Merge remote-tracking branch 'origin/develop' into empty_output_bundle

ufs-community · Jul 19, 2023 · 676b5c8 · 676b5c8
2 parents 22c4072 + a2088bf
commit 676b5c8
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Showing 80 changed files with 10,825 additions and 9,084 deletions.
diff --git a/CMEPS-interface/CMEPS b/CMEPS-interface/CMEPS
diff --git a/NOAHMP-interface/CMakeLists.txt b/NOAHMP-interface/CMakeLists.txt
@@ -21,8 +21,8 @@ list(APPEND _noahmp_ccpp_files noahmp/drivers/ccpp/noahmpdrv.F90
                                noahmp/drivers/ccpp/physcons.F90)
 
 # NoahMP
-list(APPEND _noahmp_files noahmp/src/module_sf_noahmplsm.f90
-                          noahmp/src/module_sf_noahmp_glacier.f90)
+list(APPEND _noahmp_files noahmp/src/module_sf_noahmplsm.F90
+                          noahmp/src/module_sf_noahmp_glacier.F90)
 
 #------------------------------------------------------------------------------
 # Set CCPP flags for C/C++/Fortran preprocessor 

diff --git a/NOAHMP-interface/noahmp b/NOAHMP-interface/noahmp
diff --git a/tests/bl_date.conf b/tests/bl_date.conf
@@ -1,2 +1,2 @@
-export BL_DATE=20230623
+export BL_DATE=20230713
 
diff --git a/tests/default_vars.sh b/tests/default_vars.sh
@@ -531,6 +531,7 @@ export FHZERO=6
 export FNALBC="'global_snowfree_albedo.bosu.t126.384.190.rg.grb'"
 export FNVETC="'global_vegtype.igbp.t126.384.190.rg.grb'"
 export FNSOTC="'global_soiltype.statsgo.t126.384.190.rg.grb'"
+export FNSOCC="''"
 export FNSMCC="'global_soilmgldas.t126.384.190.grb'"
 export FNSMCC_control="'global_soilmgldas.statsgo.t1534.3072.1536.grb'"
 export FNMSKH_control="'global_slmask.t1534.3072.1536.grb'"
@@ -738,6 +739,7 @@ export IOPT_STC=3
 # P8
 export IOPT_SFC=3
 export IOPT_TRS=2
+export IOPT_DIAG=2
 
 # FV3 P7 settings
 export D2_BG_K1=0.20
@@ -802,6 +804,7 @@ export FNTG3C="'C96.substrate_temperature.tileX.nc'"
 export FNVEGC="'C96.vegetation_greenness.tileX.nc'"
 export FNVETC="'C96.vegetation_type.tileX.nc'"
 export FNSOTC="'C96.soil_type.tileX.nc'"
+export FNSOCC="'C96.soil_color.tileX.nc'"
 export FNSMCC=${FNSMCC_control}
 export FNMSKH=${FNMSKH_control}
 export FNVMNC="'C96.vegetation_greenness.tileX.nc'"

diff --git a/tests/detect_machine.sh b/tests/detect_machine.sh
@@ -105,7 +105,7 @@ case $(hostname -f) in
 
 esac
 
-case $(echo $PW_CSP) in
+case $(echo $PW_CSP:-nono) in
 
   aws) MACHINE_ID=aws ;; ### parallelworks aws
   google)  MACHINE_ID=gcp ;; ### parallelworks gcp

diff --git a/tests/fv3_conf/compile_qsub.IN_acorn b/tests/fv3_conf/compile_qsub.IN_acorn
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+#PBS -o out
+#PBS -e err
+#PBS -N @[JBNME]
+#PBS -A @[ACCNR]
+#PBS -q @[QUEUE]
+#PBS -l select=1:ncpus=8:mpiprocs=1:mem=32G
+#PBS -l walltime=00:45:00
+
+set -eux
+
+cd $PBS_O_WORKDIR
+
+echo -n " $( date +%s )," >  job_timestamp.txt
+echo "Compile started:  " `date`
+
+@[PATHRT]/compile.sh @[MACHINE_ID] "@[MAKE_OPT]" @[COMPILE_NR] @[RT_COMPILER]
+
+echo "Compile ended:    " `date`
+echo -n " $( date +%s )," >> job_timestamp.txt
diff --git a/tests/fv3_conf/fv3_qsub.IN_acorn b/tests/fv3_conf/fv3_qsub.IN_acorn
@@ -0,0 +1,36 @@
+#!/bin/bash
+
+#PBS -o out
+#PBS -e err
+#PBS -N @[JBNME]
+#PBS -A @[ACCNR]
+#PBS -q @[QUEUE]
+#PBS -l place=vscatter,select=@[NODES]:ncpus=@[TPN]:mpiprocs=@[TPN]:mem=500G
+#PBS -l place=excl
+#PBS -l walltime=00:@[WLCLK]:00
+
+set -eux
+echo -n " $( date +%s )," >  job_timestamp.txt
+
+cd $PBS_O_WORKDIR
+
+set +x
+module use $PWD/modulefiles
+module load modules.fv3
+module load cray-pals
+module list
+set -x
+
+echo "Model started:  " `date`
+
+export OMP_STACKSIZE=512M
+export OMP_NUM_THREADS=@[THRD]
+export OMP_PLACES=cores
+export ESMF_RUNTIME_COMPLIANCECHECK=OFF:depth=4
+export ESMF_RUNTIME_PROFILE=ON
+export ESMF_RUNTIME_PROFILE_OUTPUT="SUMMARY"
+
+mpiexec -n @[TASKS] -ppn @[TPN] -depth @[THRD] ./fv3.exe
+
+echo "Model ended:    " `date`
+echo -n " $( date +%s )," >> job_timestamp.txt
diff --git a/tests/fv3_conf/fv3_slurm.IN_gaea b/tests/fv3_conf/fv3_slurm.IN_gaea
@@ -3,7 +3,7 @@
 #SBATCH -o out
 #SBATCH --job-name="@[JBNME]"
 #SBATCH --account=@[ACCNR]
-#SBATCH --qos=@[QUEUE]
+##SBATCH --qos=@[QUEUE]
 #SBATCH --clusters=@[PARTITION]
 #SBATCH --nodes=@[NODES]
 #SBATCH --ntasks-per-node=@[TPN]

diff --git a/tests/fv3_conf/noahmp_run.IN b/tests/fv3_conf/noahmp_run.IN
@@ -11,6 +11,7 @@ rsync -arv @[INPUTDATA_ROOT]/NOAHMP_IC/ufs-land_C96_init_fields.tile6.nc C96.ini
 rsync -arv @[INPUTDATA_ROOT]/FV3_fix_tiled/C96/C96.maximum_snow_albedo.tile*.nc .
 rsync -arv @[INPUTDATA_ROOT]/FV3_fix_tiled/C96/C96.slope_type.tile*.nc .
 rsync -arv @[INPUTDATA_ROOT]/FV3_fix_tiled/C96/C96.soil_type.tile*.nc .
+rsync -arv @[INPUTDATA_ROOT]/FV3_fix_tiled/C96/C96.soil_color.tile*.nc .
 rsync -arv @[INPUTDATA_ROOT]/FV3_fix_tiled/C96/C96.substrate_temperature.tile*.nc .
 rsync -arv @[INPUTDATA_ROOT]/FV3_fix_tiled/C96/C96.vegetation_greenness.tile*.nc .
 rsync -arv @[INPUTDATA_ROOT]/FV3_fix_tiled/C96/C96.vegetation_type.tile*.nc .

diff --git a/tests/logs/RegressionTests_acorn.log b/tests/logs/RegressionTests_acorn.log
diff --git a/tests/logs/RegressionTests_cheyenne.log b/tests/logs/RegressionTests_cheyenne.log
diff --git a/tests/logs/RegressionTests_gaea.log b/tests/logs/RegressionTests_gaea.log
diff --git a/tests/logs/RegressionTests_hera.log b/tests/logs/RegressionTests_hera.log
diff --git a/tests/logs/RegressionTests_jet.log b/tests/logs/RegressionTests_jet.log
diff --git a/tests/logs/RegressionTests_orion.log b/tests/logs/RegressionTests_orion.log
diff --git a/tests/logs/RegressionTests_wcoss2.log b/tests/logs/RegressionTests_wcoss2.log
diff --git a/tests/opnReqTest b/tests/opnReqTest
@@ -137,16 +137,13 @@ build_opnReqTests() {
 run_opnReqTests() {
   JOB_NR=0
   for rc in $run_case; do
-    # load default variables and override as necessary
-    source default_vars.sh
-    source ${PATHRT}/tests/$TEST_NAME
 
     # if TEST_NAME specifies WARM_START true, error and exit
+    source ${PATHRT}/tests/$TEST_NAME
     if [[ ${WARM_START} == .T. ]]; then
       error "test-name cannot be a restart run (i.e. WARM_START=.T.)"
     fi
 
-    application=''
     if [[ $TEST_NAME =~ regional ]]; then
       application=regional
     elif [[ $TEST_NAME =~ cpld ]]; then
@@ -251,6 +248,7 @@ run_opnReqTests() {
 			export skip_check_results=${skip_check_results}
 			export delete_rundir=${delete_rundir}
       export RT_COMPILER=${RT_COMPILER}
+      export WLCLK=${WLCLK}
 			EOF
 
     if [[ $ECFLOW == true ]]; then
@@ -345,8 +343,6 @@ if [[ $MACHINE_ID = hera ]]; then
   STMP=${dprefix}/stmp4
   PTMP=${dprefix}/stmp2
   SCHEDULER=slurm
-  cp fv3_conf/fv3_slurm.IN_hera fv3_conf/fv3_slurm.IN
-  cp fv3_conf/compile_slurm.IN_hera fv3_conf/compile_slurm.IN
 
 elif [[ $MACHINE_ID = orion ]]; then
 
@@ -364,8 +360,6 @@ elif [[ $MACHINE_ID = orion ]]; then
   STMP=$dprefix/stmp
   PTMP=$dprefix/stmp
   SCHEDULER=slurm
-  cp fv3_conf/fv3_slurm.IN_orion fv3_conf/fv3_slurm.IN
-  cp fv3_conf/compile_slurm.IN_orion fv3_conf/compile_slurm.IN
 
 elif [[ $MACHINE_ID = linux ]]; then
 
@@ -468,6 +462,9 @@ if [[ $dbg_compare == true && ! $test_case =~ dbg ]]; then
   error "$program: debug reproducibility test requires specifying dbg"
 fi
 
+# load default variables and override as necessary
+source default_vars.sh
+
 # enumerate which case to compile and run
 compile_case=
 run_case=
@@ -547,11 +544,6 @@ if [[ $ECFLOW == true ]]; then
     error "ecflow is not supported on this machine $MACHINE_ID"
   fi
 
-  if [[ $MACHINE_ID == hera ]] && [[ ! $HOSTNAME == hecflow* ]]; then
-    echo "ERROR: To use ECFlow on Hera please use the 'hecflow01' login node: ssh hecflow01."
-    exit 1
-  fi
-
 fi
 
 opnreqtest_log=${PATHRT}/logs/OpnReqTests_${TEST_NAME}_$MACHINE_ID.log

diff --git a/tests/parm/control.nml.IN b/tests/parm/control.nml.IN
@@ -165,6 +165,7 @@ deflate_level=1
   iopt_tbot    = 2
   iopt_stc     = 1
   iopt_trs     = 2
+  iopt_diag    = 2
   debug        = .false.
   oz_phys      = .false.
   oz_phys_2015 = .true.
@@ -270,6 +271,7 @@ deflate_level=1
   FNVEGC   = 'global_vegfrac.0.144.decpercent.grb'
   FNVETC   = @[FNVETC]
   FNSOTC   = @[FNSOTC]
+  FNSOCC   = @[FNSOCC]
   FNSMCC   = @[FNSMCC_control]
   FNMSKH   = @[FNMSKH_control]
   FNTSFA   = ''

diff --git a/tests/parm/control_ca.nml.IN b/tests/parm/control_ca.nml.IN
@@ -163,6 +163,7 @@ deflate_level=1
   iopt_tbot    = 2
   iopt_stc     = 1
   iopt_trs     = 2
+  iopt_diag    = 2
   debug        = .false.
   oz_phys      = .false.
   oz_phys_2015 = .true.
@@ -270,6 +271,7 @@ deflate_level=1
   FNVEGC   = 'global_vegfrac.0.144.decpercent.grb'
   FNVETC   = @[FNVETC]
   FNSOTC   = @[FNSOTC]
+  FNSOCC   = @[FNSOCC]
   FNSMCC   = 'global_soilmgldas.statsgo.t1534.3072.1536.grb'
   FNMSKH   = 'global_slmask.t1534.3072.1536.grb'
   FNTSFA   = ''

diff --git a/tests/parm/control_csawmg.nml.IN b/tests/parm/control_csawmg.nml.IN
@@ -159,6 +159,7 @@ deflate_level=1
   iopt_tbot    = 2
   iopt_stc     = 1
   iopt_trs     = 2
+  iopt_diag    = 2
   debug        = .false.
   oz_phys      = .false.
   oz_phys_2015 = .true.
@@ -214,6 +215,7 @@ deflate_level=1
   FNVEGC   = 'global_vegfrac.0.144.decpercent.grb'
   FNVETC   = @[FNVETC]
   FNSOTC   = @[FNSOTC]
+  FNSOCC   = @[FNSOCC]
   FNSMCC   = 'global_soilmgldas.statsgo.t1534.3072.1536.grb'
   FNMSKH   = 'global_slmask.t1534.3072.1536.grb'
   FNTSFA   = ''

diff --git a/tests/parm/control_flake.nml.IN b/tests/parm/control_flake.nml.IN
@@ -167,6 +167,7 @@ deflate_level=1
   iopt_tbot    = 2
   iopt_stc     = 1
   iopt_trs     = 2
+  iopt_diag    = 2
   debug        = .false.
   oz_phys      = .false.
   oz_phys_2015 = .true.
@@ -253,6 +254,7 @@ deflate_level=1
   FNVEGC   = 'global_vegfrac.0.144.decpercent.grb'
   FNVETC   = @[FNVETC]
   FNSOTC   = @[FNSOTC]
+  FNSOCC   = @[FNSOCC]
   FNSMCC   = 'global_soilmgldas.statsgo.t1534.3072.1536.grb'
   FNMSKH   = 'global_slmask.t1534.3072.1536.grb'
   FNTSFA   = ''

diff --git a/tests/parm/control_gdas.nml.IN b/tests/parm/control_gdas.nml.IN
@@ -183,6 +183,7 @@ deflate_level=1
   iopt_tbot    = 2
   iopt_stc     = 1
   iopt_trs     = 2
+  iopt_diag    = 2
   debug        = .false.
   oz_phys      = .false.
   oz_phys_2015 = .true.
@@ -276,6 +277,7 @@ deflate_level=1
   FNVEGC   = 'global_vegfrac.0.144.decpercent.grb'
   FNVETC   = @[FNVETC]
   FNSOTC   = @[FNSOTC]
+  FNSOCC   = @[FNSOCC]
   FNSMCC   = 'global_soilmgldas.statsgo.t1534.3072.1536.grb'
   FNMSKH   = 'global_slmask.t1534.3072.1536.grb'
   FNTSFA   = '        '

diff --git a/tests/parm/control_gfsv17.nml.IN b/tests/parm/control_gfsv17.nml.IN
@@ -166,6 +166,7 @@ deflate_level=1
   iopt_tbot    = 2
   iopt_stc     = 1
   iopt_trs     = 2
+  iopt_diag    = 2
   debug        = .false.
   oz_phys      = .false.
   oz_phys_2015 = .true.
@@ -269,6 +270,7 @@ deflate_level=1
   FNVEGC   = 'global_vegfrac.0.144.decpercent.grb'
   FNVETC   = @[FNVETC]
   FNSOTC   = @[FNSOTC]
+  FNSOCC   = @[FNSOCC]
   FNSMCC   = @[FNSMCC_control]
   FNMSKH   = @[FNMSKH_control]
   FNTSFA   = ''

diff --git a/tests/parm/control_noahmp.nml.IN b/tests/parm/control_noahmp.nml.IN
@@ -161,6 +161,7 @@ deflate_level=1
   iopt_tbot    = 2
   iopt_stc     = 3
   iopt_trs     = 2
+  iopt_diag    = 2
   debug        = .false.
   oz_phys      = .false.
   oz_phys_2015 = .true.
@@ -247,6 +248,7 @@ deflate_level=1
   FNVEGC   = 'global_vegfrac.0.144.decpercent.grb'
   FNVETC   = @[FNVETC]
   FNSOTC   = @[FNSOTC]
+  FNSOCC   = @[FNSOCC]
   FNSMCC   = 'global_soilmgldas.statsgo.t1534.3072.1536.grb'
   FNMSKH   = 'global_slmask.t1534.3072.1536.grb'
   FNTSFA   = ''

diff --git a/tests/parm/control_ugwpv1.nml.IN b/tests/parm/control_ugwpv1.nml.IN
@@ -161,6 +161,7 @@ deflate_level=1
   iopt_tbot    = 2
   iopt_stc     = 1
   iopt_trs     = 2
+  iopt_diag    = 2
   debug        = .false.
   oz_phys      = .false.
   oz_phys_2015 = .true.
@@ -260,6 +261,7 @@ deflate_level=1
   FNVEGC   = 'global_vegfrac.0.144.decpercent.grb'
   FNVETC   = @[FNVETC]
   FNSOTC   = @[FNSOTC]
+  FNSOCC   = @[FNSOCC]
   FNSMCC   = 'global_soilmgldas.statsgo.t1534.3072.1536.grb'
   FNMSKH   = 'global_slmask.t1534.3072.1536.grb'
   FNTSFA   = ''

diff --git a/tests/parm/cpld_control.nml.IN b/tests/parm/cpld_control.nml.IN
@@ -191,6 +191,7 @@ deflate_level=1
   iopt_run     = 1
   iopt_sfc     = @[IOPT_SFC]
   iopt_trs     = @[IOPT_TRS]
+  iopt_diag    = @[IOPT_DIAG]
   iopt_frz     = 1
   iopt_inf     = 1
   iopt_rad     = @[IOPT_RAD]
@@ -330,6 +331,7 @@ deflate_level=1
   FNVEGC   = @[FNVEGC]
   FNVETC   = @[FNVETC]
   FNSOTC   = @[FNSOTC]
+  FNSOCC   = @[FNSOCC]
   FNSMCC   = @[FNSMCC]
   FNMSKH   = @[FNMSKH]
   FNTSFA   = ''

diff --git a/tests/parm/cpt.nml.IN b/tests/parm/cpt.nml.IN
@@ -154,6 +154,7 @@
        iopt_tbot      = 2
        iopt_stc       = 1
        iopt_trs     = 2
+       iopt_diag    = 2
        oz_phys        = .false.
        oz_phys_2015   = .true.
        debug          = .false.
@@ -263,6 +264,7 @@
        FNVEGC   = "global_vegfrac.0.144.decpercent.grb",
        FNVETC   = @[FNVETC]
        FNSOTC   = @[FNSOTC]
+       FNSOCC   = @[FNSOCC]
        FNSMCC   = @[FNSMCC]
        FNMSKH   = "global_slmask.t1534.3072.1536.grb",
        FNTSFA   = "",

diff --git a/tests/parm/csawmg3shoc127.nml.IN b/tests/parm/csawmg3shoc127.nml.IN
@@ -155,6 +155,7 @@
        iopt_tbot      = 2
        iopt_stc       = 1
        iopt_trs       = 2
+       iopt_diag      = 2
        debug          = .false.
 
        ras            = .false.
@@ -213,6 +214,7 @@
        FNVEGC   = "global_vegfrac.0.144.decpercent.grb",
        FNVETC   = @[FNVETC]
        FNSOTC   = @[FNSOTC]
+       FNSOCC   = @[FNSOCC]
        FNSMCC   = @[FNSMCC]
        FNMSKH   = "global_slmask.t1534.3072.1536.grb",
        FNTSFA   = "",

diff --git a/tests/parm/csawmgshoc.nml.IN b/tests/parm/csawmgshoc.nml.IN
@@ -154,6 +154,7 @@
        iopt_tbot      = 2
        iopt_stc       = 1
        iopt_trs       = 2
+       iopt_diag      = 2
        debug          = .false.
 
        ras            = .false.

diff --git a/tests/parm/fd_nems.yaml b/tests/parm/fd_nems.yaml
@@ -763,6 +763,8 @@
        canonical_units: N m-2
      - standard_name: inst_laten_heat_flx
        canonical_units: N m-2
+     - standard_name: inst_evap_rate
+       canonical_units: kg m-2 s-1
      - standard_name: inst_tracer_mass_frac
        canonical_units: 1
      - standard_name: inst_tracer_up_surface_flx

diff --git a/tests/parm/input_global_hafs.nml.IN b/tests/parm/input_global_hafs.nml.IN
@@ -213,6 +213,7 @@
        iopt_tbot      = 2
        iopt_stc       = 1
        iopt_trs       = 2
+       iopt_diag      = 2
        debug          = .false.
        oz_phys        = .false.
        oz_phys_2015   = .true.