Use python-netcdf4 instead of python

Allow for single factor experiments
Allow running multi-site ensembles
Update for v1 parameters for RD

adjust_restart.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env/python
 import os, sys, csv, time, math
 from optparse import OptionParser
-import netcdf_functions as nffun
+import netcdf4_functions as nffun
 import glob
 
 parser = OptionParser()

case_copy.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-import netcdf_functions as nffun
+import netcdf4_functions as nffun
 import os, sys, csv, time, math, numpy
 from optparse import OptionParser
 
@@ -31,6 +31,16 @@
                   help = 'Year for initial data file')
 parser.add_option('--spin_cycle', dest='spin_cycle', default=0, \
                   help = 'Number of years in spinup cycle')
+parser.add_option('--1850_landuse', dest='nolanduse', default=False, \
+                  action='store_true', help = '1850 land use (no dynamics)')
+parser.add_option('--1850_co2', dest='noco2', default=False, \
+                  action='store_true', help = 'use 1850 CO2')
+parser.add_option('--1850_ndep', dest='nondep', default=False, \
+                  action='store_true', help = 'use 1850 NDep')
+parser.add_option('--suffix', dest='suffix', default='', \
+                  help = 'use 1850 NDep')
+parser.add_option('--machine', dest='machine', default='cades', \
+                  help = 'machine')
 
 (options, args) = parser.parse_args()
 
@@ -39,7 +49,12 @@
 #create directory from original case 
 orig_dir = str(os.path.abspath(options.runroot)+'/'+casename+'/run')
 new_dir  = orig_dir.replace(options.site_orig, options.site_new)
+if (options.suffix != ''):
+  new_dir = new_dir.replace(casename,casename+'_'+options.suffix)
 print 'Copying from '+orig_dir+' to \n'+new_dir
+if (new_dir == orig_dir):
+  print 'Error:  New and old directories are the same.  Exiting'
+  sys.exit(1)
 
 #copy files to new directory
 os.system('mkdir -p '+new_dir+'/timing/checkpoints')
@@ -60,34 +75,121 @@
         for s in myinput:
             if ('drv_in' in f and 'stop_n' in s and int(options.nyears) > 0):
                 s_out = ' stop_n = '+str(options.nyears)+'\n'
+            elif ('drv_in' in f and 'lnd_ntasks' in s):
+                np = int(s.split()[2])
+                s_out = s
             elif ('drv_in' in f and 'restart_n' in s and int(options.nyears) > 0):
                 s_out = ' restart_n = '+str(options.nyears)+'\n'
             elif ('lnd_in' in f and 'finidat =' in s and int(options.finyr) > 0):
                 year_orig = str((s.split('.')[-2:-1])[0])[0:4]
                 year_new = str(10000+int(options.finyr))[1:]
                 s_out = s.replace('.clm2.r.'+year_orig, '.clm2.r.'+year_new)
                 s_out = s_out.replace(options.site_orig, options.site_new)
+                if (options.suffix != ''):
+                  s_out = s_out.replace(casename,casename+'_'+options.suffix)
             elif ('lnd_in' in f and "hist_nhtfrq =" in s and \
                         int(options.spin_cycle) > 0):
                 nhtfrq = str(-8760*int(options.spin_cycle))
                 if ('ad_spinup' in new_dir):
                     s_out = 'hist_nhtfrq = '+nhtfrq+','+nhtfrq+'\n'
                 else:
                     s_out = 'hist_nhtfrq = '+nhtfrq+'\n'
+            elif ('lnd_in' in f and "flanduse_timeseries =" in s and \
+                     options.nolanduse == True):
+               s_out = " flanduse_timeseries = ''\n"
+            elif ('lnd_in' in f and "do_transient_pfts" in s and \
+                     options.nolanduse == True):
+               s_out = "do_transient_pfts = .false.\n"
+            elif ('lnd_in' in f and "do_harvest" in s and \
+                     options.nolanduse == True):
+               s_out = "do_harvest = .false.\n"
+            elif ('lnd_in' in f and "co2_file =" in s and \
+                     options.noco2 == True):
+               s_out = s.replace('.nc','_CON.nc')
+            elif ('lnd_in' in f and "stream_fldfilename_ndep" in s and \
+                     options.nondep == True):
+               s_out = s.replace('.nc','_CON.nc')
             elif ('diri =' not in s):
                 s_out = s.replace(options.site_orig, options.site_new)
+                if (options.suffix != ''):
+                  s_out = s_out.replace(casename,casename+'_'+options.suffix)
+            elif ('diri' in s and 'lnd' in f):
+                  exedir = s.split()[2][1:-4]
+                  print exedir
+                  s_out = s
             else:
                 s_out = s
             myoutput.write(s_out)
         myoutput.close()
         myinput.close()
         os.system(' mv '+new_dir+'/'+f+'.tmp '+new_dir+'/'+f)
 #Assume makepointdata has been run to generate surface and domain data
-os.system('cp temp/surfdata.nc '+new_dir)
-os.system('cp temp/domain.nc '+new_dir)
+if (os.path.exists(orig_dir+'/surfdata.nc')):
+  os.system('cp '+orig_dir+'/surfdata.nc '+new_dir)
+else:
+  os.system('cp temp/surfdata.nc '+new_dir)
+if (os.path.exists(orig_dir+'/domain.nc')):
+  os.system('cp '+orig_dir+'/domain.nc '+new_dir)
+else:
+  os.system('cp temp/domain.nc '+new_dir)
+
+
 os.system('pwd')
-if ('20TR' in options.casename):
+if ('20TR' in options.casename and not options.nolanduse):
    os.system('cp temp/*pftdyn*.nc '+new_dir)
 
 
+#if a global file exists, modify
+if (os.path.exists('temp/global_'+options.casename+'_0.pbs') and options.suffix != ''):
+  file_in = open('temp/global_'+options.casename+'_0.pbs','r')
+  file_out =open('temp/global_'+options.casename+'_'+options.suffix+'.pbs','w')
+  mpicmd = 'mpirun -np '+str(np)
+  if ('cades' in options.machine):
+    mpicmd = '/software/dev_tools/swtree/cs400_centos7.2_pe2016-08/openmpi/1.10.3/centos7.2_gnu5.3.0/bin/mpirun'+ \
+            ' -np '+str(np)+' --hostfile $PBS_NODEFILE ' 
+  elif (('titan' in options.machine or 'eos' in options.machine) and int(options.ninst) == 1):
+    mpicmd = 'aprun -n '+str(np)
+  elif ('cori' in options.machine or 'edison' in options.machine):
+    mpicmd = 'srun -n '+str(np)
+
+  for s in file_in:
+    if "#" in s:
+      file_out.write(s)
+  file_out.write('\n\n')
+  file_out.write('cd '+new_dir+'\n')
+  file_out.write(mpicmd+' '+exedir+'/e3sm.exe\n')
+  file_in.close()
+  file_out.close()
+  print "Submitting the job:"
+  if ('cori' in options.machine or 'edison' in options.machine):
+    os.system('sbatch temp/global_'+options.casename+'_'+options.suffix+'.pbs')
+  else:
+    os.system('qsub temp/global_'+options.casename+'_'+options.suffix+'.pbs')
+
+#if an ensemble script exists, make a copy for this site
+if (options.site_orig != ''):
+  case_prefix = options.casename.split(options.site_orig)[0][:-1]
+  ens_fname = 'scripts/'+case_prefix+'/ensemble_run_'+options.casename.replace(options.site_orig, \
+                 options.site_new)+'.pbs'
+
+  if os.path.exists('scripts/'+case_prefix+'/ensemble_run_'+options.casename+'.pbs'):
+    os.system('cp scripts/'+case_prefix+'/ensemble_run_'+options.casename+'.pbs '+ens_fname)
+    myfile = open(ens_fname,'r')
+    myfile_out = open(ens_fname+'_temp','w')
+
+    for s in myfile:
+      args = s.split(' ')
+      if ('--case' in args):
+        caseind = args.index('--case')
+        print caseind
+        args[caseind+1] = args[caseind+1].replace(options.site_orig,options.site_new)
+        siteind = args.index('--site')
+        args[siteind+1] = args[siteind+1].replace(options.site_orig,options.site_new)
+        sout = " ".join(args)
+        myfile_out.write(sout)
+      else:
+        myfile_out.write(s.replace(options.site_orig,options.site_new))
+    myfile.close()
+    myfile_out.close()
+    os.system('mv '+ens_fname+'_temp '+ens_fname)  
 

ensemble_copy.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-import netcdf_functions as nffun
+import netcdf4_functions as nffun
 import os, sys, csv, time, math, numpy
 from optparse import OptionParser
 
@@ -175,10 +175,10 @@
       elif (parm_indices[pnum] == 0):
          param = parm_values[pnum]
       else:
-         param[:] = parm_values[pnum]
+         param[...] = parm_values[pnum]
       ierr = nffun.putvar(myfile, p, param)
       if ('fr_flig' in p):
          param=nffun.getvar(myfile, 'fr_fcel')
-         param[:]=1.0-parm_values[pnum]-parm_values[pnum-1]
+         param[...]=1.0-parm_values[pnum]-parm_values[pnum-1]
          ierr = nffun.putvar(myfile, 'fr_fcel', param)
    pnum = pnum+1

ensemble_run.py

@@ -197,7 +197,13 @@ def putvar(fname, varname, varvals):
     if (isfirstcase):
         exedir = os.path.abspath(orig_dir+'/../bld/')
     if (options.norun == False):
-        os.system(exedir+'/acme.exe > ccsm_log.txt')
+        if os.path.isfile(exedir+'/acme.exe'):
+           os.system(exedir+'/acme.exe > acme_log.txt')
+        elif os.path.isfile(exedir+'/e3sm.exe'):
+           os.system(exedir+'/e3sm.exe > e3sm_log.txt')
+        elif os.path.isfile(exedir+'/cesm.exe'):
+           os.system(exedir+'/cesm.exe > cesm_log.txt')
+
     isfirstcase=False
 
 #---------  code to post-process ensebmle member and cacluate total normalized SSE ----------

global_fullrun.py

@@ -523,6 +523,8 @@ def get_regional_bounds(myregion):
     cmd_trns = cmd_trns + ' --ilambvars'
 if (options.dailyvars):
     cmd_trns = cmd_trns + ' --dailyvars'        
+if (options.dailyrunoff):
+    cmd_trns = cmd_trns+' --dailyrunoff'
 
 #transient phase 2 (CRU-NCEP only, without coupler bypass)
 if ((options.cruncep or options.gswp3) and not options.cpl_bypass):

makepointdata.py

@@ -2,7 +2,7 @@
 import os, sys, csv, time, math
 from optparse import OptionParser
 import numpy
-import netcdf_functions as nffun
+import netcdf4_functions as nffun
 
 parser = OptionParser()
 
@@ -269,11 +269,11 @@
         xv = nffun.getvar(domainfile_new, 'xv')
         yv = nffun.getvar(domainfile_new, 'yv')
         area = nffun.getvar(domainfile_new, 'area')
-        frac = 1.0
-        mask = 1
+        frac[0] = 1.0
+        mask[0] = 1
         if (options.site != ''):
-            xc= lon[n]
-            yc = lat[n]
+            xc[0] = lon[n]
+            yc[0] = lat[n]
             xv[0][0][0] = lon[n]-resx/2
             xv[0][0][1] = lon[n]+resx/2
             xv[0][0][2] = lon[n]-resx/2
@@ -282,7 +282,7 @@
             yv[0][0][1] = lat[n]-resy/2
             yv[0][0][2] = lat[n]+resy/2
             yv[0][0][3] = lat[n]+resy/2
-            area = resx*resy*math.pi/180*math.pi/180
+            area[0] = resx*resy*math.pi/180*math.pi/180
             ierr = nffun.putvar(domainfile_new, 'xc', xc)
             ierr = nffun.putvar(domainfile_new, 'yc', yc)
             ierr = nffun.putvar(domainfile_new, 'xv', xv)
@@ -400,7 +400,7 @@
         if (options.site != ''):
             longxy[0][0] = lon[n]
             latixy[0][0] = lat[n]
-            area = 111.2*resy*111.321*math.cos((lon[n]*resx)*math.pi/180)*resx
+            area[0] = 111.2*resy*111.321*math.cos((lon[n]*resx)*math.pi/180)*resx
 
         if (not options.surfdata_grid):
             pct_wetland[0][0] = 0.0

manage_ensemble.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 import sys,os, time
 import numpy as np
-import netcdf_functions as nffun
+import netcdf4_functions as nffun
 import subprocess
 from mpi4py import MPI
 from optparse import OptionParser
@@ -177,7 +177,13 @@ def postproc(myvars, myyear_start, myyear_end, myday_start, myday_end, \
                 rundir = options.runroot+'/UQ/'+options.casename+'/g'+jobst[1:]+'/'
                 os.chdir(rundir)
                 #Run the executable
-                os.system(options.exeroot+'/acme.exe > acme.log')
+                exedir = options.exeroot
+                if os.path.isfile(exedir+'/acme.exe'):
+                   os.system(exedir+'/acme.exe > acme_log.txt')
+                elif os.path.isfile(exedir+'/e3sm.exe'):
+                   os.system(exedir+'/e3sm.exe > e3sm_log.txt')
+                elif os.path.isfile(exedir+'/cesm.exe'):
+                   os.system(exedir+'/cesm.exe > cesm_log.txt')
             if (do_postproc):
                 ierr = postproc(myvars, myyear_start, myyear_end, myday_start, \
                          myday_end, myavg_pd, myfactor, myoffset, myjob, \

netcdf4_functions.py

@@ -0,0 +1,18 @@
+#Python utilities for reading and writing variables to a netcdf file
+#  using Scientific Python OR scipy, whichever available
+
+def getvar(fname, varname):
+    from netCDF4 import Dataset
+    nffile = Dataset(fname,"r")
+    varvals = nffile.variables[varname][:]
+    nffile.close()
+    return varvals
+
+def putvar(fname, varname, varvals):
+    from netCDF4 import Dataset
+    import numpy as np
+    nffile = Dataset(fname,"a")
+    nffile.variables[varname][...] = varvals
+    nffile.close()
+    ierr = 0
+    return ierr

netcdf_functions.py

@@ -32,7 +32,10 @@ def putvar(fname, varname, varvals):
     if (usescipy):
         nffile = netcdf.netcdf_file(fname,"a",mmap=False)
         var = nffile.variables[varname]
-        var[:] = varvals
+        if (len(varvals) > 1):
+          var[:] = varvals
+        else:
+
         nffile.close()
     else:
         nffile = netcdf.NetCDFFile(fname,"a")