UFS/dev PR#216

.gitmodules

@@ -4,8 +4,8 @@
 	branch = main
 [submodule "ccpp-physics"]
 	path = ccpp/physics
-	url = https://github.com/NCAR/ccpp-physics
-	branch = main
+	url = https://github.com/grantfirl/ccpp-physics
+	branch = ufs-dev-PR216
 [submodule "CMakeModules"]
 	path = CMakeModules
 	url = https://github.com/noaa-emc/CMakeModules

contrib/get_aerosol_climo.sh

@@ -20,7 +20,7 @@ data_files=("FV3_aeroclim1" "FV3_aeroclim2" "FV3_aeroclim3" "FV3_aeroclim_optics
 cd $BASEDIR/scm/data/physics_input_data/
 for file in "${data_files[@]}"; do
     echo "Retrieving $file.tar.gz"
-    wget https://github.com/NCAR/ccpp-scm/releases/download/v7.0.0-beta/${file}.tar.gz
+    wget https://github.com/NCAR/ccpp-scm/releases/download/v7.0.0/${file}.tar.gz
     tar -xvf ${file}.tar.gz
     rm -f ${file}.tar.gz
 done

contrib/get_all_static_data.sh

@@ -21,7 +21,7 @@ for file in "${data_files[@]}"; do
     mkdir -p $BASEDIR/scm/data/$file
     cd $BASEDIR/scm/data/$file
     echo "Retrieving $file"
-    wget https://github.com/NCAR/ccpp-scm/releases/download/v7.0.0-beta/${file}.tar.gz
+    wget https://github.com/NCAR/ccpp-scm/releases/download/v7.0.0/${file}.tar.gz
     tar -xf ${file}.tar.gz
     rm -f ${file}.tar.gz
 done

contrib/get_mg_inccn_data.sh

@@ -16,7 +16,7 @@ BASEDIR=$MYDIR/..
 
 # Change to directory containing the physics input data, download and extract archive
 cd $BASEDIR/scm/data/physics_input_data/
-wget https://github.com/NCAR/ccpp-scm/releases/download/v7.0.0-beta/MG_INCCN_data.tar.gz
+wget https://github.com/NCAR/ccpp-scm/releases/download/v7.0.0/MG_INCCN_data.tar.gz
 tar -xvf MG_INCCN_data.tar.gz
 rm -f MG_INCCN_data.tar.gz
 cd $BASEDIR/

contrib/get_thompson_tables.sh

@@ -15,7 +15,7 @@ BASEDIR=$MYDIR/..
 
 # Change to directory containing the physics input data, download and extract archive
 cd $BASEDIR/scm/data/physics_input_data/
-wget https://github.com/NCAR/ccpp-scm/releases/download/v7.0.0-beta/thompson_tables.tar.gz
+wget https://github.com/NCAR/ccpp-scm/releases/download/v7.0.0/thompson_tables.tar.gz
 tar -xvf thompson_tables.tar.gz
 rm -f thompson_tables.tar.gz
 cd $BASEDIR/

docker/Dockerfile

@@ -74,7 +74,7 @@ ENV w3emc_ROOT=/comsoftware/nceplibs
 # Obtain CCPP SCM source code, build code, and download static data
 RUN if [ -z "$PR_NUMBER" ]; then \
         cd /comsoftware \
-        && git clone --recursive -b main https://github.com/NCAR/ccpp-scm; \
+        && git clone --recursive -b release/public-v7 https://github.com/NCAR/ccpp-scm; \
     else \
         cd /comsoftware \
         && git clone https://github.com/NCAR/ccpp-scm \

environment-scm_analysis.yml

@@ -0,0 +1,9 @@
+name: env_scm_analysis
+
+dependencies:
+  - conda-forge::python=3.7
+  - conda-forge::netcdf4
+  - conda-forge::f90nml
+  - conda-forge::configobj
+  - conda-forge::matplotlib
+  - conda-forge::pandas

scm/doc/TechGuide/chap_cases.rst

@@ -297,6 +297,20 @@ Activate environment:
 .. code:: bash
 
   > conda activate env_ufscasegen
+
+Note that it may be possible for conda to fail to solve for the environment when attempting to use the yml file. It 
+should still be possible to create the same environment manually:
+
+.. code:: bash
+
+  > conda create --name env_ufscasegen
+  > conda install -n env_ufscasegen --channel=conda-forge python=3.8.5
+  > conda install -n env_ufscasegen --channel=conda-forge netcdf4
+  > conda install -n env_ufscasegen --channel=conda-forge f90nml
+  > conda install -n env_ufscasegen --channel=conda-forge xarray
+  > conda install -n env_ufscasegen --channel=conda-forge numpy
+  > conda install -n env_ufscasegen --channel=conda-forge shapely
+  > conda install -n env_ufscasegen --channel=conda-forge xesmf
 
 .. _`ufscasegen`:
 
@@ -422,13 +436,24 @@ appreciably different than the calculated geostrophic winds), this often leads t
 with time. An option exists within the script to assume that the mean three-dimensional winds are, in fact, identical to the 
 geostrophic winds as well. Using this option eliminates any spurious turning.
 
+Writing UFS Comparison Data
+
+The `--save_comp` (or `-sc`) options allow one to write out the UFS data for the chosen column in NetCDF format. The profiles of the state variables 
+`u`, `v`, `T`, and `q_v` are written out for the given point for each history file time. In addition, a collection of other 
+diagnostics like profiles of physics tendencies and scalar surface variables are saved and written. One can include any variable that is
+provided in the UFS history files, although the specific variables are hard-coded in the `UFS_case_gen.py` file which will require editing
+to change. The file with comparison data is automatically written out to the `scm/data/comparison_data` directory, although this is controlled
+by the `COMPARISON_DATA_DIR` global variable in the `UFS_case_gen.py` script. The filename is a concatenation of the case name (specified by the 
+`--case_name (-n)` argument) and `_comp_data.nc`.
+
 .. _`ufsforcingensemblegenerator`:
 
 UFS_forcing_ensemble_generator.py
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 There is an additional script in ``scm/etc/scripts/UFS_forcing_ensemble_generator.py`` to create UFS-caseGen case(s) starting
-with output from UFS Weather Model (UWM) Regression Tests (RTs).
+with output from UFS Weather Model (UWM) Regression Tests (RTs). This script provides a wrapper for ``UFS_case_gen.py`` for
+generating multiple cases at once.
 
 .. code:: bash
 
@@ -489,11 +514,12 @@ staged UWM RTs located at:
 Example 1: UFS-caseGen for single point
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-UFS regression test, ``control_c192``, for single point.
+UFS regression test, ``control_c192``, for a single point using calculated horizontal advective tendencies,
+supplying the vertical velocity for the vertical advective terms and nudging the horizontal winds:
 
 .. code:: bash
 
-   ./UFS_forcing_ensemble_generator.py -d [path_to_regression_tests_output]/control_c192_intel/ -sc --C_RES 192 -dt 360  -n control_c192 -lons 300 -lats 34
+   ./UFS_forcing_ensemble_generator.py -d [path_to_regression_tests_output]/control_c192_intel/ -sc --C_RES 192 -dt 360  -n control_c192 -lons 300 -lats 34 -fm 2 -vm 2 -wn
 
 Upon successful completion of the script, the command to run the case(s)
 will print to the screen. For example,
@@ -509,11 +535,11 @@ The file ``scm_ufsens_control_c192.py`` is created in ``ccpp-scm/scm/bin/``, whe
 Example 2: UFS-caseGen for list of points
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-UFS regression test, ``control_c384``, for multiple points.
+UFS regression test, ``control_c384``, for multiple points assuming the same forcing method as above:
 
 .. code:: bash
 
-   ./UFS_forcing_ensemble_generator.py -d /glade/derecho/scratch/epicufsrt/ufs-weather-model/RT/NEMSfv3gfs/develop-20240607/control_c384_intel/ -sc --C_RES 384 -dt 225 -n control_c384 -lons 300 300 300 300 -lats 34 35 35 37
+   ./UFS_forcing_ensemble_generator.py -d /glade/derecho/scratch/epicufsrt/ufs-weather-model/RT/NEMSfv3gfs/develop-20240607/control_c384_intel/ -sc --C_RES 384 -dt 225 -n control_c384 -lons 300 300 300 300 -lats 34 35 35 37 -fm 2 -vm 2 -wn
 
 Upon successful completion of the script, the command to run the case(s)
 will print to the screen. For example,

scm/doc/TechGuide/chap_quick.rst

@@ -216,13 +216,6 @@ Unified Forecast System and related applications, only a minority of which are r
 install libraries manually if they wish, but they will need to make sure the appropriate environment variables
 are set to the correct values so that the build system can find them, as described in the following paragraphs.
 
-
-<<<<<<< HEAD
-Setting up compilation environment
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-For users on a pre-configured platform, the spack-stack environment can be loaded via one of the provided modules in ``scm/etc/modules/`` as described in :numref:`Section %s <use_preconfigured_platforms>`.
-=======
 For users on a pre-configured platform, you can load the spack-stack environment via one of the provided modules in ``scm/etc/modules/``.
 For example, users on the NSF NCAR machine Derecho who wish to use Intel compilers can do the following:
 
@@ -231,7 +224,6 @@ For example, users on the NSF NCAR machine Derecho who wish to use Intel compile
    cd [path/to/ccpp-scm/]
    module use scm/etc/modules/
    module load derecho_intel
->>>>>>> feature/modulefile_updates
 
 Additionally, for users who have installed spack-stack on their own MacOS or Linux machine can use the provided ``macos_clang``
 or ``linux_gnu`` modules.
@@ -602,6 +594,12 @@ If using the main branch, you should run the above command to ensure you have th
    -  Use this to specify the timestep to use (if different than the
       default specified in ``../src/suite_info.py``).
 
+-  ``--mpi_command``
+
+   -  Provide argument to define the MPI command that will be invoked.
+      Default MPI command is ``mpirun -np 1``.
+      (Note: to run on a Derecho login node the empty argument ``--mpi_command ''`` is required.)
+
 -  ``--verbose [-v]``
 
    -  Use this option to see additional debugging output from the run
@@ -613,11 +611,7 @@ configuration files located in ``../etc/case_config`` (*without the .nml extensi
 specifying a suite other than the default, the suite name used must
 match the value of the suite name in one of the suite definition files
 located in ``../../ccpp/suites`` (Note: not the filename of the suite definition file). As
-<<<<<<< HEAD
-part of the CCPP SCM v7.0.0 release, the following suite names are supported:
-=======
 part of the seventh CCPP release, the following suite names are supported:
->>>>>>> feature/modulefile_updates
 
 #. SCM_GFS_v16
 
@@ -888,7 +882,7 @@ Running the Docker image
 
 #. To run the SCM, you can run the Docker container that was just
    created and give it the same run commands as discussed in :numref:`Section %s <singlerunscript>`
-   **Be sure to remember to include the ``-d`` and ``--mpi_command "mpirun -np 1 --allow-run-as-root"`` 
+   **Be sure to remember to include the ``-d`` and ``--mpi_command "mpirun -np 1 --allow-run-as-root"``
    options for all run commands**. For example,
 
    .. code:: bash

scm/etc/scm_qsub_example.py

@@ -34,7 +34,7 @@
 WALLTIME = "walltime=00:20:00"
 PROCESSORS = "select=1:ncpus=1"
 QUEUE = "develop"
-COMMAND = "./run_scm.py -c twpice"
+COMMAND = "cd $PBS_O_WORKDIR; ./run_scm.py -c twpice"
 EMAIL_ADDR = MY_EMAIL
 SERIAL_MEM = "512M"
 WORKING_DIR = os.path.dirname(os.path.abspath(__file__))

scm/etc/scripts/plot_configs/twpice_all_suites.ini

@@ -1,5 +1,5 @@
-scm_datasets = output_twpice_SCM_GFS_v16/output.nc, output_twpice_SCM_GFS_v17_p8/output.nc, output_twpice_SCM_RAP/output.nc, output_twpice_SCM_RRFS_v1beta/output.nc, output_twpice_SCM_WoFS_v0/output.nc, output_twpice_SCM_HRRR/output.nc
-scm_datasets_labels = GFSv16, GFSv17p8, RAP, RRFSv1b, WoFSv0, HRRR
+scm_datasets = output_twpice_SCM_GFS_v16/output.nc, output_twpice_SCM_GFS_v16_RRTMGP/output.nc, output_twpice_SCM_GFS_v17_p8_ugwpv1/output.nc, output_twpice_SCM_WoFS_v0/output.nc, output_twpice_SCM_HRRR_gf/output.nc
+scm_datasets_labels = GFSv16, GFSv16-GP, GFSv17p8-ugwpv1, WoFSv0, HRRR-gf 
 plot_dir = plots_twpice_all_suites/
 obs_file = ../data/raw_case_input/twp180iopsndgvarana_v2.1_C3.c1.20060117.000000.cdf
 obs_compare = True
@@ -23,24 +23,27 @@ time_series_resample = True
     y_log = False
     y_min_option = min             #min, max, val (if val, add y_min = float value)
     y_max_option = max              #min, max, val (if val, add y_max = float value)
-    conversion_factor = 1000.0, 1000.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0
+    conversion_factor = 1000.0, 1000.0, 1.0, 86400.0, 86400.0, 86400.0, 86400.0, 86400.0
 
   [[profiles_mean_multi]]
     [[[T_forcing]]]
       vars = T_force_tend, dT_dt_pbl, dT_dt_conv, dT_dt_micro, dT_dt_lwrad, dT_dt_swrad
       vars_labels = 'force', 'PBL', 'Conv', 'MP', 'LW', 'SW'
       x_label = 'K/day'
+      conversion_factor = 86400.0
     [[[conv_tendencies]]]
       vars = dT_dt_deepconv, dT_dt_shalconv
       vars_labels = 'deep', 'shallow'
       x_label = 'K/day'
+      conversion_factor = 86400.0
 
   [[profiles_instant]]
 
   [[time_series]]
-    vars = 'pres_s','lhf','shf','tprcp_rate_inst'
+    vars = 'pres_s','lhf','shf','tprcp_rate_accum'
     vars_labels = 'surface pressure (Pa)','latent heat flux ($W$ $m^{-2}$)','sensible heat flux ($W$ $m^{-2}$)','surface rainfall rate ($mm$ $hr{-1}$)'
-
+    conversion_factor = 1.0, 1.0, 1.0, 3600000.0
+
   [[contours]]
     vars = qv,
     vars_labels = 'Water Vapor ($g$ $kg^{-1}$)',

test/cmp_rt2bl.py

@@ -14,20 +14,22 @@
 
 #
 parser = argparse.ArgumentParser()
-parser.add_argument('-drt',  '--dir_rt',  help='Directory containing SCM RT output',      required=True)
-parser.add_argument('-dbl',  '--dir_bl',  help='Directory containing SCM RT baselines',   required=True)
+parser.add_argument('-drt',  '--dir_rt',   help='Directory containing SCM RT output',              required=True)
+parser.add_argument('-dbl',  '--dir_bl',   help='Directory containing SCM RT baselines',           required=True)
+parser.add_argument('-np',   '--no_plots', help='flag to turn off generation of difference plots', required=False, action='store_true')
 
 #
 def parse_args():
     args    = parser.parse_args()
     dir_rt  = args.dir_rt 
     dir_bl  = args.dir_bl
-    return (dir_rt, dir_bl)
+    no_plots   = args.no_plots
+    return (dir_rt, dir_bl, no_plots)
 
 #
 def main():
     #
-    (dir_rt, dir_bl) = parse_args()
+    (dir_rt, dir_bl, no_plots) = parse_args()
 
     #
     error_count = 0
@@ -38,14 +40,17 @@ def main():
             com = "cmp "+file_rt+" "+file_bl+" > logfile.txt"
             result = os.system(com)
             if (result != 0):
-                print("Output for "+run["case"]+"_"+run["suite"]+ " DIFFERS from baseline. Difference plots will be created")
+                message = "Output for "+run["case"]+"_"+run["suite"]+ " DIFFERS from baseline."
+                if (not no_plots):
+                    message += " Difference plots will be created."
+                print(message)
                 error_count = error_count + 1
             else:
                 print("Output for "+run["case"]+"_"+run["suite"]+ " is IDENTICAL to baseline")
             # end if
 
             # Create plots between RTs and baselines (only if differences exist)
-            if (result != 0):
+            if (result != 0 and not no_plots):
                 plot_files = plot_results(file_bl, file_rt)
 
                 # Setup output directories for plots.
@@ -71,7 +76,8 @@ def main():
     # end for
 
     # Create tarball with plots.
-    result = os.system('tar -cvf scm_rt_out.tar scm_rt_out/*')
+    if (not no_plots):
+        result = os.system('tar -cvf scm_rt_out.tar scm_rt_out/*')
 
     #
     if error_count == 0: