Starting to work on cosmo case

cases/cosmo-ghg-11km-test/config.yaml

@@ -0,0 +1,113 @@
+# Configuration file for the 'cosmo-ghg-11km-test' case with COSMO-GHG
+
+# GENERAL SETTINGS
+model: cosmo-ghg
+restart_step: 12
+variant: spinup
+spinup: 6
+
+# case name = pathname in cases/
+casename: null  # Set this value based on your use case
+
+# Root directory settings
+chain_src_dir: null  # Set this value based on your use case
+work_root: null  # Set this value based on your use case
+
+# PRE-PROCESSING
+input_root: null  # Set this value based on your use case
+
+# METEO
+meteo_dir: null  # Set this value based on your use case
+meteo_prefix: laf
+meteo_nameformat: "laf%Y%m%d%H"
+meteo_inc: 1
+
+# ICBC
+cams_dir_orig: null  # Set this value based on your use case
+cams_dir_proc: null  # Set this value based on your use case
+cams_parameters:
+  - suffix: cams_co2
+    inc: 3
+
+# EMISSIONS
+emissions_dir: null  # Set this value based on your use case
+emis_gridname: co2_
+
+# OAE
+oem_dir: null  # Set this value based on your use case
+oem_gridded_emissions_nc: emissions.nc
+oem_vertical_profiles_nc: vertical_profiles.nc
+oem_hourofday_nc: hourofday.nc
+oem_hourofyear_nc: hourofyear.nc
+oem_dayofweek_nc: dayofweek.nc
+oem_monthofyear_nc: monthofyear.nc
+
+# BIOFLUXES
+vprm_dir: null  # Set this value based on your use case
+vprm_prefix:
+  - vprm2_
+
+# ONLINE_VPRM
+online_vprm_dir: null  # Set this value based on your use case
+modis_filename: MODIS_sur_refl_Example_20150101-20150201.nc
+vegetation_filename: VPRM_VegClasses_example_vprm.nc
+
+# INT2LM
+int2lm_extpar_dir: null  # Set this value based on your use case
+int2lm_extpar_file: test_domain.nc
+int2lm_bin: null  # Set this value based on your use case
+int2lm_namelist: null  # Set this value based on your use case
+int2lm_runjob: null  # Set this value based on your use case
+int2lm_walltime: "01:00:00"
+int2lm_nodes: 2
+int2lm_ntasks_per_node: 12
+int2lm_np_x: 8
+int2lm_np_y: 3
+
+# POST_INT2LM
+post_int2lm_species:
+  - CO2_BG
+post_int2lm_species_spinup:
+  - CO2_BG
+  - CO2_GPP
+  - CO2_RA
+  - CO2_A
+  - CO2_GPP2
+  - CO2_RA2
+  - CO2_A2
+
+# SIMULATION
+# COSMO
+cosmo_bin: null  # Set this value based on your use case
+cosmo_namelist: null  # Set this value based on your use case
+cosmo_runjob: null  # Set this value based on your use case
+cosmo_walltime: "00:30:00"
+cosmo_np_x: 6
+cosmo_np_y: 4
+cosmo_np_io: 0
+
+# POST-PROCESSING
+# REDUCE_OUTPUT
+convert_gas: true
+output_levels: 20
+
+# POST_COSMO
+output_root: null  # Set this value based on your use case
+reference_dir: null  # Set this value based on your use case
+output_dir: null  # Set this value based on your use case
+values_to_check:
+  - - cosmo-ghg_pgi_gpu_e5e9e5a_lffd2015010200.nc
+    - lffd2015010200.nc
+    - T
+    - P
+    - U
+    - V
+    - W
+    - CO2_BG
+    - CO2_A
+    - CO2_GPP
+    - CO2_RA
+    - CO2_A2
+    - CO2_GPP2
+    - CO2_RA2
+

run_chain.py

@@ -88,61 +88,78 @@ def parse_arguments():
 
 
 def load_config_file(casename, cfg):
-    """Load the config file.
-
-    Looks for the config file in ``cases/casename/config.py`` and then imports
-    it as a module. This lets the config file contain python statements which
-    are evaluated on import.
-
-    If this is not the first config-file to be imported by run_chain.py, the
-    module has to be reloaded to overwrite the values of the old case.
-
-    Access variables declared in the config-file (``myval = 9``) with
-    ``cfg.myval``.
-
-    Add new variables with::
+    """
+    Load the configuration settings from a YAML file.
 
-        setattr(cfg, 'myval', 9)
+    This function reads the configuration settings from a YAML file located in
+    the 'cases/casename' directory and sets them as attributes of the provided
+    `cfg` object.
 
-    Parameters
-    ----------
-    casename : str
-        Name of the folder in cases/ where the configuration files are stored
-    cfg : module or None
-        If cfg is None, the module is freshly imported. If it is a module
-        object, that module is reloaded.
+    Parameters:
+    - casename (str): Name of the folder in 'cases/' where the configuration
+      files are stored.
+    - cfg (object): An object to store the configuration settings as attributes.
 
-    Returns
-    -------
-    config-object
-        Object with all variables as attributes
+    Returns:
+    - cfg (object): The same `cfg` object with configuration settings as
+      attributes.
     """
-    cfg_path = os.path.join('cases', casename, 'config')
 
-    if not os.path.exists(os.path.dirname(cfg_path)):
-        all_cases = [path.name for path in os.scandir('cases') if path.is_dir]
+    cfg_path = os.path.join('cases', casename, 'config.yaml')
+
+    if not os.path.exists(cfg_path):
+        all_cases = [path.name for path in os.scandir('cases') if path.is_dir()]
         closest_name = min([(tools.levenshtein(casename, name), name)
                             for name in all_cases],
                            key=lambda x: x[0])[1]
-        raise FileNotFoundError("Case-directory '{}' not found, did you "
-                                "mean '{}'?".format(casename, closest_name))
-
-    sys.path.append(os.path.dirname(cfg_path))
+        raise FileNotFoundError(
+            f"Case-directory '{casename}' not found, did you mean '{closest_name}'?"
+        )
 
     try:
-        if cfg is None:
-            cfg = importlib.import_module(os.path.basename(cfg_path))
-        else:
-            cfg = importlib.reload(cfg)
-    except ModuleNotFoundError:
-        raise FileNotFoundError("No file 'config.py' in " +
-                                os.path.dirname(cfg_path))
+        with open(cfg_path, 'r') as yaml_file:
+            cfg_data = yaml.load(yaml_file, Loader=yaml.FullLoader)
+    except FileNotFoundError:
+        raise FileNotFoundError(f"No file 'config.yaml' in {os.path.dirname(cfg_path)}")
+
+    for key, value in cfg_data.items():
+        setattr(cfg, key, value)
+
+    # Set additional config variables
+    cfg = set_user_account(cfg)
+
+    return cfg
+
 
-    # so that a different cfg-file can be imported later
-    sys.path.pop()
+def set_user_account(cfg):
+    setattr(cfg, user, os.environ['USER'])
+    if cfg.user == 'jenkins':
+        # g110 account for Jenkins testing
+        setattr(cfg, compute_account, 'g110')
+    elif os.path.exists(os.environ['HOME'] + '/.acct'):
+        # Use account specified in ~/.acct file
+        with open(os.environ['HOME'] + '/.acct', 'r') as file:
+            setattr(cfg, compute_account, file.read().rstrip())
+    else:
+        # Use standard account
+        setattr(cfg, compute_account, os.popen("id -gn").read().splitlines()[0])
 
     return cfg
 
+def set_node_info(cfg):
+    if cfg.constraint == 'gpu':
+        setattr(cfg, ntasks_per_node, 12)
+        setattr(cfg, mpich_cuda, ('export MPICH_RDMA_ENABLED_CUDA=1\n'
+                      'export MPICH_G2G_PIPELINE=256\n'
+                      'export CRAY_CUDA_MPS=1\n')
+               )
+    elif cfg.constraint == 'mc':
+        setattr(cfg, ntasks_per_node, 36)
+        setattr(cfg, mpich_cuda, '')
+    else:
+        raise ValueError("Invalid value for 'constraint' in the configuration."
+                         "It should be either 'gpu' or 'mc'.")
+
 
 def run_chain(work_root, model_cfg, cfg, start_time, hstart, hstop, job_names,
               force):