Cleanup CCPP cmake build, reduce number of compile jobs, use atparse …

…for variable substitution in MOM and CICE input files (#791)

* Use atparse for ice_in instead of edit_inputs
* Switch to atparse for MOM6
* Update rt.sh and tests/rt_utils.sh to guarantee only one WW3 compile job at a time
* Rearrange rt.conf and rt_gnu.conf to reduce the number of compile jobs
* Increase wallclock time for gaea to 120 minutes

Co-authored-by: denise.worthen <[email protected]>
Co-authored-by: Brian Curtis <[email protected]>

tests/default_vars.sh

@@ -403,7 +403,7 @@ fi
 WLCLK_dflt=30
 # Longer default walltime on Gaea
 if [[ $MACHINE_ID = gaea.* ]]; then
-  WLCLK_dflt=60
+  WLCLK_dflt=120
 fi
 
 export WLCLK=$WLCLK_dflt
@@ -667,8 +667,6 @@ export DT_ATMOS=900
 export DT_CICE=${DT_ATMOS}
 export DT_DYNAM_MOM6=1800
 export DT_THERM_MOM6=3600
-export CPL_SLOW=${DT_THERM_MOM6}
-export CPL_FAST=${DT_ATMOS}
 
 # nems.configure defaults
 export NEMS_CONFIGURE=nems.configure.cpld.IN
@@ -678,8 +676,8 @@ export ocn_model=mom6
 export ice_model=cice6
 export wav_model=ww3
 
-export coupling_interval_slow_sec=${CPL_SLOW}
-export coupling_interval_fast_sec=${CPL_FAST}
+export coupling_interval_slow_sec=${DT_THERM_MOM6}
+export coupling_interval_fast_sec=${DT_ATMOS}
 
 export RESTART_N=${FHMAX}
 export CPLMODE=nems_frac
@@ -730,7 +728,7 @@ export FRUNOFF=''
 export CHLCLIM=seawifs_1998-2006_smoothed_2X.nc
 # this must be set False for restart repro
 export MOM6_REPRO_LA=False
-# since CPL_SLOW is set to DT_THERM, this should be always be false
+# since coupling_interval_slow is set to DT_THERM, this should be always be false
 export MOM6_THERMO_SPAN=False
 # no WW3
 export MOM6_USE_WAVES=False
@@ -741,6 +739,11 @@ export MOM_IAU_HRS=6
 
 # CICE6 defaults; 1 degree
 export NPROC_ICE=12
+# SlenderX2
+export CICE_DECOMP=slenderX2
+export np2=`expr $NPROC_ICE / 2`
+export BLCKX=`expr $NX_GLB / $np2`
+export BLCKY=`expr $NY_GLB / 2`
 export MESHOCN_ICE=mesh.mx${OCNRES}.nc
 export CICEGRID=grid_cice_NEMS_mx${OCNRES}.nc
 export CICEMASK=kmtu_cice_NEMS_mx${OCNRES}.nc
@@ -815,6 +818,11 @@ export ice_petlist_bounds=$IPB_datm_100
 export TASKS=$TASKS_datm_100
 export TPN=$TPN_datm_100
 export NPROC_ICE=12
+# SlenderX2
+export CICE_DECOMP=slenderX2
+export np2=`expr $NPROC_ICE / 2`
+export BLCKX=`expr $NX_GLB / $np2`
+export BLCKY=`expr $NY_GLB / 2`
 
 export ENS_NUM=1
 export SYEAR=2011
@@ -828,10 +836,8 @@ export DT_ATMOS=900
 export DT_CICE=${DT_ATMOS}
 export DT_DYNAM_MOM6=1800
 export DT_THERM_MOM6=3600
-export CPL_SLOW=${DT_THERM_MOM6}
-export CPL_FAST=${DT_ATMOS}
-export coupling_interval_slow_sec=${CPL_SLOW}
-export coupling_interval_fast_sec=${CPL_FAST}
+export coupling_interval_slow_sec=${DT_THERM_MOM6}
+export coupling_interval_fast_sec=${DT_ATMOS}
 
 export RESTART_N=${FHMAX}
 export CPLMODE=nems_orig_data
@@ -861,7 +867,7 @@ export MOM_IAU=False
 export MOM_IAU_HRS=6
 # this must be set False for restart repro
 export MOM6_REPRO_LA=False
-# since CPL_SLOW is set to DT_THERM, this should be always be false
+# since coupling_interval_slow is set to DT_THERM, this should be always be false
 export MOM6_THERMO_SPAN=False
 # no WW3
 export MOM6_USE_WAVES=False
@@ -926,7 +932,12 @@ export ocn_petlist_bounds=$OPB_cdeps_100
 export ice_petlist_bounds=$IPB_cdeps_100
 export TASKS=$TASKS_cdeps_100
 export TPN=$TPN_cdeps_100
+# SlenderX2
+export CICE_DECOMP=slenderX2
 export NPROC_ICE=12
+export np2=`expr $NPROC_ICE / 2`
+export BLCKX=`expr $NX_GLB / $np2`
+export BLCKY=`expr $NY_GLB / 2`
 
 export ENS_NUM=1
 export SYEAR=2011
@@ -940,10 +951,8 @@ export DT_ATMOS=900
 export DT_CICE=${DT_ATMOS}
 export DT_DYNAM_MOM6=1800
 export DT_THERM_MOM6=3600
-export CPL_SLOW=${DT_THERM_MOM6}
-export CPL_FAST=${DT_ATMOS}
-export coupling_interval_slow_sec=${CPL_SLOW}
-export coupling_interval_fast_sec=${CPL_FAST}
+export coupling_interval_slow_sec=${DT_THERM_MOM6}
+export coupling_interval_fast_sec=${DT_ATMOS}
 
 export RESTART_N=${FHMAX}
 export CPLMODE=nems_orig_data
@@ -981,7 +990,7 @@ export MOM_IAU=False
 export MOM_IAU_HRS=6
 # this must be set False for restart repro
 export MOM6_REPRO_LA=False
-# since CPL_SLOW is set to DT_THERM, this should be always be false
+# since coupling_interval_slow is set to DT_THERM, this should be always be false
 export MOM6_THERMO_SPAN=False
 # no WW3
 export MOM6_USE_WAVES=False

tests/edit_inputs.sh

@@ -1,56 +1,6 @@
 #! /usr/bin/env bash
 set -eu
 
-function edit_ice_in {
-
-  # assumes processor shape = "slenderX2"
-  np2=$((NPROC_ICE/2))
-  BLCKX=$((NX_GLB/$np2))
-  BLCKY=$((NY_GLB/2))
-
-  sed -e "s/YEAR_INIT/$SYEAR/g" \
-      -e "s/MONTH_INIT/$SMONTH/g" \
-      -e "s/DAY_INIT/$SDAY/g" \
-      -e "s/DT_CICE/$DT_CICE/g" \
-      -e "s/CICEGRID/$CICEGRID/g" \
-      -e "s/CICEMASK/$CICEMASK/g" \
-      -e "s/NPROC_ICE/$NPROC_ICE/g" \
-      -e "s/NX_GLB/$NX_GLB/g" \
-      -e "s/NY_GLB/$NY_GLB/g" \
-      -e "s/BLCKX/$BLCKX/g" \
-      -e "s/BLCKY/$BLCKY/g" \
-      -e "s/CICERUNTYPE/$CICERUNTYPE/g" \
-      -e "s/RUNID/$RUNID/g" \
-      -e "s/CICE_HIST_AVG/$CICE_HIST_AVG/g" \
-      -e "s/RESTART_EXT/$RESTART_EXT/g" \
-      -e "s/USE_RESTART_TIME/$USE_RESTART_TIME/g" \
-      -e "s/DUMPFREQ_N/$DUMPFREQ_N/g" \
-      -e "s/DUMPFREQ/$DUMPFREQ/g" \
-      -e "s/FRAZIL_FWSALT/$FRAZIL_FWSALT/g" \
-      -e "s/TFREEZE_OPTION/$TFREEZE_OPTION/g" \
-      -e "s/KTHERM/$KTHERM/g"
-}
-
-function edit_mom_input {
-
-  sed -e "s/DT_THERM_MOM6/$DT_THERM_MOM6/g" \
-      -e "s/DT_DYNAM_MOM6/$DT_DYNAM_MOM6/g" \
-      -e "s/MOM6_RIVER_RUNOFF/$MOM6_RIVER_RUNOFF/g" \
-      -e "s/MOM6_THERMO_SPAN/$MOM6_THERMO_SPAN/g" \
-      -e "s/MOM6_REPRO_LA/$MOM6_REPRO_LA/g" \
-      -e "s/MOM6_USE_WAVES/$MOM6_USE_WAVES/g" \
-      -e "s/MOM6_ALLOW_LANDMASK_CHANGES/$MOM6_ALLOW_LANDMASK_CHANGES/g" \
-      -e "s/MOM_IAU_HRS/$MOM_IAU_HRS/g" \
-      -e "s/MOM_IAU/$MOM_IAU/g" \
-      -e "s/NX_GLB/$NX_GLB/g" \
-      -e "s/NY_GLB/$NY_GLB/g" \
-      -e "s/CHLCLIM/$CHLCLIM/g"
-}
-
-function edit_data_table {
-  sed -e "s/FRUNOFF/$FRUNOFF/g"
-}
-
 function edit_ww3_input {
 
   SDATEWW3="${SYEAR}${SMONTH}${SDAY} $(printf "%02d" $(( ${SHOUR}  )))0000"

tests/parm/MOM_input_template_025

@@ -11,10 +11,10 @@
 TRIPOLAR_N = True               !   [Boolean] default = False
                                 ! Use tripolar connectivity at the northern edge of the domain.  With
                                 ! TRIPOLAR_N, NIGLOBAL must be even.
-NIGLOBAL = NX_GLB               !
+NIGLOBAL = @[NX_GLB]            !
                                 ! The total number of thickness grid points in the x-direction in the physical
                                 ! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
-NJGLOBAL = NY_GLB               !
+NJGLOBAL = @[NY_GLB]            !
                                 ! The total number of thickness grid points in the y-direction in the physical
                                 ! domain. With STATIC_MEMORY_ this is set in MOM_memory.h at compile time.
 NIHALO = 4                      ! default = 4
@@ -40,16 +40,16 @@ THICKNESSDIFFUSE = True         !   [Boolean] default = False
 THICKNESSDIFFUSE_FIRST = True   !   [Boolean] default = False
                                 ! If true, do thickness diffusion before dynamics. This is only used if
                                 ! THICKNESSDIFFUSE is true.
-DT = DT_DYNAM_MOM6              !   [s]
+DT = @[DT_DYNAM_MOM6]           !   [s]
                                 ! The (baroclinic) dynamics time step.  The time-step that is actually used will
                                 ! be an integer fraction of the forcing time-step (DT_FORCING in ocean-only mode
                                 ! or the coupling timestep in coupled mode.)
-DT_THERM = DT_THERM_MOM6        !   [s] default = 900.0
+DT_THERM = @[DT_THERM_MOM6]     !   [s] default = 1800.0
                                 ! The thermodynamic and tracer advection time step. Ideally DT_THERM should be
                                 ! an integer multiple of DT and less than the forcing or coupling time-step,
                                 ! unless THERMO_SPANS_COUPLING is true, in which case DT_THERM can be an integer
                                 ! multiple of the coupling timestep.  By default DT_THERM is set to DT.
-THERMO_SPANS_COUPLING = MOM6_THERMO_SPAN    !   [Boolean] default = False
+THERMO_SPANS_COUPLING = @[MOM6_THERMO_SPAN]    !   [Boolean] default = False
                                 ! If true, the MOM will take thermodynamic and tracer timesteps that can be
                                 ! longer than the coupling timestep. The actual thermodynamic timestep that is
                                 ! used in this case is the largest integer multiple of the coupling timestep
@@ -58,6 +58,7 @@ HFREEZE = 20.0                  !   [m] default = -1.0
                                 ! If HFREEZE > 0, melt potential will be computed. The actual depth
                                 ! over which melt potential is computed will be min(HFREEZE, OBLD)
                                 ! where OBLD is the boundary layer depth. If HFREEZE <= 0 (default)
+                                ! melt potential will not be computed.
 USE_PSURF_IN_EOS = False        !   [Boolean] default = False
                                 ! If true, always include the surface pressure contributions in equation of
                                 ! state calculations.
@@ -118,6 +119,13 @@ GRID_CONFIG = "mosaic"          !
                                 !     mercator - use a Mercator spherical grid.
 GRID_FILE = "ocean_hgrid.nc"    !
                                 ! Name of the file from which to read horizontal grid data.
+GRID_ROTATION_ANGLE_BUGS = False  ! [Boolean] default = True
+                                ! If true, use an older algorithm to calculate the sine and
+                                ! cosines needed rotate between grid-oriented directions and
+                                ! true north and east.  Differences arise at the tripolar fold
+USE_TRIPOLAR_GEOLONB_BUG = False !   [Boolean] default = True
+                                ! If true, use older code that incorrectly sets the longitude in some points
+                                ! along the tripolar fold to be off by 360 degrees.
 TOPO_CONFIG = "file"            !
                                 ! This specifies how bathymetry is specified:
                                 !     file - read bathymetric information from the file
@@ -148,7 +156,7 @@ TOPO_FILE = "ocean_topog.nc"    ! default = "topog.nc"
                                 ! The file from which the bathymetry is read.
 TOPO_EDITS_FILE = "All_edits.nc" ! default = ""
                                 ! The file from which to read a list of i,j,z topography overrides.
-ALLOW_LANDMASK_CHANGES = MOM6_ALLOW_LANDMASK_CHANGES   ! default = "False"
+ALLOW_LANDMASK_CHANGES = @[MOM6_ALLOW_LANDMASK_CHANGES]   ! default = "False"
                                 ! If true, allow topography overrides to change ocean points to land
 MAXIMUM_DEPTH = 6500.0          !   [m]
                                 ! The maximum depth of the ocean.
@@ -157,13 +165,6 @@ MINIMUM_DEPTH = 9.5             !   [m] default = 0.0
                                 ! assumed to be land and all fluxes are masked out. If MASKING_DEPTH is
                                 ! specified, then all depths shallower than MINIMUM_DEPTH but deeper than
                                 ! MASKING_DEPTH are rounded to MINIMUM_DEPTH.
-GRID_ROTATION_ANGLE_BUGS = False  ! [Boolean] default = True
-                                ! If true, use an older algorithm to calculate the sine and
-                                ! cosines needed rotate between grid-oriented directions and
-                                ! true north and east.  Differences arise at the tripolar fold
-USE_TRIPOLAR_GEOLONB_BUG = False  ! [Boolean] default = True
-                                ! If true, use older code that incorrectly sets the longitude
-                                ! in some points along the tripolar fold to be off by 360 degrees
 
 ! === module MOM_open_boundary ===
 ! Controls where open boundaries are located, what kind of boundary condition to impose, and what data to apply,
@@ -324,6 +325,7 @@ Z_INIT_FILE_PTEMP_VAR = "temp"  ! default = "ptemp"
 Z_INIT_FILE_SALT_VAR = "salt"   ! default = "salt"
                                 ! The name of the salinity variable in
                                 ! SALT_Z_INIT_FILE.
+
 Z_INIT_ALE_REMAPPING = True     !   [Boolean] default = False
                                 ! If True, then remap straight to model coordinate from file.
 Z_INIT_REMAP_OLD_ALG = True     !   [Boolean] default = True
@@ -670,7 +672,6 @@ MAX_RINO_IT = 25                !   [nondim] default = 50
 VERTEX_SHEAR = False             !   [Boolean] default = False
                                 ! If true, do the calculations of the shear-driven mixing
                                 ! at the cell vertices (i.e., the vorticity points).
-
 KAPPA_SHEAR_ITER_BUG = True     !   [Boolean] default = True
                                 ! If true, use an older, dimensionally inconsistent estimate of the derivative
                                 ! of diffusivity with energy in the Newton's method iteration.  The bug causes
@@ -695,7 +696,7 @@ PRESSURE_DEPENDENT_FRAZIL = False !   [Boolean] default = False
 VAR_PEN_SW = True               !   [Boolean] default = False
                                 ! If true, use one of the CHL_A schemes specified by OPACITY_SCHEME to determine
                                 ! the e-folding depth of incoming short wave radiation.
-CHL_FILE = "seawifs-clim-1997-2010.1440x1080.v20180328.nc" !
+CHL_FILE = @[CHLCLIM]           !
                                 ! CHL_FILE is the file containing chl_a concentrations in the variable CHL_A. It
                                 ! is used when VAR_PEN_SW and CHL_FROM_FILE are true.
 CHL_VARNAME = "chlor_a"         ! default = "CHL_A"
@@ -740,12 +741,11 @@ MIX_LEN_EXPONENT = 1.0          !   [nondim] default = 2.0
                                 ! The exponent applied to the ratio of the distance to the MLD and the MLD depth
                                 ! which determines the shape of the mixing length. This is only used if
                                 ! USE_MLD_ITERATION is True.
-USE_LA_LI2016 = MOM6_REPRO_LA   !   [nondim] default = False
+USE_LA_LI2016 = @[MOM6_REPRO_LA]!   [nondim] default = False
                                 ! A logical to use the Li et al. 2016 (submitted) formula to determine the
                                 ! Langmuir number.
-USE_WAVES = MOM6_USE_WAVES      !   [Boolean] default = False
+USE_WAVES = @[MOM6_USE_WAVES]   !   [Boolean] default = False
                                 ! If true, enables surface wave modules.
-
 WAVE_METHOD = "SURFACE_BANDS"   ! default = "EMPTY"
                                 ! Choice of wave method, valid options include:
                                 !  TEST_PROFILE  - Prescribed from surface Stokes drift
@@ -756,19 +756,17 @@ WAVE_METHOD = "SURFACE_BANDS"   ! default = "EMPTY"
                                 !                  wave spectrum with prescribed values.
                                 !  LF17          - Infers Stokes drift profile from wind
                                 !                  speed following Li and Fox-Kemper 2017.
-
 SURFBAND_SOURCE = "COUPLER"     ! default = "EMPTY"
                                 ! Choice of SURFACE_BANDS data mode, valid options include:
                                 !  DATAOVERRIDE  - Read from NetCDF using FMS DataOverride.
                                 !  COUPLER       - Look for variables from coupler pass
                                 !  INPUT         - Testing with fixed values.
-
 STK_BAND_COUPLER = 3            ! default = 1
                                 ! STK_BAND_COUPLER is the number of Stokes drift bands in the coupler. This has
                                 ! to be consistent with the number of Stokes drift bands in WW3, or the model
                                 ! will fail.
-
 SURFBAND_WAVENUMBERS = 0.04, 0.11, 0.3305 !   [rad/m] default = 0.12566
+                                ! Central wavenumbers for surface Stokes drift bands.
 EPBL_LANGMUIR_SCHEME = "ADDITIVE" ! default = "NONE"
                                 ! EPBL_LANGMUIR_SCHEME selects the method for including Langmuir turbulence.
                                 ! Valid values are:
@@ -826,12 +824,14 @@ ENERGYSAVEDAYS = 1.00           !   [days] default = 1.0
                                 ! other globally summed diagnostics.
 
 ! === module ocean_model_init ===
+
+! === module MOM_surface_forcing ===
 OCEAN_SURFACE_STAGGER = "A"     ! default = "C"
                                 ! A case-insensitive character string to indicate the
                                 ! staggering of the surface velocity field that is
                                 ! returned to the coupler.  Valid values include
                                 ! 'A', 'B', or 'C'.
-! === module MOM_surface_forcing ===
+
 MAX_P_SURF = 0.0                !   [Pa] default = -1.0
                                 ! The maximum surface pressure that can be exerted by the atmosphere and
                                 ! floating sea-ice or ice shelves. This is needed because the FMS coupling
@@ -855,7 +855,7 @@ USE_RIGID_SEA_ICE = True        !   [Boolean] default = False
 SEA_ICE_RIGID_MASS = 100.0      !   [kg m-2] default = 1000.0
                                 ! The mass of sea-ice per unit area at which the sea-ice starts to exhibit
                                 ! rigidity
-LIQUID_RUNOFF_FROM_DATA = MOM6_RIVER_RUNOFF  !   [Boolean] default = False
+LIQUID_RUNOFF_FROM_DATA = @[MOM6_RIVER_RUNOFF]  !   [Boolean] default = False
                                 ! If true, allows liquid river runoff to be specified via
                                 ! the data_table using the component name 'OCN'.
 ! === module MOM_restart ===