#!/usr/bin/env python3 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)