test(fates): Add EDAccumulateFluxesMod unit tests and document magic constants

.gitignore

@@ -51,6 +51,7 @@ Thumbs.db
 
 # Folders created with unit/functional tests
 _build/
+build/
 _run/
 
 

CMakeLists.txt

@@ -1,8 +1,21 @@
 cmake_minimum_required(VERSION 3.10)
 
+# Determine HLM_ROOT path (compatible with CMake 3.10+)
+if (NOT DEFINED HLM_ROOT)
+  if (NOT "$ENV{HLM_ROOT}" STREQUAL "")
+    set(HLM_ROOT "$ENV{HLM_ROOT}")
+  else()
+    set(HLM_ROOT "${CMAKE_CURRENT_SOURCE_DIR}/../../")
+  endif()
+endif()
+get_filename_component(HLM_ROOT "${HLM_ROOT}" ABSOLUTE)
+
+# Force the Fortran compiler to gfortran
+set(CMAKE_Fortran_COMPILER gfortran)
+
 list(APPEND CMAKE_MODULE_PATH ${CIME_CMAKE_MODULE_DIRECTORY})
-list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../../share/cmake")
-list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../components/cmeps/cmake")
+list(APPEND CMAKE_MODULE_PATH "${HLM_ROOT}/share/cmake")
+list(APPEND CMAKE_MODULE_PATH "${HLM_ROOT}/components/cmeps/cmake")
 
 FIND_PATH(NETCDFC_FOUND libnetcdf.a ${NETCDF_C_DIR}/lib)
 FIND_PATH(NETCDFF_FOUND libnetcdff.a ${NETCDF_FORTRAN_DIR}/lib)
@@ -18,8 +31,6 @@ project(FATES_tests Fortran C)
 
 include(CIME_utils)
 
-set(HLM_ROOT "../../")
-
 if (DEFINED ENV{ESMF_ROOT})
   list(APPEND CMAKE_MODULE_PATH $ENV{ESMF_ROOT}/cmake)
 endif()
@@ -42,16 +53,16 @@ add_subdirectory(${HLM_ROOT}/share/src csm_share)
 add_subdirectory(${HLM_ROOT}/share/unit_test_stubs/util csm_share_stubs)
 
 # Add FATES source directories
-add_subdirectory(${HLM_ROOT}/src/fates/main fates_main)
-add_subdirectory(${HLM_ROOT}/src/fates/biogeochem fates_biogeochem)
-add_subdirectory(${HLM_ROOT}/src/fates/biogeophys fates_biogeophys)
-add_subdirectory(${HLM_ROOT}/src/fates/parteh fates_parteh)
-add_subdirectory(${HLM_ROOT}/src/fates/fire fates_fire)
-add_subdirectory(${HLM_ROOT}/src/fates/radiation fates_radiation)
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/main fates_main)
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/biogeochem fates_biogeochem)
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/biogeophys fates_biogeophys)
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/parteh fates_parteh)
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/fire fates_fire)
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/radiation fates_radiation)
 
 # Testing directories
-add_subdirectory(${HLM_ROOT}/src/fates/testing/tests/fortran_shr test_share)
-add_subdirectory(${HLM_ROOT}/src/fates/testing/tests/functional/fire/shr fire_share)
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/testing/tests/fortran_shr test_share)
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/testing/tests/functional/fire/shr fire_share)
 
 # Remove shr_mpi_mod from share_sources.
 # This is needed because we want to use the mock shr_mpi_mod in place of the real one
@@ -111,4 +122,4 @@ link_directories(${CMAKE_CURRENT_BINARY_DIR})
 link_libraries(esmf)
 
 # Add the main test directory
-add_subdirectory(${HLM_ROOT}/src/fates/testing)
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/testing)

biogeophys/CMakeLists.txt

@@ -1,4 +1,5 @@
 list(APPEND fates_sources
+  EDAccumulateFluxesMod.F90
   FatesHydroWTFMod.F90
   LeafBiophysicsMod.F90
   FatesLeafBiophysParamsMod.F90

biogeophys/EDAccumulateFluxesMod.F90

@@ -79,20 +79,20 @@ subroutine AccumulateFluxes_ED(nsites, sites, bc_in, bc_out, dt_time)
                    ! Accumulate fluxes from hourly to daily values. 
                    ! _tstep fluxes are KgC/indiv/timestep _acc are KgC/indiv/day
 
-                   ccohort%gpp_acc  = ccohort%gpp_acc  + ccohort%gpp_tstep 
-                   ccohort%resp_m_acc = ccohort%resp_m_acc + ccohort%resp_m_tstep
-
-                   ccohort%sym_nfix_daily = ccohort%sym_nfix_daily + ccohort%sym_nfix_tstep
-
                    ! weighted mean of D13C by gpp
-                   if((ccohort%gpp_acc + ccohort%gpp_tstep) .eq. 0.0_r8) then
+                   if((ccohort%gpp_acc + ccohort%gpp_tstep) <= 0.0_r8) then
                       ccohort%c13disc_acc = 0.0_r8
                    else
                       ccohort%c13disc_acc  = ((ccohort%c13disc_acc * ccohort%gpp_acc) + &
                            (ccohort%c13disc_clm * ccohort%gpp_tstep)) / &
                            (ccohort%gpp_acc + ccohort%gpp_tstep)
                    endif
 
+                   ccohort%gpp_acc  = ccohort%gpp_acc  + ccohort%gpp_tstep 
+                   ccohort%resp_m_acc = ccohort%resp_m_acc + ccohort%resp_m_tstep
+
+                   ccohort%sym_nfix_daily = ccohort%sym_nfix_daily + ccohort%sym_nfix_tstep
+
                    do iv=1,ccohort%nv
                       if(ccohort%year_net_uptake(iv) == 999._r8)then ! note that there were leaves in this layer this year. 
                          ccohort%year_net_uptake(iv) = 0._r8

testing/CMakeLists.txt

@@ -17,3 +17,4 @@ add_subdirectory(tests/unit/count_cohorts_test fates_count_cohorts_utest)
 add_subdirectory(tests/unit/fire_equations_test fates_fire_equations_utest)
 add_subdirectory(tests/unit/quadratic_roots_test fates_quadratic_roots_utest)
 add_subdirectory(tests/unit/great_circle_test fates_great_circle_utest)
+add_subdirectory(tests/unit/ed_accumulate_fluxes_test ed_accumulate_fluxes_test)

testing/config/unit.cfg

@@ -25,3 +25,5 @@ test_dir = fates_quadratic_roots_utest
 [great_circle]
 test_dir = fates_great_circle_utest
 
+[ed_accumulate_fluxes]
+test_dir = ed_accumulate_fluxes_test

testing/framework/builder.py

@@ -150,11 +150,11 @@ def _generate_cmake_args(self, machobj):
 
     def _find_libraries(self):
         """Locates PFUNIT and NETCDF paths."""
-        self.config.pfunit_path = self._query_makefile_var("PFUNIT_PATH")
+        self.config.pfunit_path = self._query_makefile_var("PFUNIT_PATH") or os.environ.get("PFUNIT_PATH")
 
         if "NETCDF" not in os.environ:
-            self.config.netcdf_c_path = self._query_makefile_var("NETCDF_C_PATH")
-            self.config.netcdf_f_path = self._query_makefile_var("NETCDF_FORTRAN_PATH")
+            self.config.netcdf_c_path = self._query_makefile_var("NETCDF_C_PATH") or os.environ.get("NETCDF_C_PATH")
+            self.config.netcdf_f_path = self._query_makefile_var("NETCDF_FORTRAN_PATH") or os.environ.get("NETCDF_FORTRAN_PATH")
 
     def _query_makefile_var(self, var_name: str) -> Optional[str]:
         """Helper to query variables from CIME makefile generation
@@ -233,6 +233,7 @@ def build_tests(
     make_j: int,
     clean: bool = False,
     verbose: bool = False,
+    mpilib: str = _MPI_LIBRARY,
 ):
     """Wrapper function for building tests
 
@@ -242,13 +243,15 @@ def build_tests(
         make_j (int): number of processes to build with
         clean (bool, optional): whether or not to clean the build. Defaults to False.
         verbose (bool, optional): build with verbose make. Defaults to False.
+        mpilib (str, optional): mpilib to use for building. Defaults to _MPI_LIBRARY.
     """
     config = BuildConfig(
         build_dir=build_dir,
         cmake_dir=cmake_dir,
         make_j=make_j,
         clean=clean,
         verbose=verbose,
+        mpilib=mpilib or _MPI_LIBRARY,
     )
     builder = TestBuilder(config)
     builder.build()

testing/framework/utils/path.py

@@ -1,5 +1,6 @@
 """Utility functions related to getting paths to various important places"""
 
+import os
 import sys
 import importlib
 from pathlib import Path
@@ -38,12 +39,24 @@ def path_to_cime() -> Path:
         RuntimeError: can't find path to cime
 
     Returns:
-        str: full path to cime
+        Path: full path to cime
     """
+    # 1. Check HLM_ROOT environment variable if set
+    hlm_root = os.environ.get("HLM_ROOT")
+    if hlm_root:
+        cime_path = (Path(hlm_root) / "cime").resolve()
+        if cime_path.is_dir():
+            return cime_path
+
+    # 2. Fallback to nested location relative to FATES root
     cime_path = (path_to_fates_root() / "../../cime").resolve()
     if cime_path.is_dir():
         return cime_path
-    raise RuntimeError("Cannot find cime.")
+
+    raise RuntimeError(
+        "Cannot find cime. Please define the HLM_ROOT environment variable "
+        "pointing to the parent of your local CIME directory."
+    )
 
 
 def path_to_fates_root() -> Path:

testing/run_unit_tests.py

@@ -80,6 +80,14 @@ def commandline_args():
         "--verbose", action="store_true", help="Run make with verbose output."
     )
 
+    parser.add_argument(
+        "--mpilib",
+        type=str,
+        default=None,
+        help="MPI library to use (e.g. 'mpi-serial', 'mpich'). Overrides the MPILIB\n"
+        "environment variable. Defaults to the MPILIB env var, or 'mpi-serial'.\n",
+    )
+
     parser.add_argument(
         "-t",
         "--test-list",
@@ -109,7 +117,8 @@ def main():
 
     # build tests
     build_tests(
-        build_dir, _CMAKE_BASE_DIR, args.make_j, clean=args.clean, verbose=args.verbose
+        build_dir, _CMAKE_BASE_DIR, args.make_j, clean=args.clean, verbose=args.verbose,
+        mpilib=args.mpilib,
     )
 
     # run unit tests

testing/tests/unit/ed_accumulate_fluxes_test/CMakeLists.txt

@@ -0,0 +1,5 @@
+set(pfunit_sources test_EDAccumulateFluxes.pf)
+
+add_pfunit_ctest(EDAccumulateFluxes
+  TEST_SOURCES "${pfunit_sources}"
+  LINK_LIBRARIES fates csm_share)