sep run_DART dir per exp, prior t diff to assim t

config/clusters.py

@@ -17,6 +17,9 @@ class ClusterConfig(object):
     def scripts_rundir(self):
         return self.archivedir+'/DART-WRF/'
 
+    @property
+    def dartrundir(self):
+        return '/gpfs/data/fs71386/lkugler/run_DART/'+self.expname+'/'
 
 
 #######################################################################################
@@ -31,8 +34,8 @@ vsc.tmpfiledir = '/gpfs/data/fs71386/lkugler'
 vsc.userdir = '/home/fs71386/lkugler'
 vsc.srcdir = '/gpfs/data/fs71386/lkugler/compile/WRF/WRF-4.3/run'
 vsc.archive_base = '/gpfs/data/fs71386/lkugler/sim_archive/'
-vsc.dart_srcdir = '/home/fs71386/lkugler/DART/DART-9.11.9/models/wrf/work'
-vsc.dartrundir = '/gpfs/data/fs71386/lkugler/run_DART'
+vsc.dart_srcdir = '/gpfs/data/fs71386/lkugler/compile/DART/DART-9.11.9/models/wrf/work'
+vsc.rttov_srcdir = '/gpfs/data/fs71386/lkugler/compile/RTTOV13/rtcoef_rttov13/'
 vsc.scriptsdir = '/home/fs71386/lkugler/DART-WRF/scripts/'
 
 vsc.ideal = vsc.userdir+'/compile/bin/ideal-v4.2.2_v1.16.exe'
@@ -53,7 +56,6 @@ jet.userdir = '/jetfs/home/lkugler'
 jet.srcdir = '/jetfs/home/lkugler/compile/WRF/WRF-4.1.5/run'
 jet.scriptsdir = ''
 jet.archive_base = '/jetfs/home/lkugler/data_jetfs/sim_archive/'
-jet.dartrundir = '/jetfs/home/lkugler/DART-WRF/rundir'
 
 jet.ideal = jet.userdir+'/compile/bin/ideal.exe'
 jet.wrfexe = jet.userdir+'/compile/bin/wrf-v4.2_v1.10.dmpar.exe'

scheduler.py

@@ -11,9 +11,6 @@ from config.cfg import exp, cluster
 from scripts.utils import script_to_str, symlink
 
 
-# necessary to find modules in folder, since SLURM runs the script elsewhere
-sys.path.append(os.getcwd())
-
 # allow scripts to access the configuration
 # symlink(cluster.scriptsdir+'/../config', cluster.scriptsdir+'/config')
 
@@ -153,7 +150,7 @@ def run_ENS(begin, end, depends_on=None, first_minute=True):
     #           + begin.strftime('%Y-%m-%d_%H:%M'), depends_on=[id2])
     return id
 
-def assimilate(assim_time, prior_init_time,
+def assimilate(assim_time, prior_init_time, prior_valid_time,
                prior_path_exp=False, depends_on=None):
     """Creates observations from a nature run and assimilates them.
 
@@ -171,32 +168,23 @@ def assimilate(assim_time, prior_init_time,
     elif not isinstance(prior_path_exp, str):
         raise TypeError('prior_path_exp either str or False, is '+str(type(prior_path_exp)))
 
-    # prepare state of nature run, from which observation is sampled
-    #s = my_Slurm("prepNature", cfg_update=dict(time="2"))
-    #id = s.run(cluster.python+' '+cluster.scripts_rundir+'/prepare_nature.py '
-    #           +time.strftime('%Y-%m-%d_%H:%M'), depends_on=[depends_on])
 
-    # prepare prior model state
-    s = my_Slurm("preAssim", cfg_update=dict(time="2"))
-    id = s.run(cluster.python+' '+cluster.scripts_rundir+'/pre_assim.py '
-               +assim_time.strftime('%Y-%m-%d_%H:%M ')
-               +prior_init_time.strftime('%Y-%m-%d_%H:%M ')
-               +prior_path_exp, depends_on=[depends_on])
+    # # prepare prior model state
+    # s = my_Slurm("preAssim", cfg_update=dict(time="2"))
+    # id = s.run(cluster.python+' '+cluster.scripts_rundir+'/pre_assim.py '
+    #            +assim_time.strftime('%Y-%m-%d_%H:%M ')
+    #            +prior_init_time.strftime('%Y-%m-%d_%H:%M ')
+    #            +prior_valid_time.strftime('%Y-%m-%d_%H:%M ')
+    #            +prior_path_exp, depends_on=[depends_on])
 
-    # prepare nature run, generate observations
     s = my_Slurm("Assim", cfg_update={"nodes": "1", "ntasks": "96", "time": "60",
                              "mem": "300G", "ntasks-per-node": "96", "ntasks-per-core": "2"})
     id = s.run(cluster.python+' '+cluster.scripts_rundir+'/assim_synth_obs.py '
-               +assim_time.strftime('%Y-%m-%d_%H:%M'), depends_on=[id])
- 
-    # # actuall assimilation step
-    # s = my_Slurm("Assim", cfg_update=dict(nodes="1", ntasks="48", time="50", mem="200G"))
-    # cmd = 'cd '+cluster.dartrundir+'; mpirun -np 48 ./filter; rm obs_seq_all.out'
-    # id = s.run(cmd, depends_on=[id])
+               +assim_time.strftime('%Y-%m-%d_%H:%M ')
+               +prior_init_time.strftime('%Y-%m-%d_%H:%M ')
+               +prior_valid_time.strftime('%Y-%m-%d_%H:%M ')
+               +prior_path_exp, depends_on=[id])
  
-    # s = my_Slurm("archiveAssim", cfg_update=dict(time="10"))
-    # id = s.run(cluster.python+' '+cluster.scripts_rundir+'/archive_assim.py '
-    #            + assim_time.strftime('%Y-%m-%d_%H:%M'), depends_on=[id])
 
     s = my_Slurm("updateIC", cfg_update=dict(time="8"))
     id = s.run(cluster.python+' '+cluster.scripts_rundir+'/update_wrfinput_from_filteroutput.py '
@@ -224,7 +212,7 @@ def gen_obsseq(depends_on=None):
     return id
 
 def verify(depends_on=None):
-    s = my_Slurm("verify", cfg_update={"time": "180", "mail-type": "FAIL,END", 
+    s = my_Slurm("verify", cfg_update={"time": "240", "mail-type": "FAIL,END", 
                  "ntasks": "96",  "ntasks-per-node": "96", "ntasks-per-core": "2"})
     s.run(cluster.python_enstools+' '+cluster.userdir+'/osse_analysis/analyze_fc.py '+exp.expname+' has_node',
           depends_on=[depends_on])
@@ -252,11 +240,12 @@ if __name__ == "__main__":
     is_new_run = not start_from_existing_state
 
     if is_new_run:
-        init_time = dt.datetime(2008, 7, 30, 6)
+        init_time = dt.datetime(2008, 7, 30, 9)
         id = prepare_wrfinput(init_time)  # create initial conditions
+        id = wrfinput_insert_wbubble(depends_on=id)
 
         # spin up the ensemble
-        integration_end_time = dt.datetime(2008, 7, 30, 9)
+        integration_end_time = dt.datetime(2008, 7, 30, 14)
         id = run_ENS(begin=init_time,
                     end=integration_end_time,
                     first_minute=False,
@@ -264,34 +253,34 @@ if __name__ == "__main__":
         prior_path_exp = False  # for next assimilation
         
     elif start_from_existing_state:
-        init_time = dt.datetime(2008, 7, 30, 6)
-        id = prepare_wrfinput(init_time)  # create initial conditions
+        time = dt.datetime(2008, 7, 30, 11)
 
-        # get initial conditions from archive
-        integration_end_time = dt.datetime(2008, 7, 30, 10)
-        exppath_arch = '/gpfs/data/fs71386/lkugler/sim_archive/exp_v1.16_P1_40mem'
-        id = update_wrfinput_from_archive(integration_end_time, init_time, exppath_arch, depends_on=id)
+        # prior init time
+        init_time = dt.datetime(2008, 7, 30, 6)
+        #prior_path_exp = '/gpfs/data/fs71386/lkugler/sim_archive/exp_v1.16_Pwbub_40mem'
+        #prior_path_exp = '/gpfs/data/fs71386/lkugler/sim_archive/exp_v1.18_Pwbub-1-ensprof_40mem'
+        prior_path_exp = '/gpfs/data/fs71386/lkugler/sim_archive/exp_v1.16_P1_40mem'
+        #id = update_wrfinput_from_archive(integration_end_time, init_time, prior_path_exp, depends_on=id)
         #id = wrfinput_insert_wbubble(depends_on=id)
-        prior_path_exp = exppath_arch  # for next assimilation
 
     # values for assimilation
-    time = integration_end_time
-    assim_time = integration_end_time
+    assim_time = time
     prior_init_time = init_time
 
-    while time <= dt.datetime(2008, 7, 30, 10, 30):
+    while time <= dt.datetime(2008, 7, 30, 11):
 
         id = assimilate(assim_time,
                         prior_init_time, 
+                        prior_valid_time=time+dt.timedelta(hours=2),
                         prior_path_exp=prior_path_exp,
                         depends_on=id)
-        prior_path_exp = False  # use own exp path
+        prior_path_exp = False  # use own exp path as prior
 
         # integration
         this_forecast_init = assim_time  # start integration from here
 
         timedelta_integrate = timedelta_btw_assim
-        if this_forecast_init.minute in [30, 0]:  # longer forecast every full hour
+        if this_forecast_init.minute in [0,30]:  # longer forecast every full hour
             timedelta_integrate = dt.timedelta(hours=2)
 
         this_forecast_end = assim_time + timedelta_integrate
@@ -311,4 +300,3 @@ if __name__ == "__main__":
 
     id = gen_obsseq(id)
     verify(id)
-    # copy to jet

scripts/apply_obs_op_dart.py

@@ -38,7 +38,7 @@ if __name__ == '__main__':
     # prepare dummy nature (this Hx is irrelevant)
     os.chdir(cluster.dartrundir)
     os.system('cp ./advance_temp1/wrfout_d01 ./wrfout_d01')
-    wrfout_add_geo.run(cluster.dartrundir+'/geo_em.d01.nc',
+    wrfout_add_geo.run(cluster.dartrundir+'/../geo_em.d01.nc',
                         cluster.dartrundir+'/wrfout_d01')
     aso.run_perfect_model_obs()
     aso.assimilate(nproc=96)

scripts/assim_synth_obs.py

@@ -109,44 +109,6 @@ def replace_errors_obsseqout(f, new_errors):
     print('replaced obs errors in', f)
 
 
-def set_DART_nml_singleobstype(sat_channel=False, cov_loc_radius_km=32, cov_loc_vert_km=False,
-                 just_prior_values=False):
-    """this function is outdated and will not work"""
-    cov_loc_radian = cov_loc_radius_km/earth_radius_km
-    
-    if just_prior_values:
-        template = cluster.scriptsdir+'/../templates/input.eval.nml'
-    else:
-        template = cluster.scriptsdir+'/../templates/input.nml'
-    copy(template, cluster.dartrundir+'/input.nml')
-
-    # options are overwritten with settings
-    options = {'<n_ens>': str(int(exp.n_ens)),
-               '<cov_loc_radian>': str(cov_loc_radian)}
-
-    if cov_loc_vert_km:
-        vert_norm_rad = earth_radius_km*cov_loc_vert_km/cov_loc_radius_km*1000
-        options['<horiz_dist_only>'] = '.false.'
-        options['<vert_norm_hgt>'] = str(vert_norm_rad)
-    else:
-        options['<horiz_dist_only>'] = '.true.'
-        options['<vert_norm_hgt>'] = '50000.0'  # dummy value
-
-    for key, value in options.items():
-        sed_inplace(cluster.dartrundir+'/input.nml', key, value)
-
-    # input.nml for RTTOV
-    if sat_channel > 0:
-        if sat_channel in [1, 2, 3, 12]:  # VIS channels
-            rttov_nml = cluster.scriptsdir+'/../templates/obs_def_rttov.VIS.nml'
-        else:  # IR channels
-            rttov_nml = cluster.scriptsdir+'/../templates/obs_def_rttov.IR.nml'
-        append_file(cluster.dartrundir+'/input.nml', rttov_nml)
-    else:
-        # append any rttov segment, needs to exist anyway
-        rttov_nml = cluster.scriptsdir+'/../templates/obs_def_rttov.IR.nml'
-        append_file(cluster.dartrundir+'/input.nml', rttov_nml)
-
 def set_DART_nml(just_prior_values=False):
 
     def to_radian_horizontal(cov_loc_horiz_km):
@@ -208,10 +170,6 @@ def obs_operator_ensemble():
         # DART may need a wrfinput file as well, which serves as a template for dimension sizes
         symlink(cluster.dartrundir+'/wrfout_d01', cluster.dartrundir+'/wrfinput_d01')
         
-        # I dont think this is necessary, we do this already in pre_assim.py
-        # add geodata, if istage>0, wrfout is DART output (has coords)
-        #if istage == 0:
-        #    wrfout_add_geo.run(cluster.dartrundir+'/geo_em.d01.nc', cluster.dartrundir+'/wrfout_d01')
 
         # run perfect_model obs (forward operator)
         os.system('mpirun -np 12 ./perfect_model_obs > /dev/null')
@@ -247,7 +205,70 @@ def link_nature_to_dart_truth(time):
 def prepare_nature_dart(time):
     print('linking nature to DART & georeferencing')
     link_nature_to_dart_truth(time)
-    wrfout_add_geo.run(cluster.dartrundir+'/geo_em.d01.nc', cluster.dartrundir+'/wrfout_d01')
+    wrfout_add_geo.run(cluster.dartrundir+'/../geo_em.d01.nc', cluster.dartrundir+'/wrfout_d01')
+
+
+def prepare_prior_ensemble(assim_time, prior_init_time, prior_valid_time, prior_path_exp):
+    """Prepares DART files for running filter 
+    i.e.
+    - links first guess state to DART first guess filenames
+    - creates wrfinput_d01 files
+    - adds geo-reference (xlat,xlon) coords so that DART can deal with the files
+    - writes txt files so DART knows what input and output is
+    - removes probably pre-existing files which could lead to problems
+    """
+    os.makedirs(cluster.dartrundir, exist_ok=True)
+
+    print('prepare prior state estimate')
+    for iens in range(1, exp.n_ens+1):
+        print('link wrfout file to DART background file')
+        wrfout_run = prior_path_exp \
+                    +prior_init_time.strftime('/%Y-%m-%d_%H:%M/')  \
+                    +str(iens) \
+                    +prior_valid_time.strftime('/wrfout_d01_%Y-%m-%d_%H:%M:%S')
+        dart_ensdir = cluster.dartrundir+'/advance_temp'+str(iens)
+        wrfout_dart = dart_ensdir+'/wrfout_d01'
+
+        os.makedirs(dart_ensdir, exist_ok=True)
+        print('copy', wrfout_run, 'to', wrfout_dart)
+        copy(wrfout_run, wrfout_dart)
+        symlink(wrfout_dart, dart_ensdir+'/wrfinput_d01')
+
+        # ensure prior time matches assim time (can be off intentionally)
+        if assim_time != prior_valid_time:
+            print('overwriting time in prior from nature wrfout')
+            os.system(cluster.ncks+' -A -v XTIME '
+                      +cluster.dartrundir+'/wrfout_d01 '+wrfout_dart)
+
+        # this seems to be necessary (else wrong level selection)
+        wrfout_add_geo.run(cluster.dartrundir+'/../geo_em.d01.nc', wrfout_dart) 
+
+    fpath = cluster.dartrundir+'/input_list.txt'
+    print('writing', fpath)
+    try_remove(fpath)
+    with open(fpath, 'w') as f:
+        for iens in range(1, exp.n_ens+1):
+            f.write('./advance_temp'+str(iens)+'/wrfout_d01')
+            f.write('\n')
+
+    fpath = cluster.dartrundir+'/output_list.txt'
+    print('writing', fpath)
+    try_remove(fpath)
+    with open(fpath, 'w') as f:
+        for iens in range(1, exp.n_ens+1):
+            f.write('./filter_restart_d01.'+str(iens).zfill(4))
+            f.write('\n')
+
+
+    print('removing preassim and filter_restart')
+    os.system('rm -rf '+cluster.dartrundir+'/preassim_*')
+    os.system('rm -rf '+cluster.dartrundir+'/filter_restart*')
+    os.system('rm -rf '+cluster.dartrundir+'/output_mean*')
+    os.system('rm -rf '+cluster.dartrundir+'/output_sd*')
+    os.system('rm -rf '+cluster.dartrundir+'/perfect_output_*')
+    os.system('rm -rf '+cluster.dartrundir+'/obs_seq.fina*')
+
+    os.system(cluster.python+' '+cluster.scriptsdir+'/link_rttov.py')
 
 
 def calc_obserr_WV73(Hx_nature, Hx_prior):
@@ -269,6 +290,7 @@ def calc_obserr_WV73(Hx_nature, Hx_prior):
 def run_perfect_model_obs():
     print('generating observations - running ./perfect_model_obs')
     os.chdir(cluster.dartrundir)
+
     try_remove(cluster.dartrundir+'/obs_seq.out')
     if not os.path.exists(cluster.dartrundir+'/obs_seq.in'):
         raise RuntimeError('obs_seq.in does not exist in '+cluster.dartrundir)
@@ -286,30 +308,31 @@ def assimilate(nproc=96):
     os.system('mpirun -genv I_MPI_PIN_PROCESSOR_LIST=0-'+str(int(nproc)-1)+' -np '+str(int(nproc))+' ./filter > log.filter')
     print('./filter took', int(time_module.time()-t), 'seconds')
 
-def recycle_output():
-    """Use output of assimilation (./filter) as input for another assimilation (with ./filter)
-    Specifically, this copies the state fields from filter_restart_d01.000x to the wrfout files in advance_temp folders"""
-    update_vars = ['U', 'V', 'T', 'PH', 'MU', 'QVAPOR', 'QCLOUD', 'QICE', 'QRAIN', 'U10', 'V10', 'T2', 'Q2', 'TSK', 'PSFC', 'CLDFRA']
-    updates = ','.join(update_vars)
+# currently unused
+# def recycle_output():
+#     """Use output of assimilation (./filter) as input for another assimilation (with ./filter)
+#     Specifically, this copies the state fields from filter_restart_d01.000x to the wrfout files in advance_temp folders"""
+#     update_vars = ['U', 'V', 'T', 'PH', 'MU', 'QVAPOR', 'QCLOUD', 'QICE', 'QRAIN', 'U10', 'V10', 'T2', 'Q2', 'TSK', 'PSFC', 'CLDFRA']
+#     updates = ','.join(update_vars)
 
-    print('recycle DART output to be used as input')
-    for iens in range(1, exp.n_ens+1):
-        dart_output = cluster.dartrundir+'/filter_restart_d01.'+str(iens).zfill(4)
-        dart_input = cluster.dartrundir+'/advance_temp'+str(iens)+'/wrfout_d01'
+#     print('recycle DART output to be used as input')
+#     for iens in range(1, exp.n_ens+1):
+#         dart_output = cluster.dartrundir+'/filter_restart_d01.'+str(iens).zfill(4)
+#         dart_input = cluster.dartrundir+'/advance_temp'+str(iens)+'/wrfout_d01'
 
-        #print('check for non-monotonic vertical pressure')
+#         #print('check for non-monotonic vertical pressure')
 
-        # convert link to file in order to be able to update the content
-        if os.path.islink(dart_input):
-            l = os.readlink(dart_input)
-            os.remove(dart_input)
-            copy(l, dart_input) 
+#         # convert link to file in order to be able to update the content
+#         if os.path.islink(dart_input):
+#             l = os.readlink(dart_input)
+#             os.remove(dart_input)
+#             copy(l, dart_input) 
 
-        # print('move DART output to input: '+dart_output+' -> '+dart_input)
-        # os.rename(dart_output, dart_input)  # probably doesnt work
+#         # print('move DART output to input: '+dart_output+' -> '+dart_input)
+#         # os.rename(dart_output, dart_input)  # probably doesnt work
 
-        print('updating', updates, 'in', dart_input, 'from', dart_output)
-        os.system(cluster.ncks+' -A -v '+updates+' '+dart_output+' '+dart_input)
+#         print('updating', updates, 'in', dart_input, 'from', dart_output)
+#         os.system(cluster.ncks+' -A -v '+updates+' '+dart_output+' '+dart_input)
 
 ############### archiving
 
@@ -388,18 +411,25 @@ if __name__ == "__main__":
     - x_ensemble is already linked for DART to advance_temp<iens>/wrfout_d01
 
     Example call:
-    python assim.py 2008-08-07_12:00
+    python assim.py 2008-08-07_12:00 2008-08-06:00 2008-08-07_13:00 /home/fs71386/lkugler/data/sim_archive/exp_v1.18_Pwbub-1-ensprof_40mem
     """
 
     time = dt.datetime.strptime(sys.argv[1], '%Y-%m-%d_%H:%M')
-    archive_time = cluster.archivedir+time.strftime('/%Y-%m-%d_%H:%M/')
+    prior_init_time = dt.datetime.strptime(sys.argv[2], '%Y-%m-%d_%H:%M')
+    prior_valid_time = dt.datetime.strptime(sys.argv[3], '%Y-%m-%d_%H:%M')
+    prior_path_exp = str(sys.argv[4])
 
+    archive_time = cluster.archivedir+time.strftime('/%Y-%m-%d_%H:%M/')
     os.chdir(cluster.dartrundir)
-    os.system('rm -f obs_seq.in obs_seq.out obs_seq.final')  # remove any existing observation files
+    os.system('rm -f input.nml obs_seq.in obs_seq.out obs_seq.final')  # remove any existing observation files
+    set_DART_nml()
 
-    print('create obs_seq.in from config')
+    print('prepare nature')
     prepare_nature_dart(time)  # link WRF files to DART directory
 
+    print('prepare prior ensemble')
+    prepare_prior_ensemble(time, prior_init_time, prior_valid_time, prior_path_exp)
+
     ################################################
     print(' 1) get the assimilation errors in a single vector ')
     error_assimilate = []  

scripts/create_obsseq.py

@@ -131,7 +131,7 @@ def calc_obs_locations(n_obs, coords_from_domaincenter=True,
         so that the assimilation increments are zero on the boundary
         distance to boundary = 1.5x localization-radius
         """
-        fcoords = cluster.dartrundir+'/geo_em.d01.nc'
+        fcoords = cluster.dartrundir+'/../geo_em.d01.nc'
         import xarray as xr
         ds = xr.open_dataset(fcoords)
 

scripts/pre_assim.py

 import os, sys, shutil
 import datetime as dt
 from config.cfg import exp, cluster
-from utils import symlink, copy_scp_srvx8, copy, sed_inplace
+from utils import symlink, copy_scp_srvx8, copy, sed_inplace, try_remove
 import wrfout_add_geo
 
-def run(assim_time, background_init_time, exppath_firstguess):
+def run(assim_time, prior_init_time, prior_valid_time, prior_path_exp)
     """Prepares DART files for running filter 
     i.e.
     - links first guess state to DART first guess filenames
@@ -13,28 +13,35 @@ def run(assim_time, background_init_time, exppath_firstguess):
     - writes txt files so DART knows what input and output is
     - removes probably pre-existing files which could lead to problems
     """
+    os.makedirs(cluster.dartrundir, exist_ok=True)
 
     print('prepare prior state estimate')
     for iens in range(1, exp.n_ens+1):
-        #wrfout_run = cluster.wrf_rundir(iens) + time.strftime('/wrfout_d01_%Y-%m-%d_%H:%M:%S')
-
         print('link wrfout file to DART background file')
-        wrfout_run = exppath_firstguess+background_init_time.strftime('/%Y-%m-%d_%H:%M/')  \
-                    +str(iens)+assim_time.strftime('/wrfout_d01_%Y-%m-%d_%H:%M:%S')
+        wrfout_run = prior_path_exp \
+                    +prior_init_time.strftime('/%Y-%m-%d_%H:%M/')  \
+                    +str(iens) \
+                    +prior_valid_time.strftime('/wrfout_d01_%Y-%m-%d_%H:%M:%S')
         dart_ensdir = cluster.dartrundir+'/advance_temp'+str(iens)
         wrfout_dart = dart_ensdir+'/wrfout_d01'
 
         os.makedirs(dart_ensdir, exist_ok=True)
-        print('linking', wrfout_run, 'to', wrfout_dart)
-        symlink(wrfout_run, wrfout_dart)
+        print('copy', wrfout_run, 'to', wrfout_dart)
+        copy(wrfout_run, wrfout_dart)
         symlink(wrfout_dart, dart_ensdir+'/wrfinput_d01')
 
+        # ensure prior time matches assim time (can be off intentionally)
+        if assim_time != prior_valid_time:
+            print('overwriting time in prior from nature wrfout')
+            os.system(cluster.ncks+' -A -v XTIME '
+                      +cluster.dartrundir+'/wrfout_d01 '+wrfout_dart)
+
         # this seems to be necessary (else wrong level selection)
-        wrfout_add_geo.run(cluster.dartrundir+'/geo_em.d01.nc', wrfout_dart) 
+        wrfout_add_geo.run(cluster.dartrundir+'/../geo_em.d01.nc', wrfout_dart) 
 
     fpath = cluster.dartrundir+'/input_list.txt'
     print('writing', fpath)
-    os.remove(fpath)
+    try_remove(fpath)
     with open(fpath, 'w') as f:
         for iens in range(1, exp.n_ens+1):
             f.write('./advance_temp'+str(iens)+'/wrfout_d01')
@@ -42,7 +49,7 @@ def run(assim_time, background_init_time, exppath_firstguess):
 
     fpath = cluster.dartrundir+'/output_list.txt'
     print('writing', fpath)
-    os.remove(fpath)
+    try_remove(fpath)
     with open(fpath, 'w') as f:
         for iens in range(1, exp.n_ens+1):
             f.write('./filter_restart_d01.'+str(iens).zfill(4))
@@ -62,7 +69,8 @@ def run(assim_time, background_init_time, exppath_firstguess):
 
 if __name__ == '__main__':
     assim_time = dt.datetime.strptime(sys.argv[1], '%Y-%m-%d_%H:%M')
-    background_init_time = dt.datetime.strptime(sys.argv[2], '%Y-%m-%d_%H:%M')
-    exppath_firstguess = str(sys.argv[3])
+    prior_init_time = dt.datetime.strptime(sys.argv[2], '%Y-%m-%d_%H:%M')
+    prior_valid_time = dt.datetime.strptime(sys.argv[3], '%Y-%m-%d_%H:%M')
+    prior_path_exp = str(sys.argv[4])
 
-    run(assim_time, background_init_time, exppath_firstguess)
+    run(assim_time, prior_init_time, prior_valid_time, prior_path_exp)