diff --git a/src/model_DAforcing.py b/src/model_DAforcing.py
index 2959a008b..c30b583bd 100644
--- a/src/model_DAforcing.py
+++ b/src/model_DAforcing.py
@@ -17,9 +17,10 @@
 
 from troute.routing.fast_reach.reservoir_RFC_da import _validate_RFC_data
 import netCDF4
-from nwm_routing.log_level_set import log_level_set
+from nwm_routing.log_level_set import log_level_set, MODULE_NAME
 from troute.config import Config
-LOG = logging.getLogger('')
+
+LOG = logging.getLogger(MODULE_NAME)
 
 class DAforcing_model():
 
diff --git a/src/troute-bmi/src/troute_nwm_bmi/troute_model.py b/src/troute-bmi/src/troute_nwm_bmi/troute_model.py
index f61c05711..a70cf512b 100644
--- a/src/troute-bmi/src/troute_nwm_bmi/troute_model.py
+++ b/src/troute-bmi/src/troute_nwm_bmi/troute_model.py
@@ -15,9 +15,9 @@
 
 import nwm_routing.__main__ as nwm_routing
 from nwm_routing.output import nwm_output_generator
-from nwm_routing.log_level_set import log_level_set
+from nwm_routing.log_level_set import log_level_set, MODULE_NAME
 
-LOG = logging.getLogger("")
+LOG = logging.getLogger(MODULE_NAME)
 
 
 class Model:
diff --git a/src/troute-network/troute/AbstractNetwork.py b/src/troute-network/troute/AbstractNetwork.py
index 830be578e..e54404982 100644
--- a/src/troute-network/troute/AbstractNetwork.py
+++ b/src/troute-network/troute/AbstractNetwork.py
@@ -18,7 +18,9 @@
 import troute.nhd_io as nhd_io 
 from .AbstractRouting import MCOnly, MCwithDiffusive, MCwithDiffusiveNatlXSectionNonRefactored, MCwithDiffusiveNatlXSectionRefactored
 
-LOG = logging.getLogger('')
+from nwm_routing.log_level_set import MODULE_NAME
+
+LOG = logging.getLogger(MODULE_NAME)
 
 class AbstractNetwork(ABC):
     """
diff --git a/src/troute-network/troute/AbstractRouting.py b/src/troute-network/troute/AbstractRouting.py
index 1c46dfcf2..183348efa 100644
--- a/src/troute-network/troute/AbstractRouting.py
+++ b/src/troute-network/troute/AbstractRouting.py
@@ -9,7 +9,9 @@
 from troute.nhd_network import reverse_network, reachable
 from troute.nhd_network_utilities_v02 import organize_independent_networks, build_refac_connections
 
-LOG = logging.getLogger('')
+from nwm_routing.log_level_set import MODULE_NAME
+
+LOG = logging.getLogger(MODULE_NAME)
 
 def read_diffusive_domain(domain_file):
     '''
diff --git a/src/troute-network/troute/DataAssimilation.py b/src/troute-network/troute/DataAssimilation.py
index 0c7971616..1428b4acc 100644
--- a/src/troute-network/troute/DataAssimilation.py
+++ b/src/troute-network/troute/DataAssimilation.py
@@ -11,11 +11,14 @@
 import time
 import logging
 
-LOG = logging.getLogger('')
 from troute.routing.fast_reach.reservoir_RFC_da import _validate_RFC_data
 
 from troute.network import bmi_array2df as a2df
 
+from nwm_routing.log_level_set import MODULE_NAME
+
+LOG = logging.getLogger(MODULE_NAME)
+
 # set legacy run flag: option to pass data frames through BMI formalism 
 # not to be used in regular BMI runs any longer, only for debugging
 legacy_bmi_df = False
diff --git a/src/troute-network/troute/HYFeaturesNetwork.py b/src/troute-network/troute/HYFeaturesNetwork.py
index e94cd47e5..eb84fe11a 100644
--- a/src/troute-network/troute/HYFeaturesNetwork.py
+++ b/src/troute-network/troute/HYFeaturesNetwork.py
@@ -36,6 +36,7 @@ def find_layer_name(layers, pattern):
 
 
 def read_geopkg(file_path, compute_parameters, waterbody_parameters, cpu_pool):
+    print("reading geopkg")
     # Retrieve available layers from the GeoPackage
     available_layers = fiona.listlayers(file_path)
 
@@ -50,6 +51,7 @@ def read_geopkg(file_path, compute_parameters, waterbody_parameters, cpu_pool):
     }
 
     # Match available layers to the patterns
+    print("finding layers")
     matched_layers = {key: find_layer_name(available_layers, pattern) for key, pattern in layer_patterns.items()}
 
     layers_to_read = ["flowpaths", "flowpath_attributes", "hydrolocations"]
@@ -85,12 +87,17 @@ def read_layer(layer_name):
         return pd.DataFrame()
 
     # Retrieve geopackage information using matched layer names
+    print("about to read")
     if cpu_pool > 1:
+        print("with parallel")
+        import sys
+        print(sys.executable)
         with Parallel(n_jobs=min(cpu_pool, len(layers_to_read))) as parallel:
             gpkg_list = parallel(delayed(read_layer)(matched_layers[layer]) for layer in layers_to_read)
 
         table_dict = {layers_to_read[i]: gpkg_list[i] for i in range(len(layers_to_read))}
     else:
+        print("without parallel")
         table_dict = {layer: read_layer(matched_layers[layer]) for layer in layers_to_read}
 
     # Handle different key column names between flowpaths and flowpath_attributes
@@ -350,14 +357,18 @@ def __init__(
                 from_files = False
 
             # Preprocess network objects
+            print("preprocess_network")
             self.preprocess_network(flowpaths, nexus)
 
+            print("crosswalk_nex_flowpath_poi")
             self.crosswalk_nex_flowpath_poi(flowpaths, nexus)
 
             # Preprocess waterbody objects
+            print("preprocess_waterbodies")
             self.preprocess_waterbodies(lakes, nexus)
 
             # Preprocess data assimilation objects #TODO: Move to DataAssimilation.py?
+            print("preprocess_data_assimilation")
             self.preprocess_data_assimilation(network)
 
             if self.preprocessing_parameters.get("preprocess_output_folder", None):
diff --git a/src/troute-network/troute/NHDNetwork.py b/src/troute-network/troute/NHDNetwork.py
index f8378dcf2..b3d5afd1e 100644
--- a/src/troute-network/troute/NHDNetwork.py
+++ b/src/troute-network/troute/NHDNetwork.py
@@ -12,7 +12,9 @@
 from troute.nhd_network import reverse_dict, extract_waterbody_connections, gage_mapping, extract_connections, replace_waterbodies_connections
 
 import logging
-LOG = logging.getLogger('')
+from nwm_routing.log_level_set import MODULE_NAME
+
+LOG = logging.getLogger(MODULE_NAME)
 
 __showtiming__ = True #FIXME pass flag
 __verbose__ = True #FIXME pass verbosity
diff --git a/src/troute-network/troute/hyfeature_network_utilities.py b/src/troute-network/troute/hyfeature_network_utilities.py
index e9674dc87..c4ffcf35e 100644
--- a/src/troute-network/troute/hyfeature_network_utilities.py
+++ b/src/troute-network/troute/hyfeature_network_utilities.py
@@ -14,8 +14,9 @@
 
 import troute.nhd_io as nhd_io
 
+from nwm_routing.log_level_set import MODULE_NAME
 
-LOG = logging.getLogger('')
+LOG = logging.getLogger(MODULE_NAME)
 
 
 def build_da_sets(da_params, run_sets, t0):
diff --git a/src/troute-network/troute/nhd_io.py b/src/troute-network/troute/nhd_io.py
index 57665dee1..9a8bf514c 100644
--- a/src/troute-network/troute/nhd_io.py
+++ b/src/troute-network/troute/nhd_io.py
@@ -20,7 +20,9 @@
 
 from troute.nhd_network import reverse_dict
 
-LOG = logging.getLogger('')
+from nwm_routing.log_level_set import MODULE_NAME
+
+LOG = logging.getLogger(MODULE_NAME)
 
 def read_netcdf(geo_file_path):
     '''
diff --git a/src/troute-network/troute/nhd_network_utilities_v02.py b/src/troute-network/troute/nhd_network_utilities_v02.py
index e2d353e5d..1acc4a34f 100644
--- a/src/troute-network/troute/nhd_network_utilities_v02.py
+++ b/src/troute-network/troute/nhd_network_utilities_v02.py
@@ -12,7 +12,9 @@
 import troute.nhd_io as nhd_io
 import troute.nhd_network as nhd_network
 
-LOG = logging.getLogger('')
+from nwm_routing.log_level_set import MODULE_NAME
+
+LOG = logging.getLogger(MODULE_NAME)
 
 def build_connections(supernetwork_parameters):
     '''
diff --git a/src/troute-nwm/src/nwm_routing/__main__.py b/src/troute-nwm/src/nwm_routing/__main__.py
index 3cc6bba73..172b70d3e 100644
--- a/src/troute-nwm/src/nwm_routing/__main__.py
+++ b/src/troute-nwm/src/nwm_routing/__main__.py
@@ -30,8 +30,9 @@
 import troute.hyfeature_network_utilities as hnu
 import sys
 
+from nwm_routing.log_level_set import MODULE_NAME
 
-LOG = logging.getLogger('')
+LOG = logging.getLogger(MODULE_NAME)
 
 '''
 High level orchestration of ngen t-route simulations for NWM application
diff --git a/src/troute-nwm/src/nwm_routing/input.py b/src/troute-nwm/src/nwm_routing/input.py
index 1eaf3ad93..3cd36e5c8 100644
--- a/src/troute-nwm/src/nwm_routing/input.py
+++ b/src/troute-nwm/src/nwm_routing/input.py
@@ -6,10 +6,10 @@
 
 import troute.nhd_io as nhd_io
 import troute.nhd_network_utilities_v02 as nnu
-from .log_level_set import log_level_set
+from .log_level_set import log_level_set, MODULE_NAME
 from troute.config import Config
 
-LOG = logging.getLogger('')
+LOG = logging.getLogger(MODULE_NAME)
 
 def _input_handler_v04(args):
     '''
@@ -120,7 +120,7 @@ def _input_handler_v03(args):
 
     # configure python logger
     log_level_set(log_parameters)
-    LOG = logging.getLogger('')
+    LOG = logging.getLogger(MODULE_NAME)
 
     # if log level is at or below DEBUG, then check user inputs
     if LOG.isEnabledFor(logging.DEBUG):
diff --git a/src/troute-nwm/src/nwm_routing/log_level_set.py b/src/troute-nwm/src/nwm_routing/log_level_set.py
index d1f7510e6..777ad6f68 100644
--- a/src/troute-nwm/src/nwm_routing/log_level_set.py
+++ b/src/troute-nwm/src/nwm_routing/log_level_set.py
@@ -178,24 +178,25 @@ def log_level_set(input_parameters):
         handler.setFormatter(formatter)
 
         # Setup root logger
-        logging.getLogger().handlers.clear()  # Clear any default handlers
-        logging.getLogger().setLevel(translate_ngwpc_log_level(log_level))
-        logging.getLogger().addHandler(handler)
+        logger = logging.getLogger(MODULE_NAME)
+        logger.handlers.clear()  # Clear any default handlers
+        logger.setLevel(translate_ngwpc_log_level(log_level))
+        logger.addHandler(handler)
 
         # Ensure UTC timestamps
         logging.Formatter.converter = time.gmtime
 
         # Save the current log level
-        current_level = logging.getLogger().getEffectiveLevel()
+        current_level = logger.getEffectiveLevel()
 
         try:
             # Temporarily set log level to INFO
-            logging.getLogger().setLevel(logging.INFO)
+            logger.setLevel(logging.INFO)
             
             # Log the message at INFO level
             logging.info(f"Log level set to {log_level}")
             print(f"Module {MODULE_NAME} Log Level set to {log_level}")
         finally:
             # Restore the original log level
-            logging.getLogger().setLevel(current_level)
+            logger.setLevel(current_level)
     
\ No newline at end of file
diff --git a/src/troute-nwm/src/nwm_routing/output.py b/src/troute-nwm/src/nwm_routing/output.py
index c9e59b9c7..fbbdfc604 100644
--- a/src/troute-nwm/src/nwm_routing/output.py
+++ b/src/troute-nwm/src/nwm_routing/output.py
@@ -7,7 +7,9 @@
 from build_tests import parity_check
 import logging
 
-LOG = logging.getLogger('')
+from nwm_routing.log_level_set import MODULE_NAME
+
+LOG = logging.getLogger(MODULE_NAME)
 
 def _reindex_lake_to_link_id(target_df, crosswalk):
     '''
diff --git a/src/troute-nwm/src/nwm_routing/preprocess.py b/src/troute-nwm/src/nwm_routing/preprocess.py
index 066c74412..fb751634d 100644
--- a/src/troute-nwm/src/nwm_routing/preprocess.py
+++ b/src/troute-nwm/src/nwm_routing/preprocess.py
@@ -12,7 +12,9 @@
 import troute.nhd_network as nhd_network
 import troute.nhd_io as nhd_io
 
-LOG = logging.getLogger('')
+from nwm_routing.log_level_set import MODULE_NAME
+
+LOG = logging.getLogger(MODULE_NAME)
 
 def _reindex_link_to_lake_id(target_df, crosswalk):
     '''
diff --git a/src/troute-routing/troute/routing/compute.py b/src/troute-routing/troute/routing/compute.py
index 55f529596..4b09d777a 100644
--- a/src/troute-routing/troute/routing/compute.py
+++ b/src/troute-routing/troute/routing/compute.py
@@ -16,7 +16,9 @@
 
 import logging
 
-LOG = logging.getLogger('')
+from nwm_routing.log_level_set import MODULE_NAME
+
+LOG = logging.getLogger(MODULE_NAME)
 
 _compute_func_map = defaultdict(
     compute_network_structured,
diff --git a/src/troute-routing/troute/routing/fast_reach/reservoir_GL_da.py b/src/troute-routing/troute/routing/fast_reach/reservoir_GL_da.py
index 6683e9ee3..cb9f273bb 100644
--- a/src/troute-routing/troute/routing/fast_reach/reservoir_GL_da.py
+++ b/src/troute-routing/troute/routing/fast_reach/reservoir_GL_da.py
@@ -1,7 +1,9 @@
 import numpy as np
 import logging
 from datetime import datetime, timedelta
-LOG = logging.getLogger('')
+from nwm_routing.log_level_set import MODULE_NAME
+
+LOG = logging.getLogger(MODULE_NAME)
 
 def great_lakes_da(
     gage_obs,
diff --git a/src/troute-routing/troute/routing/fast_reach/reservoir_hybrid_da.py b/src/troute-routing/troute/routing/fast_reach/reservoir_hybrid_da.py
index 0338b4faf..85a5dfaf2 100644
--- a/src/troute-routing/troute/routing/fast_reach/reservoir_hybrid_da.py
+++ b/src/troute-routing/troute/routing/fast_reach/reservoir_hybrid_da.py
@@ -1,6 +1,8 @@
 import numpy as np
 import logging
-LOG = logging.getLogger('')
+from nwm_routing.log_level_set import MODULE_NAME
+
+LOG = logging.getLogger(MODULE_NAME)
 
 def _modify_for_projected_storage(
     inflow,