
   ocn_settings:
-    OCNPETS: 120
+    OCNPETS: 240
 
   ice_settings:
     ICEPETS: 48
 
   wave_settings: 
-    WAVPETS: 40
+    WAVPETS: 136
 
   post:
     downset: 2