Add TUV-x to CAM

.gitignore

@@ -15,6 +15,8 @@ src/dynamics/fv3/atmos_cubed_sphere
 libraries/FMS
 libraries/mct
 libraries/parallelio
+libraries/musica
+libraries/json-fortran
 src/atmos_phys
 src/dynamics/mpas/dycore
 share

Externals.cfg

@@ -21,9 +21,9 @@ externals = Externals.cfg
 required = True
 
 [cmeps]
-tag = cmeps0.14.12
+branch = develop-add-linked-libs
 protocol = git
-repo_url = https://github.com/ESCOMP/CMEPS.git
+repo_url = https://github.com/mattldawson/CMEPS.git
 local_path = components/cmeps
 required = True
 

Externals_CAM.cfg

@@ -76,5 +76,19 @@ sparse = ../.mpas_sparse_checkout
 hash = ff76a231
 required = True
 
+[musica]
+local_path = libraries/musica
+protocol = git
+repo_url = https://github.com/NCAR/musica.git
+branch = main
+required = True
+
+[json-fortran]
+local_path = libraries/json-fortran
+protocol = git
+repo_url = https://github.com/jacobwilliams/json-fortran.git
+tag = 8.2.1
+required = True
+
 [externals_description]
 schema_version = 1.0.0

bld/namelist_files/namelist_definition.xml

@@ -7106,6 +7106,17 @@ Maximum zenith angle (degrees) used for photolysis.
 Default: set by build-namelist.
 </entry>
 
+<entry id="tuvx_config_path" type="char*256" input_pathname="abs" category="chemistry"
+       group="tuvx_opts" valid_values="" >
+Filepath of TUV-X configuration specification.
+Default: NONE
+</entry>
+
+<entry id="tuvx_active" type="logical" category="chemistry"
+       group="tuvx_opts" valid_values="" >
+Switch to turn on TUV-X photolysis.
+Default: FALSE
+</entry>
 
 <!-- Namelist read by seq_drydep_mod and shared by CAM and CLM -->
 

cime_config/buildlib

@@ -7,6 +7,7 @@ create the cam library
 #pylint: disable=unused-wildcard-import, bad-whitespace, too-many-locals
 #pylint: disable=invalid-name
 import sys, os, filecmp, shutil, imp
+from glob import glob
 
 _CIMEROOT = os.environ.get("CIMEROOT")
 if _CIMEROOT is None:
@@ -20,6 +21,7 @@ from CIME.case import Case
 from CIME.utils import run_cmd, expect
 from CIME.buildlib import parse_input
 from CIME.build import get_standard_makefile_args
+from CIME.XML.env_build import EnvBuild
 
 logger = logging.getLogger(__name__)
 
@@ -41,7 +43,7 @@ def _build_fms(caseroot, libroot, bldroot):
                 expect(os.path.exists(fmsbuildlib), "FMS external not found")
                 stat, _, err = run_cmd("{} {} {} {}".format(fmsbuildlib, case.get_value("EXEROOT"), fmsbuilddir, caseroot), verbose=True)
                 expect(stat==0, "FMS build Failed {}".format(err))
-                
+
                 libfms = os.path.join(bldroot,"FMS","libfms.a")
                 if os.path.exists(libfms):
                     shutil.copy(libfms, libroot)
@@ -108,10 +110,230 @@ def _build_cam(caseroot, libroot, bldroot):
         logger.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n", cmd, out, err)
         expect(rc == 0, "Command %s failed with rc=%s" % (cmd, rc))
 
+###############################################################################
+def _run_cmd(command, working_dir):
+###############################################################################
+
+    rc, out, err = run_cmd(command, from_dir=working_dir, verbose=True)
+    expect(rc == 0, "Command {} failed with rc={}".format(command, rc))
+
+###############################################################################
+def _cmake_default_args(caseroot):
+###############################################################################
+# Returns a dictionary of CMake variables based on the Macros.cmake file for
+# the build.
+
+    build = EnvBuild(case_root=caseroot)
+    with Case(caseroot) as case:
+        macro_path = os.path.abspath(os.path.join(caseroot, "cmake_macros", ""))
+        args = "-DCONVERT_TO_MAKE=ON "
+        args += "-DCASEROOT={} ".format(caseroot)
+        args += "-DCOMPILER={} ".format(build.get_value("COMPILER"))
+        args += "-DOS={} ".format(build.get_value("OS"))
+        args += "-DMACH={} ".format(case.get_value("MACH"))
+        args += "-DCMAKE_C_COMPILER_WORKS=1 "
+        args += "-DCMAKE_Fortran_COMPILER_WORKS=1 "
+        args += "-DCMAKE_CXX_COMPILER_WORKS=1 "
+        cmd = "cmake {} .".format(args)
+        rc, out, err = run_cmd(cmd, combine_output=True, from_dir=macro_path)
+        expect(rc == 0, "Command {} failed with rc={} out={} err={}".format(cmd, rc, out, err))
+
+        arg_dict = {}
+        for line in out.splitlines():
+            if ":=" in line:
+                key, val = line.split(":=")
+                arg_dict[key.replace('CIME_SET_MAKEFILE_VAR','').strip()] = val.strip()
+
+        return arg_dict
+
+###############################################################################
+def _build_json_fortran(caseroot, libroot, bldroot):
+###############################################################################
+# Builds the json-fortran library and updates the case variables used to set
+# the include paths and linked libraries
+
+    with Case(caseroot) as case:
+        bldpath = os.path.join(bldroot, "json-fortran")
+        if not os.path.exists(bldpath):
+            os.makedirs(bldpath)
+        srcpath = os.path.abspath(os.path.join(case.get_value("COMP_ROOT_DIR_ATM"), \
+                                               "libraries", "json-fortran", ""))
+        logger.info("Building json-fortran in {} from source in {}\n".format(bldpath, srcpath))
+
+        arg_dict = _cmake_default_args(caseroot)
+        cmake_args = "-DCMAKE_Fortran_COMPILER={} ".format(arg_dict["SFC"])
+        cmake_args += "-DCMAKE_C_COMPILER_WORKS=1 "
+        cmake_args += "-DCMAKE_CXX_COMPILER_WORKS=1 "
+        cmake_args += "-DCMAKE_BUILD_TYPE=Release "
+        cmake_args += "-DSKIP_DOC_GEN:BOOL=TRUE "
+        cmake_args += "-DCMAKE_INSTALL_PREFIX='{}' ".format(libroot)
+        cmake_args += srcpath
+
+        _run_cmd("cmake {}".format(cmake_args), bldpath)
+        _run_cmd(case.get_value("GMAKE"), bldpath)
+        _run_cmd("{} install".format(case.get_value("GMAKE")), bldpath)
+
+        # add json-fortran to include paths
+        incldir = os.environ.get('USER_INCLDIR')
+        if incldir is None:
+            incldir = ''
+        os.environ['USER_INCLDIR'] = incldir + \
+            " -I{} ".format(_json_fortran_include_dir(libroot))
+
+        # create simlink to library in folder CIME expects libraries to be in
+        dst = os.path.join(libroot, "libjsonfortran.a")
+        if os.path.isfile(dst):
+            os.remove(dst)
+        os.symlink(_json_fortran_lib_path(libroot), dst)
+
+###############################################################################
+def _json_fortran_include_dir(libroot):
+###############################################################################
+# Returns the path to the json-fortran include directory
+
+    jsoninc = os.path.join(_json_fortran_install_dir(libroot), "lib", "")
+    expect(os.path.exists(jsoninc), \
+           "JSON-Fortran include directory not found at {}".format(jsoninc))
+    return jsoninc
+
+###############################################################################
+def _json_fortran_lib_path(libroot):
+###############################################################################
+# Returns the path to the json-fortran library
+
+    jsonlib = os.path.join(_json_fortran_install_dir(libroot), "lib", "libjsonfortran.a")
+    expect(os.path.exists(jsonlib), \
+           "JSON-Fortran library not found at {}".format(jsonlib))
+    return jsonlib
+
+###############################################################################
+def _json_fortran_install_dir(libroot):
+###############################################################################
+# Returns the path to the json-fortran install directory
+
+    jsonpaths = glob(os.path.join(libroot, "jsonfortran*"))
+    expect(len(jsonpaths)>0, \
+           "JSON-Fortran not found at {}".format(libroot))
+    expect(len(jsonpaths)<2, \
+           "Multiple JSON-Fortran versions found at {}".format(libroot))
+    expect(os.path.exists(jsonpaths[0]), \
+           "JSON-Fortran install directory not found at {}".format(jsonpaths[0]))
+    return jsonpaths[0]
+
+###############################################################################
+def _build_musica(caseroot, libroot, bldroot):
+###############################################################################
+# Builds the musica library, including TUV-x, musica, and MICM
+# and updates the case variables used to set the include paths
+# and linked libraries
+
+    build = EnvBuild(case_root=caseroot)
+    with Case(caseroot) as case:
+        bldpath = os.path.join(bldroot, "musica")
+        if not os.path.exists(bldpath):
+            os.makedirs(bldpath)
+        jsoninc = _json_fortran_include_dir(libroot)
+        jsonlib = _json_fortran_lib_path(libroot)
+        srcpath = os.path.abspath(os.path.join(case.get_value("COMP_ROOT_DIR_ATM"), \
+                                               "libraries", "musica", ""))
+        logger.info("Building musica in {} from source in {}\n".format(bldpath, srcpath))
+
+        arg_dict = _cmake_default_args(caseroot)
+        if build.get_value("MPILIB") == "mpi-serial":
+            cmake_args = "-DCMAKE_Fortran_COMPILER={} ".format(arg_dict["SFC"])
+        else:
+            cmake_args = "-DCMAKE_Fortran_COMPILER={} ".format(arg_dict["MPIFC"])
+            cmake_args += "-DENABLE_MPI:BOOL=TRUE "
+        if case.get_value("DEBUG"):
+            cmake_args += "-DCMAKE_BUILD_TYPE=Debug "
+        else:
+            cmake_args += "-DCMAKE_BUILD_TYPE=Release "
+        cmake_args += "-DENABLE_UTIL_ONLY=ON "
+        cmake_args += "-DCMAKE_C_COMPILER_WORKS=1 "
+        cmake_args += "-DCMAKE_CXX_COMPILER_WORKS=1 "
+        cmake_args += "-DENABLE_MICM=OFF "
+        cmake_args += "-DENABLE_TUVX=ON "
+        cmake_args += "-DENABLE_TESTS=OFF "
+        cmake_args += "-DENABLE_COVERAGE=OFF "
+        cmake_args += "-DJSON_INCLUDE_DIR={} ".format(jsoninc)
+        cmake_args += "-DJSON_LIB={} ".format(jsonlib)
+        cmake_args += "-DCMAKE_Fortran_FLAGS='{}' ".format(arg_dict["FFLAGS"])
+        cmake_args += "-DCMAKE_INSTALL_PREFIX='{}' ".format(libroot)
+        cmake_args += srcpath
+
+        _run_cmd("cmake {}".format(cmake_args), bldpath)
+        _run_cmd(case.get_value("GMAKE"), bldpath)
+        _run_cmd("{} install".format(case.get_value("GMAKE")), bldpath)
+
+        # add musica to include paths
+        incldir = os.environ.get('USER_INCLDIR')
+        if incldir is None:
+            incldir = ''
+        os.environ['USER_INCLDIR'] = incldir + \
+            " -I{} ".format(_musica_include_dir(libroot))
+
+        # create simlink to library in folder CIME expects libraries to be in
+        dst = os.path.join(libroot, "libmusica.a")
+        if os.path.isfile(dst):
+            os.remove(dst)
+        os.symlink(_musica_lib_path(libroot), dst)
+
+###############################################################################
+def _musica_include_dir(libroot):
+###############################################################################
+# Returns the path to the musica include directory
+
+    coreinc = os.path.join(_musica_install_dir(libroot), "include", "")
+    expect(os.path.exists(coreinc), \
+           "musica include directory not found at {}".format(coreinc))
+    return coreinc
+
+###############################################################################
+def _musica_lib_path(libroot):
+###############################################################################
+# Returns the path to the musica library
+
+    corelib = os.path.join(_musica_install_dir(libroot), "lib64", "libmusica.a")
+    if not os.path.exists(corelib):
+        corelib = os.path.join(_musica_install_dir(libroot), "lib", "libmusica.a")
+    expect(os.path.exists(corelib), \
+           "musica library not found at {}".format(corelib))
+    return corelib
+
+###############################################################################
+def _musica_install_dir(libroot):
+###############################################################################
+# Returns the path to the musica install directory
+
+    corepaths = glob(os.path.join(libroot, "musica*"))
+    expect(len(corepaths)>0, \
+           "musica not found at {}".format(libroot))
+    expect(len(corepaths)<2, \
+           "Multiple musica versions found at {}".format(libroot))
+    expect(os.path.exists(corepaths[0]), \
+           "musica install directory not found at {}".format(corepaths[0]))
+    return corepaths[0]
+
+###############################################################################
+def _musica_package_dir(libroot):
+###############################################################################
+# Returns the path to the musica CMake package
+
+    paths = glob(os.path.join(libroot, "musica*", "cmake", "musica*" ))
+    expect(len(paths)>0, \
+           "musica package not found at {}".format(libroot))
+    expect(len(paths)<2, \
+           "Multiple musica versions found at {}".format(libroot))
+    expect(os.path.exists(paths[0]), \
+           "musica package directory not found at {}".format(paths[0]))
+    return paths[0]
+
 ###############################################################################
 
 def _main_func():
     caseroot, libroot, bldroot = parse_input(sys.argv)
+    _build_json_fortran(caseroot, libroot, bldroot)
+    _build_musica(caseroot, libroot, bldroot)
     _build_fms(caseroot, libroot, bldroot)
     _build_cam(caseroot, libroot, bldroot)
 

cime_config/buildnml

@@ -211,6 +211,17 @@ def buildnml(case, caseroot, compname):
         if (os.path.isfile(file1)) and (not os.path.isfile(file2)):
             shutil.copy(file1,file2)
 
+        # Temporary copy of TUV-x data for development
+        dest_data = os.path.join(rundir, "data")
+        if os.path.exists(dest_data):
+            shutil.rmtree(dest_data)
+        shutil.copytree(os.path.join(srcroot, "libraries", "musica", "lib", \
+                                     "tuv-x", "data"), dest_data)
+        shutil.copy2(os.path.join(srcroot, "cime_config", "tuvx_MOZART.json"), \
+                     os.path.join(rundir, "tuvx_MOZART.json"))
+        shutil.copy2(os.path.join(srcroot, "cime_config", "tuvx_MOZART_TS1.json"), \
+                     os.path.join(rundir, "tuvx_MOZART_TS1.json"))
+
 ###############################################################################
 def _main_func():
 

cime_config/config_component.xml

@@ -195,6 +195,18 @@
     </desc>
   </entry>
 
+  <entry id="CAM_LINKED_LIBS">
+    <type>char</type>
+    <valid_values></valid_values>
+    <default_value>-lmusica -ljsonfortran</default_value>
+    <group>build_component_cam</group>
+    <file>env_build.xml</file>
+    <desc>
+      CAM linked libraries. The libraries are built by CAM's buildlib script and should be included
+      during linking of the model executable.
+    </desc>
+  </entry>
+
   <entry id="CAM_NML_USE_CASE">
     <type>char</type>
     <valid_values></valid_values>