diff --git a/.gitignore b/.gitignore
index ad1f6f600..173354d9d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,9 +9,7 @@ config/**
 !config/*default*
 !config/*calibrated*
 !config/symbology/
-config/*template*.swp
-!config/*default*.swp
-!config/*calibrated*.swp
+config/*.swp
 .vscode/
 **/.DS_Store
 **/*_pytest.py
diff --git a/config/params_calibrated.env b/config/params_calibrated.env
index 57ebbb8ea..88225947a 100644
--- a/config/params_calibrated.env
+++ b/config/params_calibrated.env
@@ -22,6 +22,7 @@ export min_stream_length=0.5
 #### gms parameters ####
 export branch_id_attribute=levpa_id
 export branch_buffer_distance_meters=7000
+export branch_timeout=1000 # pass int or float. To make a percentage of median, pass a '%' at the end.
 
 #### bathy SRC estimation parameters ####
 export bathy_src_modification=True
diff --git a/config/params_template.env b/config/params_template.env
index b381d2a1f..63b415b9a 100644
--- a/config/params_template.env
+++ b/config/params_template.env
@@ -22,6 +22,7 @@ export min_stream_length=0.5
 #### gms parameters ####
 export branch_id_attribute=levpa_id
 export branch_buffer_distance_meters=7000
+export branch_timeout=1000 # pass int or float. To make a percentage of median, pass a '%' at the end.
 
 #### bathy SRC estimation parameters ####
 export bathy_src_modification=True
diff --git a/gms_run.sh b/gms_run.sh
deleted file mode 100755
index 633118278..000000000
--- a/gms_run.sh
+++ /dev/null
@@ -1,177 +0,0 @@
-#!/bin/bash -e
-:
-usage ()
-{
-    echo 'Produce GMS hydrofabric'
-    echo 'Usage : gms_run.sh [REQ: -u <hucs> -c <config file> -n <run name> ] [OPT: -h -j <job limit>]'
-    echo ''
-    echo 'REQUIRED:'
-    echo '  -u/--hucList    : HUC 4,6,or 8 to run or multiple passed in quotes. Line delimited file'
-    echo '                     also accepted. HUCs must present in inputs directory.'
-    echo '  -e/--extent     : full resolution or mainstem method; options are MS or FR'
-    echo '  -c/--config     : configuration file with bash environment variables to export'
-    echo '  -n/--runName    : a name to tag the output directories and log files as. could be a version tag.'
-    echo ''
-    echo 'OPTIONS:'
-    echo '  -h/--help       : help file'
-    echo '  -j/--jobLimit   : max number of concurrent jobs to run. Default 1 job at time. 1 outputs'
-    echo '                    stdout and stderr to terminal and logs. With >1 outputs progress and logs the rest'
-    echo '  -o/--overwrite  : overwrite outputs if already exist'
-    echo '  -p/--production : only save final inundation outputs'
-    echo '  -w/--whitelist  : list of files to save in a production run in addition to final inundation outputs'
-    echo '                     ex: file1.tif,file2.json,file3.csv'
-    echo '  -v/--viz        : compute post-processing on outputs to be used in viz'
-    exit
-}
-
-if [ "$#" -lt 7 ]
-then
-  usage
-fi
-
-while [ "$1" != "" ]; do
-case $1
-in
-    -u|--hucList)
-        shift
-        hucList="$1"
-        ;;
-    -c|--configFile )
-        shift
-        envFile=$1
-        ;;
-    -e|--extent)
-        shift
-        extent=$1
-        ;;
-    -n|--runName)
-        shift
-        runName=$1
-        ;;
-    -j|--jobLimit)
-        shift
-        jobLimit=$1
-        ;;
-    -h|--help)
-        shift
-        usage
-        ;;
-    -o|--overwrite)
-        overwrite=1
-        ;;
-    -og|--overwrite-gms)
-        overwrite_gms=1
-        ;;
-    -p|--production)
-        production=1
-        ;;
-    -w|--whitelist)
-        shift
-        whitelist="$1"
-        ;;
-    -v|--viz)
-        viz=1
-        ;;
-    *) ;;
-    esac
-    shift
-done
-
-# print usage if arguments empty
-if [ "$hucList" = "" ]
-then
-    usage
-fi
-if [ "$extent" = "" ]
-then
-    usage
-fi
-if [ "$envFile" = "" ]
-then
-    usage
-fi
-if [ "$runName" = "" ]
-then
-    usage
-fi
-if [ "$overwrite" = "" ]
-then
-    overwrite=0
-fi
-
-## SOURCE ENV FILE AND FUNCTIONS ##
-source $envFile
-source $srcDir/bash_functions.env
-
-# default values
-if [ "$jobLimit" = "" ] ; then
-    jobLimit=$default_max_jobs
-fi
-
-## Define Outputs Data Dir & Log File##
-export outputRunDataDir=$outputDataDir/$runName
-export extent=$extent
-export production=$production
-export whitelist=$whitelist
-export viz=$viz
-logFile_fr=$outputRunDataDir/logs/summary.log
-logFile_gms_unit=$outputRunDataDir/logs/summary_gms_unit.log
-logFile_gms_branch=$outputRunDataDir/logs/summary_gms_branch.log
-
-## Define inputs
-export input_WBD_gdb=$inputDataDir/wbd/WBD_National.gpkg
-export input_NWM_Lakes=$inputDataDir/nwm_hydrofabric/nwm_lakes.gpkg
-export input_NWM_Catchments_fr=$inputDataDir/nwm_hydrofabric/nwm_catchments.gpkg
-export input_NWM_Catchments_ms=$inputDataDir/nwm_hydrofabric/nwm_catchments_ms.gpkg
-export input_NWM_Flows_fr=$inputDataDir/nwm_hydrofabric/nwm_flows.gpkg
-export input_NWM_Flows_ms=$inputDataDir/nwm_hydrofabric/nwm_flows_ms.gpkg
-export input_NWM_Headwaters=$inputDataDir/nwm_hydrofabric/nwm_headwaters.gpkg
-export input_nhd_flowlines_fr=$inputDataDir/nhdplus_vectors_aggregate/NHDPlusBurnLineEvent_fr_adjusted.gpkg
-export input_nhd_flowlines_ms=$inputDataDir/nhdplus_vectors_aggregate/NHDPlusBurnLineEvent_ms_adjusted.gpkg
-export input_nhd_headwaters_fr=$inputDataDir/nhdplus_vectors_aggregate/nhd_headwaters_adjusted_fr.gpkg
-export input_nhd_headwaters_ms=$inputDataDir/nhdplus_vectors_aggregate/nhd_headwaters_adjusted_ms.gpkg
-
-## Input handling ##
-$srcDir/check_huc_inputs.py -u "$hucList"
-
-## Make output and data directories ##
-if [[ ( -d "$outputRunDataDir" ) && ( "$overwrite" -eq 1 ) && ( ( "$extent" -eq "FR" ) || ( "$extent" -eq "MS" ) ) ]]; then
-     rm -rf "$outputRunDataDir"
-elif [[ -d "$outputRunDataDir" && "$overwrite_gms" -eq 1 && "$extent" -eq "GMS" ]]; then
-     find $outputRunDataDir -iname "gms" -type d -exec rm -rf {} +
-elif [ -d "$outputRunDataDir" ] && [ -z "$overwrite" ] ; then
-    echo "$runName data directories already exist. Use -o/--overwrite to continue"
-    exit 1
-fi
-mkdir -p $outputRunDataDir/logs
-
-
-jobLimit_gms_unit=1
-## UNIT GMS FIRST ##
-if [ "$extent" = "GMS" ]; then
-    if [ -f "$hucList" ]; then
-        if [ "$jobLimit_gms_unit" -eq 1 ]; then
-            parallel --verbose --lb  -j $jobLimit_gms_unit --joblog $logFile_gms_unit --colsep ',' -- $srcDir/gms/time_and_tee_run_by_unit.sh :::: $hucList
-        else
-            parallel --eta -j $jobLimit_gms_unit --joblog $logFile_gms_unit ---colsep ',' - $srcDir/gms/time_and_tee_run_by_unit.sh :::: $hucList
-        fi
-    else 
-        if [ "$jobLimit_gms_unit" -eq 1 ]; then
-            parallel --verbose --lb  -j $jobLimit_gms_unit --joblog $logFile_gms_unit --colsep ',' -- $srcDir/gms/time_and_tee_run_by_unit.sh ::: $hucList
-        else
-            parallel --eta -j $jobLimit_gms_unit --joblog $logFile_gms_unit --colsep ',' -- $srcDir/gms/time_and_tee_run_by_unit.sh ::: $hucList
-        fi
-     fi
-    python3 $srcDir/gms/aggregate_branch_lists.py
-fi
-
-
-## RUN GMS ##
-if [ "$extent" = "GMS" ]; then
-    if [ "$jobLimit" -eq 1 ]; then
-        parallel --verbose --lb  -j $jobLimit --joblog $logFile_gms_branch --colsep ',' -- $srcDir/gms/time_and_tee_run_by_branch.sh :::: $outputRunDataDir/gms_inputs.csv
-    else
-        parallel --eta -j $jobLimit --joblog $logFile_gms_branch --colsep ',' -- $srcDir/gms/time_and_tee_run_by_branch.sh :::: $outputRunDataDir/gms_inputs.csv
-    fi
-fi
-
diff --git a/gms_run_branch.sh b/gms_run_branch.sh
index fe9d51bc7..837735769 100755
--- a/gms_run_branch.sh
+++ b/gms_run_branch.sh
@@ -103,21 +103,29 @@ export whitelist=$whitelist
 export viz=$viz
 logFile=$outputRunDataDir/logs/summary_gms_branch.log
 
-
 ## Make output and data directories ##
-if [[ -d "$outputRunDataDir" && "$overwrite" -eq 1 ]]; then
-    find $outputRunDataDir/**/gms/ -maxdepth 1 -mindepth 1 -type d -exec rm -rf {} +
-elif [ -d "$outputRunDataDir" ] && [ -z "$overwrite" ] ; then
-    echo "$runName data directories already exist. Use -o/--overwrite to continue"
+if [ -d "$outputRunDataDir" ]; then 
+    branch_directories_count=$(find $outputRunDataDir/**/gms/ -maxdepth 1 -mindepth 1 -type d | wc -l)
+
+    if [ $branch_directories_count -gt 0 ] && [ "$overwrite" -eq 1 ]; then
+        rm -rf $branch_directories_list
+    elif [ $branch_directories_count -gt 0 ] && [ "$overwrite" -eq 0 ] ; then
+        echo "GMS branch data directories for $runName already exist. Use -o/--overwrite to continue"
+        exit 1
+    fi
+else
+    echo "GMS depends on Full Resolution Data. Please produce data with fim_run.sh first."
     exit 1
 fi
+
+# make log dir
 mkdir -p $outputRunDataDir/logs
 
 
-## RUN GMS ##
+## RUN GMS BY BRANCH ##
 if [ "$jobLimit" -eq 1 ]; then
-    parallel --verbose --lb  -j $jobLimit --joblog $logFile --colsep ',' -- $srcDir/gms/time_and_tee_run_by_branch.sh :::: $outputRunDataDir/gms_inputs.csv
+    parallel --verbose --timeout $branch_timeout --lb  -j $jobLimit --joblog $logFile --colsep ',' -- $srcDir/gms/time_and_tee_run_by_branch.sh :::: $outputRunDataDir/gms_inputs.csv
 else
-    parallel --eta -j $jobLimit --joblog $logFile --colsep ',' -- $srcDir/gms/time_and_tee_run_by_branch.sh :::: $outputRunDataDir/gms_inputs.csv
+    parallel --eta --timeout $branch_timeout -j $jobLimit --joblog $logFile --colsep ',' -- $srcDir/gms/time_and_tee_run_by_branch.sh :::: $outputRunDataDir/gms_inputs.csv
 fi
 
diff --git a/gms_run_unit.sh b/gms_run_unit.sh
index a98f8e810..33d54cf0d 100755
--- a/gms_run_unit.sh
+++ b/gms_run_unit.sh
@@ -69,7 +69,7 @@ if [ "$runName" = "" ]
 then
     usage
 fi
-if [ "$overwrite" = "" ]
+if [ -z "$overwrite" ]
 then
     overwrite=0
 fi
@@ -91,27 +91,35 @@ logFile=$outputRunDataDir/logs/summary_gms_unit.log
 $srcDir/check_huc_inputs.py -u "$hucList"
 
 ## Make output and data directories ##
-if [[ -d "$outputRunDataDir" && "$overwrite" -eq 1 ]]; then
-     find $outputRunDataDir -iname "gms" -type d -exec rm -rf {} +
-elif [ -d "$outputRunDataDir" ] && [ -z "$overwrite" ] ; then
-    echo "$runName data directories already exist. Use -o/--overwrite to continue"
+if [ -d "$outputRunDataDir" ]; then
+    gms_directories_count=$(find $outputRunDataDir -iname "gms" -type d | wc -l)
+    if [ $gms_directories_count -gt 0 ] && [ "$overwrite" -eq 1 ]; then
+         rm -rf $gms_directories_list
+    elif [ $gms_directories_count -gt 0 ] && [ "$overwrite" -eq 0 ] ; then
+        echo "GMS data directory for $runName already exist. Use -o/--overwrite to continue"
+        exit 1
+    fi
+else
+    echo "GMS depends on Full Resolution Data. Please produce data with fim_run.sh first."
     exit 1
 fi
+
+# make log dir
 mkdir -p $outputRunDataDir/logs
 
 
 ## GMS BY UNIT##
 if [ -f "$hucList" ]; then
     if [ "$jobLimit" -eq 1 ]; then
-        parallel --verbose --lb  -j $jobLimit --joblog $logFile --colsep ',' -- $srcDir/gms/time_and_tee_run_by_unit.sh :::: $hucList
+        parallel --verbose --lb  -j $jobLimit --joblog $logFile -- $srcDir/gms/time_and_tee_run_by_unit.sh :::: $hucList
     else
-        parallel --eta -j $jobLimit --joblog $logFile ---colsep ',' - $srcDir/gms/time_and_tee_run_by_unit.sh :::: $hucList
+        parallel --eta -j $jobLimit --joblog $logFile -- $srcDir/gms/time_and_tee_run_by_unit.sh :::: $hucList
     fi
 else 
     if [ "$jobLimit" -eq 1 ]; then
-        parallel --verbose --lb  -j $jobLimit --joblog $logFile --colsep ',' -- $srcDir/gms/time_and_tee_run_by_unit.sh ::: $hucList
+        parallel --verbose --lb  -j $jobLimit --joblog $logFile -- $srcDir/gms/time_and_tee_run_by_unit.sh ::: $hucList
     else
-        parallel --eta -j $jobLimit --joblog $logFile --colsep ',' -- $srcDir/gms/time_and_tee_run_by_unit.sh ::: $hucList
+        parallel --eta -j $jobLimit --joblog $logFile -- $srcDir/gms/time_and_tee_run_by_unit.sh ::: $hucList
     fi
  fi
 
diff --git a/src/gms/run_by_branch.sh b/src/gms/run_by_branch.sh
index 057ac8d88..57359cb10 100755
--- a/src/gms/run_by_branch.sh
+++ b/src/gms/run_by_branch.sh
@@ -21,9 +21,6 @@ input_demDerived_raster=$outputHucDataDir/demDerived_streamPixels.tif
 input_demDerived_reaches=$outputHucDataDir/demDerived_reaches_split_filtered_addedAttributes_crosswalked.gpkg
 input_demDerived_reaches_points=$outputHucDataDir/demDerived_reaches_split_points.gpkg
 input_demDerived_pixel_points=$outputHucDataDir/flows_points_pixels.gpkg
-input_stage_list=$outputHucDataDir/stage.txt
-input_hydroTable=$outputHucDataDir/hydroTable.csv
-input_src_full=$outputHucDataDir/src_full_crosswalked.csv
 
 
 ## ECHO PARAMETERS
@@ -73,7 +70,15 @@ Tcount
 echo -e $startDiv"Subsetting vectors to branches for $current_branch_id in HUC $hucNumber"$stopDiv
 date -u
 Tstart
-$srcDir/gms/query_vectors_by_branch_polygons.py -a $outputGmsDataDir/polygons.gpkg -d $current_branch_id -i $branch_id_attribute -s $outputGmsDataDir/demDerived_reaches_levelPaths.gpkg $outputGmsDataDir/demDerived_reaches_levelPaths_dissolved.gpkg $outputGmsDataDir/demDerived_reaches_points.gpkg $outputGmsDataDir/demDerived_pixels_points.gpkg -o $outputBranchDataDir/demDerived_reaches_levelPaths.gpkg $outputBranchDataDir/demDerived_reaches_levelPaths_dissolved.gpkg $outputBranchDataDir/demDerived_reaches_points.gpkg $outputBranchDataDir/demDerived_pixels_points.gpkg -v
+echo -e "Querying demDerived_reaches_levelPaths.gpkg ..."
+ogr2ogr -f GPKG -where $branch_id_attribute="$current_branch_id" $outputBranchDataDir/demDerived_reaches_levelPaths_$current_branch_id.gpkg $outputGmsDataDir/demDerived_reaches_levelPaths.gpkg
+echo -e "Querying demDerived_reaches_levelPaths_dissolved.gpkg ..."
+ogr2ogr -f GPKG -where $branch_id_attribute="$current_branch_id" $outputBranchDataDir/demDerived_reaches_levelPaths_dissolved_$current_branch_id.gpkg $outputGmsDataDir/demDerived_reaches_levelPaths_dissolved.gpkg
+echo -e "Querying demDerived_reaches_points.gpkg ..."
+ogr2ogr -f GPKG -where $branch_id_attribute="$current_branch_id" $outputBranchDataDir/demDerived_reaches_points_$current_branch_id.gpkg $outputGmsDataDir/demDerived_reaches_points.gpkg
+echo -e "Querying demDerived_pixels_points.gpkg ..."
+ogr2ogr -f GPKG -where $branch_id_attribute="$current_branch_id" $outputBranchDataDir/demDerived_pixels_points_$current_branch_id.gpkg $outputGmsDataDir/demDerived_pixels_points.gpkg
+#$srcDir/gms/query_vectors_by_branch_polygons.py -a $outputGmsDataDir/polygons.gpkg -d $current_branch_id -i $branch_id_attribute -s $outputGmsDataDir/demDerived_reaches_levelPaths.gpkg $outputGmsDataDir/demDerived_reaches_levelPaths_dissolved.gpkg $outputGmsDataDir/demDerived_reaches_points.gpkg $outputGmsDataDir/demDerived_pixels_points.gpkg -o $outputBranchDataDir/demDerived_reaches_levelPaths.gpkg $outputBranchDataDir/demDerived_reaches_levelPaths_dissolved.gpkg $outputBranchDataDir/demDerived_reaches_points.gpkg $outputBranchDataDir/demDerived_pixels_points.gpkg -v
 Tcount
 
 ## SPLIT DERIVED REACHES ##
@@ -151,7 +156,7 @@ Tcount
 #    mkdir -p $branchOutputDir
 #fi
 
-if [ "$production" -eq 1 ]; then
+if [ $production -eq 1 ]; then
     echo -e $startDiv"Remove files for branch_id: $current_branch_id in HUC: $hucNumber"$stopDiv
     
     cd $outputBranchDataDir
diff --git a/src/gms/run_by_unit.sh b/src/gms/run_by_unit.sh
index 2d88200b8..8e6ad7ce3 100755
--- a/src/gms/run_by_unit.sh
+++ b/src/gms/run_by_unit.sh
@@ -37,7 +37,7 @@ fi
 echo -e $startDiv"Generating Level Paths for $hucNumber"$stopDiv
 date -u
 Tstart
-#$srcDir/gms/derive_level_paths.py -i $outputHucDataDir/demDerived_reaches_split_filtered_addedAttributes_crosswalked.gpkg -b $branch_id_attribute -o $outputGmsDataDir/demDerived_reaches_levelPaths.gpkg -d $outputGmsDataDir/demDerived_reaches_levelPaths_dissolved.gpkg -v
+$srcDir/gms/derive_level_paths.py -i $outputHucDataDir/demDerived_reaches_split_filtered_addedAttributes_crosswalked.gpkg -b $branch_id_attribute -o $outputGmsDataDir/demDerived_reaches_levelPaths.gpkg -d $outputGmsDataDir/demDerived_reaches_levelPaths_dissolved.gpkg -v
 Tcount
 
 ## STREAM BRANCH POLYGONS
@@ -46,7 +46,6 @@ date -u
 Tstart
 $srcDir/gms/buffer_stream_branches.py -s $outputGmsDataDir/demDerived_reaches_levelPaths_dissolved.gpkg -i $branch_id_attribute -d $branch_buffer_distance_meters -b $outputGmsDataDir/polygons.gpkg -v 
 Tcount
-exit 0
 
 ##### EDIT DEM DERIVED POINTS TO ADD BRANCH IDS ######
 echo -e $startDiv"EDITING DEM DERIVED POINTS for $hucNumber"$stopDiv
diff --git a/src/gms/test_stream_branches.py b/src/gms/test_stream_branches.py
deleted file mode 100755
index bdf90bc9e..000000000
--- a/src/gms/test_stream_branches.py
+++ /dev/null
@@ -1,101 +0,0 @@
-#!/usr/bin/env python3
-
-from stream_branches import StreamNetwork
-from stream_branches import StreamBranchPolygons
-import argparse
-
-
-if __name__ == '__main__':
-
-    # parse arguments
-    parser = argparse.ArgumentParser(description='Identifies stream branches, generates branch polygons, and clips raster to polygons')
-    parser.add_argument('-u','--huc8', help='to-do', required=True)
-    #parser.add_argument('-s','--streams', help='to-do', required=False)
-    #parser.add_argument('-b','--branches', help='to-do', required=False)
-    #parser.add_argument('-d','--buffer-distance', help='to-do', required=False)
-    #parser.add_argument('-r','--raster', help='to-do', required=False)
-    #parser.add_argument('-v','--verbose', help='to-do', required=False,action='store_true')
-
-    # extract to dictionary
-    args = vars(parser.parse_args())
-
-    from os.path import join
-    huc8 = args["huc8"] ; huc4 = huc8[0:4]
-    input_data_dir = "/data/outputs/slope_1eddd72_dem_all_mannings_6/{}/".format(huc8) #"/data/temp/stream_branches"
-    output_data_dir = "/data/temp/stream_branches/large_test/{}".format(huc8)
-    streams_file = join(output_data_dir,"NHDPlusBurnLineEvent_subset.gpkg")#'nhdplus_burnlines_subset.gpkg')
-    branches_file = join("/data/inputs/nhdplus_vectors/{}/".format(huc4),'NHDPlusFlowLineVAA{}.gpkg'.format(huc4))
-    buffer_distance = 1000
-    to_clip_raster_file = join(input_data_dir,'dem_meters.tif')
-    to_clip_vector_file = join(input_data_dir,'NHDPlusBurnLineEvent_subset.gpkg')
-
-    stream_network_processed_file = join(output_data_dir,'stream_network_processed.gpkg')
-    stream_polygons_file = join(output_data_dir,'stream_branch_polygons.gpkg')
-    clipped_raster_files = join(output_data_dir,'test_{}.tif')
-    clipped_vector_files = join(output_data_dir,'test_{}.gpkg')
-    
-    # load file
-    print('Loading file')
-    stream_network = StreamNetwork.from_file(streams_file)
-
-    # merge stream branch attributes
-    print('Merge attributes')
-    stream_network = stream_network.merge_stream_branches(stream_branch_dataset=branches_file,
-                                                          on='NHDPlusID',
-                                                          attributes=['StreamOrde','ToNode','FromNode'],
-                                                          branch_id_attribute = "LevelPathI",
-                                                          stream_branch_layer_name=None
-                                                         )
-    
-    # derive inlets and outlets
-    print('Derive inlets and outlets')
-    stream_network = stream_network.derive_inlets(toNode_attribute='ToNode',
-                                                  fromNode_attribute='FromNode',
-                                                  inlets_attribute='inlet_id'
-                                                 )
-    stream_network = stream_network.derive_outlets(toNode_attribute='ToNode',
-                                                   fromNode_attribute='FromNode',
-                                                   outlets_attribute='outlet_id'
-                                                  )
-    
-    # derive arbolate sum
-    
-    print("Calculate arbolate sum")
-    stream_network = stream_network.get_arbolate_sum(
-                                                 arbolate_sum_attribute='arbolate_sum',inlets_attribute='inlet_id',
-                                                 reach_id_attribute='NHDPlusID',toNode_attribute='ToNode',
-                                                 fromNode_attribute='FromNode',length_conversion_factor_to_km=0.001
-                                                     )
-
-    # derive stream newtork branches
-    print("Derive stream branches")
-    stream_network = stream_network.derive_stream_branches(
-                                        toNode_attribute='ToNode',fromNode_attribute='FromNode',
-                                        outlet_attribute='outlet_id',branch_id_attribute='branchID',
-                                        reach_id_attribute='NHDPlusID',comparison_attributes='arbolate_sum',
-                                        comparison_function=max
-                                                          )
-
-    # write stream network with derived stream branches
-    print("Write stream branches")
-    stream_network.write(stream_network_processed_file)
-    
-    # dissolving
-    print("Dissolve stream network by branch")
-    stream_network = stream_network.dissolve_by_branch(branch_id_attribute='branchID',attribute_excluded='StreamOrde',values_excluded=[1,2],out_vector_file_template=None)
-
-    # make stream polygons
-    print("Buffer stream branches to polygons")
-    stream_polys = StreamBranchPolygons.buffer_stream_branches(stream_network,buffer_distance=buffer_distance)
-    
-    # write polygons
-    print("Write polygons")
-    stream_polys.write(stream_polygons_file)
-
-    # clip rasters to polygons
-    print("Clip raster to polygons")
-    out_rasters = stream_polys.clip(to_clip_raster_file,clipped_raster_files)
-    
-    # clip rasters to polygons
-    print("Clip vector to polygons")
-    out_vectors = stream_polys.clip(to_clip_vector_file,clipped_vector_files)
diff --git a/src/gms/time_and_tee_run_by_branch.sh b/src/gms/time_and_tee_run_by_branch.sh
index d9119baf6..7681aa7ba 100755
--- a/src/gms/time_and_tee_run_by_branch.sh
+++ b/src/gms/time_and_tee_run_by_branch.sh
@@ -1,5 +1,5 @@
 #!/bin/bash -e
 
-/usr/bin/time -v $srcDir/gms/run_by_branch.sh $1 $2 |& tee $outputRunDataDir/logs/$1_gms.log
+/usr/bin/time -v $srcDir/gms/run_by_branch.sh $1 $2 |& tee $outputRunDataDir/logs/$1_gms_branch_$2.log
 exit ${PIPESTATUS[0]}
 
diff --git a/src/gms/toDo.md b/src/gms/toDo.md
index 1283c7989..73a8d9b3d 100644
--- a/src/gms/toDo.md
+++ b/src/gms/toDo.md
@@ -1,13 +1,18 @@
 # GMS To Do: 
 ## Immediate
-- overwrite feature in gms_run_branch and gms_run_unit. Use find command
+- test GMS overwrite
+- mannings n 0.06 test
+- branch logs with commas
+- GMS whitelist for FIM 3
+- convenience wrapper for fim_run, gms_run_unit.sh, gms_run_branch.sh. Move gms_run_branch.sh and gms_run_unit.sh to src/gms dir
+
 
 ## integration
 - merge in latest cahaba/dev
 - compatability for new rem.py, add_crosswalk.py (checking small reaches), usgs_crosswalk.py
 
 ## optimize
-- parameterize branch buffer distance by stream order
+- 
 
 ## Inundation
 - inundate_gms: "No forecast value found in passed .."
diff --git a/tools/compare_gms_srcs_to_fr.py b/tools/compare_gms_srcs_to_fr.py
index f935dbfc2..e15072506 100755
--- a/tools/compare_gms_srcs_to_fr.py
+++ b/tools/compare_gms_srcs_to_fr.py
@@ -7,10 +7,10 @@
 import argparse
 import matplotlib.pyplot as plt
 
-def join_srcs(gms_data_dir,fr_data_dir):
+def join_srcs(fr_data_dir,outputs_dir=None):
 
     gms_srcs = None
-    gms_srcs_file_list_generator = iglob( join(gms_data_dir,"**","src_full_*.csv"), recursive=True)
+    gms_srcs_file_list_generator = iglob( join(fr_data_dir,"*","gms","*","src_full_*.csv"), recursive=True)
     
     for i in gms_srcs_file_list_generator:
         current_gms_src = pd.read_csv(i)
@@ -21,7 +21,7 @@ def join_srcs(gms_data_dir,fr_data_dir):
             gms_srcs = pd.concat((gms_srcs,current_gms_src),ignore_index=True)
 
     # fr srcsi
-    fr_src_file_name = glob( join(fr_data_dir,"src_full_crosswalked.csv"))[0]
+    fr_src_file_name = glob( join(fr_data_dir,'*',"src_full_crosswalked.csv"))[0]
     fr_src = pd.read_csv( fr_src_file_name )
 
     # average out values by stage
@@ -35,7 +35,8 @@ def join_srcs(gms_data_dir,fr_data_dir):
     plt.xlabel('Discharge (m3s-1)')
     plt.ylabel('Stage (m)')
     plt.legend()
-    plt.savefig("/data/test.jpg")
+    if outputs_dir is not None:
+        plt.savefig( join(outputs_dir,"rating_curve.jpg") )
     #combined = pd.concat((gms_srcs,fr_src), ignore_index=True, axis=1)
     
     # Volume plots
@@ -45,7 +46,8 @@ def join_srcs(gms_data_dir,fr_data_dir):
     plt.xlabel('Stage (m)')
     plt.ylabel('Volume (m3)')
     plt.legend()
-    plt.savefig("/data/test_vol.jpg")
+    if outputs_dir is not None:
+        plt.savefig( join(outputs_dir,"volume.jpg") )
     
     # Bed Area plots
     plt.figure()
@@ -54,7 +56,8 @@ def join_srcs(gms_data_dir,fr_data_dir):
     plt.xlabel('Stage (m)')
     plt.ylabel('Bed Area (m2)')
     plt.legend()
-    plt.savefig("/data/test_bedarea.jpg")
+    if outputs_dir is not None:
+        plt.savefig( join(outputs_dir,"bedarea.jpg") )
     
     # Volume and Bed Area plots
     plt.figure()
@@ -67,7 +70,8 @@ def join_srcs(gms_data_dir,fr_data_dir):
     plt.xlabel('Stage (m)')
     plt.ylabel('Volume (m3s-1) ^ 5/3 divided by Bed Area (m2) ^ -2/3')
     plt.legend()
-    plt.savefig("/data/test_volume_and_bedarea.jpg")
+    if outputs_dir is not None:
+        plt.savefig( join(outputs_dir,"volume_and_bedarea.jpg") )
     
 
     # Number of Cells plots
@@ -77,7 +81,8 @@ def join_srcs(gms_data_dir,fr_data_dir):
     plt.xlabel('Stage (m)')
     plt.ylabel('Number of Cells')
     plt.legend()
-    plt.savefig("/data/test_number_of_cells.jpg")
+    if outputs_dir is not None:
+        plt.savefig( join(outputs_dir,"number_of_cells.jpg") )
 
 
 
@@ -85,8 +90,8 @@ def join_srcs(gms_data_dir,fr_data_dir):
 if __name__ == '__main__':
 
     parser = argparse.ArgumentParser(description='Comparing SRCs')
-    parser.add_argument('-g','--gms-data-dir', help='Directory with GMS data', required=True)
     parser.add_argument('-f','--fr-data-dir', help='Directory with FR data', required=True)
+    parser.add_argument('-o','--outputs-dir', help='Directory for outputs data', required=False,default=None)
 
     args = vars(parser.parse_args())
 
diff --git a/tools/gms/compile_computational_stats.py b/tools/gms/compile_computational_stats.py
new file mode 100755
index 000000000..f7ab6daed
--- /dev/null
+++ b/tools/gms/compile_computational_stats.py
@@ -0,0 +1,32 @@
+#!/usr/bin/env python3
+
+import argparse
+import pandas as pd
+import numpy as np
+from glob import iglob
+from os.path import join
+
+# desired output for branches
+# dataframe columns: HUC, branch_id, exit status, ,time, ram, 
+
+def compile_summary(gms_output_dir,ouput=None):
+
+    unit_summary = join(gms_output_dir,logs, 'summary_gms_unit.log')
+    branch_summary = join(gms_output_dir,logs, 'summary_gms_branch.log')
+
+    unit_summary = pd.read_csv(unit_summary,sep='\t')
+    branch_summary = pd.read_csv(branch_summary,sep='\t')
+
+
+
+
+if __name__ == '__main__':
+
+    parser = argparse.ArgumentParser(description='Create stream network level paths')
+    parser.add_argument('-d','--gms-output-dir', help='Input stream network', required=True)
+    parser.add_argument('-o','--output', help='Input stream network', required=True)
+    
+    args = vars(parser.parse_args())
+
+    compile_summary(**args)
+