Unit/functional test improvements to enable CTSM SystemTests

testing/functional_class.py

@@ -1,19 +1,34 @@
+import os
+import urllib.request
 from abc import ABC, abstractmethod
 from utils import str_to_bool, str_to_list
 
 class FunctionalTest(ABC):
     """Class for running FATES functional tests"""
 
     def __init__(self, name:str, test_dir:str, test_exe:str, out_file:str,
-                 use_param_file:str, other_args:str):
+                 use_param_file:str, datm_file:str, datm_file_url:str, other_args:str):
         self.name = name
         self.test_dir = test_dir
         self.test_exe = test_exe
         self.out_file = out_file
         self.use_param_file = str_to_bool(use_param_file)
+        self.datm_file = None
         self.other_args = str_to_list(other_args)
         self.plot = False
-
+
+        # Check that datm exists and save its absolute path
+        if datm_file:
+            self.datm_file = os.path.abspath(datm_file)
+            if not os.path.exists(self.datm_file):
+                if not datm_file_url:
+                    raise FileNotFoundError(f"datm_file not found: '{self.datm_file}'")
+                datm_file_dir = os.path.dirname(self.datm_file)
+                if not os.path.isdir(datm_file_dir):
+                    os.makedirs(datm_file_dir)
+                print(f"Downloading datm_file from {datm_file_url}")
+                urllib.request.urlretrieve(datm_file_url, self.datm_file)
+
     @abstractmethod
     def plot_output(self, run_dir:str, save_figs:bool, plot_dir:str):
         pass

testing/functional_testing/allometry/allometry_test.py

@@ -23,6 +23,8 @@ def __init__(self, test_dict):
             test_dict["test_exe"],
             test_dict["out_file"],
             test_dict["use_param_file"],
+            test_dict["datm_file"],
+            test_dict["datm_file_url"],
             test_dict["other_args"],
         )
         self.plot = True

testing/functional_testing/fire/fuel/fuel_test.py

@@ -20,6 +20,8 @@ def __init__(self, test_dict):
             test_dict["test_exe"],
             test_dict["out_file"],
             test_dict["use_param_file"],
+            test_dict["datm_file"],
+            test_dict["datm_file_url"],
             test_dict["other_args"],
         )
         self.plot = True

testing/functional_testing/fire/ros/ros_test.py

@@ -26,6 +26,8 @@ def __init__(self, test_dict):
             test_dict["test_exe"],
             test_dict["out_file"],
             test_dict["use_param_file"],
+            test_dict["datm_file"],
+            test_dict["datm_file_url"],
             test_dict["other_args"],
         )
         self.plot = True

testing/functional_testing/fire/shr/SyntheticFuelModels.F90

@@ -178,7 +178,7 @@ integer function FuelModelPosition(this, fuel_model_index)
       end if
     end do
     write(*, '(a, i2, a)') "Cannot find the fuel model index ", fuel_model_index, "."
-    stop
+    call abort()
 
   end function FuelModelPosition
 

testing/functional_testing/math_utils/math_utils_test.py

@@ -22,6 +22,8 @@ def __init__(self, test_dict):
             test_dict["test_exe"],
             test_dict["out_file"],
             test_dict["use_param_file"],
+            test_dict["datm_file"],
+            test_dict["datm_file_url"],
             test_dict["other_args"],
         )
         self.plot = True

testing/functional_testing/patch/patch_test.py

@@ -23,6 +23,8 @@ def __init__(self, test_dict):
             test_dict["test_exe"],
             test_dict["out_file"],
             test_dict["use_param_file"],
+            test_dict["datm_file"],
+            test_dict["datm_file_url"],
             test_dict["other_args"],
         )
         self.plot = True

testing/functional_tests.cfg

@@ -3,32 +3,42 @@ test_dir = fates_allom_ftest
 test_exe = FATES_allom_exe
 out_file = allometry_out.nc
 use_param_file = True
+datm_file =
+datm_file_url =
 other_args = []
 
 [quadratic]
 test_dir = fates_math_ftest
 test_exe = FATES_math_exe
 out_file = quad_out.nc
 use_param_file = False
+datm_file =
+datm_file_url =
 other_args = []
 
 [fuel]
 test_dir = fates_fuel_ftest
 test_exe = FATES_fuel_exe
 out_file = fuel_out.nc
 use_param_file = True
-other_args = ['../testing/test_data/BONA_datm.nc']
+datm_file = ../testing/test_data/BONA_datm.nc
+datm_file_url = https://www.dropbox.com/scl/fi/l7ik0xhnww3snlk2lqngr/BONA_datm.nc?rlkey=15kwixoofokyyj936xkxmfq8t&e=1&dl=1
+other_args = []
 
 [ros]
 test_dir = fates_ros_ftest
 test_exe = FATES_ros_exe
 out_file = ros_out.nc
 use_param_file = True
+datm_file =
+datm_file_url =
 other_args = []
 
 [patch]
 test_dir = fates_patch_ftest
 test_exe = FATES_patch_exe
 out_file = None
 use_param_file = True
+datm_file =
+datm_file_url =
 other_args = []

testing/run_functional_tests.py

@@ -28,6 +28,7 @@
 """
 import os
 import argparse
+import subprocess
 import matplotlib.pyplot as plt
 
 from build_fortran_tests import build_tests, build_exists
@@ -39,12 +40,18 @@
 
 add_cime_lib_to_path()
 
-from CIME.utils import run_cmd_no_fail
+from CIME.utils import run_cmd
 
 # constants for this script
-_DEFAULT_CONFIG_FILE = "functional_tests.cfg"
-_DEFAULT_CDL_PATH = os.path.abspath("../parameter_files/fates_params_default.cdl")
-_CMAKE_BASE_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "../")
+_FILE_DIR = os.path.dirname(__file__)
+_DEFAULT_CONFIG_FILE = os.path.join(_FILE_DIR, "functional_tests.cfg")
+_DEFAULT_CDL_PATH = os.path.abspath(os.path.join(
+    _FILE_DIR,
+    os.pardir,
+    "parameter_files",
+    "fates_params_default.cdl",
+))
+_CMAKE_BASE_DIR = os.path.join(_FILE_DIR, os.pardir)
 _TEST_SUB_DIR = "testing"
 
 
@@ -74,6 +81,13 @@ def commandline_args():
         "parameter_files directory.\n",
     )
 
+    parser.add_argument(
+        "--config-file",
+        type=str,
+        default=_DEFAULT_CONFIG_FILE,
+        help=f"Configuration file where test list is defined. Default: '{_DEFAULT_CONFIG_FILE}'",
+    )
+
     parser.add_argument(
         "-b",
         "--build-dir",
@@ -196,7 +210,7 @@ def check_param_file(param_file):
             None, "Must supply parameter file with .cdl or .nc ending."
         )
     if not os.path.isfile(param_file):
-        raise argparse.ArgumentError(None, f"Cannot find file {param_file}.")
+        raise FileNotFoundError(param_file)
 
 
 def check_build_dir(build_dir, test_dict):
@@ -295,8 +309,11 @@ def run_functional_tests(
     if run_executables:
         print("Running executables")
         for _, test in test_dict.items():
-            # prepend parameter file (if required) to argument list
             args = test.other_args
+            # prepend datm file (if required) to argument list
+            if test.datm_file:
+                args.insert(0, test.datm_file)
+            # prepend parameter file (if required) to argument list
             if test.use_param_file:
                 args.insert(0, param_file)
             # run
@@ -386,7 +403,11 @@ def run_fortran_exectuables(build_dir, test_dir, test_exe, run_dir, args):
     run_command.extend(args)
 
     os.chdir(run_dir)
-    out = run_cmd_no_fail(" ".join(run_command), combine_output=True)
+    cmd = " ".join(run_command)
+    stat, out, _ = run_cmd(cmd, combine_output=True)
+    if stat:
+        print(out)
+        raise subprocess.CalledProcessError(stat, cmd, out)
     print(out)
 
 
@@ -395,13 +416,13 @@ def main():
     Reads in command-line arguments and then runs the tests.
     """
 
-    full_test_dict = config_to_dict(_DEFAULT_CONFIG_FILE)
-    subclasses = FunctionalTest.__subclasses__()
-
     args = commandline_args()
+
+    full_test_dict = config_to_dict(args.config_file)
     config_dict = parse_test_list(full_test_dict, args.test_list)
 
     test_dict = {}
+    subclasses = FunctionalTest.__subclasses__()
     for name in config_dict.keys():
         test_class = list(filter(lambda subclass: subclass.name == name, subclasses))[
             0

testing/run_unit_tests.py

@@ -29,8 +29,9 @@
 from CIME.utils import run_cmd_no_fail  # pylint: disable=wrong-import-position,import-error,wrong-import-order
 
 # constants for this script
-_CMAKE_BASE_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "../")
-_DEFAULT_CONFIG_FILE = "unit_tests.cfg"
+_FILE_DIR = os.path.dirname(os.path.abspath(__file__))
+_CMAKE_BASE_DIR = os.path.join(_FILE_DIR, os.pardir)
+_DEFAULT_CONFIG_FILE = os.path.join(_FILE_DIR, "unit_tests.cfg")
 _TEST_SUB_DIR = "testing"
 
 
@@ -58,6 +59,13 @@ def commandline_args():
         "Will be created if it does not exist.\n",
     )
 
+    parser.add_argument(
+        "--config-file",
+        type=str,
+        default=_DEFAULT_CONFIG_FILE,
+        help=f"Configuration file where test list is defined. Default: '{_DEFAULT_CONFIG_FILE}'",
+    )
+
     parser.add_argument(
         "--make-j",
         type=int,
@@ -129,9 +137,8 @@ def main():
     Reads in command-line arguments and then runs the tests.
     """
 
-    full_test_dict = config_to_dict(_DEFAULT_CONFIG_FILE)
-
     args = commandline_args()
+    full_test_dict = config_to_dict(args.config_file)
     test_dict = parse_test_list(full_test_dict, args.test_list)
 
     run_unit_tests(

testing/testing_shr/FatesArgumentUtils.F90

@@ -24,7 +24,7 @@ function command_line_arg(arg_position)
 
       if (n_args < arg_position) then
         write(*, '(a, i2, a, i2)') "Incorrect number of arguments: ", n_args, ". Should be at least", arg_position, "."
-        stop
+        call abort()
       end if 
 
       call get_command_argument(arg_position, length=arglen)

testing/testing_shr/FatesFactoryMod.F90

@@ -520,7 +520,7 @@ subroutine CreateTestPatchList(patch, heights, dbhs)
     if (present(dbhs)) then 
       if (size(heights) /= size(dbhs)) then 
         write(*, '(a)') "Size of heights array must match size of dbh array."
-        stop
+        call abort()
       end if 
     end if 
 

testing/testing_shr/FatesUnitTestIOMod.F90

@@ -106,7 +106,7 @@ subroutine Check(status)
 
     if (status /= nf90_noerr) then
       write(*,*) trim(nf90_strerror(status))
-      stop
+      call abort()
     end if
 
   end subroutine Check
@@ -134,11 +134,11 @@ subroutine OpenNCFile(nc_file, ncid, fmode)
         call Check(nf90_create(trim(nc_file), NF90_CLOBBER, ncid))
       case DEFAULT
         write(*,*) 'Need to specify read, write, or readwrite'
-        stop
+        call abort()
       end select
     else
       write(*,*) 'Problem reading file'
-      stop
+      call abort()
     end if
 
   end subroutine OpenNCFile
@@ -480,7 +480,7 @@ subroutine RegisterVar(ncid, var_name, dimID, type, att_names, atts, num_atts, v
       nc_type = NF90_CHAR
     else
       write(*, *) "Must pick correct type"
-      stop
+      call abort()
     end if
 
     call Check(nf90_def_var(ncid, var_name, nc_type, dimID, varID))

testing/testing_shr/FatesUnitTestParamReaderMod.F90

@@ -89,7 +89,7 @@ subroutine ReadParameters(this, fates_params)
           case default
             write(*, '(a,a)') 'dimension shape:', dimension_shape
             write(*, '(a)') 'unsupported number of dimensions reading parameters.'
-            stop
+            call abort()
         end select
     end do
 

testing/testing_shr/SyntheticPatchTypes.F90

@@ -163,7 +163,7 @@ integer function PatchDataPosition(this, patch_id, patch_name)
     ! can't supply both
     if (present(patch_id) .and. present(patch_name)) then 
       write(*, '(a)') "Can only supply either a patch_id or a patch_name - not both"
-      stop
+      call abort()
     end if 
 
     do i = 1, this%num_patches
@@ -179,11 +179,11 @@ integer function PatchDataPosition(this, patch_id, patch_name)
         end if
       else 
         write(*, '(a)') "Must supply either a patch_id or a patch_name."
-        stop
+        call abort()
       end if
     end do
     write(*, '(a)') "Cannot find the synthetic patch type supplied"
-    stop
+    call abort()
 
   end function PatchDataPosition