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site_fullrun.py
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#!/usr/bin/env python
import socket, getpass, os, sys, csv, math
from optparse import OptionParser
import subprocess
import numpy
import re
### Run options
parser = OptionParser();
# general OLMT options
parser.add_option("--no_submit", dest="no_submit", default=False, action="store_true", \
help = 'do NOT submit built model to queue, i.e. build only')
parser.add_option("--caseidprefix", dest="mycaseid", default="", \
help="Unique identifier to include as a prefix to the case name")
parser.add_option("--caseroot", dest="caseroot", default='', \
help = "case root directory, where submission scripts live (default = '', i.e., under model_root/scripts/)")
parser.add_option("--runroot", dest="runroot", default="", \
help="Directory where the run would be created")
parser.add_option("--exeroot", dest="exeroot", default="", \
help="Location of executable")
parser.add_option("--archiveroot", dest="archiveroot", default='', \
help = "archive root directory only for mesabi")
parser.add_option("--batch_build", action="store_true", default=False, \
help="Do build as part of submitted batch script")
parser.add_option("--constraints", dest="constraints", default="", \
help="Directory containing model constraints")
parser.add_option("--compare_cases", dest="compare", default='', \
help = 'caseidprefix(es) to compare')
parser.add_option("--ninst", dest="ninst", default=1, \
help = 'number of land model instances')
parser.add_option("--mc_ensemble", dest="mc_ensemble", default=-1, \
help = 'Monte Carlo ensemble (argument is # of simulations)')
parser.add_option("--ng", dest="ng", default=256, \
help = 'number of groups to run in ensemble mode')
parser.add_option("--parm_list", dest="parm_list", default='parm_list', \
help = 'File containing list of parameters to vary')
parser.add_option("--mod_parm_file", dest="mod_parm_file", default='', \
help = "adding the path to the modified parameter file")
parser.add_option("--mod_parm_file_P", dest="mod_parm_file_P", default='', \
help = "adding the path to the modified parameter file")
parser.add_option("--ensemble_file", dest="ensemble_file", default='', \
help = 'Parameter sample file to generate ensemble')
parser.add_option("--postproc_file", dest="postproc_file", default="postproc_vars", \
help = 'File for ensemble post processing')
parser.add_option("--nopftdyn", dest="nopftdyn", default=False, action="store_true", \
help='Do not use dynamic PFT file')
# general model build options
parser.add_option("--model_root", dest="csmdir", default='', \
help = "base CESM directory")
parser.add_option("--compiler", dest="compiler", default = '', \
help = "compiler to use (pgi*, gnu)")
parser.add_option("--mpilib", dest="mpilib", default="mpi-serial", \
help = "mpi library (openmpi, mpich, ibm, mpi-serial)")
parser.add_option("--debugq", dest="debug", default=False, action="store_true", \
help='Use debug queue and options')
parser.add_option("--clean_build", action="store_true", default=False, \
help="Perform a clean build")
parser.add_option("--cpl_bypass", dest = "cpl_bypass", default=False, action="store_true", \
help = "Bypass coupler")
parser.add_option("--machine", dest="machine", default = '', \
help = "machine to use")
parser.add_option("--np", dest="np", default=1, \
help = 'number of processors')
parser.add_option("--walltime", dest="walltime", default=6, \
help = "desired walltime for each job (hours)")
parser.add_option("--pio_version", dest="pio_version", default='2', \
help = "PIO version (1 or 2)")
# CASE options
parser.add_option("--nyears_ad_spinup", dest="ny_ad", default=250, \
help = 'number of years to run ad_spinup')
parser.add_option("--nyears_final_spinup", dest="nyears_final_spinup", default='200', \
help="base no. of years for final spinup")
parser.add_option("--nyears_transient", dest="nyears_transient", default=-1, \
help = 'number of years to run transient')
parser.add_option("--ad_Pinit", dest="ad_Pinit", default=False, action="store_true", \
help="Initialize AD spinup with P pools and use CNP mode")
parser.add_option("--noad", action="store_true", dest="noad", default=False, \
help='Do not perform ad spinup simulation')
parser.add_option("--nofnsp", action="store_true", dest="nofnsp", default=False, \
help='Do not perform final spinup simulation')
parser.add_option("--notrans", action="store_true", dest="notrans", default=False, \
help='Do not perform transient simulation (spinup only)')
# model input options
parser.add_option("--site", dest="site", default='', \
help = '6-character FLUXNET code to run (required)')
parser.add_option("--sitegroup", dest="sitegroup",default="AmeriFlux", \
help = "site group to use (default AmeriFlux)")
parser.add_option("--ccsm_input", dest="ccsm_input", default='', \
help = "input data directory for CESM (required)")
# metdata
parser.add_option("--nopointdata", dest="nopointdata", default=False, action="store_true", \
help="Do NOT make point data (use data already created)")
parser.add_option("--metdir", dest="metdir", default="none", \
help = 'subdirectory for met data forcing')
parser.add_option("--metdata_dir", dest="metdata_dir", default='none', \
help = 'Directory containing cpl_bypass met data (site only)')
parser.add_option("--makemetdata", action="store_true", dest="makemet", default=False, \
help="generate site meteorology")
parser.add_option("--cruncep", dest="cruncep", default=False, action="store_true", \
help = 'Use CRU-NCEP meteorology')
parser.add_option("--cruncepv8", dest="cruncepv8", default=False, action="store_true", \
help = 'Use CRU-NCEP meteorology')
parser.add_option("--gswp3", dest="gswp3", default=False, action="store_true", \
help = 'Use GSWP3 meteorology')
parser.add_option("--gswp3_w5e5", dest="gswp3_w5e5", default=False, action="store_true", \
help = 'Use GSWP3 meteorology')
parser.add_option("--princeton", dest="princeton", default=False, action="store_true", \
help = 'Use Princeton meteorology')
parser.add_option("--co2_file", dest="co2_file", default="fco2_datm_rcp4.5_1765-2500_c130312.nc", \
help = 'co2 data filename')
parser.add_option("--eco2_file", dest="eco2_file", default="", \
help = 'elevated co2 data filename, will spawn three transient simulations, using this file for an elevated co2 sim')
parser.add_option("--add_co2", dest="addco2", default=0.0, \
help = 'CO2 (ppmv) to add to atmospheric forcing')
parser.add_option("--startdate_add_co2", dest="sd_addco2", default="99991231", \
help = 'Date (YYYYMMDD) to begin addding CO2')
parser.add_option("--add_temperature", dest="addt", default=0.0, \
help = 'Temperature to add to atmospheric forcing')
parser.add_option("--startdate_add_temperature", dest="sd_addt", default="99991231", \
help = 'Date (YYYYMMDD) to begin addding temperature')
# surface data
parser.add_option("--surfdata_grid", dest="surfdata_grid", default=False, action="store_true", \
help = 'Use gridded surface data instead of site data')
parser.add_option("--surffile", dest="surffile", default='', \
help = 'Use specified surface data file')
parser.add_option("--domainfile", dest="domainfile", default="", \
help = 'Domain file to use')
# parameters
parser.add_option("--pft", dest="mypft", default=-1, \
help = 'Use this PFT (override site default)')
parser.add_option("--siteparms",dest = "siteparms", default=False, action="store_true", \
help = 'Use default PFT parameters')
parser.add_option("--parm_file", dest="parm_file", default="", \
help = 'parameter file to use')
parser.add_option("--parm_file_P", dest="parm_file_P", default="", \
help = 'parameter file to use')
parser.add_option("--fates_paramfile", dest="fates_paramfile", default="", \
help = 'Fates parameter file to use')
parser.add_option("--parm_vals", dest="parm_vals", default="", \
help = 'User specified parameter values')
# model structural config options
parser.add_option("--namelist_file", dest="namelist_file", default='', \
help="File containing custom namelist options for user_nl_clm")
parser.add_option("--tstep", dest="tstep", default=0.5, \
help = 'CLM timestep (hours)')
parser.add_option("--SP", dest="sp", default=False, action="store_true", \
help = 'Use satellite phenology mode')
parser.add_option("--lai", dest="lai", default=-999, \
help = 'Set constant LAI (SP mode only)')
parser.add_option("--run_startyear", dest="run_startyear", default="1850", \
help="Starting year for simulation (SP mode only)")
parser.add_option("--crop", action="store_true", default=False, \
help="Perform a crop model simulation")
parser.add_option("--humhol", dest="humhol", default=False, action="store_true", \
help = 'Use hummock/hollow microtopography')
parser.add_option("--marsh", dest="marsh", default=False, \
help = 'Use marsh hydrology/elevation', action="store_true")
parser.add_option("--tide_components_file", dest="tide_components_file", default='', \
help = 'NOAA tide components file')
parser.add_option("--nofire", dest="nofire", default=False, action="store_true", \
help='Turn off fire algorithms')
parser.add_option("--C13", dest="C13", default=False, action="store_true", \
help = 'Switch to turn on C13')
parser.add_option("--C14", dest="C14", default=False, action="store_true", \
help = 'Use C14 as C13 (no decay)')
parser.add_option("--aero_rcp85",dest="aerorcp85", action="store_true", default=False,help="Use RCP8.5 aerosols")
parser.add_option("--ndep_rcp85",dest="ndeprcp85", action="store_true", default=False,help="Use RCP8.5 N dep")
parser.add_option("--harvmod", action="store_true", dest='harvmod', default=False, \
help="turn on harvest modification: All harvest at first timestep")
parser.add_option("--no_dynroot", dest="no_dynroot", default=False, action="store_true", \
help = 'Turn off dynamic root distribution')
parser.add_option("--vertsoilc", dest="vsoilc", default=False, action="store_true", \
help = 'To turn on CN with multiple soil layers, excluding CENTURY C module (CLM4ME on as well)')
parser.add_option("--centbgc", dest="centbgc", default=False, action="store_true", \
help = 'To turn on CN with multiple soil layers, CENTURY C module (CLM4ME on as well)')
parser.add_option("--CH4", dest="CH4", default=False, action="store_true", \
help = 'To turn on CN with CLM4me')
parser.add_option("--fates", dest="fates", default=False, action="store_true", \
help = 'Use fates model')
parser.add_option("--fates_nutrient", dest="fates_nutrient", default="", \
help = 'Which version of fates_nutrient to use (RD or ECA)')
parser.add_option("--ECA", dest="eca", default=False, action="store_true", \
help = 'Use ECA compset')
parser.add_option("--c_only", dest="c_only", default=False, action ="store_true", \
help='Carbon only (saturated N&P)')
parser.add_option("--cn_only", dest="cn_only", default=False, action ="store_true", \
help='Carbon/Nitrogen only (saturated P)')
parser.add_option("--srcmods_loc", dest="srcmods_loc", default='', \
help = 'Copy sourcemods from this location')
parser.add_option("--daymet", dest="daymet", default=False, \
action="store_true", help = 'Use Daymet corrected meteorology')
parser.add_option("--daymet4", dest="daymet4", default=False, \
action="store_true", help = "Daymet v4 downscaled GSWP3-v2 forcing with user-provided domain and surface data)")
parser.add_option("--dailyvars", dest="dailyvars", default=False, \
action="store_true", help="Write daily ouptut variables")
parser.add_option("--var_soilthickness",dest="var_soilthickness", default=False, \
help = 'Use variable soil depth from surface data file',action='store_true')
parser.add_option("--no_budgets", dest="no_budgets", default=False, \
help = 'Turn off CNP budget calculations', action='store_true')
parser.add_option("--use_hydrstress", dest="use_hydrstress", default=False, \
help = 'Turn on hydraulic stress', action='store_true')
parser.add_option("--spruce_treatments", dest="spruce_treatments", default=False, \
help = 'Run SPRUCE treatment simulations (ensemble mode)', action='store_true')
# model output options
parser.add_option("--hist_vars", dest="hist_vars", default='', \
help = 'Output only selected variables in h0 file (comma delimited)')
parser.add_option("--diags", dest="diags", default=False, action="store_true",
help="Write special outputs for diagnostics")
parser.add_option("--trans_varlist", dest = "trans_varlist", default='', \
help = "Transient outputs")
parser.add_option("--hist_mfilt_trans", dest="hist_mfilt", default="365", \
help = 'number of output timesteps per file (transient only)')
parser.add_option("--hist_nhtfrq_trans", dest="hist_nhtfrq", default="-24", \
help = 'output file timestep (transient only)')
parser.add_option("--spinup_vars", dest = "spinup_vars", default=False, action="store_true", \
help = "limit output variables for spinup")
parser.add_option("--hist_mfilt_spinup", dest="hist_mfilt_spinup", default="-999", \
help = 'number of output timesteps per file (spinup only)')
parser.add_option("--hist_nhtfrq_spinup", dest="hist_nhtfrq_spinup", default="-999", \
help = 'output file timestep (spinup only)')
#datasets for user-defined PFTs (by F-M Yuan, NGEE-Arctic)
parser.add_option("--maxpatch_pft", dest="maxpatch_pft", default=17, \
help = "user-defined max. patch PFT number, default is 17")
parser.add_option("--landusefile", dest="pftdynfile", default='', \
help='user-defined dynamic PFT file')
parser.add_option("--var_list_pft", dest="var_list_pft", default="",help='Comma-separated list of vars to output at PFT level')
parser.add_option("--dryrun",dest="dryrun",default=False,action="store_true",help="Do not execute commands")
(options, args) = parser.parse_args()
def runcmd(cmd,echo=True):
if echo:
print(cmd)
if not options.dryrun:
return os.system(cmd)
else:
return 0
#----------------------------------------------------------
# define function for pbs submission
def submit(fname, submit_type='qsub', job_depend=''):
job_depend_flag = ' -W depend=afterok:'
if ('sbatch' in submit_type):
job_depend_flag = ' --dependency=afterok:'
if (job_depend != '' and submit_type != ''):
runcmd(submit_type+job_depend_flag+job_depend+' '+fname+' > temp/jobinfo')
else:
if (submit_type == ''):
runcmd('chmod a+x '+fname)
runcmd('./'+fname+' > temp/jobinfo')
else:
runcmd(submit_type+' '+fname+' > temp/jobinfo')
if (submit_type != '' and not options.dryrun):
myinput = open('temp/jobinfo')
for s in myinput:
thisjob = re.search('[0-9]+', s).group(0)
myinput.close()
else:
thisjob="0"
runcmd('rm temp/jobinfo')
return thisjob
#----------------------------------------------------------
# Set default model root
if (options.csmdir == ''):
if (os.path.exists('../E3SM')):
options.csmdir = os.path.abspath('../E3SM')
print('Model root not specified. Defaulting to '+options.csmdir)
else:
print('Error: Model root not specified. Please set using --model_root')
sys.exit(1)
elif (not os.path.exists(options.csmdir)):
print('Error: Model root '+options.csmdir+' does not exist.')
sys.exit(1)
#check whether model named clm or elm
if (os.path.exists(options.csmdir+'/components/elm')):
model_name='elm'
else:
model_name='clm2'
#get machine info if not specified
npernode=32
if (options.machine == ''):
hostname = socket.gethostname()
print('')
print('Machine not specified. Using hostname '+hostname+' to determine machine')
if ('or-slurm' in hostname):
options.machine = 'cades'
npernode=32
elif ('cori' in hostname):
print('Cori machine not specified. Setting to cori-haswell')
options.machine = 'cori-haswell'
npernode=32
elif ('blues' in hostname or 'blogin' in hostname):
print('Hostname = '+hostname+' and machine not specified. Assuming anvil')
options.machine = 'anvil'
npernode=36
elif ('compy' in hostname):
options.machine = 'compy'
npernode=40
elif ('ubuntu' in hostname):
options.machine = 'ubuntu'
npernode = 8
elif ('chrlogin' in hostname):
options.machine = 'chrysalis'
npernode = 64
else:
print('ERROR in site_fullrun.py: Machine not specified. Aborting')
sys.exit(1)
if (options.ccsm_input != ''):
ccsm_input = options.ccsm_input
elif (options.machine == 'titan' or options.machine == 'eos'):
ccsm_input = '/lustre/atlas/world-shared/cli900/cesm/inputdata'
elif (options.machine == 'cades'):
ccsm_input = '/nfs/data/ccsi/proj-shared/E3SM/inputdata/'
elif (options.machine == 'edison' or 'cori' in options.machine):
ccsm_input = '/project/projectdirs/acme/inputdata'
elif ('anvil' in options.machine or 'chrysalis' in options.machine):
ccsm_input = '/home/ccsm-data/inputdata'
elif ('compy' in options.machine):
ccsm_input = '/compyfs/inputdata/'
#if (options.compiler != ''):
# if (options.machine == 'titan'):
# options.compiler = 'pgi'
# if (options.machine == 'eos' or options.machine == 'edison' or 'cori' in options.machine):
# options.compiler = 'intel'
# if (options.machine == 'cades'):
# options.compiler = 'gnu'
mycaseid = options.mycaseid
srcmods = options.srcmods_loc
if (mycaseid == ''):
myscriptsdir = 'none'
else:
myscriptsdir = mycaseid
#get start and year of input meteorology from site data file
PTCLMfiledir = ccsm_input+'/lnd/clm2/PTCLM'
fname = PTCLMfiledir+'/'+options.sitegroup+'_sitedata.txt'
AFdatareader = csv.reader(open(fname, "rt"))
translen = int(options.nyears_transient)
csmdir = options.csmdir
#case run and case root directories
myproject='e3sm'
if (options.runroot == '' or (os.path.exists(options.runroot) == False)):
myuser = getpass.getuser()
if (options.machine == 'titan' or options.machine == 'eos'):
myinput = open('/ccs/home/'+myuser+'/.cesm_proj','r')
for s in myinput:
myproject=s[:-1]
runroot='/lustre/atlas/scratch/'+myuser+'/'+myproject
elif (options.machine == 'cades'):
runroot='/lustre/or-scratch/cades-ccsi/scratch/'+myuser
elif ('cori' in options.machine):
runroot='/global/cscratch1/sd/'+myuser
myinput = open(os.environ.get('HOME')+'/.cesm_proj','r')
for s in myinput:
myproject=s[:-1]
print('Project = '+myproject)
elif ('edison' in options.machine):
runroot=os.environ.get('CSCRATCH')+'/acme_scratch/edison/'
elif ('anvil' in options.machine or 'chrysalis' in options.machine):
runroot="/lcrc/group/acme/"+myuser
myproject='e3sm'
elif ('compy' in options.machine):
runroot='/compyfs/'+myuser+'/e3sm_scratch'
myproject='e3sm'
else:
runroot = csmdir+'/run'
else:
runroot = os.path.abspath(options.runroot)
if (options.caseroot == options.runroot):
caseroot = os.path.abspath(options.caseroot)+'/cime_case_dirs'
os.system('mkdir -p '+caseroot)
elif (options.caseroot == '' or (os.path.exists(options.caseroot) == False)):
caseroot = os.path.abspath(csmdir+'/cime/scripts')
else:
caseroot = os.path.abspath(options.caseroot)
sitenum=0
# create ensemble file if requested (so that all cases use the same)
if (int(options.mc_ensemble) != -1):
if (not(os.path.isfile(options.parm_list))):
print('parm_list file does not exist')
sys.exit()
else:
param_names=[]
param_min=[]
param_max=[]
input = open(options.parm_list,'r')
for s in input:
if (s):
param_names.append(s.split()[0])
if (int(options.mc_ensemble) > 0):
if (len(s.split()) == 3):
param_min.append(float(s.split()[1]))
param_max.append(float(s.split()[2]))
else:
param_min.append(float(s.split()[2]))
param_max.append(float(s.split()[3]))
input.close()
n_parameters = len(param_names)
nsamples = int(options.mc_ensemble)
samples=numpy.zeros((n_parameters,nsamples), dtype=float)
for i in range(0,nsamples):
for j in range(0,n_parameters):
samples[j][i] = param_min[j]+(param_max[j]-param_min[j])*numpy.random.rand(1)
numpy.savetxt('mcsamples_'+options.mycaseid+'_'+str(options.mc_ensemble)+'.txt', \
numpy.transpose(samples))
options.ensemble_file = 'mcsamples_'+options.mycaseid+'_'+str(options.mc_ensemble)+'.txt'
mysites = options.site.split(',')
nnode=1
if(int(options.np)>1): #in case of a single site in name but with multiple unstructured gridcells
npernode=min(int(npernode),int(options.np))
nnode=-(int(options.np)//-int(npernode))
elif (not 'all' in mysites and (options.ensemble_file == '')):
npernode = len(mysites)
for row in AFdatareader:
if (row[0] in mysites) or ('all' in mysites and row[0] !='site_code' \
and row[0] != ''):
site = row[0]
if (sitenum == 0):
firstsite=site
site_lat = row[4]
site_lon = row[3]
if (options.cruncepv8 or options.cruncep or options.gswp3 or options.gswp3_w5e5 or options.princeton):
startyear = 1901
endyear = 1920
if (options.cruncepv8):
endyear_trans=2016
elif (options.gswp3):
endyear_trans=2014
elif (options.gswp3_w5e5):
endyear_trans=2019
elif (options.princeton):
endyear_trans=2012
else:
endyear_trans=2010
else:
startyear = int(row[6])
endyear = int(row[7])
if (options.diags):
timezone = int(row[9])
site_endyear = int(row[7])
ncycle = endyear-startyear+1 #number of years in met cycle
ny_ad = options.ny_ad
ny_fin = options.nyears_final_spinup
#AD spinup and final spinup lengths must be multiples of met data cyle.
if (int(options.ny_ad) % ncycle != 0):
ny_ad = str(int(ny_ad) + ncycle - (int(ny_ad) % ncycle))
# APW TCOFD
#if (int(options.nyears_final_spinup) % ncycle !=0 and options.noad == False):
if (int(options.nyears_final_spinup) % ncycle !=0):
ny_fin = str(int(ny_fin) + ncycle - (int(ny_fin) % ncycle))
if (options.nyears_transient == -1):
translen = endyear-1850+1 # length of transient run
if (options.eco2_file != ''):
translen = translen - ncycle # if experiment sim, stop first transient at exp start yr - 1
if (options.cpl_bypass and (options.cruncep or options.gswp3 or \
options.princeton or options.cruncepv8 or options.gswp3_w5e5)):
print(endyear_trans, site_endyear)
translen = min(site_endyear,endyear_trans)-1850+1
fsplen = int(ny_fin)
#get align_year
year_align = (endyear-1850+1) % ncycle
#use site parameter file if it exists
if (options.siteparms):
if (os.path.exists(PTCLMfiledir+'/parms_'+site)):
print ('Using parameter file PTCLM_Files/parms_'+site)
options.parm_file = PTCLMfiledir+'/parms_'+site
else:
options.parm_file = ''
#---------------- build base command for all calls to runcase.py -----------------------------
#print year_align, fsplen
basecmd = 'python runcase.py --site '+site+' --ccsm_input '+ \
os.path.abspath(ccsm_input)+' --rmold --no_submit --sitegroup ' + \
options.sitegroup
if (options.machine != ''):
basecmd = basecmd+' --machine '+options.machine
if (options.csmdir != ''):
basecmd = basecmd+' --model_root '+options.csmdir
if (srcmods != ''):
srcmods = os.path.abspath(srcmods)
basecmd = basecmd+' --srcmods_loc '+srcmods
elif (options.ad_Pinit):
srcmods = os.path.abspath('srcmods_Pinit')
basecmd = basecmd+' --srcmods_loc '+srcmods
if (mycaseid != ''):
basecmd = basecmd+' --caseidprefix '+mycaseid
if (options.parm_file != ''):
basecmd = basecmd+' --parm_file '+options.parm_file
if (options.parm_file_P != ''):
basecmd = basecmd+' --parm_file_P '+options.parm_file_P
if (options.parm_vals != ''):
basecmd = basecmd+' --parm_vals '+options.parm_vals
if (options.clean_build):
basecmd = basecmd+' --clean_build '
if (options.namelist_file != ''):
basecmd = basecmd+' --namelist_file '+options.namelist_file
if (options.metdir !='none'):
basecmd = basecmd+' --metdir '+options.metdir
if (options.metdata_dir !='none'):
basecmd = basecmd+' --metdata_dir '+options.metdata_dir
if (options.C13):
basecmd = basecmd+' --C13 '
if (options.C14):
basecmd = basecmd+' --C14 '
if (options.debug):
basecmd = basecmd+' --debugq'
if (options.ninst > 1):
basecmd = basecmd+' --ninst '+str(options.ninst)
if (int(options.mypft) >= 0):
basecmd = basecmd+' --pft '+str(options.mypft)
if (options.nofire):
basecmd = basecmd+' --nofire'
if (options.harvmod):
basecmd = basecmd+' --harvmod'
if (options.humhol):
basecmd = basecmd+' --humhol'
if (options.marsh):
basecmd = basecmd+' --marsh'
if (options.tide_components_file != ''):
basecmd = basecmd + ' --tide_components_file %s'%options.tide_components_file
if (float(options.lai) >= 0):
basecmd = basecmd+' --lai '+str(options.lai)
if (options.nopftdyn):
basecmd = basecmd+' --nopftdyn'
if (options.no_dynroot):
basecmd = basecmd+' --no_dynroot'
if (options.vsoilc):
basecmd = basecmd+' --vertsoilc'
if (options.centbgc):
basecmd = basecmd+' --centbgc'
if (options.c_only):
basecmd = basecmd+' --c_only'
if (options.cn_only):
basecmd = basecmd+' --cn_only'
if (options.CH4):
basecmd = basecmd+' --CH4'
if (options.cruncep):
basecmd = basecmd+' --cruncep'
if (options.cruncepv8):
basecmd = basecmd+' --cruncepv8'
if (options.gswp3):
basecmd = basecmd+' --gswp3'
if (options.gswp3_w5e5):
basecmd = basecmd+' --gswp3_w5e5'
if (options.princeton):
basecmd = basecmd+' --princeton'
if (options.daymet):
basecmd = basecmd+' --daymet'
if (options.daymet4): # gswp3 v2 spatially-downscaled by daymet v4, usually together with user-defined domain and surface data
basecmd = basecmd+' --daymet4'
if (not options.gswp3): basecmd = basecmd+' --gswp3'
if (options.fates_paramfile != ''):
basecmd = basecmd+ ' --fates_paramfile '+options.fates_paramfile
if (options.fates_nutrient != ''):
basecmd = basecmd+ ' --fates_nutrient '+options.fates_nutrient
if (options.surfdata_grid):
basecmd = basecmd+' --surfdata_grid'
if (options.ensemble_file != ''):
basecmd = basecmd+' --ensemble_file '+options.ensemble_file
basecmd = basecmd+' --parm_list '+options.parm_list
if (options.archiveroot !=''):
basecmd = basecmd+' --archiveroot '+options.archiveroot
if (options.mod_parm_file !=''):
basecmd = basecmd+' --mod_parm_file '+options.mod_parm_file
if (options.mod_parm_file_P !=''):
basecmd = basecmd+' --mod_parm_file_P '+options.mod_parm_file_P
if (options.addt != 0):
basecmd = basecmd+' --add_temperature '+str(options.addt)
basecmd = basecmd+' --startdate_add_temperature '+str(options.sd_addt)
if (options.addco2 != 0):
basecmd = basecmd+' --add_co2 '+str(options.addco2)
basecmd = basecmd+' --startdate_add_co2 '+str(options.sd_addco2)
if (options.surffile != ''):
basecmd = basecmd+' --surffile '+options.surffile
basecmd = basecmd + ' --ng '+str(options.ng)
basecmd = basecmd + ' --np '+str(options.np)
basecmd = basecmd + ' --tstep '+str(options.tstep)
basecmd = basecmd + ' --co2_file '+options.co2_file
if (options.aerorcp85):
basecmd = basecmd + ' --aero_rcp85'
if (options.ndeprcp85):
basecmd = basecmd + ' --ndep_rcp85'
if (options.compiler != ''):
basecmd = basecmd + ' --compiler '+options.compiler
basecmd = basecmd + ' --mpilib '+options.mpilib
basecmd = basecmd + ' --pio_version '+options.pio_version
basecmd = basecmd+' --caseroot '+caseroot
basecmd = basecmd+' --runroot '+runroot
basecmd = basecmd+' --walltime '+str(options.walltime)
if (options.constraints != ''):
basecmd = basecmd+' --constraints '+options.constraints
if (options.hist_vars != ''):
basecmd = basecmd+' --hist_vars '+options.hist_vars
if (options.maxpatch_pft!=17):
basecmd = basecmd + ' --maxpatch_pft '+options.maxpatch_pft
if (options.pftdynfile != ''):
basecmd = basecmd + ' --landusefile '+options.pftdynfile
if (options.var_soilthickness):
basecmd = basecmd + ' --var_soilthickness'
if (options.var_list_pft != ''):
basecmd = basecmd + ' --var_list_pft '+options.var_list_pft
if (options.no_budgets):
basecmd = basecmd+' --no_budgets'
if (options.use_hydrstress):
basecmd = basecmd+' --use_hydrstress'
if (options.spruce_treatments):
basecmd = basecmd+' --spruce_treatments'
if (myproject != ''):
basecmd = basecmd+' --project '+myproject
if (options.domainfile != ''):
basecmd = basecmd+' --domainfile '+options.domainfile
#---------------- build commands for runcase.py -----------------------------
# define compsets
# C, CN, CNP
if (options.c_only):
nutrients = 'C'
elif (options.cn_only):
nutrients = 'CN'
else:
nutrients = 'CNP'
# CENTURY or CTC
if (options.centbgc):
decomp_model = 'CNT'
else:
decomp_model = 'CTC'
# ECA or RD
if (options.eca):
mycompset = nutrients+'ECA'+decomp_model
else:
mycompset = nutrients+'RD'+decomp_model+'BC'
#note - RD / ECA in FATES handled with namelist options, not compsets
if (options.fates):
if (model_name == 'elm'):
mycompset = 'ELMFATES'
else:
mycompset = 'CLM45ED'
else:
mycompset = nutrients+'RD'+decomp_model+'BC'
# add P during initial spinup
if (not options.ad_Pinit):
mycompset_adsp = mycompset.replace('CNP','CN')
else:
mycompset_adsp = mycompset
# crop model
if (options.crop):
if (model_name == 'elm'):
mycompset = 'ELMCNCROP'
else:
mycompset = 'CLM45CNCROP'
mycompset_adsp = mycompset
# model executable E3SM / CESM
myexe = 'e3sm.exe'
if ('clm5' in options.csmdir):
mycompset = 'Clm50BgcGs'
mycompset_adsp = 'Clm50BgcGs'
myexe = 'cesm.exe'
# develop calls to runcase.py
# AD spinup
cmd_adsp = basecmd+' --ad_spinup --nyears_ad_spinup '+ \
str(ny_ad)+' --align_year '+str(year_align+1)
if (int(options.hist_mfilt_spinup) == -999):
cmd_adsp = cmd_adsp+' --hist_mfilt 1 --hist_nhtfrq -'+ \
str((endyear-startyear+1)*8760)
else:
cmd_adsp = cmd_adsp+' --hist_mfilt '+str(options.hist_mfilt_spinup) \
+' --hist_nhtfrq '+str(options.hist_nhtfrq_spinup)
if (sitenum == 0):
if (options.exeroot != ''):
if (os.path.isfile(options.exeroot+'/'+myexe) == False):
print('Error: '+options.exeroot+' does not exist or does '+ \
'not contain an executable. Exiting')
sys.exit(1)
else:
ad_exeroot = options.exeroot
cmd_adsp = cmd_adsp+' --exeroot '+ad_exeroot+' --no_build'
elif options.batch_build:
cmd_adsp = cmd_adsp+' --no_build'
else:
cmd_adsp = cmd_adsp+' --exeroot '+ad_exeroot+' --no_build'
if (options.cpl_bypass):
if (options.crop):
cmd_adsp = cmd_adsp+' --compset ICB'+mycompset_adsp
ad_case = site+'_ICB'+mycompset_adsp
else:
cmd_adsp = cmd_adsp+' --compset ICB1850'+mycompset_adsp
ad_case = site+'_ICB1850'+mycompset_adsp
if (options.sp):
if (model_name == 'elm'):
ad_case = site+'_ICBELMBC'
else:
ad_case = site+'_ICBCLM45BC'
else:
cmd_adsp = cmd_adsp+' --compset I1850'+mycompset_adsp
ad_case = site+'_I1850'+mycompset_adsp
if (options.noad == False):
ad_case = ad_case+'_ad_spinup'
if (options.makemet):
cmd_adsp = cmd_adsp+' --makemetdat'
if (options.spinup_vars):
cmd_adsp = cmd_adsp+' --spinup_vars'
if (mycaseid != ''):
ad_case = mycaseid+'_'+ad_case
if (sitenum == 0 and options.exeroot == ''):
ad_exeroot = os.path.abspath(runroot+'/'+ad_case+'/bld')
# final spinup
if mycaseid !='':
basecase=mycaseid+'_'+site
if (options.cpl_bypass):
if (options.crop):
basecase = basecase+'_ICB'+mycompset
else:
basecase = basecase+'_ICB1850'+mycompset
else:
basecase = basecase+'_I1850'+mycompset
else:
if (options.cpl_bypass):
if (options.crop):
basecase = site+'_ICB'+mycompset
else:
basecase=site+'_ICB1850'+mycompset
else:
basecase=site+'_I1850'+mycompset
if (options.sp):
if (model_name == 'elm'):
basecase=site+'_ICBELMBC'
else:
basecase=site+'_ICBCLM45BC'
if (options.noad):
cmd_fnsp = basecmd+' --run_units nyears --run_n '+str(fsplen)+' --align_year '+ \
str(year_align+1)+' --coldstart'
if (sitenum > 0):
cmd_fnsp = cmd_fnsp+' --exeroot '+ad_exeroot+' --no_build'
if (options.sp):
cmd_fnsp = cmd_fnsp+' --run_startyear '+str(options.run_startyear)
if (options.exeroot != ''):
if (os.path.isfile(options.exeroot+'/'+myexe) == False):
print('Error: '+options.exeroot+' does not exist or does '+ \
'not contain an executable. Exiting')
sys.exit(1)
else:
ad_exeroot=options.exeroot
cmd_fnsp = cmd_fnsp+' --no_build --exeroot '+ad_exeroot
elif options.batch_build:
cmd_fnsp = cmd_fnsp+' --no_build'
else:
cmd_fnsp = basecmd+' --finidat_case '+ad_case+ \
' --finidat_year '+str(int(ny_ad)+1)+' --run_units nyears --run_n '+ \
str(fsplen)+' --align_year '+str(year_align+1)+' --no_build' + \
' --exeroot '+ad_exeroot+' --nopointdata'
if (int(options.hist_mfilt_spinup) == -999):
if (options.sp):
cmd_fnsp = cmd_fnsp+' --hist_mfilt 365 --hist_nhtfrq -24'
else:
cmd_fnsp = cmd_fnsp+' --hist_mfilt 1 --hist_nhtfrq -'+ \
str((endyear-startyear+1)*8760)
else:
cmd_fnsp = cmd_fnsp+' --hist_mfilt '+str(options.hist_mfilt_spinup) \
+' --hist_nhtfrq '+str(options.hist_nhtfrq_spinup)
if (options.cpl_bypass):
if (options.sp):
if (model_name == 'elm'):
cmd_fnsp = cmd_fnsp+' --compset ICBELMBC'
else:
cmd_fnsp = cmd_fnsp+' --compset ICBCLM45BC'
else:
if (options.crop):
cmd_fnsp = cmd_fnsp+' --compset ICB'+mycompset
else:
cmd_fnsp = cmd_fnsp+' --compset ICB1850'+mycompset
else:
cmd_fnsp = cmd_fnsp+' --compset I1850'+mycompset
if (options.spinup_vars):
cmd_fnsp = cmd_fnsp+' --spinup_vars'
#if (options.ensemble_file != '' and options.notrans):
# cmd_fnsp = cmd_fnsp+' --spinup_vars'
if (options.ensemble_file != '' and options.notrans and options.constraints == ''):
cmd_fnsp = cmd_fnsp + ' --postproc_file '+options.postproc_file
#transient
cmd_trns = basecmd+' --finidat_case '+basecase+ \
' --finidat_year '+str(fsplen+1)+' --run_units nyears' \
+' --run_n '+str(translen)+' --align_year '+ \
str(year_align+1850)+' --hist_nhtfrq '+ \
options.hist_nhtfrq+' --hist_mfilt '+options.hist_mfilt+' --no_build' + \
' --exeroot '+ad_exeroot+' --nopointdata'
if (options.cpl_bypass):
if (options.crop or options.fates):
cmd_trns = cmd_trns+' --istrans --compset ICB'+mycompset
else:
cmd_trns = cmd_trns+' --compset ICB20TR'+mycompset
else:
cmd_trns = cmd_trns+' --compset I20TR'+mycompset
if (options.spinup_vars):
cmd_trns = cmd_trns + ' --spinup_vars'
if (options.trans_varlist != ''):
cmd_trns = cmd_trns + ' --trans_varlist '+options.trans_varlist
if (options.dailyvars):
cmd_trns = cmd_trns + ' --dailyvars'
if (options.ensemble_file != ''): #Transient post-processing
cmd_trns = cmd_trns + ' --postproc_file '+options.postproc_file
if (options.diags):
cmd_trns = cmd_trns + ' --diags'
if (not options.nofire):
#Turn wildfire off in transient simulations (disturbances are known)
cmd_trns = cmd_trns + ' --nofire'
#transient phase 2
#(CRU-NCEP only, without coupler bypass)
if ((options.cruncep or options.cruncepv8 or options.gswp3 or options.princeton \
or options.gswp3_w5e5) and not options.cpl_bypass):
basecase=basecase.replace('1850','20TR')+'_phase1'
thistranslen = site_endyear - 1921 + 1
cmd_trns2 = basecmd+' --trans2 --finidat_case '+basecase+ \
' --finidat_year 1921 --run_units nyears --branch ' \
+' --run_n '+str(thistranslen)+' --align_year 1921'+ \
' --hist_nhtfrq '+options.hist_nhtfrq+' --hist_mfilt '+ \
options.hist_mfilt+' --no_build'+' --exeroot '+ad_exeroot + \
' --compset I20TR'+mycompset+' --nopointdata'
#print(cmd_trns2)
# experimental manipulation transients, without coupler bypass
# APW: check align_year is correct,
# APW: do we want different outputs? Maybe the full set here and a reduced set for the initial transient?
elif ((options.eco2_file != '') and not options.cpl_bypass):
basecase=basecase.replace('1850','20TR')
# ambient CO2 run
cmd_trns2 = basecmd+' --transtag aCO2 --finidat_case '+basecase+ \
' --finidat_year '+str(startyear)+' --run_startyear '+str(startyear)+' --run_units nyears ' \
+' --run_n '+str(ncycle)+' --align_year '+str(startyear)+ \
' --hist_nhtfrq '+options.hist_nhtfrq+' --hist_mfilt '+ \
options.hist_mfilt+' --no_build'+' --exeroot '+ad_exeroot + \
' --compset I20TR'+mycompset+' --nopointdata'
# elevated CO2 run
basecmd_eco2=basecmd.replace(options.co2_file,options.eco2_file)
cmd_trns3 = basecmd_eco2+' --transtag eCO2 --finidat_case '+basecase+ \
' --finidat_year '+str(startyear)+' --run_startyear '+str(startyear)+' --run_units nyears ' \
+' --run_n '+str(ncycle)+' --align_year '+str(startyear)+ \
' --hist_nhtfrq '+options.hist_nhtfrq+' --hist_mfilt '+ \
options.hist_mfilt+' --no_build'+' --exeroot '+ad_exeroot + \
' --compset I20TR'+mycompset+' --nopointdata'
#---------------------------------------------------------------------------------
#set site environment variable
os.environ['SITE']=site
basecase = site
if (mycaseid != ''):
basecase = mycaseid+'_'+site
runcmd('mkdir -p temp')
runcmd('mkdir -p scripts/'+myscriptsdir)
mymodel = 'ELM'
if ('clm5' in csmdir):
mymodel = 'CLM5'
#If not the first site, create point data here
if ((sitenum > 0) and not options.nopointdata):
print('\n\nCreating point data for '+site+'\n')
ptcmd = 'python makepointdata.py '+ \
' --site '+site+' --sitegroup '+options.sitegroup+ \
' --ccsm_input '+ccsm_input+' --model '+mymodel
if (options.nopftdyn):
ptcmd = ptcmd+' --nopftdyn'
if (int(options.mypft) >= 0):
ptcmd = ptcmd+' --pft '+str(options.mypft)
if (options.humhol):
ptcmd = ptcmd+' --humhol'
if (options.marsh):
ptcmd = ptcmd+' --marsh'
result = runcmd(ptcmd)
if (result > 0):
print('Site_fullrun: Error creating point data for '+site)
sys.exit(1)
#Build Cases
if (options.noad == False):
print('\n\nSetting up ad_spinup case\n')
if (sitenum == 0):
ad_case_firstsite = ad_case
result = runcmd(cmd_adsp)
else:
ptcmd = 'python case_copy.py --runroot '+runroot+' --case_copy '+ \
ad_case_firstsite+' --site_orig '+firstsite +\
' --site_new '+site+' --nyears '+str(ny_ad)+' --spin_cycle ' \
+str(endyear-startyear+1)
result = runcmd(ptcmd)
if (result > 0):
print('Site_fullrun: Error in runcase.py for ad_spinup ')
sys.exit(1)
else:
if (sitenum == 0):
ad_case_firstsite = ad_case
if (options.nofnsp == False):
print('\n\nSetting up final spinup case\n')
if (sitenum == 0):
fin_case_firstsite = ad_case_firstsite.replace('_ad_spinup','')
if (nutrients == 'CNP' and not options.ad_Pinit):
fin_case_firstsite = fin_case_firstsite.replace('1850CN','1850CNP')
print(cmd_fnsp+'\n')
result = os.system(cmd_fnsp)
else:
ptcmd = 'python case_copy.py --runroot '+runroot+' --case_copy '+ \
fin_case_firstsite+' --site_orig '+firstsite +\
' --site_new '+site+' --nyears '+str(ny_fin)
if (not options.sp):
ptcmd = ptcmd+' --finidat_year ' \
+str(int(ny_ad)+1)+' --spin_cycle '+str(endyear-startyear+1)
print(ptcmd)
result = os.system(ptcmd)
if (result > 0):
print('Site_fullrun: Error in runcase.py final spinup')
sys.exit(1)
else:
fin_case_firstsite = ad_case_firstsite.replace('_ad_spinup','')
if (nutrients == 'CNP' and not options.ad_Pinit):
fin_case_firstsite = fin_case_firstsite.replace('1850CN','1850CNP')
if (options.notrans == False):
print('\n\nSetting up transient case\n')
if (sitenum == 0):
if (options.crop):
tr_case_firstsite = fin_case_firstsite+'_trans'
else:
tr_case_firstsite = fin_case_firstsite.replace('1850','20TR')
result = runcmd(cmd_trns)
else:
ptcmd = 'python case_copy.py --runroot '+runroot+' --case_copy '+ \
tr_case_firstsite+' --site_orig '+firstsite +\
' --site_new '+site+' --finidat_year '+str(int(ny_fin)+1)+ \
' --nyears '+str(translen)
result = runcmd(ptcmd)
if ((options.cruncep or options.cruncepv8 or options.gswp3 or options.princeton) and not options.cpl_bypass):