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case_copy.py
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case_copy.py
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#!/usr/bin/env python
import netcdf4_functions as nffun
import os, sys, csv, time, math, numpy
from optparse import OptionParser
#Create, run and process a CLM/ELM model ensemble member
# given specified case and parameters (see parm_list and parm_data files)
# Parent case must be pre-built and all namelists in run directory.
# Post-processing calcuates normalized sum of squared errors (SSE) given
# data constraints specified in "constraints" directory"
# DMRicciuto 12/1/2015
#
# Note: This will only work for single-point CLM/ELM compiled with MPI_SERIAL
#-------------------Parse options-----------------------------------------------
parser = OptionParser()
parser.add_option("--runroot", dest="runroot", default="../../run", \
help="Directory where the run would be created")
parser.add_option("--case_copy", dest="casename", default="", \
help="Name of case to copy from")
parser.add_option("--site_orig", dest="site_orig", default='', \
help = 'Site being run in original case')
parser.add_option("--site_new", dest="site_new", default='', \
help = 'Site to run')
parser.add_option("--nyears", dest="nyears", default=0, \
help = 'Number of years to run')
parser.add_option("--finidat_year", dest='finyr', default=0, \
help = 'Year for initial data file')
parser.add_option("--finidat_thiscase", dest='fincase', default=False, \
action="store_true", help = 'Use this case for finidat')
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')
parser.add_option('--warming', dest='warming', default='0.0', \
help = 'warming level to apply')
(options, args) = parser.parse_args()
casename = options.casename
#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')
os.system('rm '+new_dir+'/*.nc')
os.system('rm -f '+new_dir+'/*.nc.orig')
os.system('cp '+orig_dir+'/*_in* '+new_dir)
os.system('cp '+orig_dir+'/*nml '+new_dir)
if (not ('ICB' in casename)):
os.system('cp '+orig_dir+'/*stream* '+new_dir)
os.system('cp '+orig_dir+'/*.rc '+new_dir)
os.system('cp '+orig_dir+'/*para*.nc '+new_dir)
#Change site name in relevant files
for f in os.listdir(new_dir):
if (os.path.isfile(new_dir+'/'+f) and (f[-2:] == 'in' or f[-3:] == 'nml' or 'streams' in f)):
myinput=open(new_dir+'/'+f)
myoutput=open(new_dir+'/'+f+'.tmp','w')
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
if (options.site_orig == options.site_new and 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 (options.site_orig == options.site_new and 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 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)