Allow running on NERSC debug queue, but don't use DEBUG build option

Temporary fix for using CRUNCEPv7

global_fullrun.py

@@ -23,7 +23,7 @@
                   help="Perform a clean build")
 parser.add_option("--compiler", dest="compiler", default = '', \
                   help = "compiler to use (pgi*, gnu)")
-parser.add_option("--debug", dest="debug", default=False, \
+parser.add_option("--debugq", dest="debug", default=False, \
                  action="store_true", help='Use debug queue and options')
 parser.add_option("--dailyrunoff", dest="dailyrunoff", default=False, \
                  action="store_true", help="Write daily output for hydrology")
@@ -123,6 +123,8 @@
                   help = 'To turn on CN with CLM4me', action="store_true")
 parser.add_option("--cruncep", dest="cruncep", default=False, \
                   action="store_true", help = 'Use CRU-NCEP meteorology')
+parser.add_option("--cruncepv7", dest="cruncepv7", default=False, \
+                  help = "use cru-ncep data", action="store_true")
 parser.add_option("--cplhist", dest="cplhist", default=False, \
                   help= "use CPLHIST forcing", action="store_true")
 parser.add_option("--gswp3", dest="gswp3", default=False, \
@@ -237,7 +239,7 @@ def get_regional_bounds(myregion):
     ccsm_input = '/lustre/or-hydra/cades-ccsi/proj-shared/project_acme/ACME_inputdata/'
 elif (options.machine == 'edison' or 'cori' in options.machine):
     ccsm_input = '/project/projectdirs/acme/inputdata'
-
+print options.machine
 #default compilers
 if (options.compiler == ''):
     if (options.machine == 'titan' or options.machine == 'metis'):
@@ -289,18 +291,23 @@ def get_regional_bounds(myregion):
     caseroot = os.path.abspath(options.caseroot)
 
 
-if (options.cruncep or options.gswp3 or options.princeton):
+if (options.cruncep or options.cruncepv7 or options.gswp3 or options.princeton):
     startyear = 1901
     endyear = 1920
-    site_endyear = 2010
+    if (options.cruncep):
+       site_endyear = 2013
+    elif (options.cruncepv7):
+       site_endyear = 2016   
+    elif (options.gswp3):
+       site_endyear = 2010
+    elif (options.princeton):
+       site_endyear = 2012
     if (options.livneh):
         startyear = 1950
         endyear = 1969
-        site_endyear = 2013
     if (options.daymet):
         startyear = 1980
         endyear = 2010
-        site_endyear = 2010
 else:
     #Qian input data
     startyear = 1948
@@ -318,7 +325,7 @@ def get_regional_bounds(myregion):
 
 if (translen == -1):
     translen = endyear-1850+1        #length of transient run
-    if (options.cpl_bypass and (options.cruncep or options.gswp3 or options.princeton)):
+    if (options.cpl_bypass and (options.cruncep or options.cruncepv7 or options.gswp3 or options.princeton)):
         translen = site_endyear-1850+1
 
 fsplen = int(ny_fin)
@@ -374,7 +381,7 @@ def get_regional_bounds(myregion):
 if (options.C14):
     basecmd = basecmd+' --C14 '
 if (options.debug):
-    basecmd = basecmd+' --debug'
+    basecmd = basecmd+' --debugq'
 if (options.monthly_metdata != ''):
     basecmd = basecmd+' --monthly_metdata '+options.monthly_metdata
 if (options.nofire):
@@ -397,6 +404,8 @@ def get_regional_bounds(myregion):
     basecmd = basecmd+' --CH4'
 if (options.cruncep):
     basecmd = basecmd+' --cruncep'
+if (options.cruncepv7):
+    basecmd = basecmd+' --cruncepv7'
 if (options.gswp3):
     basecmd = basecmd+' --gswp3'
 if (options.princeton):
@@ -527,7 +536,7 @@ def get_regional_bounds(myregion):
     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):
+if ((options.cruncep or options.gswp3 or options.cruncepv7) and not options.cpl_bypass):
     basecase=basecase.replace('1850','20TR')+'_phase1'
     thistranslen = site_endyear - 1921 + 1
     cmd_trns2 = basecmd+' --trans2 --finidat_case '+basecase+ \
@@ -552,7 +561,7 @@ def get_regional_bounds(myregion):
 if (options.notrans == False):
     print('\nSetting up transient case\n')
     os.system(cmd_trns)
-if ((options.cruncep or options.gswp3) and not options.cpl_bypass):
+if ((options.cruncep or options.gswp3 or options.cruncepv7) and not options.cpl_bypass):
     print('\nSetting up transient case phase 2\n')
     os.system(cmd_trns2)
 
@@ -605,6 +614,8 @@ def get_regional_bounds(myregion):
             if ("perl" in s or "python" in s):
                 timestr=str(int(float(options.walltime)))+':'+str(int((float(options.walltime)- \
                             int(float(options.walltime)))*60))+':00'
+                if (options.debug):
+                    timestr='00:30:00'
                 output.write("#!/bin/csh -f\n")
                 if (mysubmit_type == 'qsub'):
                     output.write('#PBS -l walltime='+timestr+'\n')

runcase.py

@@ -29,8 +29,8 @@
                  action="store_true", help="Write daily output for hydrology")
 parser.add_option("--diags", dest="diags", default=False, \
                  action="store_true", help="Write special outputs for diagnostics")
-parser.add_option("--debug", dest="debug", default=False, \
-                 action="store_true", help='Use debug queue and options')
+parser.add_option("--debugq", dest="debug", default=False, \
+                 action="store_true", help='Use debug queue')
 parser.add_option("--runroot", dest="runroot", default="", \
                   help="Directory where the run would be created")
 parser.add_option('--project', dest='project',default='', \
@@ -69,6 +69,8 @@
                          "Currently supports ONLY *CLM45(CN) compsets")
 parser.add_option("--cruncep", dest="cruncep", default=False, \
                   help = "use cru-ncep data", action="store_true")
+parser.add_option("--cruncepv7", dest="cruncepv7", default=False, \
+                  help = "use cru-ncep data", action="store_true")
 parser.add_option("--cplhist", dest="cplhist", default=False, \
                   help= "use CPLHIST forcing", action="store_true")
 parser.add_option("--gswp3", dest="gswp3", default=False, \
@@ -81,7 +83,7 @@
                   action="store_true", help = "Daymet correction to GSWP3 precip (CONUS only)")
 parser.add_option("--machine", dest="machine", default = '', \
                   help = "machine to\n")
-parser.add_option("--compiler", dest="compiler", default='gnu', \
+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)")
@@ -405,7 +407,7 @@
 
 #CRU-NCEP 2 transient phases
 if ('CRU' in compset or options.cruncep or options.gswp3 or \
-            options.princeton or options.cplhist):
+            options.cruncepv7 or options.princeton or options.cplhist):
     use_reanalysis = True
 else:
     use_reanalysis = False
@@ -673,13 +675,15 @@
 
 #create new case
 cmd = './create_newcase --case '+casename+' --mach '+options.machine+' --compset '+ \
-	   options.compset+' --res '+options.res+' --compiler '+options.compiler+' --mpilib '+ \
+	   options.compset+' --res '+options.res+' --mpilib '+ \
            options.mpilib+' > create_newcase.log'+' --walltime '+str(options.walltime)+ \
           ':00:00'
 if (options.mymodel == 'CLM5'):
    cmd = cmd+' --run-unsupported'
 if (options.project != ''):
    cmd = cmd+' --project '+options.project
+if (options.compiler != ''):
+   cmd = cmd+' --compiler '+options.compiler
 resut = os.system(cmd)
 
 if (os.path.isdir(casename)):
@@ -696,13 +700,13 @@
 result = os.system('./xmlchange EXEROOT='+exeroot)
 if (options.mymodel == 'ELM'):
     result = os.system('./xmlchange MOSART_MODE=NULL')
-if (options.debug):
-    result = os.system('./xmlchange DEBUG=TRUE')
+#if (options.debug):
+#    result = os.system('./xmlchange DEBUG=TRUE')
 
 #clm 4_5 cn config options
-clmcn_opts = "'-phys clm4_5'"
-if (options.mymodel == 'ELM'):
-    os.system("./xmlchange CLM_CONFIG_OPTS="+clmcn_opts)
+#clmcn_opts = "'-phys clm4_5 -cppdefs -DMODAL_AER'"
+#if (options.mymodel == 'ELM'):
+#    os.system("./xmlchange CLM_CONFIG_OPTS="+clmcn_opts)
 
 if (options.machine == 'userdefined'):
     os.system("./xmlchange COMPILER="+options.compiler)
@@ -889,8 +893,13 @@
         if (options.ad_spinup):
             output.write(" hist_mfilt = "+str(options.hist_mfilt)+", "+str(options.hist_mfilt)+"\n")
         else:
-            if (options.dailyrunoff or options.dailyvars):
+            if (options.dailyrunoff):
+                #include daily variables related to runoff only
                 output.write(" hist_mfilt = "+ str(options.hist_mfilt)+",365\n")
+            if (options.dailyvars):
+                #include daily column and PFT level output
+                output.write(" hist_dov2xy = .true., .true., .false.\n")
+                output.write(" hist_mfilt = "+ str(options.hist_mfilt)+",365,365\n")
             else:
                 output.write(" hist_mfilt = "+ str(options.hist_mfilt)+"\n")
 
@@ -899,13 +908,17 @@
             output.write(" hist_nhtfrq = "+ str(options.hist_nhtfrq)+", "+str(options.hist_nhtfrq)+"\n")
         else:
             if (options.dailyvars):
-                output.write(" hist_nhtfrq = "+ str(options.hist_nhtfrq)+",-24\n")
+                output.write(" hist_nhtfrq = "+ str(options.hist_nhtfrq)+",-24,-24\n")
                 h1varst = "fincl2 = "
+                h2varst = "fincl3 = "
                 for v in var_list_hourly:
                     h1varst = h1varst+"'"+v+"',"
                 for v in var_list_daily:
                     h1varst = h1varst+"'"+v+"',"
-                output.write(h1varst+"\n")
+                for v in var_list_pft:
+                    h2varst = h2varst+"'"+v+"',"
+                output.write(h1varst[:-1]+"\n")
+                output.write(h2varst[:-1]+"\n")
             elif (options.dailyrunoff):
                 output.write(" hist_nhtfrq = "+ str(options.hist_nhtfrq)+",-24\n")
                 output.write(" hist_fincl2 = 'TBOT','QBOT','RAIN','SNOW','QBOT','PBOT','WIND','FPSN','QVEGT'," \
@@ -1046,7 +1059,12 @@
             output.write(" spinup_mortality_factor = 10\n")
     if (cpl_bypass):
         if (use_reanalysis):
-            if (options.cruncep):
+            if (options.cruncepv7):
+                    output.write(" metdata_type = 'cru-ncep'\n")
+                    output.write(" metdata_bypass = '"+options.ccsm_input+"/atm/datm7/" \
+                         +"atm_forcing.datm7.cruncep_qianFill.0.5d.V7.c160715" + \
+                         "/cpl_bypass_full'\n")
+            elif (options.cruncep):
                 if (options.livneh):
                     output.write(" metdata_type = 'cru-ncep_livneh'\n")
                     output.write(" metdata_bypass = '"+options.ccsm_input+"/atm/datm7/" \
@@ -1217,7 +1235,7 @@
         elif ('streams' in s):
             continue  #do nothing
         elif ('taxmode' in s):
-            if (options.cruncep):
+            if (options.cruncep or options.cruncepv7):
                 taxst = "taxmode = 'cycle', 'cycle', 'cycle', 'extend', 'extend'"
             else:
                 taxst = "taxmode = 'cycle', 'extend', 'extend'"
@@ -1352,6 +1370,8 @@
         output_run  = open(PTCLMdir+'/scripts/'+myscriptsdir+'/ensemble_run_'+casename+'.pbs','w')
         timestr=str(int(float(options.walltime)))+':'+str(int((float(options.walltime)- \
                                      int(float(options.walltime)))*60))+':00'
+        if (options.debug):
+           timestr='00:30:00'
         output_run.write("#!/bin/csh -f\n")
         if (mysubmit_type == 'qsub'):
             output_run.write('#PBS -l walltime='+timestr+'\n')

site_fullrun.py

@@ -25,11 +25,11 @@
                   help="Perform a clean build")
 parser.add_option("--model_root", dest="csmdir", default='', \
                   help = "base CESM directory")
-parser.add_option("--compiler", dest="compiler", default = 'gnu', \
+parser.add_option("--compiler", dest="compiler", default = '', \
                   help = "compiler to use (pgi*, gnu)")
 parser.add_option("--diags", dest="diags", default=False, \
                  action="store_true", help="Write special outputs for diagnostics")
-parser.add_option("--debug", dest="debug", default=False, \
+parser.add_option("--debugq", dest="debug", default=False, \
                  action="store_true", help='Use debug queue and options')
 parser.add_option("--hist_mfilt_trans", dest="hist_mfilt", default="365", \
                   help = 'number of output timesteps per file (transient only)')
@@ -210,13 +210,13 @@ def submit(fname, project='', submit_type='qsub', job_depend=''):
 elif (options.machine == 'edison' or 'cori' in options.machine):
     ccsm_input = '/project/projectdirs/acme/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'
+#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
@@ -375,7 +375,7 @@ def submit(fname, project='', submit_type='qsub', job_depend=''):
         if (options.C14):
             basecmd = basecmd+' --C14 '
         if (options.debug):
-            basecmd = basecmd+' --debug'
+            basecmd = basecmd+' --debugq'
         if (options.ninst > 1):
             basecmd = basecmd+' --ninst '+str(options.ninst)
         if (options.nofire):
@@ -419,7 +419,8 @@ def submit(fname, project='', submit_type='qsub', job_depend=''):
         basecmd = basecmd + ' --np '+str(options.np)
         basecmd = basecmd + ' --tstep '+str(options.tstep)
         basecmd = basecmd + ' --co2_file '+options.co2_file
-        basecmd = basecmd + ' --compiler '+options.compiler
+        if (options.compiler != ''):
+            basecmd = basecmd + ' --compiler '+options.compiler
         basecmd = basecmd + ' --mpilib '+options.mpilib
         basecmd = basecmd+' --caseroot '+caseroot
         basecmd = basecmd+' --runroot '+runroot
@@ -648,7 +649,8 @@ def submit(fname, project='', submit_type='qsub', job_depend=''):
             case_list.append('ad_spinup')
             case_list.append('iniadjust')
         case_list.append('fn_spinup')
-        case_list.append('spinup_diags')
+        if (options.diags):
+            case_list.append('spinup_diags')
         if (options.notrans == False):
             case_list.append('transient')
             if (options.diags):
@@ -674,6 +676,8 @@ def submit(fname, project='', submit_type='qsub', job_depend=''):
                         output.write("#!/bin/csh -f\n")
                         timestr=str(int(float(options.walltime)))+':'+str(int((float(options.walltime)- \
                                      int(float(options.walltime)))*60))+':00'
+                        if (options.debug):
+                            timestr = '00:30:00'
                         if (mysubmit_type == 'qsub'):
                             output.write('#PBS -l walltime='+timestr+'\n')
                         else: