<p><b>mhoffman@lanl.gov</b> 2013-03-11 08:47:30 -0600 (Mon, 11 Mar 2013)</p><p>BRANCH COMMIT - land ice -ocean coupler<br>
<br>
Progress on the coupler script.<br>
Commented out ocean-related code. Still working on getting it working properly with the ice sheet model only.<br>
</p><hr noshade><pre><font color="gray">Modified: branches/landice_ocean_coupler/landice-ocean-coupler.py
===================================================================
--- branches/landice_ocean_coupler/landice-ocean-coupler.py 2013-03-09 00:48:01 UTC (rev 2578)
+++ branches/landice_ocean_coupler/landice-ocean-coupler.py 2013-03-11 14:47:30 UTC (rev 2579)
@@ -4,6 +4,7 @@
import numpy
import os, sys, subprocess
+import time
#import matplotlib.pyplot as plt
try:
from Scientific.IO.NetCDF import NetCDFFile
@@ -28,10 +29,7 @@
# =======================================
# Setup needed files
ocnInput = 'grid.nc'
-ocnOutput = 'output.nc'
-
liceInput = 'land_ice_grid.nc'
-liceOutput = 'output.nc'
# Setup needed executables
runLICE = 'mpirun -np 4 land_ice_model.exe'
@@ -39,7 +37,7 @@
# Define number of coupling intervals (assumes you have set dt for each model accordingly, and ocean dt is evenly divisble in land ice dt)
# (We may want to do more sophisticated time-keeping of the coupling if there is a need.)
-numCoupleIntervals = 3
+numCoupleIntervals = 2
# Some parameters
rhoi = 900.0 # land ice model's ice density (kg m^-3)
@@ -47,26 +45,34 @@
# =======================================
+# clean up previous runs
+os.system('rm -rf land_ice/output*')
+os.system('rm -rf land_ice/restart*')
+os.system('rm -rf ocean/output*')
+os.system('rm -rf ocean/restart*')
-
-
-for t in range(coupleIntervals):
+for t in range(numCoupleIntervals):
+ print '============================================================'
print 'Starting coupling number ', t
# Get the appropriate source and destination files for the input needed by the coupler
if t==0:
# Use I.C. from input files at initial time
liceSourceFile = NetCDFFile('./land_ice/'+liceInput,'r')
- ocnSourceFile = NetCDFFile('./ocean/'+ocnInput,'r')
+# ocnSourceFile = NetCDFFile('./ocean/'+ocnInput,'r')
# At initial time, we want to write to the input files
liceDestFile = NetCDFFile('./land_ice/'+liceInput,'r+')
- ocnDestFile = NetCDFFile('./ocean/'+ocnInput,'r+')
+# ocnDestFile = NetCDFFile('./ocean/'+ocnInput,'r+')
else:
# Use values from output files at other times.
- liceSourceFile = NetCDFFile('./land_ice/'+liceOutput,'r')
- ocnSourceFile = NetCDFFile('./ocean/'+ocnOutput,'r')
+ p = os.popen('ls -1t ./land_ice/output.*.nc | head -n 1') # get the most recent output file
+ liceOutput = p.read().rstrip() # get stdout
+ liceSourceFile = NetCDFFile(liceOutput, 'r')
+# p = os.popen('ls -1t ./ocean/output.*.nc | head -n 1') # get the most recent output file
+# ocnOutput = p.read().rstrip() # get stdout
+# ocnSourceFile = NetCDFFile(ocnOutput, 'r')
# At other times we want to write to the restart files
# Need to choose the appropriate restart file - there may be smarter ways to do this, but an easy way is to take the most recent
@@ -74,27 +80,27 @@
p = os.popen('ls -1t ./land_ice/restart.*.nc | head -n 1')
liceRestart = p.read().rstrip() # get stdout
liceDestFile = NetCDFFile(liceRestart,'r+')
- p = os.popen('ls -1t ./ocean/restart.*.nc | head -n 1')
- ocnRestart = p.read().rstrip() # get stdout
- ocnDestFile = NetCDFFile(ocnRestart,'r+')
+# p = os.popen('ls -1t ./ocean/restart.*.nc | head -n 1')
+# ocnRestart = p.read().rstrip() # get stdout
+# ocnDestFile = NetCDFFile(ocnRestart,'r+')
# Get the source fields needed by the coupler
# (Get the -1 time level for all variables - this will be the last whether this is from input or output
liceThickness = liceSourceFile.variables['thickness'][-1,:]
liceBasalTemp = liceSourceFile.variables['temperature'][-1,:,-1]
- ocnSurfTemp = ocnSourceFile.variables['temperature'][-1,:,0]
- ocnSurfSalin = ocnSourceFile.variables['salinity'][-1,:,0]
+# ocnSurfTemp = ocnSourceFile.variables['temperature'][-1,:,0]
+# ocnSurfSalin = ocnSourceFile.variables['salinity'][-1,:,0]
# Get the destination fields needed by the coupler
- liceBMB = liceDestFile.variables['marineBasalMassBalanceTimeSeries'][:,0] # There should only be on time level
+ liceBMB = liceDestFile.variables['marineBasalMassBalTimeSeries'][:,0] # There should only be on time level
#liceBHF = liceDestFile.variables['basalHeatFluxTimeSeries'][:,0] # NEED TO RESTRICT THIS TO CELLS WITH ICE
- ocnSurfPressure = ocnDestFile.variables['ssh'][0,:] # TODO WHAT IS THE PROPER VARIABLE HERE?
+# ocnSurfPressure = ocnDestFile.variables['ssh'][0,:] # TODO WHAT IS THE PROPER VARIABLE HERE?
# TODO WHAT ARE THE PROPER VARIABLE FOR MASS, HEAT, AND SALINITY FLUXES?
# Calculate the ocean surface pressure - this could be a function call
# TODO WHAT TO DO ABOUT NON-ICE SHELF OCEAN CELLS?
- ocnSurfPressure = rhoi * grav * liceThickness # TODO ARE THESE THE PROPER UNITS?
+# ocnSurfPressure = rhoi * grav * liceThickness # TODO ARE THESE THE PROPER UNITS?
# Calculate boundary layer fluxes - this could be an internal or external function call
#calculateBdyLyrFluxes(liceBasalTemp, ocnSurfTemp, ocnSurfSalin, liceBHF, ocnMassFlux, ocnHeatFlux, ocnSalinFlux) #TODO
@@ -104,60 +110,71 @@
# =======================================
# Run the models # TODO Do we want to do this in parallel?
- try:
- os.chdir('ocean')
- # Set the namelist file properly for a restart or no
- print 'Setting up ocean namelist file'
- if t==0:
- subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_do_restart.*/ config_do_restart = .false./" namelist.input" ' , shell=True, executable='/bin/bash') # no restart
- subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_write_output_on_startup.*/ config_write_output_on_startup = .true./" namelist.input" ' , shell=True, executable='/bin/bash') # write the initial time
- subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_start_time.*/ config_start_time = '0000-01-01_00:00:00'/" namelist.input" ' , shell=True, executable='/bin/bash') # set the start time
- else:
- subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_do_restart.*/ config_do_restart = .true./" namelist.input" ' , shell=True, executable='/bin/bash') # do a restart
- subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_write_output_on_startup.*/ config_write_output_on_startup = .false./" namelist.input" ' , shell=True, executable='/bin/bash') # don't write the initial time
- # Get the old stop time so we can set it to be the new start time.
- p = os.popen('ls -1t output*nc | head -n 1')
- oldoutputfile=p.read().rstrip()
- p = os.popen('ncks -v xtime -H -s "%c" ' + oldoutputfile + ' | tail -r -c 65')
- oldstoptime=p.read().rstrip()
- subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_start_time.*/ config_start_time = "' + oldstoptime '"/" namelist.input" ' , shell=True, executable='/bin/bash') # set the start time to the old stop time
+# try:
+# os.chdir('ocean')
+# # Set the namelist file properly for a restart or no
+# print 'Setting up ocean namelist file'
+# if t==0:
+# subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_do_restart.*/ config_do_restart = .false./" namelist.input' , shell=True, executable='/bin/bash') # no restart
+# subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_write_output_on_startup.*/ config_write_output_on_startup = .true./" namelist.input' , shell=True, executable='/bin/bash') # write the initial time
+# subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_start_time.*/ config_start_time = \'0000-01-01_00:00:00\'/" namelist.input' , shell=True, executable='/bin/bash') # set the start time
+# else:
+# subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_do_restart.*/ config_do_restart = .true./" namelist.input' , shell=True, executable='/bin/bash') # do a restart
+# subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_write_output_on_startup.*/ config_write_output_on_startup = .false./" namelist.input' , shell=True, executable='/bin/bash') # don't write the initial time
+# # Get the old stop time so we can set it to be the new start time.
+# p = os.popen('ls -1t output*nc | head -n 1')
+# oldoutputfile=p.read().rstrip()
+# p = os.popen('ncks -v xtime -H -s "%c" ' + oldoutputfile + ' | tail -r -c 65')
+# oldstoptime=p.read().rstrip()
+# subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_start_time.*/ config_start_time = ' + oldstoptime + '/" namelist.input ' , shell=True, executable='/bin/bash') # set the start time to the old stop time
- print 'Starting ocean model.'
- subprocess.check_call(runOCN, shell=True, executable='/bin/bash')
- print 'Ocean model completed.'
- # Copy output file so we don't lose it when the model restarts - could use Python's shutil module. TODO Also may want to change format of the string conversion of t
- subprocess.check_call('cp ' + ocnOutput + ' output.' + str(t) + '.nc', shell=True, executable='/bin/bash')
- os.chdir('..')
- except:
- sys.exit('Ocean model failed!')
+# print 'Starting ocean model.'
+# subprocess.check_call(runOCN, shell=True, executable='/bin/bash')
+# print 'Ocean model completed.'
+# # Don't need to copy output file if the namelist is setup properly
+# ### Copy output file so we don't lose it when the model restarts - could use Python's shutil module. TODO Also may want to change format of the string conversion of t
+# ##subprocess.check_call('cp ' + ocnOutput + ' output.' + str(t) + '.nc', shell=True, executable='/bin/bash')
+# os.chdir('..')
+# except:
+# sys.exit('Ocean model failed!')
+
try:
os.chdir('land_ice')
# Set the namelist file properly for a restart or no and set the start and stop times
print 'Setting up land ice namelist file'
if t==0:
- subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_do_restart.*/ config_do_restart = .false./" namelist.input" ' , shell=True, executable='/bin/bash') # no restart
- subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_write_output_on_startup.*/ config_write_output_on_startup = .true./" namelist.input" ' , shell=True, executable='/bin/bash') # write the initial time
- subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_start_time.*/ config_start_time = '0000-01-01_00:00:00'/" namelist.input" ' , shell=True, executable='/bin/bash') # set the start time
+ subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_do_restart.*/ config_do_restart = .false./" namelist.input' , shell=True, executable='/bin/bash') # no restart
+ print 'set no restart'
+ subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_write_output_on_startup.*/ config_write_output_on_startup = .true./" namelist.input' , shell=True, executable='/bin/bash') # write the initial time
+ print 'set write initial time'
+ subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_start_time.*/ config_start_time = \'0000-01-01_00:00:00\'/" namelist.input' , shell=True, executable='/bin/bash') # set the start time
+ print 'set start time'
else:
- subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_do_restart.*/ config_do_restart = .true./" namelist.input" ' , shell=True, executable='/bin/bash') # do a restart
- subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_write_output_on_startup.*/ config_write_output_on_startup = .false./" namelist.input" ' , shell=True, executable='/bin/bash') # don't write the initial time
- # Get the old stop time so we can set it to be the new start time.
- p = os.popen('ls -1t output*nc | head -n 1')
- oldoutputfile=p.read().rstrip()
- p = os.popen('ncks -v xtime -H -s "%c" ' + oldoutputfile + ' | tail -r -c 65')
+ subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_do_restart.*/ config_do_restart = .true./" namelist.input' , shell=True, executable='/bin/bash') # do a restart
+ print 'set restart'
+ subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_write_output_on_startup.*/ config_write_output_on_startup = .true./" namelist.input' , shell=True, executable='/bin/bash') # don't write the initial time
+ print 'disabled initial write'
+ # Get the old stop time so we can set it to be the new start time. - it seems more reliable to search for the most recent restart file rather than the most recent output file.
+ p = os.popen('ls -1t restart*nc | head -n 1')
+ lastrestartfile=p.read().rstrip()
+ p = os.popen('ncks -v xtime -H -s "%c" ' + lastrestartfile + ' | tail -r -c 65')
oldstoptime=p.read().rstrip()
- subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_start_time.*/ config_start_time = "' + oldstoptime '"/" namelist.input" ' , shell=True, executable='/bin/bash') # set the start time to the old stop time
+ subprocess.check_call('sed -i.SEDBACKUP "s/^.*config_start_time.*/ config_start_time = ' + oldstoptime + '/" namelist.input ' , shell=True, executable='/bin/bash') # set the start time to the old stop time
+ print 'set start time'
print 'Starting land ice model.'
subprocess.check_call(runLICE, shell=True, executable='/bin/bash')
print 'Land ice model completed.'
- # Copy output file so we don't lose it when the model restarts - could use Python's shutil module. TODO Also may want to change format of the string conversion of t
- subprocess.check_call('cp ' + liceOutput + ' output.' + str(t) + '.nc', shell=True, executable='/bin/bash')
+ # Don't need to copy output file if the namelist is setup properly
+ ### Copy output file so we don't lose it when the model restarts - could use Python's shutil module. TODO Also may want to change format of the string conversion of t
+ ##subprocess.check_call('cp ' + liceOutput + ' output.' + str(t) + '.nc', shell=True, executable='/bin/bash')
os.chdir('..')
except:
sys.exit('Land Ice model failed!')
+ #time.sleep(62)
+
# =======================================
print 'Coupled model run complete!'
</font>
</pre>