diff --git a/README.md b/README.md
index b3d42a9..8001d6d 100644
--- a/README.md
+++ b/README.md
@@ -1,23 +1,22 @@
 ## 3DCS Parallel Workflow
-This workflow enables running a 3DCS Monte Carlo or contributor analysis job using multiple workers on a SLURM cluster in the cloud. Here’s how to use it:
+This workflow enables running a 3DCS Monte Carlo or contributor analysis job using multiple workers on a SLURM cluster in the cloud. Here's how to use it:
 
 ### 1. Upload Files
-- Upload your model’s files to a cloud bucket on the platform (see this [link](https://parallelworks.com/docs/storage/transferring-data/obtaining-credentials)).
+- Upload your model's files to a cloud bucket on the platform (see this [link](https://parallelworks.com/docs/storage/transferring-data/obtaining-credentials)).
 
 ### 2. Run the Job
-- Fill in the workflow’s input form.
+- Fill in the workflow's input form.
 - Click the execute button.
 - For parameter descriptions, hover over the help (?) icon next to each parameter's name.
 
 ### 3. Job Execution
-- The job is divided into sub-jobs based on the selected number of workers.
-- Each worker uses the specified number of threads.
+- Before running, the workflow checks that your group has sufficient 3DCS allocation balance.
+- The job is divided into sub-jobs based on the selected number of workers (up to 20).
+- Each worker is submitted as an individual SLURM job and uses the specified number of threads.
 - The simulation runs in the resource defined in the simulation executor section of the input form.
 
 ### 4. Node Utilization
-- The "max workers per node" parameter sets the maximum number of workers per node.
-- To reduce compute costs, estimate the required memory for a single worker and maximize memory utilization by fitting as many workers as possible on a single node.
-- Required memory for N workers is N times the memory for a single worker. However, the required memory for N threads is more than N times the memory for a single thread.
+- The `#SBATCH --exclusive` flag is set by default in the SLURM directives due to issues running multiple 3DCS workers on a single node. This means each worker occupies a full node.
 
 ![Sample Configuration](https://raw.githubusercontent.com/parallelworks/dcs-workflow/main/2-Nodes_4-Workers_2-Threads_Per_Worker_Configuration.png)
 
@@ -33,3 +32,4 @@ This workflow enables running a 3DCS Monte Carlo or contributor analysis job usi
 - 3DCS usage is calculated based on the total number of hours a node uses any number of 3DCS workers.
 - For example, if 2 nodes run a 3DCS job for 10 hours with 3 workers per node and 4 threads per worker, the usage is 2 nodes x 10 hours = 20 hours.
 - To minimize 3DCS license usage, fit as many workers as possible on a single node.
+- Usage data is continuously transferred to the metering server during the run.
diff --git a/honda-japan.yaml b/honda-japan.yaml
index 208bd28..3f62fe1 100644
--- a/honda-japan.yaml
+++ b/honda-japan.yaml
@@ -1,30 +1,471 @@
 permissions:
   - '*'
+env:
+  MAX_JOBS: '40'
 jobs:
-  main:
+
+  local_preprocessing:
     steps:
-      - name: Main
-        run: bash main.sh > logs/main/step_0/logs.out 2>&1 
-        cleanup: |
-          touch COMPLETED
-          source resources/001_simulation_executor/inputs.sh
-          timeout 180 bash cancel.sh  || true
-          exit 0
-  stream:
+
+      - name: Checkout
+        uses: parallelworks/checkout
+        with:
+          repo: https://github.com/parallelworks/dcs-workflow.git
+          branch: v4
+
+      - name: Sanity Checks
+        run: |
+          source /etc/profile.d/parallelworks.sh
+          source /etc/profile.d/parallelworks-env.sh
+
+          python3 scripts/get_group_allocation_balance.py ${{ inputs.run_hours_3dcs_group }} ${{ inputs.org_name }}
+          if [ $? -ne 0 ]; then
+              echo "$(date) ERROR: No 3DCS balance is available. Exiting workflow." >&2
+              exit 1
+          fi
+
+  usage_metering:
+    needs:
+      - local_preprocessing
     steps:
-      - name: Stream Logs
+      - name: Usage Metering
         early-cancel: any-job-failed
-        run: bash stream.sh > logs/stream/step_0/logs.out 2>&1 
+        run: |
+          #!/bin/bash
+          mkdir -p usage
+          while true; do
+              sleep 60
+              echo "$(date) INFO: Transferring usage data" 
+              set -x
+              rsync -avz --delete ${{ inputs.resource.ip }}:${PW_PARENT_JOB_DIR}/usage/ usage
+              rsync -avz ${PWD}/usage/ ${{ inputs.metering_user }}@${{ inputs.metering_ip }}:~/.3dcs/usage-pending
+              set +x
+          done
+
+  remote_preprocessing:
+    needs:
+      - local_preprocessing
+    ssh:
+      remoteHost: ${{ inputs.resource.ip }}
+    steps:
+      - name: Checkout
+        uses: parallelworks/checkout
+        with:
+          repo: https://github.com/parallelworks/dcs-workflow.git
+          branch: v4
+
+
+      - name: Sanity Checks
+        run: |
+          if [[ "${{ inputs.dcs.output_directory }}" == "${{ inputs.dcs.model_directory }}" || "${{ inputs.dcs.output_directory }}" == "${{ inputs.dcs.model_directory }}/"* ]]; then
+              echo "$(date) ERROR: Output directory ${{ inputs.dcs.output_directory }} is a subdirectory of model directory ${{ inputs.dcs.model_directory }}. Exiting workflow" >&2
+              exit 1
+          fi
+
+          # Check if file is provided as an argument
+          if ! [ -f "dcs_environment/${{ inputs.dcs.version }}.sh" ]; then
+              echo "$(date) ERROR: Missing file dcs_environment/${{ inputs.dcs.version }}.sh required to load and run 3DCS. Exiting workflow." >&2
+              exit 1
+          fi
+
+      - name: Transfer and Process Input Files
+        run: |
+          set -x
+
+          mkdir tmp-data-transfer
+          cd tmp-data-transfer
+
+          pw buckets cp -r ${{ inputs.dcs.bucket.uri }}/${{ inputs.dcs.model_directory }} .
+
+          # Find all files ending in ".wtx" in the current directory, excluding subdirectories
+          export dcs_model_file=$(find . -type f -name "*.wtx")
+
+          # Check if dcs_model_file is empty
+          if [ -z "$dcs_model_file" ]; then
+              echo "$(date) ERROR: No '.wtx' files found. Exiting workflow" >&2
+              exit 1
+          fi
+
+          echo "dcs_model_file=${PW_PARENT_JOB_DIR}/${dcs_model_file}" >> $OUTPUTS
+
+          # Count the number of files found
+          file_count=$(echo "$dcs_model_file" | wc -l)
+
+          # Check if only one file ending in ".wtx" is found
+          if [ "$file_count" -eq 1 ]; then
+              echo "Found file ${dcs_model_file}"
+          else
+              echo "$(date) ERROR: Found $file_count '.wtx' files. Expected only one. Exiting workflow" >&2
+              exit 1
+          fi
+
+          # Get the count of directories in the current directory
+          dir_count=$(ls -d */ | wc -l)
+
+          # If there's only one directory
+          if [ "$dir_count" -eq 1 ]; then
+              # Get the name of the directory
+              fea_dir=$(ls -d */ | head -n 1)
+              export fea_dir=${fea_dir%/}  # Remove trailing slash
+              echo "Directory found: $fea_dir"
+          else
+              # If no directory or multiple directories exist
+              echo "Error: Either no FEA directory found or multiple directories exist." >&2
+              exit 1
+          fi
+
+          # Process WTX file to adapt the paths to the files
+          retries=5
+          while true; do
+              python3 ${PW_PARENT_JOB_DIR}/scripts/adapt_wtx_paths.py ${dcs_model_file} ${fea_dir}
+              exit_code=$?
+              if [ ${exit_code} -ne 0 ]; then
+                retries=$((retries-1))
+                if [ ${retries} -gt 0 ]; then
+                    sleep 10
+                else
+                    echo
+                    echo "$(date) ERROR: Failed to process WTX file with adapt_wtx_paths.py"  >&2
+                    exit 1
+                fi
+              else
+                break
+              fi
+          done
+
+          # List all downloaded file
+          find . -mindepth 1 > downloaded_files.txt
+
+          cd ..
+          mv tmp-data-transfer/*  .
+          rmdir tmp-data-transfer
+
+      - name: General Preprocessing
+        run: |
+          set -x
+          source dcs_environment/${{ inputs.dcs.version }}.sh 
+          ls -latd ${WINEPREFIX}
+          sudo chown -R ${USER}:pwuser ${WINEPREFIX}
+          ls -latd ${WINEPREFIX}
+
+          mkdir ./usage
+          mkdir ./usage_completed
+
+          cat <<'EOF' >> inputs.sh
+          export PATH=$HOME/pw:$PATH
+          export dcs_model_file="${{ needs.remote_preprocessing.outputs.dcs_model_file }}"
+          export dcs_dry_run="${{ inputs.dcs.dry_run }}"
+          export dcs_version="${{ inputs.dcs.version }}"
+          export dcs_analysis_type="${{ inputs.dcs.analysis_type }}"
+          export dcs_bucket_uri="${{ inputs.dcs.bucket.uri }}"
+          export dcs_model_directory="${{ inputs.dcs.model_directory }}"
+          export dcs_output_directory="${{ inputs.dcs.output_directory }}"
+          export dcs_num_seeds="${{ inputs.dcs.num_seeds }}"
+          export dcs_concurrency="${{ inputs.dcs.concurrency }}"
+          export dcs_thread="${{ inputs.dcs.thread }}"
+          export metering_user="${{ inputs.metering_user }}"
+          export metering_ip="${{ inputs.metering_ip }}"
+          export run_hours_3dcs_group="${{ inputs.run_hours_3dcs_group }}"
+          export org_name="${{ inputs.org_name }}"
+          export monitoring_conda_dir="${{ inputs.monitoring_conda_dir }}"
+          export monitoring_conda_env="${{ inputs.monitoring_conda_env }}"
+          EOF
+          echo "export PW_PARENT_JOB_DIR=${PW_PARENT_JOB_DIR}" >> inputs.sh
+          echo "export PW_WORKFLOW_NAME=${PW_WORKFLOW_NAME}" >> inputs.sh
+          echo "export PW_JOB_NUMBER=${PW_JOB_NUMBER}" >> inputs.sh
+
+          echo "$(date) INFO: Inputs file"
+          cat inputs.sh
+
+      - name: Installing Python Dependencies for CPU and Memory Monitoring
+        run: |
+          source inputs.sh
+
+          install_miniconda() {
+              local install_dir=$1
+              local conda_repo="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"
+              local ID="${RANDOM}-$(date +%s)" # This script may run at the same time!
+              echo "Installing Miniconda to ${install_dir}"
+              wget --no-check-certificate "${conda_repo}" -O "/tmp/miniconda-${ID}.sh" > "/tmp/miniconda_wget-${ID}.out" 2>&1
+              rm -rf "${install_dir}"
+              mkdir -p "$(dirname "${install_dir}")"
+              bash "/tmp/miniconda-${ID}.sh" -b -p "${install_dir}" > "/tmp/miniconda_sh-${ID}.out" 2>&1
+          }
+
+          create_conda_env_from_yaml() {
+              local CONDA_DIR=$1
+              local CONDA_ENV=$2
+              local CONDA_YAML=$3
+              local CONDA_SH="${CONDA_DIR}/etc/profile.d/conda.sh"
+
+              # Remove name/prefix fields and empty lines so conda env update accepts the file
+              sed -i -e 's/name.*$//' -e 's/prefix.*$//' -e '/^$/d' "${CONDA_YAML}"
+
+              if [ ! -d "${CONDA_DIR}" ]; then
+                  echo "Conda directory <${CONDA_DIR}> not found. Installing Conda..."
+                  install_miniconda "${CONDA_DIR}"
+              fi
+
+              echo "Sourcing Conda: ${CONDA_SH}"
+              source "${CONDA_SH}"
+
+              if conda env list | grep -q "^${CONDA_ENV} "; then
+                  echo "Conda environment <${CONDA_ENV}> already exists. Skipping installation."
+              else
+                  echo "Conda environment <${CONDA_ENV}> not found. Creating from <${CONDA_YAML}>..."
+                  conda env update -n "${CONDA_ENV}" -q -f "${CONDA_YAML}" || {
+                      echo "ERROR: Failed to create conda environment <${CONDA_ENV}>. Exiting."
+                      exit 1
+                  }
+              fi
+
+              conda activate "${CONDA_ENV}"
+          }
+
+
+          create_conda_env_from_yaml ${monitoring_conda_dir} ${monitoring_conda_env} scripts/cpu_and_memory_usage_requirements.yaml
+
+      - name: Dry Run
+        if: ${{ inputs.dcs.dry_run == true }}
+        run: |
+          echo "$(date) INFO: Running the workflow in dry run mode"
+          echo > scripts/activate_monitoring.sh
+          echo > scripts/plot_monitoring.sh
+          echo > scripts/activate_monitoring.sh
+          mv scripts/dry_run.sh scripts/run_dcs.sh
+          mv scripts/merge/dry_run.sh scripts/merge/run_dcs.sh
+
+
+      - name: Create Job Scripts
+        run: |
+          set -x
+
+          source inputs.sh
+
+          if [ ${dcs_concurrency} -gt ${MAX_JOBS} ]; then
+            echo "$(date) ERROR: Selected number of jobs is greater than maximum number of jobs. Exiting workflow."
+            exit 1
+          fi
+
+          for nj in $(seq 1 ${dcs_concurrency}); do
+            echo "$(date) INFO: Preparing directory for job ${nj}"
+            job_dir=job_dir_${nj}
+            mkdir -p ${job_dir}
+
+            echo '#!/bin/bash' > ${job_dir}/cancel.sh
+            chmod +x ${job_dir}/cancel.sh
+
+            cat inputs.sh >> ${job_dir}/run_case.sh
+            echo "export case_index=${nj}" >> ${job_dir}/run_case.sh
+
+            cat dcs_environment/${dcs_version}.sh >> ${job_dir}/run_case.sh
+            echo >> ${job_dir}/run_case.sh
+            echo "touch job.started" >> ${job_dir}/run_case.sh
+            echo >> ${job_dir}/run_case.sh
+
+            cat scripts/${dcs_analysis_type}.sh >> ${job_dir}/run_case.sh
+            cat scripts/activate_monitoring.sh >> ${job_dir}/run_case.sh
+            cat scripts/run_dcs.sh >> ${job_dir}/run_case.sh
+            cat scripts/plot_monitoring.sh >> ${job_dir}/run_case.sh
+            cat scripts/transfer_outputs.sh >> ${job_dir}/run_case.sh
+          done
+
 
   estimate_end_time:
+    needs:
+      - remote_preprocessing
+    ssh:
+      remoteHost: ${{ inputs.resource.ip }}
     steps:
       - name: Estimate End Time
-        early-cancel: any-job-failed
-        run: bash estimate_end_time.sh > logs/estimate_end_time/step_0/logs.out 2>&1 
-        cleanup: |
-          bash cancel_stream.sh || true
+        run: |
+
+          # Source the inputs file
+          source inputs.sh
+
+          if [ ${dcs_thread} -eq 1 ]; then
+              echo "$(date) INFO: Number of threads must be larger than 1 to enable estimates"
+              echo "$(date) INFO: Exiting job..."
+          fi 
+
+          log_path="TempData/dcsSimuMacro_SA_log_x64_$(echo ${dcs_version} | tr '.' '_').txt"
+
+          wait_for_all_simulations_to_start() {
+              while true; do
+                  n_running_workers=$(ls -d job_dir_*/job.started | wc -l)
+                  if [ $? -ne 0 ]; then
+                      n_running_workers=0
+                  fi
+                  if [ "${n_running_workers}" -lt "${dcs_concurrency}" ]; then
+                      echo "$(date) INFO: ${n_running_workers}/${dcs_concurrency} simulations started"
+                      echo "$(date) INFO: Waiting for all simulations to start..."
+                      sleep 15
+                  else
+                      break
+                  fi
+              done
+          }
+
+          wait_for_all_simulations_to_start
+
+          echo "$(date) INFO: All simulations are started!"
+          echo; echo
+          echo "$(date) INFO: Calculating completion time estimates"
+
+          while true; do
+            log_files=$(ls -d ./job_dir_*/${log_path})
+            log_files=$(echo ${log_files} | tr ' ' ',')
+
+            echo "$(date) INFO: Log files:"
+            echo ${log_files} | tr ',' '\n'
+
+            python3 scripts/estimate_end_time.py ${log_files}
+            sleep 120
+          done
           exit 0
 
+  workers:
+    needs:
+      - remote_preprocessing
+    strategy:
+      fail-fast: true
+      max-parallel: ${{ inputs.dcs.concurrency }}
+      matrix:
+        job_id:
+          - 1
+          - 2
+          - 3
+          - 4
+          - 5
+          - 6
+          - 7
+          - 8
+          - 9
+          - 10
+          - 11
+          - 12
+          - 13
+          - 14
+          - 15
+          - 16
+          - 17
+          - 18
+          - 19
+          - 20
+          - 21
+          - 22
+          - 23
+          - 24
+          - 25
+          - 26
+          - 27
+          - 28
+          - 29
+          - 30
+          - 31
+          - 32
+          - 33
+          - 34
+          - 35
+          - 36
+          - 37
+          - 38
+          - 39
+          - 40
+    if: ${{ matrix.job_id <= inputs.dcs.concurrency }}
+    working-directory: ${PW_PARENT_JOB_DIR}/job_dir_${{ matrix.job_id }}
+    ssh:
+      remoteHost: ${{ inputs.resource.ip }}
+    steps:
+      - uses: github/parallelworks/workflows@canary
+        early-cancel: any-job-failed
+        with:
+          $yaml: workflows/script_submitter/v3.6/general.yaml
+          resource: ${{ inputs.resource }}
+          shebang: '#!/bin/bash'
+          rundir: ${PW_PARENT_JOB_DIR}/job_dir_${{ matrix.job_id }}
+          use_existing_script: true
+          script_path: ./run_case.sh
+          define_cleanup_script: true
+          cleanup_script_path: ./cancel.sh
+          scheduler: true
+          use_scheduler_agent: false
+          slurm:
+            is_enabled: true
+            partition: ${{ inputs.slurm.partition }}
+            scheduler_directives: ${{ inputs.slurm.scheduler_directives }}
+            time: ${{ inputs.slurm.time }}
+          pbs:
+            is_enabled: false
+
+  merge:
+    if: ${{ always }}
+    needs:
+      - workers
+    ssh:
+      remoteHost: ${{ inputs.resource.ip }}
+    steps:
+      - name: Cancel End Time Estimation
+        uses: parallelworks/cancel-jobs
+        with:
+          jobs:
+            - estimate_end_time
+      - name: Create Merge Script
+        early-cancel: any-job-failed
+        run: |
+          set -x 
+          source inputs.sh
+
+          # Only run merge if more than one job was submitted
+          if [ ${dcs_concurrency} == 1 ]; then
+            echo "$(date) INFO: 3DCS concurrency is 1. Exiting workflow."
+            echo "run_merge=false" | tee -a $OUTPUTS
+            exit 0
+          fi
+          echo "run_merge=true" | tee -a $OUTPUTS
+
+          echo "$(date) INFO: Preparing merge job"
+          mkdir -p merge
+
+          echo '#!/bin/bash' > merge/cancel.sh
+          chmod +x merge/cancel.sh
+
+          cat inputs.sh > merge/merge.sh
+          cat dcs_environment/${dcs_version}.sh >> merge/merge.sh
+          cat scripts/merge/transfer_inputs.sh >> merge/merge.sh
+          cat scripts/merge/${dcs_analysis_type}.sh >> merge/merge.sh
+          cat scripts/merge/run_dcs.sh >> merge/merge.sh
+          cat scripts/merge/clean_job_directory.sh >> merge/merge.sh
+          cat scripts/merge/transfer_outputs.sh >> merge/merge.sh
+ 
+      - uses: github/parallelworks/workflows@canary
+        if: ${{ needs.merge.outputs.run_merge == "true" }}
+        early-cancel: any-job-failed
+        with:
+          $yaml: workflows/script_submitter/v3.6/general.yaml
+          resource: ${{ inputs.resource }}
+          shebang: '#!/bin/bash'
+          rundir: ${PW_PARENT_JOB_DIR}/merge
+          use_existing_script: true
+          script_path: ./merge.sh
+          define_cleanup_script: true
+          cleanup_script_path: ./cancel.sh
+          scheduler: true
+          use_scheduler_agent: false
+          slurm:
+            is_enabled: true
+            partition: ${{ inputs.slurm.partition }}
+            scheduler_directives: ${{ inputs.slurm.scheduler_directives }}
+            time: ${{ inputs.slurm.time }}
+          pbs:
+            is_enabled: false
+
+      - name: Cancel Usage Metering
+        uses: parallelworks/cancel-jobs
+        with:
+          jobs:
+            - usage_metering
+
 
 'on':
   execute:
@@ -49,6 +490,21 @@ jobs:
         type: string
         default: honda
         hidden: true
+      monitoring_conda_dir:
+        label: PW Conda Directory
+        type: string
+        default: /dcs/pw/miniconda
+        hidden: true
+      monitoring_conda_env:
+        label: PW Conda Environment
+        type: string
+        default: psutil
+        hidden: true
+      resource:
+        type: compute-clusters
+        label: Service host
+        include-workspace: false
+        tooltip: Resource to host the service
       dcs:
         type: group
         label: 3DCS Options
@@ -80,10 +536,10 @@ jobs:
                 label: Monte Carlo Simulation
               - value: sensitivity
                 label: Contributor Analysis
-          bucket_id:
-            label: Bucket ID or namespace
-            type: string
-            tooltip: Type in the bucket ID string or namespace in the format [bucket-owner]/[bucket-name]
+          bucket:
+            label: Bucket
+            type: bucket
+            tooltip: Select the storage bucket used to download input files and upload output files.
           model_directory:
             label: Model Path
             type: string
@@ -105,7 +561,7 @@ jobs:
             label: Number of Workers
             type: number
             min: 1
-            max: 50
+            max: 40
             default: 1
             tooltip: Number of workers used to run the simulations. A SLURM job is submitted for each worker.
           thread:
@@ -115,84 +571,25 @@ jobs:
             max: 64
             default: 1
             tooltip: Number of threads used to run the simulation. Be aware that N threads require more than N times the memory needed for a single thread.
-
-      pwrl_001_simulation_executor:
+      slurm:
         type: group
-        label: Simulation Executor
+        label: SLURM Directives
         items:
-          monitoring_conda_dir:
-            label: PW Conda Directory
-            type: string
-            default: /dcs/pw/miniconda
-            hidden: true
-          monitoring_conda_env:
-            label: PW Conda Environment
-            type: string
-            default: psutil
-            hidden: true
-          resource:
-            label: Resource
-            type: compute-clusters
-            tooltip: Resource to run the simulation task
-            include-workspace: false
-          jobschedulertype:
-            label: Select Controller, SLURM Partition or PBS Queue
-            type: string
-            default: SLURM
-            hidden: true
-          _sch__dd_partition_e_:
+          partition:
             type: slurm-partitions
             label: SLURM partition
             optional: true
-            tooltip: Partition to submit the job. Leave empty to let SLURM pick the optimal option.
-            resource: ${{ inputs.pwrl_001_simulation_executor.resource }}
-          _sch__dd_time_e_:
+            resource: ${{ inputs.resource }}
+            tooltip: Select a partition from the drop down menu.
+          time:
             label: Walltime
             type: string
             default: '999:00:00'
-            tooltip: Maximum walltime per job
+            tooltip: '--time= SLURM directive to set the maximum wall-clock time limit for the job'
           scheduler_directives:
-            label: Scheduler directives
-            type: string
-            default: '--exclusive'
-            tooltip: e.g. --mem=1000;--gpus-per-node=1 - Use the semicolon character ; to separate parameters. Do not include the SBATCH keyword.
-      pwrl_002_merge_executor:
-        type: group
-        label: Merge Executor
-        items:
-          monitoring_conda_dir:
-            label: PW Conda Directory
-            type: string
-            default: /dcs/pw/miniconda
-            hidden: true
-          monitoring_conda_env:
-            label: PW Conda Environment
-            type: string
-            default: psutil
-            hidden: true
-          resource:
-            label: Resource
-            type: compute-clusters
-            tooltip: Resource to run the simulation task
-            include-workspace: false
-          jobschedulertype:
-            label: Select Controller, SLURM Partition or PBS Queue
-            type: string
-            default: SLURM
-            hidden: true
-          _sch__dd_partition_e_:
-            type: slurm-partitions
-            label: SLURM partition
+            type: editor
             optional: true
-            tooltip: Partition to submit the job. Leave empty to let SLURM pick the optimal option.
-            resource: ${{ inputs.pwrl_002_merge_executor.resource }}
-          _sch__dd_time_e_:
-            label: Walltime
-            type: string
-            default: '999:00:00'
-            tooltip: Maximum walltime per job
-          scheduler_directives:
-            label: Scheduler directives
-            type: string
-            default: '--exclusive'
-            tooltip: e.g. --mem=1000;--gpus-per-node=1 - Use the semicolon character ; to separate parameters. Do not include the SBATCH keyword.
+            tooltip: |
+              Type in additional scheduler directives.
+            default: |
+              #SBATCH --exclusive
\ No newline at end of file
diff --git a/main.sh b/main.sh
index 1f1d348..650b5f5 100755
--- a/main.sh
+++ b/main.sh
@@ -2,17 +2,6 @@
 source inputs.sh
 chmod +x cancel.sh
 
-if [[ "${dcs_output_directory}" == "${dcs_model_directory}" || "${dcs_output_directory}" == "${dcs_model_directory}/"* ]]; then
-    echo "Error: Output directory is a subdirectory of model directory." >&2
-    exit 1
-fi
-
-# Check if file is provided as an argument
-if ! [ -f "dcs_environment/${dcs_version}.sh" ]; then
-    echo "Error: Missing file dcs_environment/${dcs_version}.sh required to load and run 3DCS. Exiting workflow."
-    exit 1
-fi
-
 
 # Use the resource wrapper
 source /etc/profile.d/parallelworks.sh
@@ -38,7 +27,7 @@ fi
 
 # Check balance
 echo; echo "3DCS allocation balance"
-python3 get_group_allocation_balance.py ${run_hours_3dcs_group} ${org_name}
+python3 utils/get_group_allocation_balance.py ${run_hours_3dcs_group} ${org_name}
 
 
 if [ $? -ne 0 ]; then
@@ -102,6 +91,8 @@ scp bucket_credentials ${resource_publicIp}:${resource_jobdir}/bucket_credential
 reload_bucket_credential_pid=$!
 echo "kill ${reload_bucket_credential_pid} || true # bucket credentials" >> cancel.sh
 
+# HERE
+
 echo; echo; echo "PREPARING AND SUBMITTING 3DCS RUN JOBS"
 single_cluster_rsync_exec resources/001_simulation_executor/cluster_rsync_exec.sh
 return_code=$?
diff --git a/metering.sh b/metering.sh
deleted file mode 100755
index aa26f66..0000000
--- a/metering.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/bash
-mkdir -p usage
-while true; do
-    sleep 60
-    rsync -avz --delete ${resource_publicIp}:${resource_jobdir}/usage/ usage >> metering.out 2>&1
-    rsync -avz ${resource_jobdir}/usage/ ${metering_user}@${metering_ip}:~/.3dcs/usage-pending >> metering.out 2>&1
-done
\ No newline at end of file
diff --git a/reload_bucket_credentials.sh b/reload_bucket_credentials.sh
deleted file mode 100755
index 265f945..0000000
--- a/reload_bucket_credentials.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-source resources/001_simulation_executor/inputs.sh
-set -x
-while true; do
-    sleep 300
-    date
-    pw buckets get-token pw://${dcs_bucket_id} > bucket_credentials
-    source bucket_credentials
-    # Check if BUCKET_NAME is empty
-    if ! [ -n "${BUCKET_URI}" ]; then
-        echo "ERROR: Unable to load bucket credentials!"
-        exit 1
-    fi
-    scp bucket_credentials ${resource_publicIp}:${resource_jobdir}/bucket_credentials
-done
diff --git a/resources/001_simulation_executor/activate_monitoring.sh b/resources/001_simulation_executor/activate_monitoring.sh
deleted file mode 100644
index 5d809a2..0000000
--- a/resources/001_simulation_executor/activate_monitoring.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-source ${monitoring_conda_dir}/etc/profile.d/conda.sh 
-conda activate ${monitoring_conda_env}
-monitoring_txt="case-${case_index}-${HOSTNAME}-jobid-${SLURM_JOB_ID}.txt"
-python ${resource_jobdir}/${resource_label}/cpu_and_memory_usage.py --write-usage --txt ${monitoring_txt} &
-monitoring_pid=$!
-echo "kill ${monitoring_pid}" >> ${resource_jobdir}/${resource_label}/cancel.sh
diff --git a/resources/001_simulation_executor/cluster_rsync_exec.sh b/resources/001_simulation_executor/cluster_rsync_exec.sh
deleted file mode 100644
index 87f82f7..0000000
--- a/resources/001_simulation_executor/cluster_rsync_exec.sh
+++ /dev/null
@@ -1,122 +0,0 @@
-#!/bin/bash
-cd $(dirname $0)
-
-source inputs.sh
-source workflow-libs.sh
-
-source dcs_environment/${dcs_version}.sh 
-sudo chown -R ${USER}:pwuser ${WINEPREFIX}
-
-# Prepare for metering
-mkdir ${resource_jobdir}/usage
-mkdir ${resource_jobdir}/usage_completed
-
-echo '#!/bin/bash' > cancel.sh
-chmod +x cancel.sh
-
-create_case(){
-    # The merge tasks syncs the results from an S3 bucket. To simplify the path to the
-    # results in the S3 bucket ww use the resource job dir
-    case_dir=${resource_jobdir}/worker_${case_index}
-    mkdir -p ${case_dir}
-
-    echo "    Writing job script"
-    cp batch_header.sh  ${case_dir}/run_case.sh
-
-    if [[ ${jobschedulertype} == "SLURM" ]]; then 
-        echo "#SBATCH -o ${case_dir}/logs_${case_index}.out" >> ${case_dir}/run_case.sh
-        echo "#SBATCH -e ${case_dir}/logs_${case_index}.out" >> ${case_dir}/run_case.sh
-    elif [[ ${jobschedulertype} == "PBS" ]]; then
-        echo "#PBS -o ${case_dir}/logs_${case_index}.out" >> ${case_dir}/run_case.sh
-        echo "#PBS -e ${case_dir}/logs_${case_index}.out" >> ${case_dir}/run_case.sh
-    fi
-    
-    # Main script
-    echo "mkdir -p ${case_dir}" >> ${case_dir}/run_case.sh
-    echo "cd ${case_dir}" >> ${case_dir}/run_case.sh
-    
-    # FIXME: This is needed because run directory is not shared between controller and compute nodes
-    #echo "rsync -avzq ${resource_privateIp}:${case_dir}/ ."  >> ${case_dir}/run_case.sh
-
-    # Main script
-    echo >> ${case_dir}/run_case.sh
-    cat inputs.sh >> ${case_dir}/run_case.sh
-    cat dcs_environment/${dcs_version}.sh >> ${case_dir}/run_case.sh
-    echo "export case_index=${case_index}" >> ${case_dir}/run_case.sh
-    echo "export dcs_model_file=${dcs_model_file}" >> ${case_dir}/run_case.sh
-    echo >> ${case_dir}/run_case.sh
-
-    cat ${dcs_analysis_type}.sh >> ${case_dir}/run_case.sh
-    cat activate_monitoring.sh >> ${case_dir}/run_case.sh
-    cat run_dcs.sh >> ${case_dir}/run_case.sh
-    cat plot_monitoring.sh >> ${case_dir}/run_case.sh
-    echo "source ${resource_jobdir}/bucket_credentials" >> ${case_dir}/run_case.sh
-    cat transfer_outputs.sh >> ${case_dir}/run_case.sh
-
-}
-
-cat_slurm_logs() {
-    for f in  $(find ${resource_jobdir} -name logs_*.out); do
-	    echo; echo "Contents of ${f}:"
-	    cat ${f}
-    done
-	      
-}
-
-
-echo; echo; echo "STARTING INPUT DATA TRANSFER"
-source ${resource_jobdir}/bucket_credentials
-source transfer_inputs.sh
-
-if [[ ${dcs_dry_run} == "true" ]]; then
-    echo "RUNNING THE WORKFLOW IN DRY RUN MODE"
-    unset monitoring_conda_dir monitoring_conda_env
-    echo > activate_monitoring.sh
-    echo > plot_monitoring.sh
-    echo > activate_monitoring.sh
-    mv dry_run.sh run_dcs.sh
-else
-    rm dry_run.sh
-fi
-
-# If no conda environment is specified for the CPU and Mem python monitoring utility
-# the workflow assumes monitoring is disabled
-if [ -z "${monitoring_conda_dir}" ] || [ -z "${monitoring_conda_env}" ]; then
-    echo "CPU and Memory monitoring are disabled"
-    echo > activate_monitoring.sh
-    echo > plot_monitoring.sh
-else
-    echo; echo; echo "INSTALLING PYTHON DEPENDENCIES FOR CPU AND MEMORY MONITORING"
-    create_conda_env_from_yaml ${monitoring_conda_dir} ${monitoring_conda_env} ./cpu_and_memory_usage_requirements.yaml
-fi
-
-echo; echo; echo "CREATING JOB SCRIPTS"
-for case_index in $(seq 1 ${dcs_concurrency}); do
-    echo; echo "  Case ${case_index}"
-    create_case
-done
-
-echo; echo; echo "SUBMITTING JOB SCRIPTS"
-for case_index in $(seq 1 ${dcs_concurrency}); do
-    case_dir=${resource_jobdir}/worker_${case_index}
-    echo; echo "  Case ${case_index}"
-    cp ${resource_jobdir}/${dcs_model_file} ${case_dir}
-
-    submit_job_sh=${case_dir}/run_case.sh
-    echo "  Job script ${submit_job_sh}"
-
-    if [[ ${jobschedulertype} == "SLURM" ]]; then 
-        job_id=$(${submit_cmd} ${submit_job_sh} | tail -1 | awk -F ' ' '{print $4}')
-    elif [[ ${jobschedulertype} == "PBS" ]]; then
-        job_id=$(${submit_cmd} ${submit_job_sh} | tail -1)
-    fi
-    
-    if [ -z "${job_id}" ]; then
-        echo "  ERROR: ${submit_cmd} ${submit_job_sh} failed"
-        exit 1
-    else
-        echo "  Submitted job ${job_id}"
-        echo "${cancel_cmd} ${job_id}" >> ${resource_jobdir}/${resource_label}/cancel.sh
-        echo ${job_id} > ${case_dir}/job_id.submitted
-    fi
-done
\ No newline at end of file
diff --git a/resources/001_simulation_executor/plot_monitoring.sh b/resources/001_simulation_executor/plot_monitoring.sh
deleted file mode 100644
index 7327892..0000000
--- a/resources/001_simulation_executor/plot_monitoring.sh
+++ /dev/null
@@ -1 +0,0 @@
-python ${resource_jobdir}/${resource_label}/cpu_and_memory_usage.py --plot-usage --txt ${monitoring_txt}
diff --git a/resources/001_simulation_executor/run_dcs.sh b/resources/001_simulation_executor/run_dcs.sh
deleted file mode 100644
index b3aaff3..0000000
--- a/resources/001_simulation_executor/run_dcs.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-# run in bat file to get correct exit code from the software
-#echo set DCS2FLMD_LICENSE_FILE="$DCS2FLMD_LICENSE_FILE" > run.bat
-
-# Create metering script
-cat >> metering.sh <<HERE
-#!/bin/bash 
-while true; do
-    date >> ${resource_jobdir}/usage/$(hostname)-${job_number}
-    sleep \$((RANDOM % 30 + 30))
-done
-HERE
-
-chmod +x metering.sh
-./metering.sh &
-metering_pid=$!
-
-# Run 3dcs
-SECONDS=0
-eval "${dcs_run}"  macroScript.txt
-kill ${metering_pid}
-mv ${resource_jobdir}/usage/$(hostname)-${job_number} ${resource_jobdir}/usage_completed/$(hostname)-${job_number}
-
-# Results is own by root
-sudo chmod 777 Results/ -R
-echo ${SECONDS} > Results/dcs-runtime_${case_index}.txt
-
diff --git a/resources/001_simulation_executor/transfer_outputs.sh b/resources/001_simulation_executor/transfer_outputs.sh
deleted file mode 100644
index 7ff846d..0000000
--- a/resources/001_simulation_executor/transfer_outputs.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-# HARDCODED TO AWS
-# A dynamicStorage parameter type would be very helpful for this
-unset BUCKET_URI
-unset AWS_ACCESS_KEY_ID
-unset AWS_SECRET_ACCESS_KEY
-unset AWS_SESSION_TOKEN
-
-source ${resource_jobdir}/bucket_credentials
-
-# Loop until all variables are non-empty
-while [[ -z "$BUCKET_URI" \
-     || -z "$AWS_ACCESS_KEY_ID" \
-     || -z "$AWS_SECRET_ACCESS_KEY" \
-     || -z "$AWS_SESSION_TOKEN" ]]
-do
-    echo "$(date) Waiting for required environment variables to be set..."
-    sleep 5
-    source ${resource_jobdir}/bucket_credentials
-done
-
-# Copy path/to/worker_<i> to bucket
-aws s3 cp --recursive ${PWD} ${BUCKET_URI}/${dcs_output_directory}/${USER}/${workflow_name}/${job_number}/$(basename ${PWD})
diff --git a/resources/002_merge_executor/cluster_rsync_exec.sh b/resources/002_merge_executor/cluster_rsync_exec.sh
deleted file mode 100644
index 038d050..0000000
--- a/resources/002_merge_executor/cluster_rsync_exec.sh
+++ /dev/null
@@ -1,62 +0,0 @@
-#!/bin/bash
-cd $(dirname $0)
-
-source inputs.sh
-source workflow-libs.sh
-
-if [[ ${dcs_dry_run} == "true" ]]; then
-    echo "RUNNING THE WORKFLOW IN DRY RUN MODE"
-    mv dry_run.sh run_dcs.sh 
-else
-    rm dry_run.sh
-fi
-
-echo; echo; echo "MERGING RESULTS"
-pwd
-echo "    Writing job script"
-cp batch_header.sh merge.sh
-
-if [[ ${jobschedulertype} == "SLURM" ]]; then 
-    echo "#SBATCH -o ${PWD}/${case_dir}/logs_merge.out" >> merge.sh
-    echo "#SBATCH -e ${PWD}/${case_dir}/logs_merge.out" >> merge.sh
-elif [[ ${jobschedulertype} == "PBS" ]]; then
-    echo "#PBS -o ${PWD}/${case_dir}/logs_merge.out" >> merge.sh
-    echo "#PBS -e ${PWD}/${case_dir}/logs_merge.out" >> merge.sh
-fi
-    
-# FIXME: This is needed because run directory is not shared between controller and compute nodes
-#echo "rsync -avzq ${resource_privateIp}:${PWD}/ ."  >> merge.sh
-
-
-# Main script
-cat inputs.sh >> merge.sh
-cat dcs_environment/${dcs_version}.sh >> merge.sh
-echo "source ${resource_jobdir}/bucket_credentials" >> merge.sh
-cat transfer_inputs.sh >> merge.sh
-cat ${dcs_analysis_type}.sh >> merge.sh
-cat run_dcs.sh >> merge.sh
-echo "source ${resource_jobdir}/bucket_credentials" >> merge.sh
-cat clean_job_directory.sh >> merge.sh
-cat transfer_outputs.sh >> merge.sh
-
-# FIXME: This is needed because run directory is not shared between controller and compute nodes
-#echo "rsync -avzq . ${resource_privateIp}:${PWD}/"  >> merge.sh
-
-echo; echo; echo "SUBMITTING MERGE JOB"
-submit_job_sh=./merge.sh
-echo "  Job script ${submit_job_sh}"
-
-if [[ ${jobschedulertype} == "SLURM" ]]; then 
-    jobid=$(${submit_cmd} ${submit_job_sh} | tail -1 | awk -F ' ' '{print $4}')
-elif [[ ${jobschedulertype} == "PBS" ]]; then
-    jobid=$(${submit_cmd} ${submit_job_sh} | tail -1)
-fi
-    
-if [ -z "${jobid}" ]; then
-    echo "  ERROR: ${submit_cmd} ${submit_job_sh} failed"
-    cat ${PWD}/${case_dir}/logs_merge.out
-    exit 1
-fi
-
-echo ${jobid} > ${resource_jobdir}/job_id.submitted
-echo "${cancel_cmd} ${jobid}" >> ${resource_jobdir}/${resource_label}/cancel.sh
\ No newline at end of file
diff --git a/resources/002_merge_executor/transfer_inputs.sh b/resources/002_merge_executor/transfer_inputs.sh
deleted file mode 100644
index 5e59b4c..0000000
--- a/resources/002_merge_executor/transfer_inputs.sh
+++ /dev/null
@@ -1,27 +0,0 @@
-# HARDCODED TO AWS
-# A dynamicStorage parameter type would be very helpful for this
-
-# Transfer model
-# dcs_model_directory can end with or without /
-aws s3 sync ${BUCKET_URI}/${dcs_model_directory} .
-aws s3 sync ${BUCKET_URI}/${dcs_output_directory}/${USER}/${workflow_name}/${job_number} .
-
-# Find all files ending in ".wtx" in the current directory, excluding subdirectories
-dcs_model_file=$(find . -maxdepth 1 -type f -name "*.wtx")
-
-# Check if dcs_model_file is empty
-if [ -z "$dcs_model_file" ]; then
-    echo "Error: No '.wtx' files found."
-    exit 1
-fi
-
-# Count the number of files found
-file_count=$(echo "$dcs_model_file" | wc -l)
-
-# Check if only one file ending in ".wtx" is found
-if [ "$file_count" -eq 1 ]; then
-    echo "Found file ${dcs_model_file}"
-else
-    echo "Error: Found $file_count '.wtx' files. Expected only one."
-    exit 1
-fi
diff --git a/resources/002_merge_executor/transfer_outputs.sh b/resources/002_merge_executor/transfer_outputs.sh
deleted file mode 100644
index 4ab73ab..0000000
--- a/resources/002_merge_executor/transfer_outputs.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-# HARDCODED TO AWS
-# A dynamicStorage parameter type would be very helpful for this
-
-aws s3 cp ${resource_label}/merge.sh ${BUCKET_URI}/${dcs_output_directory}/${USER}/${workflow_name}/${job_number}/merge.sh
-aws s3 cp --recursive Results ${BUCKET_URI}/${dcs_output_directory}/${USER}/${workflow_name}/${job_number}/Results
-aws s3 cp --recursive TempData ${BUCKET_URI}/${dcs_output_directory}/${USER}/${workflow_name}/${job_number}/TempData
diff --git a/scripts/activate_monitoring.sh b/scripts/activate_monitoring.sh
new file mode 100644
index 0000000..1a4d243
--- /dev/null
+++ b/scripts/activate_monitoring.sh
@@ -0,0 +1,6 @@
+source ${monitoring_conda_dir}/etc/profile.d/conda.sh 
+conda activate ${monitoring_conda_env}
+monitoring_txt="case-${case_index}-${HOSTNAME}-jobid-${SLURM_JOB_ID}.txt"
+python ${PW_PARENT_JOB_DIR}/scripts/cpu_and_memory_usage.py --write-usage --txt ${monitoring_txt} &
+monitoring_pid=$!
+echo "kill ${monitoring_pid} || true # kill monitoring" >> cancel.sh
diff --git a/resources/001_simulation_executor/adapt_wtx_paths.py b/scripts/adapt_wtx_paths.py
similarity index 79%
rename from resources/001_simulation_executor/adapt_wtx_paths.py
rename to scripts/adapt_wtx_paths.py
index b686555..f7c6a75 100644
--- a/resources/001_simulation_executor/adapt_wtx_paths.py
+++ b/scripts/adapt_wtx_paths.py
@@ -2,7 +2,6 @@
 import sys
 
 wtx_file_path = sys.argv[1]
-fea_dir = sys.argv[2].replace('/', '')
 
 def replace_between_angle_brackets(input_string, replacement):
     """
@@ -27,14 +26,6 @@ def write_lines_to_file(lines, file_path, encoding='utf-8'):
     with open(file_path, 'w', encoding=encoding) as file:
         file.writelines(lines)
 
-def get_search_file_paths(file_paths):
-    """
-    Create search patterns for the file paths.
-
-    :param file_paths: List of file paths.
-    :return: List of search patterns for the file paths.
-    """
-    return [os.path.basename(file_path) for file_path in file_paths]
 
 def read_file_with_encodings(file_path, encodings=['utf-8', 'shift_jis', 'euc-jp', 'iso-2022-jp', 'latin-1']):
     """
@@ -53,20 +44,22 @@ def read_file_with_encodings(file_path, encodings=['utf-8', 'shift_jis', 'euc-jp
             continue
     raise UnicodeDecodeError(f"Unable to decode file {file_path} with any of the provided encodings.")
 
-def process_wtx_file(wtx_file_path, search_file_paths):
+def process_wtx_file(wtx_file_path, file_paths):
     """
     Process the WTX file, replacing text between angle brackets.
 
     :param wtx_file_path: Path to the WTX file.
-    :param search_file_paths: List of search patterns for file paths.
+    :param file_paths: List of relative file paths found in the current directory.
     :return: List of processed lines from the WTX file.
     """
     new_wtx_file_lines = []
     lines, encoding = read_file_with_encodings(wtx_file_path)
     for line in lines:
-        for file_path in search_file_paths:
-            if file_path in line:
-                line = replace_between_angle_brackets(line, '..\\' + fea_dir + '\\' + file_path)
+        for file_path in file_paths:
+            basename = os.path.basename(file_path)
+            if basename in line:
+                win_path = '..\\'  + file_path.replace('/', '\\')
+                line = replace_between_angle_brackets(line, win_path)
         new_wtx_file_lines.append(line)
     return new_wtx_file_lines, encoding
 
@@ -84,9 +77,8 @@ def main():
     wtx_file_path = sys.argv[1]
 
     file_paths = find_all_files_os()
-    search_file_paths = get_search_file_paths(file_paths)
 
-    new_wtx_file_lines, encoding = process_wtx_file(wtx_file_path, search_file_paths)
+    new_wtx_file_lines, encoding = process_wtx_file(wtx_file_path, file_paths)
     write_lines_to_file(new_wtx_file_lines, wtx_file_path, encoding=encoding)
 
 if __name__ == '__main__':
diff --git a/scripts/cpu_and_memory_usage.py b/scripts/cpu_and_memory_usage.py
new file mode 100644
index 0000000..1586bfe
--- /dev/null
+++ b/scripts/cpu_and_memory_usage.py
@@ -0,0 +1,101 @@
+import argparse
+import psutil
+import matplotlib.pyplot as plt
+from datetime import datetime
+import time
+import os
+import subprocess
+
+"""
+This script monitors CPU and memory usage over time and provides options to either write the data to a text file or plot it. 
+If '--write-usage' option is provided, it continuously monitors CPU and memory usage and writes the data to the specified text file.
+If '--plot-usage' option is provided, it reads CPU and memory usage data from the specified text file and plots it over time.
+"""
+
+def kill_job():
+    try:
+        with open("job_id.submitted", "r") as file:
+            job_id = file.readline().strip()
+            if job_id:
+                subprocess.run(["scancel", job_id], check=True)
+                print(f"Job {job_id} cancelled successfully.")
+            else:
+                print("No job ID found in job_id.submitted.")
+    except FileNotFoundError:
+        print("File job_id.submitted not found.")
+    except subprocess.CalledProcessError as e:
+        print(f"Failed to cancel job {job_id}. Error: {e}")
+
+def get_usage():
+    cpu_percent = psutil.cpu_percent()
+    memory_percent = psutil.virtual_memory().percent
+    return cpu_percent, memory_percent
+
+def write_usage_data(txt_file):
+    with open(txt_file, "w") as data_file:
+        print("Monitoring CPU and memory usage...")
+        while True:
+            timestamp = datetime.now()
+            cpu_usage, memory_usage = get_usage()
+            if memory_usage > 98:
+                print('Memory exceeded 98%. Killing job.', flush = True)
+                kill_job()
+
+            # Write data to file
+            data_file.write(f"{timestamp},{cpu_usage},{memory_usage}\n")
+            data_file.flush()
+
+            # Wait for 1 second before collecting next data point
+            time.sleep(1)
+
+
+def plot_usage_data(txt_file):
+    timestamps = []
+    cpu_usages = []
+    memory_usages = []
+
+    try:
+        with open(txt_file, "r") as data_file:
+            print("Reading CPU and memory usage data...")
+            for line in data_file:
+                parts = line.strip().split(",")
+                timestamp = datetime.fromisoformat(parts[0])
+                cpu_usage = float(parts[1])
+                memory_usage = float(parts[2])
+                timestamps.append(timestamp)
+                cpu_usages.append(cpu_usage)
+                memory_usages.append(memory_usage)
+
+        # Plot CPU and memory usage over time
+        plt.figure(figsize=(10, 6))
+        plt.plot(timestamps, cpu_usages, label='CPU Usage (%)')
+        plt.plot(timestamps, memory_usages, label='Memory Usage (%)')
+        plt.xlabel('Time')
+        plt.ylabel('Usage (%)')
+        plt.title('CPU and Memory Usage Over Time')
+        plt.legend()
+        plt.grid(True)
+        plt.xticks(rotation=45)
+        plt.tight_layout()
+
+        # Save plot image
+        img_path = os.path.splitext(txt_file)[0] + ".png"
+        plt.savefig(img_path)
+        print(f"Plot image saved as {img_path}")
+    except FileNotFoundError:
+        print(f"File '{txt_file}' not found.")
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="CPU and Memory Usage Monitor and Plotter")
+    parser.add_argument("--write-usage", action="store_true", help="Write CPU and memory usage data to a text file")
+    parser.add_argument("--plot-usage", action="store_true", help="Plot CPU and memory usage data from a text file")
+    parser.add_argument("--txt", type=str, help="Specify the text file to read/write usage data")
+
+    args = parser.parse_args()
+
+    if args.write_usage and args.txt:
+        write_usage_data(args.txt)
+    elif args.plot_usage and args.txt:
+        plot_usage_data(args.txt)
+    else:
+        print("Invalid arguments. Please specify '--write-usage' or '--plot-usage' along with '--txt' option.")
diff --git a/scripts/cpu_and_memory_usage_requirements.yaml b/scripts/cpu_and_memory_usage_requirements.yaml
new file mode 100644
index 0000000..e73c7d8
--- /dev/null
+++ b/scripts/cpu_and_memory_usage_requirements.yaml
@@ -0,0 +1,153 @@
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - alsa-lib=1.2.11=hd590300_1
+  - attr=2.5.1=h166bdaf_1
+  - brotli=1.1.0=hd590300_1
+  - brotli-bin=1.1.0=hd590300_1
+  - bzip2=1.0.8=hd590300_5
+  - ca-certificates=2024.2.2=hbcca054_0
+  - cairo=1.18.0=h3faef2a_0
+  - certifi=2024.2.2=pyhd8ed1ab_0
+  - contourpy=1.2.1=py312h8572e83_0
+  - cycler=0.12.1=pyhd8ed1ab_0
+  - dbus=1.13.6=h5008d03_3
+  - expat=2.6.2=h59595ed_0
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=h77eed37_1
+  - fontconfig=2.14.2=h14ed4e7_0
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - fonttools=4.51.0=py312h98912ed_0
+  - freetype=2.12.1=h267a509_2
+  - gettext=0.22.5=h59595ed_2
+  - gettext-tools=0.22.5=h59595ed_2
+  - glib=2.80.0=hf2295e7_5
+  - glib-tools=2.80.0=hde27a5a_5
+  - graphite2=1.3.13=h59595ed_1003
+  - gst-plugins-base=1.24.1=hfa15dee_1
+  - gstreamer=1.24.1=h98fc4e7_1
+  - harfbuzz=8.3.0=h3d44ed6_0
+  - icu=73.2=h59595ed_0
+  - keyutils=1.6.1=h166bdaf_0
+  - kiwisolver=1.4.5=py312h8572e83_1
+  - krb5=1.21.2=h659d440_0
+  - lame=3.100=h166bdaf_1003
+  - lcms2=2.16=hb7c19ff_0
+  - ld_impl_linux-64=2.40=h41732ed_0
+  - lerc=4.0.0=h27087fc_0
+  - libasprintf=0.22.5=h661eb56_2
+  - libasprintf-devel=0.22.5=h661eb56_2
+  - libblas=3.9.0=22_linux64_openblas
+  - libbrotlicommon=1.1.0=hd590300_1
+  - libbrotlidec=1.1.0=hd590300_1
+  - libbrotlienc=1.1.0=hd590300_1
+  - libcap=2.69=h0f662aa_0
+  - libcblas=3.9.0=22_linux64_openblas
+  - libclang-cpp15=15.0.7=default_h127d8a8_5
+  - libclang13=18.1.3=default_h5d6823c_0
+  - libcups=2.3.3=h4637d8d_4
+  - libdeflate=1.20=hd590300_0
+  - libedit=3.1.20191231=he28a2e2_2
+  - libevent=2.1.12=hf998b51_1
+  - libexpat=2.6.2=h59595ed_0
+  - libffi=3.4.2=h7f98852_5
+  - libflac=1.4.3=h59595ed_0
+  - libgcc-ng=13.2.0=h807b86a_5
+  - libgcrypt=1.10.3=hd590300_0
+  - libgettextpo=0.22.5=h59595ed_2
+  - libgettextpo-devel=0.22.5=h59595ed_2
+  - libgfortran-ng=13.2.0=h69a702a_5
+  - libgfortran5=13.2.0=ha4646dd_5
+  - libglib=2.80.0=hf2295e7_5
+  - libgomp=13.2.0=h807b86a_5
+  - libgpg-error=1.48=h71f35ed_0
+  - libiconv=1.17=hd590300_2
+  - libjpeg-turbo=3.0.0=hd590300_1
+  - liblapack=3.9.0=22_linux64_openblas
+  - libllvm15=15.0.7=hb3ce162_4
+  - libllvm18=18.1.3=h2448989_0
+  - libnsl=2.0.1=hd590300_0
+  - libogg=1.3.4=h7f98852_1
+  - libopenblas=0.3.27=pthreads_h413a1c8_0
+  - libopus=1.3.1=h7f98852_1
+  - libpng=1.6.43=h2797004_0
+  - libpq=16.2=h33b98f1_1
+  - libsndfile=1.2.2=hc60ed4a_1
+  - libsqlite=3.45.2=h2797004_0
+  - libstdcxx-ng=13.2.0=h7e041cc_5
+  - libsystemd0=255=h3516f8a_1
+  - libtiff=4.6.0=h1dd3fc0_3
+  - libuuid=2.38.1=h0b41bf4_0
+  - libvorbis=1.3.7=h9c3ff4c_0
+  - libwebp-base=1.4.0=hd590300_0
+  - libxcb=1.15=h0b41bf4_0
+  - libxcrypt=4.4.36=hd590300_1
+  - libxkbcommon=1.7.0=h662e7e4_0
+  - libxml2=2.12.6=h232c23b_2
+  - libzlib=1.2.13=hd590300_5
+  - lz4-c=1.9.4=hcb278e6_0
+  - matplotlib=3.8.4=py312h7900ff3_0
+  - matplotlib-base=3.8.4=py312he5832f3_0
+  - mpg123=1.32.6=h59595ed_0
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - mysql-common=8.3.0=hf1915f5_4
+  - mysql-libs=8.3.0=hca2cd23_4
+  - ncurses=6.4.20240210=h59595ed_0
+  - nspr=4.35=h27087fc_0
+  - nss=3.98=h1d7d5a4_0
+  - numpy=1.26.4=py312heda63a1_0
+  - openjpeg=2.5.2=h488ebb8_0
+  - openssl=3.2.1=hd590300_1
+  - packaging=24.0=pyhd8ed1ab_0
+  - pcre2=10.43=hcad00b1_0
+  - pillow=10.3.0=py312hdcec9eb_0
+  - pip=24.0=pyhd8ed1ab_0
+  - pixman=0.43.2=h59595ed_0
+  - ply=3.11=pyhd8ed1ab_2
+  - psutil=5.9.8=py312h98912ed_0
+  - pthread-stubs=0.4=h36c2ea0_1001
+  - pulseaudio-client=17.0=hb77b528_0
+  - pyparsing=3.1.2=pyhd8ed1ab_0
+  - pyqt=5.15.9=py312h949fe66_5
+  - pyqt5-sip=12.12.2=py312h30efb56_5
+  - python=3.12.3=hab00c5b_0_cpython
+  - python-dateutil=2.9.0=pyhd8ed1ab_0
+  - python_abi=3.12=4_cp312
+  - qt-main=5.15.8=hc9dc06e_21
+  - readline=8.2=h8228510_1
+  - setuptools=69.5.1=pyhd8ed1ab_0
+  - sip=6.7.12=py312h30efb56_0
+  - six=1.16.0=pyh6c4a22f_0
+  - tk=8.6.13=noxft_h4845f30_101
+  - toml=0.10.2=pyhd8ed1ab_0
+  - tomli=2.0.1=pyhd8ed1ab_0
+  - tornado=6.4=py312h98912ed_0
+  - tzdata=2024a=h0c530f3_0
+  - wheel=0.43.0=pyhd8ed1ab_1
+  - xcb-util=0.4.0=hd590300_1
+  - xcb-util-image=0.4.0=h8ee46fc_1
+  - xcb-util-keysyms=0.4.0=h8ee46fc_1
+  - xcb-util-renderutil=0.3.9=hd590300_1
+  - xcb-util-wm=0.4.1=h8ee46fc_1
+  - xkeyboard-config=2.41=hd590300_0
+  - xorg-kbproto=1.0.7=h7f98852_1002
+  - xorg-libice=1.1.1=hd590300_0
+  - xorg-libsm=1.2.4=h7391055_0
+  - xorg-libx11=1.8.9=h8ee46fc_0
+  - xorg-libxau=1.0.11=hd590300_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xorg-libxext=1.3.4=h0b41bf4_2
+  - xorg-libxrender=0.9.11=hd590300_0
+  - xorg-renderproto=0.11.1=h7f98852_1002
+  - xorg-xextproto=7.3.0=h0b41bf4_1003
+  - xorg-xf86vidmodeproto=2.3.1=h7f98852_1002
+  - xorg-xproto=7.0.31=h7f98852_1007
+  - xz=5.2.6=h166bdaf_0
+  - zlib=1.2.13=hd590300_5
+  - zstd=1.5.5=hfc55251_0
\ No newline at end of file
diff --git a/resources/001_simulation_executor/dry_run.sh b/scripts/dry_run.sh
similarity index 100%
rename from resources/001_simulation_executor/dry_run.sh
rename to scripts/dry_run.sh
diff --git a/resources/001_simulation_executor/estimate_end_time.py b/scripts/estimate_end_time.py
similarity index 100%
rename from resources/001_simulation_executor/estimate_end_time.py
rename to scripts/estimate_end_time.py
diff --git a/get_group_allocation_balance.py b/scripts/get_group_allocation_balance.py
similarity index 100%
rename from get_group_allocation_balance.py
rename to scripts/get_group_allocation_balance.py
diff --git a/resources/002_merge_executor/clean_job_directory.sh b/scripts/merge/clean_job_directory.sh
similarity index 100%
rename from resources/002_merge_executor/clean_job_directory.sh
rename to scripts/merge/clean_job_directory.sh
diff --git a/resources/002_merge_executor/dry_run.sh b/scripts/merge/dry_run.sh
similarity index 100%
rename from resources/002_merge_executor/dry_run.sh
rename to scripts/merge/dry_run.sh
diff --git a/resources/002_merge_executor/montecarlo.sh b/scripts/merge/montecarlo.sh
similarity index 100%
rename from resources/002_merge_executor/montecarlo.sh
rename to scripts/merge/montecarlo.sh
diff --git a/resources/002_merge_executor/run_dcs.sh b/scripts/merge/run_dcs.sh
similarity index 50%
rename from resources/002_merge_executor/run_dcs.sh
rename to scripts/merge/run_dcs.sh
index d23ebb6..c609dd7 100644
--- a/resources/002_merge_executor/run_dcs.sh
+++ b/scripts/merge/run_dcs.sh
@@ -6,7 +6,7 @@
 cat >> metering.sh <<HERE
 #!/bin/bash
 while true; do
-    date >> ${resource_jobdir}/usage/$(hostname)-${job_number}-merge
+    date >> ${PW_PARENT_JOB_DIR}/usage/$(hostname)-${PW_JOB_NUMBER}-merge
     sleep \$((RANDOM % 30 + 30))
 done
 HERE
@@ -14,12 +14,20 @@ HERE
 chmod +x metering.sh
 ./metering.sh &
 metering_pid=$!
+echo "kill ${metering_pid} || true # Metering" >> cancel.sh
+
+# Stream logs
+log_path="TempData/dcsSimuMacro_SA_log_x64_$(echo ${dcs_version} | tr '.' '_').txt"
+touch ${log_path}
+tail -f ${log_path} &
+tail_pid=$!
+echo "kill ${tail_pid} || true # Tail logs" >> cancel.sh
 
 # Run 3dcs
 SECONDS=0
 eval "${dcs_run}"  macroScript.txt
 kill ${metering_pid}
-mv ${resource_jobdir}/usage/$(hostname)-${job_number}-merge ${resource_jobdir}/usage_completed/$(hostname)-${job_number}-merge
+mv ${PW_PARENT_JOB_DIR}/usage/$(hostname)-${PW_JOB_NUMBER}-merge ${PW_PARENT_JOB_DIR}/usage_completed/$(hostname)-${PW_JOB_NUMBER}-merge
 
 
 # Results is own by root
diff --git a/resources/002_merge_executor/sensitivity.sh b/scripts/merge/sensitivity.sh
similarity index 100%
rename from resources/002_merge_executor/sensitivity.sh
rename to scripts/merge/sensitivity.sh
diff --git a/scripts/merge/transfer_inputs.sh b/scripts/merge/transfer_inputs.sh
new file mode 100644
index 0000000..9f75e0e
--- /dev/null
+++ b/scripts/merge/transfer_inputs.sh
@@ -0,0 +1,3 @@
+
+
+pw buckets cp -r ${dcs_bucket_uri}/${dcs_output_directory}/${USER}/${PW_WORKFLOW_NAME}/${PW_JOB_NUMBER} .  > bucket_download.log 2>&1
diff --git a/scripts/merge/transfer_outputs.sh b/scripts/merge/transfer_outputs.sh
new file mode 100644
index 0000000..f6cad30
--- /dev/null
+++ b/scripts/merge/transfer_outputs.sh
@@ -0,0 +1,15 @@
+
+pw buckets cp merge.sh ${dcs_bucket_uri}/${dcs_output_directory}/${USER}/${PW_WORKFLOW_NAME}/${PW_JOB_NUMBER}/merge.sh > bucket_upload.log 2>&1
+echo >> bucket_upload.log
+
+# The pw CLI mis-signs S3 keys that contain spaces (403 SignatureDoesNotMatch),
+# and 3DCS names some result files with spaces (e.g. "CMRailTraining .hsu"),
+# which aborts the whole Results upload. Strip spaces before uploading.
+find Results -depth -name '* *' | while IFS= read -r f; do
+    mv "$f" "$(dirname "$f")/$(basename "$f" | tr -d ' ')"
+done
+
+pw buckets cp -r Results ${dcs_bucket_uri}/${dcs_output_directory}/${USER}/${PW_WORKFLOW_NAME}/${PW_JOB_NUMBER}/Results >> bucket_upload.log 2>&1
+echo >> bucket_upload.log
+pw buckets cp -r TempData ${dcs_bucket_uri}/${dcs_output_directory}/${USER}/${PW_WORKFLOW_NAME}/${PW_JOB_NUMBER}/TempData >> bucket_upload.log 2>&1
+
diff --git a/resources/001_simulation_executor/montecarlo.sh b/scripts/montecarlo.sh
similarity index 100%
rename from resources/001_simulation_executor/montecarlo.sh
rename to scripts/montecarlo.sh
diff --git a/scripts/plot_monitoring.sh b/scripts/plot_monitoring.sh
new file mode 100644
index 0000000..06cda51
--- /dev/null
+++ b/scripts/plot_monitoring.sh
@@ -0,0 +1 @@
+python ${PW_PARENT_JOB_DIR}/scripts/cpu_and_memory_usage.py --plot-usage --txt ${monitoring_txt}
diff --git a/scripts/run_dcs.sh b/scripts/run_dcs.sh
new file mode 100644
index 0000000..2704946
--- /dev/null
+++ b/scripts/run_dcs.sh
@@ -0,0 +1,34 @@
+# run in bat file to get correct exit code from the software
+#echo set DCS2FLMD_LICENSE_FILE="$DCS2FLMD_LICENSE_FILE" > run.bat
+
+# Create metering script
+cat >> metering.sh <<HERE
+#!/bin/bash 
+while true; do
+    date >> ${PW_PARENT_JOB_DIR}/usage/$(hostname)-${PW_JOB_NUMBER}
+    sleep \$((RANDOM % 30 + 30))
+done
+HERE
+
+chmod +x metering.sh
+./metering.sh &
+metering_pid=$!
+echo "kill ${metering_pid} || true # Metering" >> cancel.sh
+
+# Stream logs
+log_path="TempData/dcsSimuMacro_SA_log_x64_$(echo ${dcs_version} | tr '.' '_').txt"
+touch ${log_path}
+tail -f ${log_path} &
+tail_pid=$!
+echo "kill ${tail_pid} || true # Tail logs" >> cancel.sh
+
+# Run 3dcs
+SECONDS=0
+eval "${dcs_run}"  macroScript.txt
+kill ${metering_pid}
+mv ${PW_PARENT_JOB_DIR}/usage/$(hostname)-${PW_JOB_NUMBER} ${PW_PARENT_JOB_DIR}/usage_completed/$(hostname)-${PW_JOB_NUMBER}
+
+# Results is own by root
+sudo chmod 777 Results/ -R
+echo ${SECONDS} > Results/dcs-runtime-${case_index}.txt
+
diff --git a/resources/001_simulation_executor/sensitivity.sh b/scripts/sensitivity.sh
similarity index 100%
rename from resources/001_simulation_executor/sensitivity.sh
rename to scripts/sensitivity.sh
diff --git a/resources/001_simulation_executor/transfer_inputs.sh b/scripts/transfer_and_process_inputs.sh
similarity index 68%
rename from resources/001_simulation_executor/transfer_inputs.sh
rename to scripts/transfer_and_process_inputs.sh
index 9022ae0..627ac6f 100644
--- a/resources/001_simulation_executor/transfer_inputs.sh
+++ b/scripts/transfer_and_process_inputs.sh
@@ -4,8 +4,7 @@
 mkdir tmp-data-transfer
 cd tmp-data-transfer
 
-# dcs_model_directory can end with or without /
-aws s3 sync ${BUCKET_URI}/${dcs_model_directory} . --cli-read-timeout 60
+pw buckets cp -r ${BUCKET_URI}/${dcs_model_directory} .
 
 # User aws s3 cp --recursive ../test ${BUCKET_URI}/path/to/dir/test to transfer to the bucket
 
@@ -30,25 +29,10 @@ else
 fi
 
 
-# Get the count of directories in the current directory
-dir_count=$(ls -d */ | wc -l)
-
-# If there's only one directory
-if [ "$dir_count" -eq 1 ]; then
-    # Get the name of the directory
-    fea_dir=$(ls -d */ | head -n 1)
-    export fea_dir=${fea_dir%/}  # Remove trailing slash
-    echo "Directory found: $fea_dir"
-else
-    # If no directory or multiple directories exist
-    echo "Error: Either no FEA directory found or multiple directories exist." >&2
-    exit 1
-fi
-
 # Process WTX file to adapt the paths to the files
 retries=5
 while true; do
-    python3 ../adapt_wtx_paths.py ${dcs_model_file} ${fea_dir}
+    python3 ../adapt_wtx_paths.py ${dcs_model_file}
     exit_code=$?
     if [ ${exit_code} -ne 0 ]; then
 	    retries=$((retries-1))
diff --git a/scripts/transfer_outputs.sh b/scripts/transfer_outputs.sh
new file mode 100644
index 0000000..81d9e2d
--- /dev/null
+++ b/scripts/transfer_outputs.sh
@@ -0,0 +1,6 @@
+
+# Copy path/to/worker_<i> to bucket
+set -x
+pw buckets cp -r ${PWD} ${dcs_bucket_uri}/${dcs_output_directory}/${USER}/${PW_WORKFLOW_NAME}/${PW_JOB_NUMBER}/$(basename ${PWD}) > bucket_upload.log 2>&1
+
+
diff --git a/stream.sh b/stream.sh
deleted file mode 100755
index 8e87a10..0000000
--- a/stream.sh
+++ /dev/null
@@ -1,88 +0,0 @@
-#!/bin/bash
-while [ ! -f "SUBMITTED" ]; do
-    echo "$(date '+%Y-%m-%d %H:%M:%S') - Waiting for simulations to be submitted"
-    sleep 10
-done
-
-# Source the inputs file
-source resources/001_simulation_executor/inputs.sh
-
-export sshcmd="ssh -o StrictHostKeyChecking=no -o ServerAliveInterval=60 -o ServerAliveCountMax=3 ${resource_publicIp}"
-
-log_path="TempData/dcsSimuMacro_SA_log_x64_$(echo ${dcs_version} | tr '.' '_').txt"
-
-wait_for_all_simulations_to_start() {
-    while true; do
-        n_running_workers=$(${sshcmd} ls -d ${resource_jobdir}/worker_*/${log_path} | wc -l)
-        if [ $? -ne 0 ]; then
-            n_running_workers=0
-        fi
-        if [ "${n_running_workers}" -lt "${dcs_concurrency}" ]; then
-            echo "$(date '+%Y-%m-%d %H:%M:%S') - ${n_running_workers}/${dcs_concurrency} simulations started"
-            echo "$(date '+%Y-%m-%d %H:%M:%S') - Waiting for all simulations to start..."
-            sleep 15
-        else
-            break
-        fi
-        if [ -f "COMPLETED" ]; then
-            echo "$(date '+%Y-%m-%d %H:%M:%S') - Simulations are completed"
-            exit 0
-        fi
-    done
-}
-
-wait_for_all_simulations_to_start
-
-echo "$(date '+%Y-%m-%d %H:%M:%S') - All simulations are started!"
-echo; echo
-echo "$(date '+%Y-%m-%d %H:%M:%S') - Initiating streaming"
-
-stream_logs() {
-    local max_retries=5
-    local retry_delay=10
-    local attempt=1
-
-    while [ $attempt -le $max_retries ]; do
-        if [ -f "COMPLETED" ]; then
-            echo "$(date '+%Y-%m-%d %H:%M:%S') - COMPLETED file detected, stopping log streaming"
-            return 0
-        fi
-        echo "$(date '+%Y-%m-%d %H:%M:%S') - Attempt $attempt of $max_retries to stream logs"
-        ${sshcmd} "tail -f ${resource_jobdir}/worker_*/${log_path}"
-        local exit_code=$?
-        if [ $exit_code -eq 0 ]; then
-            echo "$(date '+%Y-%m-%d %H:%M:%S') - Streaming completed successfully"
-            return 0
-        else
-            echo "$(date '+%Y-%m-%d %H:%M:%S') - SSH tail failed with exit code $exit_code. Retrying in $retry_delay seconds..."
-            sleep $retry_delay
-            attempt=$((attempt + 1))
-        fi
-    done
-
-    if [ $attempt -gt $max_retries ]; then
-        if [ -f "COMPLETED" ]; then
-            echo "$(date '+%Y-%m-%d %H:%M:%S') - COMPLETED file detected, ignoring retry limit"
-            return 0
-        else
-            echo "$(date '+%Y-%m-%d %H:%M:%S') - Failed to stream logs after $max_retries attempts"
-            return 1
-        fi
-    fi
-}
-
-# Start log streaming in the background
-echo "$(date '+%Y-%m-%d %H:%M:%S') - Starting background log streaming"
-stream_logs &
-stream_pid=$!
-echo "kill ${stream_pid}" > cancel_stream.sh
-
-# Wait for either COMPLETED file or stream_logs to exit
-while [ ! -f "COMPLETED" ]; do
-    # Check if the stream_logs process is still running
-    if ! ps -p $stream_pid > /dev/null; then
-        echo "$(date '+%Y-%m-%d %H:%M:%S') - Stream logs process (PID: $stream_pid) has exited"
-        break
-    fi
-    sleep 10
-done
\ No newline at end of file
diff --git a/update-3dcs-usage.py b/update-3dcs-usage.py
index e318430..f77c2b4 100755
--- a/update-3dcs-usage.py
+++ b/update-3dcs-usage.py
@@ -35,20 +35,16 @@ def encode_string_to_base64(text):
 os.makedirs(DCS_PROCESSED_USAGE_DIR, exist_ok=True)
 LOCK_FILE_PATH = os.path.join(DCS_DIR, 'update-3dcs-usage.lock')
 
-# See https://cloud.parallel.works/api/v2/organization
+# See https://cloud.parallel.works/api/organizations
 CUSTOMER_ORG_ID = '63572a4c1129281e00477a0c'
 PW_PLATFORM_HOST = os.environ.get('PW_PLATFORM_HOST')
 PW_API_KEY = os.environ.get('PW_API_KEY')
-CUSTOMER_ORG_NAME = os.environ.get('CUSTOMER_ORG_NAME')
+CUSTOMER_ORG_NAME = 'honda'
+HEADERS = {"Authorization": "Basic {}".format(encode_string_to_base64(PW_API_KEY))}
 
-group_name_to_id_mapping = {}
-HEADERS = {"Authorization": "Basic {}".format(encode_string_to_base64(os.environ['PW_API_KEY']))}
-
-GROUP_NAME: str = '3dcs-run-hours'
-# ORGANIZATION_URL: str = f'https://{PW_PLATFORM_HOST}/api/v2/organization/teams?organization={CUSTOMER_ORG_ID}'
-# ORGANIZATION_URL: str = f'https://{PW_PLATFORM_HOST}/api/v2/organization/teams'
+GROUP_NAME: str = 'japan-3dcs-run-hours'
 ORGANIZATION_URL = f'https://{PW_PLATFORM_HOST}/api/organizations/{CUSTOMER_ORG_NAME}/groups'
-
+#ORGANIZATION_URL = f'https://{PW_PLATFORM_HOST}/api/organization/{CUSTOMER_ORG_NAME}/groups/{GROUP_NAME}'
 
 CONNECTED_WORKERS = {}
 
@@ -79,23 +75,24 @@ def get_group_info():
 
 def get_allocation_used(group):
     if 'used' in group['allocations']:
-        return group['allocations']['used']['value']
-    return 0    
+        return group['allocations']['used']
+    return 0
 
 def http_put_sync(url, payload):
     response = requests.put(url, json=payload,  headers = HEADERS)
     return response.json()
 
-def update_group_allocation_used(group_id, allocation_used):
-    #logger.info(f'Updating {group_id} used allocation to {allocation_used}')
-    url = f"https://{PW_PLATFORM_HOST}/api/v2/organization/teams/{group_id}"
+def update_group_allocation_used(group_name, allocation_used):
+    #logger.info(f'Updating {group_name} used allocation to {allocation_used}')
+    url = f"https://{PW_PLATFORM_HOST}/api/organizations/{CUSTOMER_ORG_NAME}/groups/{group_name}/allocations"
     payload = {
-        "allocation_used": allocation_used
+        "allocation": float(group_info['allocations']['total']),
+        "allocationUsed": float(allocation_used)
     }
-    return http_put_sync(url, payload)
+    response = requests.patch(url, json=payload, headers=HEADERS)
+    return response.json()
 
 def get_group_id(group_name):
-
     res = requests.get(ORGANIZATION_URL, headers = get_headers())
 
     for group in res.json():
@@ -221,7 +218,7 @@ def process_worker_files(worker_files, allocation_used):
     if cached_usage > 0:
         allocation_used += cached_usage
         logger.info(f'Updating allocation used to {allocation_used}.')
-        update_group_allocation_used(group_id, round(allocation_used,2))
+        update_group_allocation_used(GROUP_NAME, round(allocation_used,2))
     
     return allocation_used
 
diff --git a/windows-aws-credentials.yaml b/windows-aws-credentials.yaml
deleted file mode 100644
index c5525b9..0000000
--- a/windows-aws-credentials.yaml
+++ /dev/null
@@ -1,18 +0,0 @@
-permissions:
-  - '*'
-jobs:
-  main:
-    steps:
-      - name: Generate Windows S3 Credentials
-        run: |
-          source /etc/profile.d/parallelworks.sh
-          source /etc/profile.d/parallelworks-env.sh
-          source /pw/.miniconda3/etc/profile.d/conda.sh
-          python3 bucket_token_generator.py --bucket_id ${{ inputs.bucket_id }} --token_format text --platform windows
-'on':
-  execute:
-    inputs:
-      bucket_id:
-        label: Bucket ID or namespace
-        type: string
-        tooltip: Type in the bucket ID string or namespace in the format [bucket-owner]/[bucket-name]
diff --git a/workflow.xml b/workflow.xml
deleted file mode 100644
index a44814a..0000000
--- a/workflow.xml
+++ /dev/null
@@ -1,201 +0,0 @@
-<tool id='NA' name='NA'>
-  <command interpreter='bash'>main.sh</command>
-  <cancel interpreter='bash'>cancel.sh</cancel>
-  <inputs>
-    <param 
-        name='metering_user' 
-        label='metering_user' 
-        type='hidden' 
-        value='__metering_user__'  
-    ></param>
-    <param 
-        name='metering_ip' 
-        label='metering_ip' 
-        type='hidden' 
-        value='34.132.102.65'  
-    ></param>
-<section name='dcs' type='section' title='3DCS Options' expanded='true'>
-        <param 
-            name="dry_run" 
-            type="boolean" 
-            truevalue="Yes" 
-            falsevalue="No" 
-            checked="False" 
-            value="false"
-            label="Dry run?" 
-            help='Dry run generates the macroScript.txt file and executes every step of the workflow except running 3DCS'  
-        ></param>
-        <param 
-            name='version' 
-            type='select' 
-            label='3DCS Version' 
-            help='Select the 3DCS version' 
-            multiple='false'
-        >
-            <option value="8.0.0.2"  selected="true">8.0.0.2</option>
-            <option value="7.10.0.2" >7.10.0.2</option>
-        </param>
-        <param 
-            name='analysis_type' 
-            type='select' 
-            label='Analysis Type' 
-            help='Select Montecarlo simulation or contributor analysis (sensitivity)' 
-            multiple='false'
-        >
-            <option value="montecarlo"  selected="true">Monte Carlo Simulation</option>
-            <option value="sensitivity" >Contributor Analysis</option>
-        </param>
-        <param name='bucket_id' 
-            label='Bucket ID or namespace' 
-            type='text' 
-            help='Type in the bucket ID string or namespace in the format [bucket-owner]/[bucket-name]' 
-        ></param>
-        <param 
-            name='model_directory' 
-            label='Model Path' 
-            type='text' 
-            help='Directory within the bucket with the model and all the required files' 
-        ></param>
-        <param 
-            name='output_directory' 
-            label='Output Path' 
-            type='text' 
-            help='Output directory within the bucket to store outputs and logs. It cannot be inside the Model Directory!' 
-        ></param>
-        <param 
-            name='num_seeds' 
-            type='integer' 
-            label='Number of Monte Carlo Simulations' 
-            min='1' 
-            max='100000' 
-            value='2000'
-            depends_on='dcs.analysis_type'
-            show_if="montecarlo"
-        ></param>
-        <param 
-            name='concurrency' 
-            type='integer' 
-            label='Number of Workers' 
-            min='1' 
-            max='100' 
-            value='2' 
-            help='Number of workers used to run the simulations. A SLURM job is submitted for each worker.' 
-        ></param>
-        <param 
-            name='thread' 
-            type='integer' 
-            label='Number of Threads per Worker' 
-            min='1' 
-            max='64' 
-            value='1' 
-            help='Number of threads used to run the simulation. Be aware that N threads require more than N times the memory needed for a single thread.'
-        ></param>
-    </section>
-    <section name='pwrl_001_simulation_executor' type='section' title='Simulation Executor' expanded='true'>
-        <param 
-            name='monitoring_conda_dir' 
-            label='PW Conda Directory' 
-            type='hidden' 
-            value='/dcs/pw/miniconda'
-        ></param>
-        <param 
-            name='monitoring_conda_env' 
-            label='PW Conda Directory' 
-            type='hidden' 
-            value='psutil'
-        ></param>
-        <param 
-            name='resource' 
-            type='computeResource' 
-            label='Resource' 
-            hideUserWorkspace='true' 
-            help='Resource to run the simulation task'>
-        </param>
-        <param 
-            name='jobschedulertype' 
-            label='Select Controller, SLURM Partition or PBS Queue' 
-            type='hidden' 
-            value='SLURM' 
-        >
-        </param>
-       <param
-           name='_sch__dd_partition_e_'
-           label='SLURM partition'
-           type='dynamicPartitionDropdown'
-           resource='pwrl_001_simulation_executor.resource'
-           help='Partition to submit the interactive job. Leave empty to let SLURM pick the optimal option.'
-           optional='true'  
-           dependent='false'
-       ></param>
-        <param 
-            name='_sch__dd_time_e_' 
-            label='Walltime' 
-            type='text' 
-            help='Maximum walltime per job' 
-            value='999:00:00'
-            optional='true' 
-        ></param>
-        <param 
-            name='scheduler_directives' 
-            label='Scheduler directives' 
-            type='text' 
-            help='e.g. --mem=1000;--gpus-per-node=1 - Use the semicolon character ; to separate parameters. Do not include the SBATCH keyword.' 
-            value='--exclusive'
-            optional='true'  
-        ></param>
-    </section>
-    <section name='pwrl_002_merge_executor' type='section' title='Merge Executor' expanded='true'>
-        <param 
-            name='monitoring_conda_dir' 
-            label='PW Conda Directory' 
-            type='hidden' 
-            value='/dcs/pw/miniconda'
-        ></param>
-        <param 
-            name='monitoring_conda_env' 
-            label='PW Conda Directory' 
-            type='hidden' 
-            value='psutil'
-        ></param>
-        <param 
-            name='resource' 
-            type='computeResource' 
-            label='Resource' 
-            hideUserWorkspace='true' 
-            help='Resource to run the simulation task'>
-        </param>
-        <param 
-            name='jobschedulertype' 
-            label='Select Controller, SLURM Partition or PBS Queue' 
-            type='hidden' 
-            value='SLURM' 
-        >
-        </param>
-        <param
-           name='_sch__dd_partition_e_'
-           label='SLURM partition'
-           type='dynamicPartitionDropdown'
-           resource='pwrl_002_merge_executor.resource'
-           help='Partition to submit the interactive job. Leave empty to let SLURM pick the optimal option.'
-           optional='true'  
-           dependent='false'
-        ></param>
-        <param 
-            name='_sch__dd_time_e_' 
-            label='Walltime' 
-            type='text' 
-            help='Maximum walltime per job' 
-            value='999:00:00'
-            optional='true' 
-        ></param>
-        <param 
-            name='scheduler_directives' 
-            label='Scheduler directives' 
-            type='text' 
-            help='e.g. --mem=1000;--gpus-per-node=1 - Use the semicolon character ; to separate parameters. Do not include the SBATCH keyword.' 
-            value='--exclusive'
-            optional='true'  
-        ></param>
-    </section>
-    </inputs>
-</tool>
diff --git a/workflow.yaml b/workflow.yaml
deleted file mode 100644
index 55434b5..0000000
--- a/workflow.yaml
+++ /dev/null
@@ -1,172 +0,0 @@
-permissions:
-  - '*'
-jobs:
-  main:
-    steps:
-      - name: Main
-        run: bash main.sh
-        cleanup: |
-          bash cancel.sh  || true
-          exit 0
-'on':
-  execute:
-    inputs:
-      metering_user:
-        label: Metering User
-        type: string
-        default: __metering_user__
-        hidden: true
-      metering_ip:
-        label: Metering IP
-        type: string
-        default: 34.132.102.65
-        hidden: true
-      dcs:
-        type: group
-        label: 3DCS Options
-        items:
-          dry_run:
-            label: Dry run?
-            type: boolean
-            default: false
-            tooltip: Dry run generates the macroScript.txt file and executes every step of the workflow except running 3DCS
-          version:
-            label: 3DCS Version
-            type: dropdown
-            default: 8.0.0.2
-            tooltip: Select the 3DCS version
-            options:
-              - value: 8.0.0.2
-                label: 8.0.0.2
-              - value: 7.10.0.2
-                label: 7.10.0.2
-          analysis_type:
-            label: Analysis Type
-            type: dropdown
-            tooltip: Select Montecarlo simulation or contributor analysis (sensitivity)
-            default: montecarlo
-            options:
-              - value: montecarlo
-                label: Monte Carlo Simulation
-              - value: sensitivity
-                label: Contributor Analysis
-          bucket_id:
-            label: Bucket ID or namespace
-            type: string
-            tooltip: Type in the bucket ID string or namespace in the format [bucket-owner]/[bucket-name]
-          model_directory:
-            label: Model Path
-            type: string
-            tooltip: Directory within the bucket with the model and all the required files
-          output_directory:
-            label: Output Path
-            type: string
-            tooltip: Output directory within the bucket to store outputs and logs. It cannot be inside the Model Directory!
-          num_seeds:
-            label: Number of Monte Carlo Simulations
-            type: number
-            min: 1
-            max: 100000
-            default: 2000
-            hidden: ${{ 'montecarlo' !=inputs.dcs.analysis_type }}
-            ignore: ${{ .hidden }}
-            optional: ${{ .hidden }}
-          concurrency:
-            label: Number of Workers
-            type: number
-            min: 1
-            max: 50
-            default: 1
-            tooltip: Number of workers used to run the simulations. A SLURM job is submitted for each worker.
-          thread:
-            label: Number of Threads per Worker
-            type: number
-            min: 1
-            max: 64
-            default: 1
-            tooltip: Number of threads used to run the simulation. Be aware that N threads require more than N times the memory needed for a single thread.
-
-      pwrl_001_simulation_executor:
-        type: group
-        label: Simulation Executor
-        items:
-          monitoring_conda_dir:
-            label: PW Conda Directory
-            type: string
-            default: /dcs/pw/miniconda
-            hidden: true
-          monitoring_conda_env:
-            label: PW Conda Environment
-            type: string
-            default: psutil
-            hidden: true
-          resource:
-            label: Resource
-            type: compute-clusters
-            tooltip: Resource to run the simulation task
-            include-workspace: false
-          jobschedulertype:
-            label: Select Controller, SLURM Partition or PBS Queue
-            type: string
-            default: SLURM
-            hidden: true
-          _sch__dd_partition_e_:
-            type: slurm-partitions
-            label: SLURM partition
-            hidden: ${{ 'SLURM' !=inputs.pwrl_001_simulation_executor.jobschedulertype }}
-            ignore: ${{ .hidden }}
-            optional: true
-            tooltip: Partition to submit the job. Leave empty to let SLURM pick the optimal option.
-            resource: ${{ inputs.pwrl_001_simulation_executor.resource }}
-          _sch__dd_time_e_:
-            label: Walltime
-            type: string
-            default: '999:00:00'
-            tooltip: Maximum walltime per job
-          scheduler_directives:
-            label: Scheduler directives
-            type: string
-            default: '--exclusive'
-            tooltip: e.g. --mem=1000;--gpus-per-node=1 - Use the semicolon character ; to separate parameters. Do not include the SBATCH keyword.
-      pwrl_002_merge_executor:
-        type: group
-        label: Merge Executor
-        items:
-          monitoring_conda_dir:
-            label: PW Conda Directory
-            type: string
-            default: /dcs/pw/miniconda
-            hidden: true
-          monitoring_conda_env:
-            label: PW Conda Environment
-            type: string
-            default: psutil
-            hidden: true
-          resource:
-            label: Resource
-            type: compute-clusters
-            tooltip: Resource to run the simulation task
-            include-workspace: false
-          jobschedulertype:
-            label: Select Controller, SLURM Partition or PBS Queue
-            type: string
-            default: SLURM
-            hidden: true
-          _sch__dd_partition_e_:
-            type: slurm-partitions
-            label: SLURM partition
-            hidden: ${{ 'SLURM' !=inputs.pwrl_002_merge_executor.jobschedulertype }}
-            ignore: ${{ .hidden }}
-            optional: true
-            tooltip: Partition to submit the job. Leave empty to let SLURM pick the optimal option.
-            resource: ${{ inputs.pwrl_002_merge_executor.resource }}
-          _sch__dd_time_e_:
-            label: Walltime
-            type: string
-            default: '999:00:00'
-            tooltip: Maximum walltime per job
-          scheduler_directives:
-            label: Scheduler directives
-            type: string
-            default: '--exclusive'
-            tooltip: e.g. --mem=1000;--gpus-per-node=1 - Use the semicolon character ; to separate parameters. Do not include the SBATCH keyword.