Update feature/nssl_micro branch to latest main

scm/etc/Hera_setup_intel.csh

@@ -28,54 +28,6 @@ setenv CMAKE_CXX_COMPILER icpc
 setenv CMAKE_Fortran_COMPILER ifort
 setenv CMAKE_Platform hera.intel
 
-echo "Loading the anaconda python distribution"
-module use -a /contrib/anaconda/modulefiles
-module load anaconda/anaconda3-4.4.0
-
-#install f90nml for the local user
-
-#check to see if f90nml is installed locally
-echo "Checking if f90nml python module is installed"
-python -c "import f90nml"
-
-if ( $? != 0 ) then
-	echo "Not found; installing f90nml"
-	pip install -e git://github.com/marshallward/f90nml.git@v0.19\#egg=f90nml --user
-else
-	echo "f90nml is installed"
-endif
-
-#install shapely for the local user
-
-#check to see if shapely is installed locally
-echo "Checking if shapely python module is installed"
-python -c "import shapely"
-
-if ( $? != 0 ) then
-	echo "Not found; installing shapely"
-	pip install --index-url http://anaconda.rdhpcs.noaa.gov/simple --trusted-host anaconda.rdhpcs.noaa.gov shapely --user
-else
-	echo "shapely is installed"
-endif
-
-#check to see if configobj is installed locally
-echo "Checking if configobj python module is installed"
-python -c "import configobj"
-
-if ( $? != 0 ) then
-	echo "Not found; installing configobj"
-	pip install --index-url http://anaconda.rdhpcs.noaa.gov/simple --trusted-host anaconda.rdhpcs.noaa.gov configobj --user
-else
-	echo "configobj is installed"
-endif
-
-#check to see if netCDF4 is installed locally
-echo "Checking if netCDF4 python module is installed"
-python -c "import netCDF4"
-
-if ( $? != 0 ) then
-	echo "Not found; installing netCDF4"
-	pip install --index-url http://anaconda.rdhpcs.noaa.gov/simple --trusted-host anaconda.rdhpcs.noaa.gov netCDF4 --user
-else
-	echo "netCDF4 is installed"
-endif
+echo "Loading the SCM python environment"
+source /scratch1/BMC/gmtb/SCM_anaconda/etc/profile.d/conda.csh
+conda activate pyccpp

scm/etc/Hera_setup_intel.sh

@@ -25,54 +25,6 @@ export CMAKE_CXX_COMPILER=icpc
 export CMAKE_Fortran_COMPILER=ifort
 export CMAKE_Platform=hera.intel
 
-echo "Loading the anaconda python distribution"
-module use -a /contrib/anaconda/modulefiles
-module load anaconda/anaconda3-4.4.0
-
-#install f90nml for the local user
-
-#check to see if f90nml is installed locally
-echo "Checking if f90nml python module is installed"
-python -c "import f90nml"
-
-if [ $? -ne 0 ]; then
-	echo "Not found; installing f90nml"
-	pip install -e git://github.com/marshallward/f90nml.git@v0.19#egg=f90nml --user
-else
-	echo "f90nml is installed"
-fi
-
-#install shapely for the local user
-
-#check to see if shapely is installed locally
-echo "Checking if shapely python module is installed"
-python -c "import shapely"
-
-if [ $? -ne 0 ]; then
-	echo "Not found; installing shapely"
-	pip install --index-url http://anaconda.rdhpcs.noaa.gov/simple --trusted-host anaconda.rdhpcs.noaa.gov shapely --user
-else
-	echo "shapely is installed"
-fi
-
-#check to see if configobj is installed locally
-echo "Checking if configobj python module is installed"
-python -c "import configobj"
-
-if [ $? -ne 0 ]; then
-	echo "Not found; installing configobj"
-	pip install --index-url http://anaconda.rdhpcs.noaa.gov/simple --trusted-host anaconda.rdhpcs.noaa.gov configobj --user
-else
-	echo "configobj is installed"
-fi
-
-#check to see if netCDF4 is installed locally
-echo "Checking if netCDF4 python module is installed"
-python -c "import netCDF4"
-
-if [ $? -ne 0 ]; then
-	echo "Not found; installing netCDF4"
-	pip install --index-url http://anaconda.rdhpcs.noaa.gov/simple --trusted-host anaconda.rdhpcs.noaa.gov netCDF4 --user
-else
-	echo "netCDF4 is installed"
-fi
+echo "Loading the SCM python environment"
+. "/scratch1/BMC/gmtb/SCM_anaconda/etc/profile.d/conda.sh"
+conda activate pyccpp

scm/etc/case_config/gabls3_ruc.nml

@@ -0,0 +1,29 @@
+$case_config
+model_name = 'FV3',
+n_columns = 1,
+case_name = 'gabls3_ruc',
+dt = 600.0,
+time_scheme = 1,
+runtime = 86400,
+n_itt_out = 1,
+n_itt_diag = 6,
+n_levels = 64,
+output_file = 'output',
+case_data_dir = '../data/processed_case_input',
+vert_coord_data_dir = '../data/vert_coord_data',
+thermo_forcing_type = 2,
+mom_forcing_type = 2,
+relax_time = 7200.0,
+sfc_flux_spec = .false.,
+lsm_ics = .true.,
+do_spinup = .true.,
+spinup_timesteps = 12,
+sfc_roughness_length_cm = 15.0,
+sfc_type = 1,
+reference_profile_choice = 2,
+year = 2006,
+month = 7,
+day = 1,
+hour = 12,
+column_area = 1.45E8,
+$end

scm/etc/scm_qsub_example.py

@@ -21,7 +21,7 @@
 USER = os.getenv('USER')
 STRINGS = [USER, 'ucar.edu']
 MY_EMAIL = '@'.join(STRINGS)
-PROC = Popen('qsub', shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE, close_fds=True)
+PROC = Popen('qsub -V', shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE, close_fds=True)
 
 ### Begin User-editable section ###
 JOB_NAME = "test_job"

scm/etc/scripts/GABLS3_LSM.ncl

@@ -431,7 +431,11 @@ begin
   tg3@units = "K"
   tg3@long_name = "deep soil temperature"
 
-  zorlw = 15.0 ;(cm) from case specs
+  zorl = 15.0 ;(cm) from case specs
+  zorl@long_name = "composite surface roughness length"
+  zorl@units = "cm"
+
+  zorlw = zorl ;(cm) from case specs
   zorlw@long_name = "surface roughness length over ocean"
   zorlw@units = "cm"
 
@@ -482,7 +486,7 @@ begin
 
   ;derive friction velocity from known values
   wind1 = sqrt(u_specified(1)^2 + v_specified(1)^2)
-  uustar = von_K*wind1/log(u_h(1)/(0.01*zorlw))
+  uustar = von_K*wind1/log(u_h(1)/(0.01*zorl))
   uustar@units = "m s-1"
   uustar@long_name = "friction velocity"
 
@@ -533,19 +537,19 @@ begin
   tsfcl@long_name = "surface skin temperature over land"
   tsfcl@units     = "K"
 
-  zorll = zorlw ;(cm) from case specs
+  zorll = zorl ;(cm) from case specs
   zorll@long_name = "surface roughness length over land"
   zorll@units = "cm"
 
-  zorli = zorlw ;(cm) from case specs
+  zorli = zorl ;(cm) from case specs
   zorli@long_name = "surface roughness length over ice"
   zorli@units = "cm"
 
   stc = (/ 292.55, 289.9, 285.35, 283.15 /)
   stc@units = "K"
   stc@long_name = "initial profile of soil temperature"
 
-  smc = (/ 0.197, 0.197, 0.197, 0.197 /)
+  smc = (/ 0.203, 0.203, 0.203, 0.203 /)
   smc@units = "m3 m-3"
   smc@long_name = "initial profile of soil moisture"
 
@@ -636,6 +640,10 @@ begin
   filevarattdef(g1,"tg3",tg3)
   g1->tg3 = tg3
 
+  filevardef(g1,"zorl",typeof(zorl),"ncl_scalar")
+  filevarattdef(g1,"zorl",zorl)
+  g1->zorl = zorl
+
   filevardef(g1,"zorlw",typeof(zorlw),"ncl_scalar")
   filevarattdef(g1,"zorlw",zorlw)
   g1->zorlw = zorlw

scm/etc/scripts/GABLS3_LSM_NoahMP.ncl

@@ -431,7 +431,11 @@ begin
   tg3@units = "K"
   tg3@long_name = "deep soil temperature"
 
-  zorlw = 15.0 ;(cm) from case specs
+  zorl = 15.0 ;(cm) from case specs
+  zorl@long_name = "composite surface roughness length"
+  zorl@units = "cm"
+
+  zorlw = zorl ;(cm) from case specs
   zorlw@long_name = "surface roughness length over ocean"
   zorlw@units = "cm"
 
@@ -482,7 +486,7 @@ begin
 
   ;derive friction velocity from known values
   wind1 = sqrt(u_specified(1)^2 + v_specified(1)^2)
-  uustar = von_K*wind1/log(u_h(1)/(0.01*zorlw))
+  uustar = von_K*wind1/log(u_h(1)/(0.01*zorl))
   uustar@units = "m s-1"
   uustar@long_name = "friction velocity"
 
@@ -533,11 +537,11 @@ begin
   tsfcl@long_name = "surface skin temperature over land"
   tsfcl@units     = "K"
 
-  zorll = zorlw ;(cm) from case specs
+  zorll = zorl ;(cm) from case specs
   zorll@long_name = "surface roughness length over land"
   zorll@units = "cm"
 
-  zorli = zorlw ;(cm) from case specs
+  zorli = zorl ;(cm) from case specs
   zorli@long_name = "surface roughness length over ice"
   zorli@units = "cm"
 
@@ -636,6 +640,10 @@ begin
   filevarattdef(g1,"tg3",tg3)
   g1->tg3 = tg3
 
+  filevardef(g1,"zorl",typeof(zorl),"ncl_scalar")
+  filevarattdef(g1,"zorl",zorl)
+  g1->zorl = zorl
+
   filevardef(g1,"zorlw",typeof(zorlw),"ncl_scalar")
   filevarattdef(g1,"zorlw",zorlw)
   g1->zorlw = zorlw