Merge remote-tracking branch 'UFS/develop' into develop

JessicaMeixner-NOAA · Dec 16, 2019 · e36fafc · e36fafc
2 parents cd134bc + 798b8aa
commit e36fafc
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Showing 38 changed files with 3,086 additions and 584 deletions.
diff --git a/CICE_SRC b/CICE_SRC
diff --git a/FV3 b/FV3
diff --git a/MOM6 b/MOM6
diff --git a/compsets/benchmark_cold.input b/compsets/benchmark_cold.input
@@ -2,6 +2,7 @@
 
 test cpld_fv3_384_mom6_cice_cold_bmark: fv3_mom6_cice.exe {
     use cpld_fv3_mom6_cice_cold_atm_flux
+    use plat%default_cpl_benchmark
 
     ATMRES='384'
     TEST_DESCR="Fully coupled FV3-MOM6-CICE system - cold 384"
@@ -25,15 +26,6 @@ test cpld_fv3_384_mom6_cice_cold_bmark: fv3_mom6_cice.exe {
      OZONE_data="@[FV3_input_data]/ozprdlos_2015_new_sbuvO3_tclm15_nuchem.f77"
        CO2_data="@[plat%INPUTS]/FV3_input_bm2/INPUT"
 
-    # - set total number of tasks to satisfy coupled application need 
-    #TASKS=480
-    #WRITE_GROUP=1
-    #WRTTASK_PER_GROUP=24
-    #INPES=6
-    #JNPES=8
-    #THRD=3
-    #TPN=8
-
     # - set date YYYYMMDDHH
     SYEAR='2012'
     SMONTH='01'
@@ -53,19 +45,6 @@ test cpld_fv3_384_mom6_cice_cold_bmark: fv3_mom6_cice.exe {
        MOM6_IC="@[BM_IC]/mom6_da"
       CICE5_IC="@[BM_IC]/cpc"    
 
-    # - nems.configure --- 
-    #nems_configure="medcold_atm_ocn_ice" 
-    #med_model="nems" 
-    #med_petlist_bounds="0 311"
-    #atm_model="fv3"
-    #atm_petlist_bounds="0 311"
-    #ocn_model="mom6"
-    #ocn_petlist_bounds="312 431"
-    #ice_model="cice"
-    #ice_petlist_bounds="432 479"
-    #coupling_interval_slow_sec="@[CPL_SLOW]"
-    #coupling_interval_fast_sec="@[CPL_FAST]"
-
     # Specify output files:
     criteria output {
         # WORKFILE                            .comparison. TARGET

diff --git a/compsets/benchmark_warm.input b/compsets/benchmark_warm.input
@@ -2,6 +2,7 @@
 
 test cpld_fv3_384_mom6_cice_2d_bmark: fv3_mom6_cice.exe {
     use cpld_fv3_mom6_cice_2d_atm_flux
+    use plat%default_cpl_benchmark
 
     ATMRES='384'
     TEST_DESCR="Fully coupled FV3-MOM6-CICE system - cold 384"
@@ -40,15 +41,6 @@ test cpld_fv3_384_mom6_cice_2d_bmark: fv3_mom6_cice.exe {
      OZONE_data="@[FV3_input_data]/ozprdlos_2015_new_sbuvO3_tclm15_nuchem.f77"
        CO2_data="@[plat%INPUTS]/FV3_input_bm2/INPUT"
 
-    # - set total number of tasks to satisfy coupled application need 
-    #TASKS=480
-    #WRITE_GROUP=1
-    #WRTTASK_PER_GROUP=24
-    #INPES=6
-    #JNPES=8
-    #THRD=3
-    #TPN=8
-
     # - set date YYYYMMDDHH
     SYEAR='2012'
     SMONTH='01'
@@ -74,19 +66,6 @@ test cpld_fv3_384_mom6_cice_2d_bmark: fv3_mom6_cice.exe {
     MED_restart_data="full-path-to-user-coldstart"
     RESTART_MED="mediator_*"    
 
-    # - nems.configure --- 
-    #nems_configure="med_atm_ocn_ice" 
-    #med_model="nems" 
-    #med_petlist_bounds="0 311"
-    #atm_model="fv3"
-    #atm_petlist_bounds="0 311"
-    #ocn_model="mom6"
-    #ocn_petlist_bounds="312 431"
-    #ice_model="cice"
-    #ice_petlist_bounds="432 479"
-    #coupling_interval_slow_sec="@[CPL_SLOW]"
-    #coupling_interval_fast_sec="@[CPL_FAST]"
-
     # Specify output files:
     criteria output {
         # WORKFILE                            .comparison. TARGET

diff --git a/compsets/cpld_fv3_mom6_cice_2d_atm_flux.input b/compsets/cpld_fv3_mom6_cice_2d_atm_flux.input
@@ -1,7 +1,7 @@
 ########################################################################
 test cpld_fv3_mom6_cice_2d_atm_flux: fv3_mom6_cice.exe { 
     use plat 
-    use plat%default_resources 
+    use plat%default_cpl
     use fv3_defaults 
     use cpl_defaults 
 
@@ -30,13 +30,8 @@ test cpld_fv3_mom6_cice_2d_atm_flux: fv3_mom6_cice.exe {
     RUNDIR="@[RUNDIR]",modules="@[fv3_mom6_cice.exe%modules.nems]",
     CNTL="@[CNTL]")
 
-    # - set total number of tasks to satisfy coupled application need 
-    TASKS=318
-
     # - set component and coupling timesteps
           DT_CICE="@[DT_ATMOS]"
-    DT_DYNAM_MOM6='900'
-    DT_THERM_MOM6='1800'
          CPL_SLOW="@[DT_THERM_MOM6]"
          CPL_FAST="@[DT_ATMOS]"
 
@@ -54,19 +49,11 @@ test cpld_fv3_mom6_cice_2d_atm_flux: fv3_mom6_cice.exe {
     # set default locations of ICs
         FV3_IC="@[FV3_input_data]/INPUT"
        MOM6_IC="@[UGCS_input_data]/MOM6_IC"
-      CICE5_IC="@[UGCS_input_data]/CICE"
+      CICE5_IC="@[UGCS_input_data]/CICE_IC"
     FV3_mosaic="C96"    
 
     # - nems.configure --- 
     nems_configure="med_atm_ocn_ice" 
-    med_model="nems" 
-    med_petlist_bounds="0 149"
-    atm_model="fv3"
-    atm_petlist_bounds="0 149"
-    ocn_model="mom6"
-    ocn_petlist_bounds="150 269"
-    ice_model="cice"
-    ice_petlist_bounds="270 317"
     coupling_interval_slow_sec="@[CPL_SLOW]"
     coupling_interval_fast_sec="@[CPL_FAST]"
 
@@ -82,17 +69,16 @@ test cpld_fv3_mom6_cice_2d_atm_flux: fv3_mom6_cice.exe {
            'global_o3prdlos.f77'  <=copy=     "@[OZONE_data]"
                           '*grb'  <=copyfrom= "@[FV3_input_data]"
                    'field_table'  <=copy=     "@[FV3_input_data]/@[FIELD_TABLE]"
-            'INPUT/grid_spec.nc'  <=copy=     "@[UGCS_input_data]/COUPLED@[ATMRES]/grid_spec.nc"
+            'INPUT/grid_spec.nc'  <=copy=     "@[UGCS_input_data]/CPL_FIX/a@[FV3_mosaic]o@[OCNRES]/grid_spec.nc"
    "INPUT/@[FV3_mosaic]_grid*nc"  <=copyfrom= "@[FV3_input_data]/INPUT"
              'INPUT/oro_data*nc'  <=copyfrom= "@[FV3_input_data]/INPUT"
  "INPUT/@[FV3_mosaic]_mosaic.nc"  <=copy=     "@[FV3_input_data]/INPUT/grid_spec.nc"
              'INPUT/gfs_ctrl.nc'  <=copyfrom= "@[FV3_input_data]/INPUT"
 #MOM6 fixed input
-                       'INPUT/*'  <=copyfrom= "@[UGCS_input_data]/MOM6_FIX_025deg"
-                    'data_table'  <=copy=     "@[UGCS_input_data]/MOM6_FIX_025deg/data_table"
+                       'INPUT/*'  <=copyfrom= "@[UGCS_input_data]/MOM6_FIX/@[OCNRES]"          
 #CICE5 fixed input
-       'grid_cice_NEMS_mx025.nc'  <=copy=     "@[UGCS_input_data]/CICE/grid_cice_NEMS_mx025.nc"
-       'kmtu_cice_NEMS_mx025.nc'  <=copy=     "@[UGCS_input_data]/CICE/kmtu_cice_NEMS_mx025.nc"
+       'grid_cice_NEMS_mx025.nc'  <=copy=     "@[UGCS_input_data]/CICE_FIX/@[OCNRES]/grid_cice_NEMS_mx025.nc"
+       'kmtu_cice_NEMS_mx025.nc'  <=copy=     "@[UGCS_input_data]/CICE_FIX/@[OCNRES]/kmtu_cice_NEMS_mx025.nc"
 # ICs
             'INPUT/sfc_data*.nc'  <=copyfrom= "@[FV3_IC]"
             'INPUT/gfs_data*.nc'  <=copyfrom= "@[FV3_IC]"
@@ -105,6 +91,7 @@ test cpld_fv3_mom6_cice_2d_atm_flux: fv3_mom6_cice.exe {
                'ice_in_template'  <=copy=     "@[PARMnems]/ice_in_template"
       'INPUT/MOM_input_template'  <=copy=     "@[PARMnems]/MOM_input_template"
            'diag_table_template'  <=copy=     "@[PARMnems]/diag_table_template"
+                    'data_table'  <=copy=     "@[PARMnems]/data_table"
                 "nems.configure"  <=atparse=  "@[PARMnems]/nems.configure.@[nems_configure].IN"
     } 
 
@@ -121,7 +108,8 @@ test cpld_fv3_mom6_cice_2d_atm_flux: fv3_mom6_cice.exe {
                   DUMPFREQ_N="@[DUMPFREQ_N]",
                     DUMPFREQ="@[DUMPFREQ]",
                     DT_THERM="@[DT_THERM_MOM6]",
-                    DT_DYNAM="@[DT_DYNAM_MOM6]")
+                    DT_DYNAM="@[DT_DYNAM_MOM6]",
+           MOM6_RIVER_RUNOFF="@[MOM6_RIVER_RUNOFF]")
 
     # Specify output files:
     criteria output {

diff --git a/compsets/cpld_fv3_mom6_cice_cold_atm_flux.input b/compsets/cpld_fv3_mom6_cice_cold_atm_flux.input
@@ -2,7 +2,7 @@
 
 test cpld_fv3_mom6_cice_cold_atm_flux: fv3_mom6_cice.exe { 
     use plat 
-    use plat%default_resources 
+    use plat%default_cpl
     use fv3_defaults 
     use cpl_defaults
 
@@ -28,13 +28,8 @@ test cpld_fv3_mom6_cice_cold_atm_flux: fv3_mom6_cice.exe {
     RUNDIR="@[RUNDIR]",modules="@[fv3_mom6_cice.exe%modules.nems]", 
     CNTL="@[CNTL]") 
 
-    # - set total number of tasks to satisfy coupled application need 
-    TASKS=318
-
     # - set component and coupling timesteps
     DT_CICE="@[DT_ATMOS]"
-    DT_DYNAM_MOM6='900'
-    DT_THERM_MOM6='1800'
     CPL_SLOW="@[DT_THERM_MOM6]"
     CPL_FAST="@[DT_ATMOS]"
 
@@ -52,19 +47,11 @@ test cpld_fv3_mom6_cice_cold_atm_flux: fv3_mom6_cice.exe {
     # set default locations of ICs
         FV3_IC="@[FV3_input_data]/INPUT"
        MOM6_IC="@[UGCS_input_data]/MOM6_IC"
-      CICE5_IC="@[UGCS_input_data]/CICE"
+      CICE5_IC="@[UGCS_input_data]/CICE_IC"
     FV3_mosaic="C96"
 
     # - nems.configure --- 
     nems_configure="medcold_atm_ocn_ice" 
-    med_model="nems" 
-    med_petlist_bounds="0 149"
-    atm_model="fv3"
-    atm_petlist_bounds="0 149"
-    ocn_model="mom6"
-    ocn_petlist_bounds="150 269"
-    ice_model="cice"
-    ice_petlist_bounds="270 317"
     coupling_interval_slow_sec="@[CPL_SLOW]"
     coupling_interval_fast_sec="@[CPL_FAST]"
 
@@ -80,17 +67,16 @@ test cpld_fv3_mom6_cice_cold_atm_flux: fv3_mom6_cice.exe {
            'global_o3prdlos.f77'  <=copy=     "@[OZONE_data]"
                           '*grb'  <=copyfrom= "@[FV3_input_data]"
                    'field_table'  <=copy=     "@[FV3_input_data]/@[FIELD_TABLE]"
-            'INPUT/grid_spec.nc'  <=copy=     "@[UGCS_input_data]/COUPLED@[ATMRES]/grid_spec.nc"
+            'INPUT/grid_spec.nc'  <=copy=     "@[UGCS_input_data]/CPL_FIX/a@[FV3_mosaic]o@[OCNRES]/grid_spec.nc"
    "INPUT/@[FV3_mosaic]_grid*nc"  <=copyfrom= "@[FV3_input_data]/INPUT"
              'INPUT/oro_data*nc'  <=copyfrom= "@[FV3_input_data]/INPUT"
  "INPUT/@[FV3_mosaic]_mosaic.nc"  <=copy=     "@[FV3_input_data]/INPUT/grid_spec.nc"
              'INPUT/gfs_ctrl.nc'  <=copyfrom= "@[FV3_input_data]/INPUT"
 #MOM6 fixed input
-                       'INPUT/*'  <=copyfrom= "@[UGCS_input_data]/MOM6_FIX_025deg"
-                    'data_table'  <=copy=     "@[UGCS_input_data]/MOM6_FIX_025deg/data_table"
+                       'INPUT/*'  <=copyfrom= "@[UGCS_input_data]/MOM6_FIX/@[OCNRES]"
 #CICE5 fixed input
-       'grid_cice_NEMS_mx025.nc'  <=copy=     "@[UGCS_input_data]/CICE/grid_cice_NEMS_mx025.nc"
-       'kmtu_cice_NEMS_mx025.nc'  <=copy=     "@[UGCS_input_data]/CICE/kmtu_cice_NEMS_mx025.nc"
+       'grid_cice_NEMS_mx025.nc'  <=copy=     "@[UGCS_input_data]/CICE_FIX/@[OCNRES]/grid_cice_NEMS_mx025.nc"
+       'kmtu_cice_NEMS_mx025.nc'  <=copy=     "@[UGCS_input_data]/CICE_FIX/@[OCNRES]/kmtu_cice_NEMS_mx025.nc"
 # ICs
             'INPUT/sfc_data*.nc'  <=copyfrom= "@[FV3_IC]"
             'INPUT/gfs_data*.nc'  <=copyfrom= "@[FV3_IC]"
@@ -102,6 +88,7 @@ test cpld_fv3_mom6_cice_cold_atm_flux: fv3_mom6_cice.exe {
                'ice_in_template'  <=copy=     "@[PARMnems]/ice_in_template"
       'INPUT/MOM_input_template'  <=copy=     "@[PARMnems]/MOM_input_template"
            'diag_table_template'  <=copy=     "@[PARMnems]/diag_table_template"
+                    'data_table'  <=copy=     "@[PARMnems]/data_table"
                 "nems.configure"  <=atparse=  "@[PARMnems]/nems.configure.@[nems_configure].IN"
     } 
 
@@ -118,7 +105,8 @@ test cpld_fv3_mom6_cice_cold_atm_flux: fv3_mom6_cice.exe {
                   DUMPFREQ_N="@[DUMPFREQ_N]",
                     DUMPFREQ="@[DUMPFREQ]",
                     DT_THERM="@[DT_THERM_MOM6]",
-                    DT_DYNAM="@[DT_DYNAM_MOM6]")
+                    DT_DYNAM="@[DT_DYNAM_MOM6]",
+           MOM6_RIVER_RUNOFF="@[MOM6_RIVER_RUNOFF]")
 
     # Specify output files:
     criteria output {

diff --git a/compsets/datesuite_warm.input b/compsets/datesuite_warm.input
@@ -6,13 +6,16 @@ load 'benchmark_warm.input'
    # eg: "/scratch2/NCEPDEV/stmp1/First.LastName/rtgen.NUMBER"
    ROOTDIR = "path-to-user-coldstarts"
 
+datesuite_defaults = {
     DAYS='5'
    FHMAX='120'
    walltime=10800   # seconds
+}
 
 ########################################################################
 test cpld_fv3_384_mom6_cice_5d_2012010100: fv3_mom6_cice.exe {
     use cpld_fv3_384_mom6_cice_2d_bmark
+    use datesuite_defaults
 
     # - set date YYYYMMDDHH
     SYEAR='2012'
@@ -21,11 +24,12 @@ test cpld_fv3_384_mom6_cice_5d_2012010100: fv3_mom6_cice.exe {
     SHOUR='00'
     CDATE="@[SYEAR]@[SMONTH]@[SDAY]@[SHOUR]"
 
-    MED_restart_data="@[ROOTDIR]/tmp/cpld_fv3_384_mom6_cice_cold_@[CDATE]"
+    MED_restart_data="@[ROOTDIR]/tmp/cpld_fv3_384_mom6_cice_cold_2012010100"
 }
 
 test cpld_fv3_384_mom6_cice_5d_2012040100: fv3_mom6_cice.exe {
     use cpld_fv3_384_mom6_cice_2d_bmark
+    use datesuite_defaults
 
     # - set date YYYYMMDDHH
     SYEAR='2012'
@@ -34,11 +38,12 @@ test cpld_fv3_384_mom6_cice_5d_2012040100: fv3_mom6_cice.exe {
     SHOUR='00'
     CDATE="@[SYEAR]@[SMONTH]@[SDAY]@[SHOUR]"
 
-    MED_restart_data="@[ROOTDIR]/tmp/cpld_fv3_384_mom6_cice_cold_@[CDATE]"
+    MED_restart_data="@[ROOTDIR]/tmp/cpld_fv3_384_mom6_cice_cold_2012040100"
 }
 
 test cpld_fv3_384_mom6_cice_5d_2012070100: fv3_mom6_cice.exe {
     use cpld_fv3_384_mom6_cice_2d_bmark
+    use datesuite_defaults
 
     # - set date YYYYMMDDHH
     SYEAR='2012'
@@ -47,11 +52,12 @@ test cpld_fv3_384_mom6_cice_5d_2012070100: fv3_mom6_cice.exe {
     SHOUR='00'
     CDATE="@[SYEAR]@[SMONTH]@[SDAY]@[SHOUR]"
 
-    MED_restart_data="@[ROOTDIR]/tmp/cpld_fv3_384_mom6_cice_cold_@[CDATE]"
+    MED_restart_data="@[ROOTDIR]/tmp/cpld_fv3_384_mom6_cice_cold_2012070100"
 }
 
 test cpld_fv3_384_mom6_cice_5d_2012100100: fv3_mom6_cice.exe {
     use cpld_fv3_384_mom6_cice_2d_bmark
+    use datesuite_defaults
 
     # - set date YYYYMMDDHH
     SYEAR='2012'
@@ -60,5 +66,5 @@ test cpld_fv3_384_mom6_cice_5d_2012100100: fv3_mom6_cice.exe {
     SHOUR='00'
     CDATE="@[SYEAR]@[SMONTH]@[SDAY]@[SHOUR]"
 
-    MED_restart_data="@[ROOTDIR]/tmp/cpld_fv3_384_mom6_cice_cold_@[CDATE]"
+    MED_restart_data="@[ROOTDIR]/tmp/cpld_fv3_384_mom6_cice_cold_2012100100"
 }
diff --git a/compsets/fv3.input b/compsets/fv3.input
@@ -54,7 +54,7 @@ embed bash compile.sh(MAKE_OPTS=' ',BUILD_NR='',fv3,modules,md5) [[[
                 ./compile.sh "@[plat%HOMEnems]/FV3" \
                 $( echo @[plat%MACHINE_ID] | sed 's,\.,_,g' ) \
                 @[MAKE_OPTS] @[BUILD_NR]
-        elif [[ @[plat%PLATFORM_NAME] == hera* || @[plat%PLATFORM_NAME] == cheyenne* || @[plat%PLATFORM_NAME] == gaea* || @[plat%PLATFORM_NAME] == jet* ]] ; then
+        elif [[ @[plat%PLATFORM_NAME] == hera* || @[plat%PLATFORM_NAME] == cheyenne* || @[plat%PLATFORM_NAME] == gaea* || @[plat%PLATFORM_NAME] == *jet* ]] ; then
             # Don't substitute the . with a _ on Cheyenne
             echo "DON'T SUBSTITUTE _ for . on @[plat%PLATFORM_NAME]"
             ./compile.sh "@[plat%HOMEnems]/FV3" \
@@ -468,7 +468,6 @@ test fv3_ccpp_control: fv3_ccpp_control.exe {
            '*configure' <=copyfrom= "@[FV3_input_data]"
                 'INPUT' <=copy=     "@[FV3_input_data]/INPUT"
   'global_o3prdlos.f77' <=copy= "@[FV3_input_data]/INPUT/global_o3prdlos.f77"
-       'ccpp_suite.xml' <=copy= "@[HOMEnems]/ccpp/suites/suite_FV3_GFS_2017.xml"
     }
 
     # Specify output files:
@@ -1211,10 +1210,10 @@ test fv3_gfdlmprad: fv3_ww3.exe {
         'RESTART/sfc_data.tile4.nc'             .bitcmp. "@[CNTL]/RESTART/"
         'RESTART/sfc_data.tile5.nc'             .bitcmp. "@[CNTL]/RESTART/"
         'RESTART/sfc_data.tile6.nc'             .bitcmp. "@[CNTL]/RESTART/"
+        'out_grd.glo_30m'                       .bitcmp. "@[CNTL]"
         "@[build%target]" .md5cmp. "@[fv3_ww3.exe%md5sum]"
     }
 
-
     spawn execute {
         {"@[build%target]", ranks="@[TASKS]" }
     }
@@ -1635,7 +1634,6 @@ test fv3_wrtGauss_netcdf_esmf: fv3.exe {
     }
 }
 
-
 ########################################################################
 
 test fv3_wrtGauss_nemsio_c192: fv3.exe {
@@ -1764,7 +1762,6 @@ test fv3_wrtGauss_nemsio_c768: fv3_ww3.exe {
     CNTL_NAME="fv3_wrtGauss_nemsio_c768"
 
     TASKS='1752'
-    TPN='12'
     PPN="@[plat%C768_PPN]"
     INPES='16'
     JNPES='16'
@@ -1879,7 +1876,7 @@ test fv3_wrtGauss_nemsio_c768: fv3_ww3.exe {
         'RESTART/sfc_data.tile4.nc'             .bitcmp. "@[CNTL]/RESTART/"
         'RESTART/sfc_data.tile5.nc'             .bitcmp. "@[CNTL]/RESTART/"
         'RESTART/sfc_data.tile6.nc'             .bitcmp. "@[CNTL]/RESTART/"
-
+        'out_grd.glo_30m'                       .bitcmp. "@[CNTL]"
       # Executable validation.  This makes an MD5 sum of the fv3.exe
       # for comparison against the MD5 sum made in the build job.
       # This is to ensure the executable did not change during the
+86 −0		lanl_cice/bld/Macros.Linux.NEMS.cheyenne
+660 −3		lanl_cice_cap/cice_cap.F90
+1 −1		lanl_cice_cap/makefile.nuopc
+1 −1		atmos_cubed_sphere
+1 −1		ccpp/physics
+6 −1		fv3_cap.F90
+1 −1		gfsphysics/GFS_layer/GFS_physics_driver.F90
+10 −1		gfsphysics/GFS_layer/GFS_restart.F90
+11 −1		gfsphysics/GFS_layer/GFS_typedefs.F90
+4 −4		gfsphysics/physics/gfdl_cloud_microphys.F90
+27 −26		gfsphysics/physics/satmedmfvdifq.f
+3 −9		io/FV3GFS_io.F90
+1 −0		io/module_fv3_io_def.F90
+360 −43		io/module_wrt_grid_comp.F90
+40 −29		io/post_gfs.F90