Developing a solution for u-cp647

bgcval2/download_from_mass.py

@@ -409,15 +409,18 @@ def download_from_mass(
     outputFold = folder([paths.ModelFolder_pref,  jobID,] )
     # make this folder group writeable. 
     st = os.stat(outputFold)
-    os.chmod(outputFold, st.st_mode | stat.S_IWGRP)
+
+    try: os.chmod(outputFold, st.st_mode | stat.S_IWGRP)
+    except: pass
 
     deleteBadLinksAndZeroSize(outputFold, jobID)
 
     fixFilePaths(outputFold, jobID)
     deleteBadLinksAndZeroSize(outputFold, jobID)
 
     # Set up a file to save command to a new file.
-    download_script_path = ''.join([folder('mass_scripts/'), jobID,'.sh'])
+    username = os.getlogin()
+    download_script_path = ''.join([folder('mass_scripts/'), jobID,'_',username, '.sh'])
     header_lines = ['# Run this script on mass-cli1.jasmin.ac.uk\n',]
     header_lines.append('# from login1.jasmin.ac.uk, ssh to the mass machine:\n#     ssh -X  mass-cli\n')
     header_lines.append(''.join(['# run script with:\n# source ', os.path.abspath(download_script_path),'\n']))
@@ -483,7 +486,8 @@ def download_from_mass(
     if auto_download:
         shared_file_path = os.path.join(paths.shared_mass_scripts, os.path.basename(download_script_path))
         print('writing file in shared path', shared_file_path)
-        shutil.copy(download_script_path, shared_file_path)
+        try: shutil.copy(download_script_path, shared_file_path)
+        except: pass
 
     fixFilePaths(outputFold, jobID, debug=False,)
     deleteBadLinksAndZeroSize(outputFold, jobID, debug=False,)

bgcval2/functions/AirSeaFluxCO2.py

@@ -32,6 +32,7 @@
 import numpy as np
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
+from bgcval2.functions.tools import load_area
 
 global loaded_area_and_mask
 global tmask
@@ -46,7 +47,7 @@ def load_area_and_mask(areafile):
     if isinstance(areafile, list) and len(areafile)==1:
         areafile = areafile[0]
     nc = dataset(areafile, 'r')
-    area = nc.variables['e2t'][:] * nc.variables['e1t'][:]
+    area = load_area(nc)
     nc.close()
     loaded_area_and_mask = True
     return area

bgcval2/functions/BenCa.py

@@ -32,6 +32,7 @@
 import numpy as np
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
+from bgcval2.functions.tools import load_area
 
 global loaded_area_and_mask
 global tmask
@@ -48,7 +49,7 @@ def load_area_and_mask(areafile):
     else:
         raise ValueError(f"{areafile} must be a length=1 list containing a single file descriptor.")
     nc = dataset(areafile, 'r')
-    area = nc.variables['e2t'][:] * nc.variables['e1t'][:]
+    area = load_area(nc)
     nc.close()
     loaded_area_and_mask = True
     return area

bgcval2/functions/InvtAlk.py

@@ -32,6 +32,7 @@
 import numpy as np
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
+from bgcval2.functions.tools import load_area
 
 global loaded_area_and_mask
 global tmask
@@ -48,7 +49,7 @@ def load_area_and_mask(areafile):
     else:
         raise ValueError(f"{areafile} must be a length=1 list containing a single file descriptor.")
     nc = dataset(areafile, 'r')
-    area = nc.variables['e2t'][:] * nc.variables['e1t'][:]
+    area = load_area(nc)
     nc.close()
     loaded_area_and_mask = True
     return area

bgcval2/functions/TotalIntPP.py

@@ -31,6 +31,7 @@
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
 from bgcval2.functions.standard_functions import find_best_var
+from bgcval2.functions.tools import load_area
 
 global loadedArea
 global model_area
@@ -41,10 +42,7 @@
 
 def loadDataMask(gridfn):
     nc = dataset(gridfn,'r')
-    try:
-        model_area = nc.variables['area'][:]
-    except:
-         model_area = nc.variables['e1t'][:]*nc.variables['e2t'][:]
+    model_area = load_area(nc)
     nc.close()
     loadedArea = True
     return model_area

bgcval2/functions/dust.py

@@ -42,7 +42,8 @@ def loadDataMask(gridfn):
     global loadedArea
     global masked_area
     nc = dataset(gridfn,'r')
-    masked_area = nc.variables['e2t'][:] * nc.variables['e1t'][:]*nc.variables['tmask'][0]
+    area = load_area(nc)
+    masked_area = area *nc.variables['tmask'][0]
     nc.close()
     loadedArea = True
 

bgcval2/functions/globalVolMean.py

@@ -31,15 +31,18 @@
 
 import numpy as np
 from bgcval2.functions.standard_functions import choose_best_var 
-
+from bgcval2.functions.tools import load_area
 
 def calc_vol(nc):
     """
     Calculate volume from the (grid-T) netcdf file.
     """
-    area = nc.variables['area'][:]
+    area = load_area(area)
     thkcello = nc.variables['thkcello'][:]
-    area = area[None, None,:, :]
+    if area.ndim == 4:
+        area = area[None, None,:, :]
+    if area.ndim == 3:
+        area = area[None, :, :]
     return thkcello * area
 
 

bgcval2/functions/ice.py

@@ -32,6 +32,7 @@
 import numpy as np
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
+from bgcval2.functions.tools import load_area
 
 global loaded_area_and_mask
 global tmask
@@ -50,7 +51,7 @@ def load_area_and_mask(gridfn, maskname,):
         gridfn = gridfn[0]
     nc = dataset(gridfn, 'r')
     tmask = nc.variables[maskname][0]
-    area = nc.variables['e2t'][:] * nc.variables['e1t'][:]
+    area = load_area(nc)
     lat = nc.variables['nav_lat'][:]
     nc.close()
     loaded_area_and_mask = True
@@ -74,7 +75,7 @@ def calculate_ice_extent(nc, keys, **kwargs):
     if 'area' not in nc.variables and not loaded_area_and_mask:
         area, tmask, lat = load_area_and_mask(areafile, maskname)
     else:
-        area = nc.variables['area'][:]
+        area = load_area(nc)
         lat = nc.variables['nav_lat'][:]
         tmask = nc.variables[keys[0]][:].squeeze().mask
 

bgcval2/functions/tools.py

@@ -0,0 +1,49 @@
+# Copyright 2023, Plymouth Marine Laboratory
+#
+# This file is part of the bgc-val library.
+#
+# bgc-val is free software: you can redistribute it and/or modify it
+# under the terms of the Revised Berkeley Software Distribution (BSD) 3-clause license.
+
+# bgc-val is distributed in the hope that it will be useful, but
+# without any warranty; without even the implied warranty of merchantability
+# or fitness for a particular purpose. See the revised BSD license for more details.
+# You should have received a copy of the revised BSD license along with bgc-val.
+# If not, see <http://opensource.org/licenses/BSD-3-Clause>.
+#
+# Address:
+# Plymouth Marine Laboratory
+# Prospect Place, The Hoe
+# Plymouth, PL1 3DH, UK
+#
+# Email:
+# ledm@pml.ac.uk
+#
+"""
+.. module:: tools
+   :platform: Unix
+   :synopsis: This uses some tools for the functions library.
+
+.. moduleauthor:: Lee de Mora <ledm@pml.ac.uk>
+
+"""
+
+
+
+import numpy as np
+from bgcval2.functions.standard_functions import choose_best_var
+
+
+def load_area(nc):
+    """
+    Generic tool for loading area:
+    """
+    area_keys = ['area', 'area_grid_T', 'area_grid_W', 'area_grid_V', 'area_grid_U']
+    if set(area_keys).intersection(set(nc.variables.keys())): 
+        area = choose_best_var(nc, area_keys)
+    elif set(['e1t', 'e2t']).intersection(set(nc.variables.keys())):
+        area = nc.variables['e1t'][:]*nc.variables['e2t'][:]
+    else:
+        raise ValueError('Unable to load or calculate area from this file.')
+    return area
+