explicitly load modules

config/jet.py

@@ -55,7 +55,7 @@ cluster.python_verif = '/jetfs/home/lkugler/miniconda3/envs/enstools/bin/python'
 cluster.ncks = '/jetfs/spack/opt/spack/linux-rhel8-skylake_avx512/intel-2021.7.1/nco-5.1.0-izrhxv24jqco5epjhf5ledsqwanojc5m/bin/ncks'
 cluster.ideal = '/jetfs/home/lkugler/bin/ideal-v4.3_v1.22.exe'
 cluster.wrfexe = '/jetfs/home/lkugler/bin/wrf-v4.3_v1.22_ifort_20230413.exe'
-cluster.container = ''
+cluster.dart_modules = 'module purge; module load netcdf-fortran/4.5.3-gcc-8.5.0-qsqbozc;'
 
 # paths for data output
 cluster.wrf_rundir_base = '/jetfs/home/lkugler/data/run_WRF/'  # path for temporary files

config/srvx1.py

@@ -53,7 +53,6 @@ cluster.python_verif = '/users/staff/lkugler/miniconda3/bin/python'
 cluster.ncks = '/home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/nco-5.0.1-ntu44aoxlvwtr2tsrobfr4lht7cpvccf/bin/ncks'
 cluster.ideal = '' #/jetfs/home/lkugler/bin/ideal-v4.3_v1.22.exe'
 cluster.wrfexe = '' #/jetfs/home/lkugler/bin/wrf-v4.3_v1.22.exe'
-cluster.container = ''
 
 # paths for data output
 cluster.wrf_rundir_base = utils.userhome+'/AdvDA23/run_WRF/'  # path for temporary files

dartwrf/assim_synth_obs.py

@@ -169,7 +169,7 @@ def run_perfect_model_obs(nproc=12, verbose=True):
     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)
-    shell('mpirun -np '+str(nproc)+' '+cluster.container+" ./perfect_model_obs > log.perfect_model_obs")
+    shell(cluster.dart_modules+' mpirun -np '+str(nproc)+" ./perfect_model_obs > log.perfect_model_obs")
     if not os.path.exists(cluster.dartrundir + "/obs_seq.out"):
         raise RuntimeError(
             "obs_seq.out does not exist in " + cluster.dartrundir,
@@ -182,9 +182,9 @@ def filter(nproc=12):
     try_remove(cluster.dartrundir + "/obs_seq.final")
     t = time_module.time()
     if nproc < 12:
-        shell('mpirun -np 12 '+cluster.container+' ./filter &> log.filter')
+        shell(cluster.dart_modules+' mpirun -np 12 ./filter &> log.filter')
     else:  # -genv I_MPI_PIN_PROCESSOR_LIST=0-"+str(int(nproc) - 1)
-        shell("mpirun -np "+str(int(nproc))+' '+cluster.container+" ./filter > log.filter")
+        shell(cluster.dart_modules+" mpirun -np "+str(int(nproc))+" ./filter > log.filter")
     print("./filter took", int(time_module.time() - t), "seconds")
     if not os.path.isfile(cluster.dartrundir + "/obs_seq.final"):
         raise RuntimeError(

dartwrf/run_obs_diag.py

@@ -39,7 +39,7 @@ def run_obsdiag(filepaths, f_out='./obsdiag.nc'):
         print('------ running obs_diag program')
         os.chdir(rundir_program)
         symlink(cluster.dart_srcdir+'/obs_diag', rundir_program+'/obs_diag')
-        shell(cluster.container, './obs_diag >& obs_diag.log')  # caution, this overwrites obs_seq_to_netcdf
+        shell(cluster.dart_modules+' ./obs_diag >& obs_diag.log')  # caution, this overwrites obs_seq_to_netcdf
 
         # move output to archive
         #outdir = os.path.dirname(f_out)  #'/'.join(folder_obs_seq_final.split('/')[:-1])
@@ -57,7 +57,7 @@ def run_obs_seq_to_netcdf(filepaths, f_out='./obs_epoch.nc'):
     print('------ running obs_seq_to_netcdf program')
     #shutil.copy(cluster.dart_srcdir+'/obs_seq_to_netcdf-bak', rundir_program+'/obs_seq_to_netcdf')
     os.chdir(rundir_program)
-    shell(cluster.container, './obs_seq_to_netcdf  >& obs_seq_to_netcdf.log')  # caution, overwrites its own binary?!
+    shell(cluster.dart_modules+' ./obs_seq_to_netcdf  >& obs_seq_to_netcdf.log')  # caution, overwrites its own binary?!
     shutil.move(rundir_program+'/obs_epoch_001.nc', f_out)
     print(f_out, 'saved.')
 

dartwrf/utils.py

@@ -14,6 +14,7 @@ class ClusterConfig(object):
     """Collection of variables regarding the cluster configuration"""
     def __init__(self, exp):
         self.exp = exp
+        self.dart_modules = ''  # default value
 
     @property
     def archivedir(self):

dartwrf/workflows.py

@@ -29,6 +29,9 @@ class WorkFlows(object):
             exp (str): Path to exp config file
             config (str): Path to the cluster config file
 
+        Attributes:
+            cluster (obj): cluster configuration as defined in server_config file
+
         Note:
             in WorkFlows, we load the config from the git cloned folder
             in all other dartwrf scripts, load the config from cluster.scripts_rundir
@@ -196,7 +199,7 @@ class WorkFlows(object):
         runtime_wallclock_mins_expected = int(8+time_in_simulation_hours*9.5)  # usually below 9 min/hour
 
         id = self.cluster.run_job(cmd, "WRF", cfg_update={"array": "1-"+str(self.cluster.size_jobarray), "ntasks": "10", "nodes": "1",
-                            "time": str(runtime_wallclock_mins_expected), "mem": "140G"}, depends_on=[id])
+                            "time": str(runtime_wallclock_mins_expected), "mem": "100G"}, depends_on=[id])
         return id