Merge pull request #2 from UU-Hydro/develop_before_release

Updating files.

model/landSurface.py

@@ -653,7 +653,7 @@ def waterDemandOptions(self,iniItems):
         if iniItems.landSurfaceOptions['desalinationWater'] not in ["None", "False"]:
             logger.info("Monthly desalination water is included.")
             self.includeDesalination = True
-            self.desalinationWaterFile = iniItems.landSurfaceOptions['desalinationWater']
+            self.desalinationWaterFile = vos.getFullPath(iniItems.landSurfaceOptions['desalinationWater'], self.inputDir)
         else:    
             logger.info("Monthly desalination water is NOT included.")
 

model/parallel_pcrglobwb_runner.py

@@ -0,0 +1,181 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# PCR-GLOBWB (PCRaster Global Water Balance) Global Hydrological Model
+#
+# Copyright (C) 2016, Ludovicus P. H. (Rens) van Beek, Edwin H. Sutanudjaja, Yoshihide Wada,
+# Joyce H. C. Bosmans, Niels Drost, Inge E. M. de Graaf, Kor de Jong, Patricia Lopez Lopez,
+# Stefanie Pessenteiner, Oliver Schmitz, Menno W. Straatsma, Niko Wanders, Dominik Wisser,
+# and Marc F. P. Bierkens,
+# Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program 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
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+import os
+import sys
+import shutil
+import glob
+import datetime
+
+import pcraster as pcr
+
+import configuration
+import virtualOS as vos
+
+import logging
+logger = logging.getLogger(__name__)
+
+import disclaimer
+
+# print disclaimer
+disclaimer.print_disclaimer()
+
+# get the configuration/ini file given in the system argument
+iniFileName = os.path.abspath(sys.argv[1])
+
+# option for debuging and paralelization 
+debug_option = "parallel"
+if len(sys.argv) > 2: debug_option = str(sys.argv[2]) 
+
+# object to handle configuration/ini file
+generalConfiguration = configuration.Configuration(iniFileName = iniFileName, debug_mode = False, no_modification = False)
+
+clean_previous_output = True
+if generalConfiguration.globalOptions['cloneAreas'] == "part_one" or\
+   generalConfiguration.globalOptions['cloneAreas'] == "part_two":
+    clean_previous_output = False
+
+# clean any files exists on the ouput directory (this can be done for global runs)
+if clean_previous_output and os.path.exists(generalConfiguration.globalOptions['outputDir']): shutil.rmtree(generalConfiguration.globalOptions['outputDir'])
+
+# make log folder and initialize logging
+generalOutputFolder = generalConfiguration.globalOptions['outputDir']
+logFileFolder = generalOutputFolder + "/global/log/"
+if os.path.exists(logFileFolder) and clean_previous_output:  
+    shutil.rmtree(logFileFolder)
+    os.makedirs(logFileFolder)
+if os.path.exists(logFileFolder) == False: 
+    os.makedirs(logFileFolder)
+generalConfiguration.initialize_logging(logFileFolder)
+
+# copy ini file to the log folder:
+timestamp = datetime.datetime.now()
+logger.info('Copying ini file to the folder %s', logFileFolder)
+shutil.copy(iniFileName, logFileFolder + \
+                         os.path.basename(iniFileName) + '_' +  str(timestamp.isoformat()).replace(":",".") + '.ini')
+
+# make global output maps directory (it will contain a "maps" directory that will contain merged pcraster maps)
+global_maps_folder = generalConfiguration.globalOptions['outputDir']+"/global/maps/"
+if os.path.exists(global_maps_folder):
+    shutil.rmtree(global_maps_folder)
+    os.makedirs(global_maps_folder)
+else:
+    os.makedirs(global_maps_folder)
+
+# make the backup of these python scripts to a specific backup folder and go to the backup folder
+scriptDir = generalConfiguration.globalOptions['outputDir'] + "/global/scripts/"
+if generalConfiguration.globalOptions['cloneAreas'] == "part_one" or\
+   generalConfiguration.globalOptions['cloneAreas'] == "part_two":
+    scriptDir = scriptDir + "/" + generalConfiguration.globalOptions['cloneAreas'] + "/"
+logger.info('Making the backup of the python scripts used to the folder %s', scriptDir)
+if os.path.exists(scriptDir): shutil.rmtree(scriptDir)
+os.makedirs(scriptDir)
+path_of_this_module = os.path.abspath(os.path.dirname(__file__))
+# working/starting directory where all script files are used
+for filename in glob.glob(os.path.join(path_of_this_module, '*.py')):
+    shutil.copy(filename, scriptDir)
+os.chdir(scriptDir)    
+
+
+# option to include merging process:
+with_merging_or_modflow = True
+# - in the ini file, we can also skip merging (e.g. for runs with spin-ups): 
+
+
+# Note that for parallel runs with spin-up, we cannot do any merging and/or combine them with modflow 
+if float(generalConfiguration.globalOptions['maxSpinUpsInYears']) > 0:
+    msg = "The run is set with some spin-ups. We can NOT combine this with merging processes and modflow calculation. "
+    logger.warning(msg)
+    logger.warning(msg)
+    logger.warning(msg)
+    logger.warning(msg)
+    logger.warning(msg)
+    if "with_merging" in generalConfiguration.globalOptions.keys() and generalConfiguration.globalOptions["with_merging"] == "False":
+        with_merging_or_modflow = False
+    else:
+        msg = "You set this run (with spin-ups) either with modflow or merging processes. That is not possible."
+        logger.warning(msg)
+        sys.exit()
+
+
+# pcr-globwb clone areas (for pcr-globwb multiple runs)
+clone_codes = list(set(generalConfiguration.globalOptions['cloneAreas'].split(",")))
+#
+# - for one global run (that should be using a fat node):
+if clone_codes[0] == "Global": 
+    clone_codes = ['M%02d'%i for i in range(1,54,1)]
+#
+# - using two (thick) nodes:
+if clone_codes[0] == "part_one": 
+     # the relative big ones
+    clone_codes  = ["M17","M19","M26","M13","M18","M20","M05","M03","M21","M46","M27","M49","M16","M44","M52","M25","M09","M08","M11","M42","M12","M39"]
+    #~ # - and plus one of the two smallest ones
+    #~ clone_codes += ["M29"]
+    #~ # - and plus two of the smallest ones 
+    #~ clone_codes += ["M30","M29"]
+if clone_codes[0] == "part_two": 
+    # the relative small ones
+    clone_codes = ["M07","M15","M38","M48","M40","M41","M22","M14","M23","M51","M04","M06","M10","M02","M45","M35","M47","M50","M24","M01","M36","M53","M33","M43","M34","M37","M31","M32","M28","M30","M29"]
+    #~ # the relative small ones minus one of the the two smallest ones
+    #~ clone_codes = ["M07","M15","M38","M48","M40","M41","M22","M14","M23","M51","M04","M06","M10","M02","M45","M35","M47","M50","M24","M01","M36","M53","M33","M43","M34","M37","M31","M32","M28","M30"]
+    #~ # the relative small ones minus two of the smallest ones
+    #~ clone_codes = ["M07","M15","M38","M48","M40","M41","M22","M14","M23","M51","M04","M06","M10","M02","M45","M35","M47","M50","M24","M01","M36","M53","M33","M43","M34","M37","M31","M32","M28"]
+    # the execution of merging and modflow processes are done in another node
+    with_merging_or_modflow = False
+
+
+# command line(s) for PCR-GLOBWB 
+logger.info('Running transient PCR-GLOBWB with/without MODFLOW ')
+i_clone = 0
+cmd = ''
+for clone_code in clone_codes:
+
+   cmd += "python deterministic_runner_glue_with_parallel_and_modflow_options.py " + iniFileName  + " " + debug_option + " " + clone_code + " "
+   cmd = cmd + " & "
+   i_clone += 1
+
+
+# Note that for runs with spin-up, we should not combine it with modflow 
+
+
+# command line(s) for merging and MODFLOW processes:       
+if with_merging_or_modflow:
+
+   logger.info('Also with merging and/or MODFLOW processes ')
+
+   cmd += "python deterministic_runner_for_monthly_modflow_and_merging.py " + iniFileName +" "+debug_option +" transient"
+
+   cmd = cmd + " & "       
+
+
+# don't foget to add the following line
+cmd = cmd + "wait"       
+
+print cmd
+msg = "Call: "+str(cmd)
+logger.debug(msg)
+
+
+# execute PCR-GLOBWB and MODFLOW
+vos.cmd_line(cmd, using_subprocess = False)