From 5cdb30180ebbefee1d5e6092dcac1d1e695c60fd Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Tue, 8 Jul 2025 22:35:19 -0400
Subject: [PATCH 01/14] first attempt with CB

---
 .github/workflows/cont-bench.yml | 75 ++++++++++++++++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100644 .github/workflows/cont-bench.yml

diff --git a/.github/workflows/cont-bench.yml b/.github/workflows/cont-bench.yml
new file mode 100644
index 000000000..0e6500ccb
--- /dev/null
+++ b/.github/workflows/cont-bench.yml
@@ -0,0 +1,75 @@
+name: Continuous Benchmarking
+
+on:
+  pull_request:
+  pull_request_review:
+    types: [submitted]
+  workflow_dispatch:
+
+
+permissions:
+  contents: write
+  deployments: write
+
+jobs:
+  file-changes:
+    name: Detect File Changes
+    runs-on: 'ubuntu-latest'
+    outputs: 
+      checkall: ${{ steps.changes.outputs.checkall }}
+    steps:
+      - name: Clone
+        uses: actions/checkout@v4
+
+      - name: Detect Changes
+        uses: dorny/paths-filter@v3
+        id: changes
+        with: 
+          filters: ".github/file-filter.yml"
+
+  self:
+    name: "Continuous Benchmarking"
+    if: ${{ github.repository == 'MFlowCode/MFC' && needs.file-changes.outputs.checkall == 'true' && (
+             (github.event_name == 'pull_request_review' && github.event.review.state == 'approved') ||
+             (github.event_name == 'pull_request' && github.event.pull_request.user.login == 'sbryngelson')
+           ) }}
+    needs: file-changes
+    continue-on-error: true
+    runs-on: ubuntu-latest
+    steps:
+      - name: Clone - PR
+        uses: actions/checkout@v4
+        with:
+          path: pr
+
+      - name: Setup
+        run: | 
+          sudo apt update -y
+          sudo apt install -y cmake gcc g++ python3 python3-dev hdf5-tools \
+                    libfftw3-dev libhdf5-dev openmpi-bin libopenmpi-dev
+
+      - name: Run Fortran Benchmark
+        run: |
+          (cd pr     && ./mfc.sh bench -o bench)
+      - name: Store benchmark result
+        uses: benchmark-action/github-action-benchmark@v1
+        with:
+          name: Fortran Benchmark
+          tool: 'googlecpp'
+          output-file-path: pr/bench.json
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          auto-push: true
+          alert-threshold: '200%'
+          comment-on-alert: true
+          fail-on-alert: true
+          # alert-comment-cc-users: '@sbryngelson'
+      
+      - name: Archive Results
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          path: |
+            pr/bench-*
+            pr/build/benchmarks/*
+            pr/bench.json
+      - uses: actions/checkout@v4
\ No newline at end of file

From 3db57c0ca98234b9fc8bd5d0ed44173871d154c2 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Wed, 9 Jul 2025 12:33:56 -0400
Subject: [PATCH 02/14] cont-bench testing

---
 .github/workflows/cont-bench.yml | 204 +++++++++++++++++++++++++++++--
 1 file changed, 194 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/cont-bench.yml b/.github/workflows/cont-bench.yml
index 0e6500ccb..b7257745f 100644
--- a/.github/workflows/cont-bench.yml
+++ b/.github/workflows/cont-bench.yml
@@ -5,11 +5,14 @@ on:
   pull_request_review:
     types: [submitted]
   workflow_dispatch:
-
+  push:
+    branches: [main, master]
 
 permissions:
   contents: write
   deployments: write
+  pages: write
+  id-token: write
 
 jobs:
   file-changes:
@@ -20,21 +23,24 @@ jobs:
     steps:
       - name: Clone
         uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 
 
       - name: Detect Changes
         uses: dorny/paths-filter@v3
         id: changes
         with: 
           filters: ".github/file-filter.yml"
+          base: ${{ github.event.repository.default_branch || 'main' }}
 
   self:
     name: "Continuous Benchmarking"
-    if: ${{ github.repository == 'MFlowCode/MFC' && needs.file-changes.outputs.checkall == 'true' && (
-             (github.event_name == 'pull_request_review' && github.event.review.state == 'approved') ||
-             (github.event_name == 'pull_request' && github.event.pull_request.user.login == 'sbryngelson')
-           ) }}
-    needs: file-changes
-    continue-on-error: true
+    # if: ${{ github.repository == 'MFlowCode/MFC' && needs.file-changes.outputs.checkall == 'true' && (
+    #          (github.event_name == 'pull_request_review' && github.event.review.state == 'approved') ||
+    #          (github.event_name == 'pull_request' && github.event.pull_request.user.login == 'sbryngelson')
+    #        ) }}
+    # needs: file-changes
+    # continue-on-error: true
     runs-on: ubuntu-latest
     steps:
       - name: Clone - PR
@@ -51,25 +57,203 @@ jobs:
       - name: Run Fortran Benchmark
         run: |
           (cd pr     && ./mfc.sh bench -o bench)
+
       - name: Store benchmark result
         uses: benchmark-action/github-action-benchmark@v1
         with:
           name: Fortran Benchmark
           tool: 'googlecpp'
-          output-file-path: pr/bench.json
+          output-file-path: pr/bench-*
           github-token: ${{ secrets.GITHUB_TOKEN }}
           auto-push: true
           alert-threshold: '200%'
           comment-on-alert: true
           fail-on-alert: true
+          gh-pages-branch: 'gh-pages'
+          benchmark-data-dir-path: benchmarks
           # alert-comment-cc-users: '@sbryngelson'
       
+
+      - name: Create Benchmark Documentation
+        run: |
+          mkdir -p pr/docs/documentation
+          cat > pr/docs/documentation/cont-bench.md << 'EOF'
+          # Continuous Benchmarking
+
+          This page provides an overview of MFC's continuous benchmarking system and results.
+
+          ## Overview
+
+          The continuous benchmarking system automatically runs performance tests on every approved pull request and main branch commit to track performance regressions and improvements over time.
+
+          ## Benchmark Results
+
+          ### Live Dashboard
+          
+          View the interactive benchmark dashboard with historical performance data:
+          
+          **[🔗 Live Benchmark Results](https://mflowcode.github.io/MFC/benchmarks/)**
+
+          ### Key Metrics
+
+          Our benchmarking system tracks the following performance metrics:
+
+          - **Execution Time**: Overall runtime of benchmark cases
+          - **Memory Usage**: Peak memory consumption during execution
+          - **Computational Efficiency**: Performance per computational unit
+          - **Scalability**: Performance across different problem sizes
+
+          ### Benchmark Cases
+
+          The benchmark suite includes:
+
+          1. **Standard Test Cases**: Representative fluid dynamics problems
+          2. **Scaling Tests**: Performance evaluation across different core counts
+          3. **Memory Tests**: Memory efficiency and usage patterns
+          4. **Accuracy Tests**: Verification of numerical accuracy
+
+          ## Performance Trends
+
+          ```mermaid
+          graph LR
+              A[PR Submitted] --> B[Benchmark Run]
+              B --> C[Results Stored]
+              C --> D[Performance Comparison]
+              D --> E{Performance OK?}
+              E -->|Yes| F[PR Approved]
+              E -->|No| G[Alert Generated]
+              G --> H[Developer Notified]
+          ```
+
+          ## Alert System
+
+          The system automatically:
+
+          - 🚨 **Generates alerts** when performance degrades by more than 200%
+          - 📊 **Comments on PRs** with performance impact analysis
+          - 📈 **Tracks trends** to identify gradual performance changes
+          - 👥 **Notifies maintainers** of significant performance issues
+
+          ## Configuration
+
+          ### Benchmark Triggers
+
+          Benchmarks are automatically triggered on:
+
+          - ✅ Approved pull request reviews
+          - 🔄 Pull requests from trusted contributors
+          - 📦 Pushes to main/master branches
+          - 🎯 Manual workflow dispatch
+
+          ### Performance Thresholds
+
+          - **Alert Threshold**: 200% performance degradation
+          - **Fail Threshold**: Critical performance regressions
+          - **Comparison Base**: Previous main branch performance
+
+          ## Interpreting Results
+
+          ### Performance Metrics
+
+          | Metric | Description | Good Trend | Bad Trend |
+          |--------|-------------|------------|-----------|
+          | Runtime | Execution time | ⬇️ Decreasing | ⬆️ Increasing |
+          | Memory | Peak memory usage | ⬇️ Decreasing | ⬆️ Increasing |
+          | Efficiency | Ops per second | ⬆️ Increasing | ⬇️ Decreasing |
+
+          ### Reading the Dashboard
+
+          1. **Timeline View**: Shows performance evolution over time
+          2. **Comparison View**: Compares current vs. baseline performance
+          3. **Detailed Metrics**: Drill down into specific performance aspects
+          4. **Regression Detection**: Automatically highlights performance issues
+
+          ## Contributing to Benchmarks
+
+          ### Adding New Benchmarks
+
+          To add new benchmark cases:
+
+          1. Add test case to `benchmarks/` directory
+          2. Update benchmark configuration
+          3. Ensure proper performance metrics collection
+          4. Test locally before submitting PR
+
+          ### Best Practices
+
+          - 🎯 **Focus on representative cases** that reflect real-world usage
+          - 📊 **Include scalability tests** for different problem sizes
+          - 🔄 **Maintain benchmark stability** to ensure reliable comparisons
+          - 📝 **Document benchmark purpose** and expected performance characteristics
+
+          ## Troubleshooting
+
+          ### Common Issues
+
+          | Issue | Cause | Solution |
+          |-------|-------|----------|
+          | Benchmark timeout | Long-running test | Optimize test case or increase timeout |
+          | Memory errors | Insufficient resources | Check memory requirements |
+          | Inconsistent results | System variability | Multiple runs or statistical analysis |
+
+          ### Getting Help
+
+          - 📧 Contact: @sbryngelson for benchmark-related issues
+          - 🐛 Issues: Report problems via GitHub issues
+          - 📖 Documentation: Check MFC documentation for detailed guides
+
+          ---
+
+          *Last updated: $(date '+%Y-%m-%d %H:%M:%S UTC')*
+          *Generated automatically by the continuous benchmarking workflow*
+          EOF
+
+      - name: Commit Documentation
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        run: |
+          cd pr
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add docs/documentation/cont-bench.md
+          if git diff --staged --quiet; then
+            echo "No changes to commit"
+          else
+            git commit -m "Update continuous benchmarking documentation [skip ci]"
+            git push
+          fi
+      
       - name: Archive Results
         uses: actions/upload-artifact@v4
         if: always()
         with:
+          name: benchmark-results
           path: |
             pr/bench-*
             pr/build/benchmarks/*
-            pr/bench.json
-      - uses: actions/checkout@v4
\ No newline at end of file
+            pr/docs/documentation/cont-bench.md
+
+  deploy-pages:
+    name: Deploy Benchmark Pages
+    if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+    needs: self
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v2
+        with:
+          path: .
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v3

From 85cd57c58a3cae0912642a38749e94bed06491b1 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Wed, 9 Jul 2025 12:45:54 -0400
Subject: [PATCH 03/14] cont-bench testing

---
 .github/workflows/cont-bench.yml | 39 ++++++++++++++++----------------
 1 file changed, 19 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/cont-bench.yml b/.github/workflows/cont-bench.yml
index b7257745f..c929850ff 100644
--- a/.github/workflows/cont-bench.yml
+++ b/.github/workflows/cont-bench.yml
@@ -15,23 +15,23 @@ permissions:
   id-token: write
 
 jobs:
-  file-changes:
-    name: Detect File Changes
-    runs-on: 'ubuntu-latest'
-    outputs: 
-      checkall: ${{ steps.changes.outputs.checkall }}
-    steps:
-      - name: Clone
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0 
-
-      - name: Detect Changes
-        uses: dorny/paths-filter@v3
-        id: changes
-        with: 
-          filters: ".github/file-filter.yml"
-          base: ${{ github.event.repository.default_branch || 'main' }}
+  # file-changes:
+  #   name: Detect File Changes
+  #   runs-on: 'ubuntu-latest'
+  #   outputs: 
+  #     checkall: ${{ steps.changes.outputs.checkall }}
+  #   steps:
+  #     - name: Clone
+  #       uses: actions/checkout@v4
+  #       with:
+  #         fetch-depth: 0 
+
+  #     - name: Detect Changes
+  #       uses: dorny/paths-filter@v3
+  #       id: changes
+  #       with: 
+  #         filters: ".github/file-filter.yml"
+  #         base: ${{ github.event.repository.default_branch || 'main' }}
 
   self:
     name: "Continuous Benchmarking"
@@ -64,7 +64,7 @@ jobs:
           name: Fortran Benchmark
           tool: 'googlecpp'
           output-file-path: pr/bench-*
-          github-token: ${{ secrets.GITHUB_TOKEN }}
+          github-token: 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
           auto-push: true
           alert-threshold: '200%'
           comment-on-alert: true
@@ -73,7 +73,6 @@ jobs:
           benchmark-data-dir-path: benchmarks
           # alert-comment-cc-users: '@sbryngelson'
       
-
       - name: Create Benchmark Documentation
         run: |
           mkdir -p pr/docs/documentation
@@ -218,7 +217,7 @@ jobs:
           if git diff --staged --quiet; then
             echo "No changes to commit"
           else
-            git commit -m "Update continuous benchmarking documentation [skip ci]"
+            git commit -m "Update continuous benchmarking documentation"
             git push
           fi
       

From 93a093a2adfea00b87e4f7640d073108a5671fc4 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Wed, 9 Jul 2025 12:50:38 -0400
Subject: [PATCH 04/14] cont-bench testing

---
 .github/workflows/cont-bench.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cont-bench.yml b/.github/workflows/cont-bench.yml
index c929850ff..9d7743a72 100644
--- a/.github/workflows/cont-bench.yml
+++ b/.github/workflows/cont-bench.yml
@@ -64,7 +64,7 @@ jobs:
           name: Fortran Benchmark
           tool: 'googlecpp'
           output-file-path: pr/bench-*
-          github-token: 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
+          github-token: ${{ secrets.TOKEN }}
           auto-push: true
           alert-threshold: '200%'
           comment-on-alert: true

From d7d8e7af5d7e6f0e83709127ad5ae3a4f85d8caa Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Wed, 9 Jul 2025 15:41:37 -0400
Subject: [PATCH 05/14] test bench setup

---
 .github/workflows/cont-bench.yml | 334 +++++++++++++++----------------
 1 file changed, 156 insertions(+), 178 deletions(-)

diff --git a/.github/workflows/cont-bench.yml b/.github/workflows/cont-bench.yml
index 9d7743a72..ce5002604 100644
--- a/.github/workflows/cont-bench.yml
+++ b/.github/workflows/cont-bench.yml
@@ -2,8 +2,6 @@ name: Continuous Benchmarking
 
 on:
   pull_request:
-  pull_request_review:
-    types: [submitted]
   workflow_dispatch:
   push:
     branches: [main, master]
@@ -15,32 +13,8 @@ permissions:
   id-token: write
 
 jobs:
-  # file-changes:
-  #   name: Detect File Changes
-  #   runs-on: 'ubuntu-latest'
-  #   outputs: 
-  #     checkall: ${{ steps.changes.outputs.checkall }}
-  #   steps:
-  #     - name: Clone
-  #       uses: actions/checkout@v4
-  #       with:
-  #         fetch-depth: 0 
-
-  #     - name: Detect Changes
-  #       uses: dorny/paths-filter@v3
-  #       id: changes
-  #       with: 
-  #         filters: ".github/file-filter.yml"
-  #         base: ${{ github.event.repository.default_branch || 'main' }}
-
   self:
     name: "Continuous Benchmarking"
-    # if: ${{ github.repository == 'MFlowCode/MFC' && needs.file-changes.outputs.checkall == 'true' && (
-    #          (github.event_name == 'pull_request_review' && github.event.review.state == 'approved') ||
-    #          (github.event_name == 'pull_request' && github.event.pull_request.user.login == 'sbryngelson')
-    #        ) }}
-    # needs: file-changes
-    # continue-on-error: true
     runs-on: ubuntu-latest
     steps:
       - name: Clone - PR
@@ -53,206 +27,210 @@ jobs:
           sudo apt update -y
           sudo apt install -y cmake gcc g++ python3 python3-dev hdf5-tools \
                     libfftw3-dev libhdf5-dev openmpi-bin libopenmpi-dev
+          export TOKEN=$(gh auth token)
+          sudo wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64
+          sudo chmod +x /usr/local/bin/yq
+          yq --version
 
       - name: Run Fortran Benchmark
         run: |
-          (cd pr     && ./mfc.sh bench -o bench)
-
-      - name: Store benchmark result
-        uses: benchmark-action/github-action-benchmark@v1
-        with:
-          name: Fortran Benchmark
-          tool: 'googlecpp'
-          output-file-path: pr/bench-*
-          github-token: ${{ secrets.TOKEN }}
-          auto-push: true
-          alert-threshold: '200%'
-          comment-on-alert: true
-          fail-on-alert: true
-          gh-pages-branch: 'gh-pages'
-          benchmark-data-dir-path: benchmarks
-          # alert-comment-cc-users: '@sbryngelson'
+          (cd pr     && ./mfc.sh bench -o bench.yaml)
+          find pr/ -maxdepth 1 -name "*.yaml" -exec sh -c 'yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
+
+      # - name: Store benchmark result
+      #   uses: benchmark-action/github-action-benchmark@v1
+      #   with:
+      #     name: Fortran Benchmark
+      #     tool: 'googlecpp'
+      #     output-file-path: pr/bench*.json
+      #     github-token: ${{ secrets.GITHUB_TOKEN }}
+      #     auto-push: true
+      #     alert-threshold: '200%'
+      #     comment-on-alert: true
+      #     fail-on-alert: true
+      #     gh-pages-branch: 'gh-pages'
+      #     benchmark-data-dir-path: benchmarks
       
-      - name: Create Benchmark Documentation
-        run: |
-          mkdir -p pr/docs/documentation
-          cat > pr/docs/documentation/cont-bench.md << 'EOF'
-          # Continuous Benchmarking
+      # - name: Create Benchmark Documentation
+      #   run: |
+      #     mkdir -p pr/docs/documentation
+      #     cat > pr/docs/documentation/cont-bench.md << 'EOF'
+      #     # Continuous Benchmarking
 
-          This page provides an overview of MFC's continuous benchmarking system and results.
+      #     This page provides an overview of MFC's continuous benchmarking system and results.
 
-          ## Overview
+      #     ## Overview
 
-          The continuous benchmarking system automatically runs performance tests on every approved pull request and main branch commit to track performance regressions and improvements over time.
+      #     The continuous benchmarking system automatically runs performance tests on every approved pull request and main branch commit to track performance regressions and improvements over time.
 
-          ## Benchmark Results
+      #     ## Benchmark Results
 
-          ### Live Dashboard
+      #     ### Live Dashboard
           
-          View the interactive benchmark dashboard with historical performance data:
+      #     View the interactive benchmark dashboard with historical performance data:
           
-          **[🔗 Live Benchmark Results](https://mflowcode.github.io/MFC/benchmarks/)**
+      #     **[🔗 Live Benchmark Results](https://mflowcode.github.io/MFC/benchmarks/)**
 
-          ### Key Metrics
+      #     ### Key Metrics
 
-          Our benchmarking system tracks the following performance metrics:
+      #     Our benchmarking system tracks the following performance metrics:
 
-          - **Execution Time**: Overall runtime of benchmark cases
-          - **Memory Usage**: Peak memory consumption during execution
-          - **Computational Efficiency**: Performance per computational unit
-          - **Scalability**: Performance across different problem sizes
+      #     - **Execution Time**: Overall runtime of benchmark cases
+      #     - **Memory Usage**: Peak memory consumption during execution
+      #     - **Computational Efficiency**: Performance per computational unit
+      #     - **Scalability**: Performance across different problem sizes
 
-          ### Benchmark Cases
+      #     ### Benchmark Cases
 
-          The benchmark suite includes:
+      #     The benchmark suite includes:
 
-          1. **Standard Test Cases**: Representative fluid dynamics problems
-          2. **Scaling Tests**: Performance evaluation across different core counts
-          3. **Memory Tests**: Memory efficiency and usage patterns
-          4. **Accuracy Tests**: Verification of numerical accuracy
+      #     1. **Standard Test Cases**: Representative fluid dynamics problems
+      #     2. **Scaling Tests**: Performance evaluation across different core counts
+      #     3. **Memory Tests**: Memory efficiency and usage patterns
+      #     4. **Accuracy Tests**: Verification of numerical accuracy
 
-          ## Performance Trends
+      #     ## Performance Trends
 
-          ```mermaid
-          graph LR
-              A[PR Submitted] --> B[Benchmark Run]
-              B --> C[Results Stored]
-              C --> D[Performance Comparison]
-              D --> E{Performance OK?}
-              E -->|Yes| F[PR Approved]
-              E -->|No| G[Alert Generated]
-              G --> H[Developer Notified]
-          ```
+      #     ```mermaid
+      #     graph LR
+      #         A[PR Submitted] --> B[Benchmark Run]
+      #         B --> C[Results Stored]
+      #         C --> D[Performance Comparison]
+      #         D --> E{Performance OK?}
+      #         E -->|Yes| F[PR Approved]
+      #         E -->|No| G[Alert Generated]
+      #         G --> H[Developer Notified]
+      #     ```
 
-          ## Alert System
+      #     ## Alert System
 
-          The system automatically:
+      #     The system automatically:
 
-          - 🚨 **Generates alerts** when performance degrades by more than 200%
-          - 📊 **Comments on PRs** with performance impact analysis
-          - 📈 **Tracks trends** to identify gradual performance changes
-          - 👥 **Notifies maintainers** of significant performance issues
+      #     - 🚨 **Generates alerts** when performance degrades by more than 200%
+      #     - 📊 **Comments on PRs** with performance impact analysis
+      #     - 📈 **Tracks trends** to identify gradual performance changes
+      #     - 👥 **Notifies maintainers** of significant performance issues
 
-          ## Configuration
+      #     ## Configuration
 
-          ### Benchmark Triggers
+      #     ### Benchmark Triggers
 
-          Benchmarks are automatically triggered on:
+      #     Benchmarks are automatically triggered on:
 
-          - ✅ Approved pull request reviews
-          - 🔄 Pull requests from trusted contributors
-          - 📦 Pushes to main/master branches
-          - 🎯 Manual workflow dispatch
+      #     - ✅ Approved pull request reviews
+      #     - 🔄 Pull requests from trusted contributors
+      #     - 📦 Pushes to main/master branches
+      #     - 🎯 Manual workflow dispatch
 
-          ### Performance Thresholds
+      #     ### Performance Thresholds
 
-          - **Alert Threshold**: 200% performance degradation
-          - **Fail Threshold**: Critical performance regressions
-          - **Comparison Base**: Previous main branch performance
+      #     - **Alert Threshold**: 200% performance degradation
+      #     - **Fail Threshold**: Critical performance regressions
+      #     - **Comparison Base**: Previous main branch performance
 
-          ## Interpreting Results
+      #     ## Interpreting Results
 
-          ### Performance Metrics
+      #     ### Performance Metrics
 
-          | Metric | Description | Good Trend | Bad Trend |
-          |--------|-------------|------------|-----------|
-          | Runtime | Execution time | ⬇️ Decreasing | ⬆️ Increasing |
-          | Memory | Peak memory usage | ⬇️ Decreasing | ⬆️ Increasing |
-          | Efficiency | Ops per second | ⬆️ Increasing | ⬇️ Decreasing |
+      #     | Metric | Description | Good Trend | Bad Trend |
+      #     |--------|-------------|------------|-----------|
+      #     | Runtime | Execution time | ⬇️ Decreasing | ⬆️ Increasing |
+      #     | Memory | Peak memory usage | ⬇️ Decreasing | ⬆️ Increasing |
+      #     | Efficiency | Ops per second | ⬆️ Increasing | ⬇️ Decreasing |
 
-          ### Reading the Dashboard
+      #     ### Reading the Dashboard
 
-          1. **Timeline View**: Shows performance evolution over time
-          2. **Comparison View**: Compares current vs. baseline performance
-          3. **Detailed Metrics**: Drill down into specific performance aspects
-          4. **Regression Detection**: Automatically highlights performance issues
+      #     1. **Timeline View**: Shows performance evolution over time
+      #     2. **Comparison View**: Compares current vs. baseline performance
+      #     3. **Detailed Metrics**: Drill down into specific performance aspects
+      #     4. **Regression Detection**: Automatically highlights performance issues
 
-          ## Contributing to Benchmarks
+      #     ## Contributing to Benchmarks
 
-          ### Adding New Benchmarks
+      #     ### Adding New Benchmarks
 
-          To add new benchmark cases:
+      #     To add new benchmark cases:
 
-          1. Add test case to `benchmarks/` directory
-          2. Update benchmark configuration
-          3. Ensure proper performance metrics collection
-          4. Test locally before submitting PR
+      #     1. Add test case to `benchmarks/` directory
+      #     2. Update benchmark configuration
+      #     3. Ensure proper performance metrics collection
+      #     4. Test locally before submitting PR
 
-          ### Best Practices
+      #     ### Best Practices
 
-          - 🎯 **Focus on representative cases** that reflect real-world usage
-          - 📊 **Include scalability tests** for different problem sizes
-          - 🔄 **Maintain benchmark stability** to ensure reliable comparisons
-          - 📝 **Document benchmark purpose** and expected performance characteristics
+      #     - 🎯 **Focus on representative cases** that reflect real-world usage
+      #     - 📊 **Include scalability tests** for different problem sizes
+      #     - 🔄 **Maintain benchmark stability** to ensure reliable comparisons
+      #     - 📝 **Document benchmark purpose** and expected performance characteristics
 
-          ## Troubleshooting
+      #     ## Troubleshooting
 
-          ### Common Issues
+      #     ### Common Issues
 
-          | Issue | Cause | Solution |
-          |-------|-------|----------|
-          | Benchmark timeout | Long-running test | Optimize test case or increase timeout |
-          | Memory errors | Insufficient resources | Check memory requirements |
-          | Inconsistent results | System variability | Multiple runs or statistical analysis |
+      #     | Issue | Cause | Solution |
+      #     |-------|-------|----------|
+      #     | Benchmark timeout | Long-running test | Optimize test case or increase timeout |
+      #     | Memory errors | Insufficient resources | Check memory requirements |
+      #     | Inconsistent results | System variability | Multiple runs or statistical analysis |
 
-          ### Getting Help
+      #     ### Getting Help
 
-          - 📧 Contact: @sbryngelson for benchmark-related issues
-          - 🐛 Issues: Report problems via GitHub issues
-          - 📖 Documentation: Check MFC documentation for detailed guides
+      #     - 📧 Contact: @sbryngelson for benchmark-related issues
+      #     - 🐛 Issues: Report problems via GitHub issues
+      #     - 📖 Documentation: Check MFC documentation for detailed guides
 
-          ---
+      #     ---
 
-          *Last updated: $(date '+%Y-%m-%d %H:%M:%S UTC')*
-          *Generated automatically by the continuous benchmarking workflow*
-          EOF
+      #     *Last updated: $(date '+%Y-%m-%d %H:%M:%S UTC')*
+      #     *Generated automatically by the continuous benchmarking workflow*
+      #     EOF
 
-      - name: Commit Documentation
-        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-        run: |
-          cd pr
-          git config --local user.email "action@github.com"
-          git config --local user.name "GitHub Action"
-          git add docs/documentation/cont-bench.md
-          if git diff --staged --quiet; then
-            echo "No changes to commit"
-          else
-            git commit -m "Update continuous benchmarking documentation"
-            git push
-          fi
+      # - name: Commit Documentation
+      #   if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+      #   run: |
+      #     cd pr
+      #     git config --local user.email "action@github.com"
+      #     git config --local user.name "GitHub Action"
+      #     git add docs/documentation/cont-bench.md
+      #     if git diff --staged --quiet; then
+      #       echo "No changes to commit"
+      #     else
+      #       git commit -m "Update continuous benchmarking documentation"
+      #       git push
+      #     fi
       
-      - name: Archive Results
-        uses: actions/upload-artifact@v4
-        if: always()
-        with:
-          name: benchmark-results
-          path: |
-            pr/bench-*
-            pr/build/benchmarks/*
-            pr/docs/documentation/cont-bench.md
-
-  deploy-pages:
-    name: Deploy Benchmark Pages
-    if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
-    needs: self
-    runs-on: ubuntu-latest
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-        with:
-          ref: gh-pages
+      # - name: Archive Results
+      #   uses: actions/upload-artifact@v4
+      #   if: always()
+      #   with:
+      #     name: benchmark-results
+      #     path: |
+      #       pr/bench-*
+      #       pr/build/benchmarks/*
+      #       pr/docs/documentation/cont-bench.md
+
+  # deploy-pages:
+  #   name: Deploy Benchmark Pages
+  #   if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+  #   needs: self
+  #   runs-on: ubuntu-latest
+  #   environment:
+  #     name: github-pages
+  #     url: ${{ steps.deployment.outputs.page_url }}
+  #   steps:
+  #     - name: Checkout
+  #       uses: actions/checkout@v4
+  #       with:
+  #         ref: gh-pages
 
-      - name: Setup Pages
-        uses: actions/configure-pages@v4
+  #     - name: Setup Pages
+  #       uses: actions/configure-pages@v4
       
-      - name: Upload artifact
-        uses: actions/upload-pages-artifact@v2
-        with:
-          path: .
+  #     - name: Upload artifact
+  #       uses: actions/upload-pages-artifact@v2
+  #       with:
+  #         path: .
 
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v3
+  #     - name: Deploy to GitHub Pages
+  #       id: deployment
+  #       uses: actions/deploy-pages@v3

From eeffaa4cfcbfeb4a2238f3f0562aa81fa679c791 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Wed, 9 Jul 2025 15:45:32 -0400
Subject: [PATCH 06/14] another test

---
 .github/workflows/cont-bench.yml | 203 +------------------------------
 1 file changed, 1 insertion(+), 202 deletions(-)

diff --git a/.github/workflows/cont-bench.yml b/.github/workflows/cont-bench.yml
index ce5002604..84008dc62 100644
--- a/.github/workflows/cont-bench.yml
+++ b/.github/workflows/cont-bench.yml
@@ -2,9 +2,6 @@ name: Continuous Benchmarking
 
 on:
   pull_request:
-  workflow_dispatch:
-  push:
-    branches: [main, master]
 
 permissions:
   contents: write
@@ -35,202 +32,4 @@ jobs:
       - name: Run Fortran Benchmark
         run: |
           (cd pr     && ./mfc.sh bench -o bench.yaml)
-          find pr/ -maxdepth 1 -name "*.yaml" -exec sh -c 'yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
-
-      # - name: Store benchmark result
-      #   uses: benchmark-action/github-action-benchmark@v1
-      #   with:
-      #     name: Fortran Benchmark
-      #     tool: 'googlecpp'
-      #     output-file-path: pr/bench*.json
-      #     github-token: ${{ secrets.GITHUB_TOKEN }}
-      #     auto-push: true
-      #     alert-threshold: '200%'
-      #     comment-on-alert: true
-      #     fail-on-alert: true
-      #     gh-pages-branch: 'gh-pages'
-      #     benchmark-data-dir-path: benchmarks
-      
-      # - name: Create Benchmark Documentation
-      #   run: |
-      #     mkdir -p pr/docs/documentation
-      #     cat > pr/docs/documentation/cont-bench.md << 'EOF'
-      #     # Continuous Benchmarking
-
-      #     This page provides an overview of MFC's continuous benchmarking system and results.
-
-      #     ## Overview
-
-      #     The continuous benchmarking system automatically runs performance tests on every approved pull request and main branch commit to track performance regressions and improvements over time.
-
-      #     ## Benchmark Results
-
-      #     ### Live Dashboard
-          
-      #     View the interactive benchmark dashboard with historical performance data:
-          
-      #     **[🔗 Live Benchmark Results](https://mflowcode.github.io/MFC/benchmarks/)**
-
-      #     ### Key Metrics
-
-      #     Our benchmarking system tracks the following performance metrics:
-
-      #     - **Execution Time**: Overall runtime of benchmark cases
-      #     - **Memory Usage**: Peak memory consumption during execution
-      #     - **Computational Efficiency**: Performance per computational unit
-      #     - **Scalability**: Performance across different problem sizes
-
-      #     ### Benchmark Cases
-
-      #     The benchmark suite includes:
-
-      #     1. **Standard Test Cases**: Representative fluid dynamics problems
-      #     2. **Scaling Tests**: Performance evaluation across different core counts
-      #     3. **Memory Tests**: Memory efficiency and usage patterns
-      #     4. **Accuracy Tests**: Verification of numerical accuracy
-
-      #     ## Performance Trends
-
-      #     ```mermaid
-      #     graph LR
-      #         A[PR Submitted] --> B[Benchmark Run]
-      #         B --> C[Results Stored]
-      #         C --> D[Performance Comparison]
-      #         D --> E{Performance OK?}
-      #         E -->|Yes| F[PR Approved]
-      #         E -->|No| G[Alert Generated]
-      #         G --> H[Developer Notified]
-      #     ```
-
-      #     ## Alert System
-
-      #     The system automatically:
-
-      #     - 🚨 **Generates alerts** when performance degrades by more than 200%
-      #     - 📊 **Comments on PRs** with performance impact analysis
-      #     - 📈 **Tracks trends** to identify gradual performance changes
-      #     - 👥 **Notifies maintainers** of significant performance issues
-
-      #     ## Configuration
-
-      #     ### Benchmark Triggers
-
-      #     Benchmarks are automatically triggered on:
-
-      #     - ✅ Approved pull request reviews
-      #     - 🔄 Pull requests from trusted contributors
-      #     - 📦 Pushes to main/master branches
-      #     - 🎯 Manual workflow dispatch
-
-      #     ### Performance Thresholds
-
-      #     - **Alert Threshold**: 200% performance degradation
-      #     - **Fail Threshold**: Critical performance regressions
-      #     - **Comparison Base**: Previous main branch performance
-
-      #     ## Interpreting Results
-
-      #     ### Performance Metrics
-
-      #     | Metric | Description | Good Trend | Bad Trend |
-      #     |--------|-------------|------------|-----------|
-      #     | Runtime | Execution time | ⬇️ Decreasing | ⬆️ Increasing |
-      #     | Memory | Peak memory usage | ⬇️ Decreasing | ⬆️ Increasing |
-      #     | Efficiency | Ops per second | ⬆️ Increasing | ⬇️ Decreasing |
-
-      #     ### Reading the Dashboard
-
-      #     1. **Timeline View**: Shows performance evolution over time
-      #     2. **Comparison View**: Compares current vs. baseline performance
-      #     3. **Detailed Metrics**: Drill down into specific performance aspects
-      #     4. **Regression Detection**: Automatically highlights performance issues
-
-      #     ## Contributing to Benchmarks
-
-      #     ### Adding New Benchmarks
-
-      #     To add new benchmark cases:
-
-      #     1. Add test case to `benchmarks/` directory
-      #     2. Update benchmark configuration
-      #     3. Ensure proper performance metrics collection
-      #     4. Test locally before submitting PR
-
-      #     ### Best Practices
-
-      #     - 🎯 **Focus on representative cases** that reflect real-world usage
-      #     - 📊 **Include scalability tests** for different problem sizes
-      #     - 🔄 **Maintain benchmark stability** to ensure reliable comparisons
-      #     - 📝 **Document benchmark purpose** and expected performance characteristics
-
-      #     ## Troubleshooting
-
-      #     ### Common Issues
-
-      #     | Issue | Cause | Solution |
-      #     |-------|-------|----------|
-      #     | Benchmark timeout | Long-running test | Optimize test case or increase timeout |
-      #     | Memory errors | Insufficient resources | Check memory requirements |
-      #     | Inconsistent results | System variability | Multiple runs or statistical analysis |
-
-      #     ### Getting Help
-
-      #     - 📧 Contact: @sbryngelson for benchmark-related issues
-      #     - 🐛 Issues: Report problems via GitHub issues
-      #     - 📖 Documentation: Check MFC documentation for detailed guides
-
-      #     ---
-
-      #     *Last updated: $(date '+%Y-%m-%d %H:%M:%S UTC')*
-      #     *Generated automatically by the continuous benchmarking workflow*
-      #     EOF
-
-      # - name: Commit Documentation
-      #   if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-      #   run: |
-      #     cd pr
-      #     git config --local user.email "action@github.com"
-      #     git config --local user.name "GitHub Action"
-      #     git add docs/documentation/cont-bench.md
-      #     if git diff --staged --quiet; then
-      #       echo "No changes to commit"
-      #     else
-      #       git commit -m "Update continuous benchmarking documentation"
-      #       git push
-      #     fi
-      
-      # - name: Archive Results
-      #   uses: actions/upload-artifact@v4
-      #   if: always()
-      #   with:
-      #     name: benchmark-results
-      #     path: |
-      #       pr/bench-*
-      #       pr/build/benchmarks/*
-      #       pr/docs/documentation/cont-bench.md
-
-  # deploy-pages:
-  #   name: Deploy Benchmark Pages
-  #   if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
-  #   needs: self
-  #   runs-on: ubuntu-latest
-  #   environment:
-  #     name: github-pages
-  #     url: ${{ steps.deployment.outputs.page_url }}
-  #   steps:
-  #     - name: Checkout
-  #       uses: actions/checkout@v4
-  #       with:
-  #         ref: gh-pages
-
-  #     - name: Setup Pages
-  #       uses: actions/configure-pages@v4
-      
-  #     - name: Upload artifact
-  #       uses: actions/upload-pages-artifact@v2
-  #       with:
-  #         path: .
-
-  #     - name: Deploy to GitHub Pages
-  #       id: deployment
-  #       uses: actions/deploy-pages@v3
+          find pr/ -maxdepth 1 -name "*.yaml" -exec sh -c 'yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
\ No newline at end of file

From 68d3733bf77d68140c8adac0a6bfecbf5aa36f82 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Wed, 9 Jul 2025 15:46:43 -0400
Subject: [PATCH 07/14] another way

---
 .github/workflows/cont-bench.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/cont-bench.yml b/.github/workflows/cont-bench.yml
index 84008dc62..e50ee256c 100644
--- a/.github/workflows/cont-bench.yml
+++ b/.github/workflows/cont-bench.yml
@@ -1,7 +1,6 @@
 name: Continuous Benchmarking
 
-on:
-  pull_request:
+on: [push, pull_request, workflow_dispatch]
 
 permissions:
   contents: write

From 82fa00402868b4dae4f356a597dfac5671b1fe36 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Wed, 9 Jul 2025 15:56:34 -0400
Subject: [PATCH 08/14] added detect file change

---
 .github/workflows/cont-bench.yml | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cont-bench.yml b/.github/workflows/cont-bench.yml
index e50ee256c..2de64924c 100644
--- a/.github/workflows/cont-bench.yml
+++ b/.github/workflows/cont-bench.yml
@@ -9,8 +9,28 @@ permissions:
   id-token: write
 
 jobs:
+  file-changes:
+    name: Detect File Changes
+    runs-on: 'ubuntu-latest'
+    outputs: 
+      checkall: ${{ steps.changes.outputs.checkall }}
+    steps:
+      - name: Clone
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 
+
+      - name: Detect Changes
+        uses: dorny/paths-filter@v3
+        id: changes
+        with: 
+          filters: ".github/file-filter.yml"
+          base: ${{ github.event.repository.default_branch || 'main' }}
+
   self:
     name: "Continuous Benchmarking"
+    needs: file-changes
+    continue-on-error: true
     runs-on: ubuntu-latest
     steps:
       - name: Clone - PR
@@ -28,7 +48,7 @@ jobs:
           sudo chmod +x /usr/local/bin/yq
           yq --version
 
-      - name: Run Fortran Benchmark
+      - name: Run Benchmark Cases
         run: |
           (cd pr     && ./mfc.sh bench -o bench.yaml)
           find pr/ -maxdepth 1 -name "*.yaml" -exec sh -c 'yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
\ No newline at end of file

From 963aff2ea6b9db5512f036f51c941bb8298d60bb Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Wed, 9 Jul 2025 16:00:39 -0400
Subject: [PATCH 09/14] addedArchive Results

---
 .github/workflows/cont-bench.yml | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cont-bench.yml b/.github/workflows/cont-bench.yml
index 2de64924c..6bcdf7c86 100644
--- a/.github/workflows/cont-bench.yml
+++ b/.github/workflows/cont-bench.yml
@@ -51,4 +51,14 @@ jobs:
       - name: Run Benchmark Cases
         run: |
           (cd pr     && ./mfc.sh bench -o bench.yaml)
-          find pr/ -maxdepth 1 -name "*.yaml" -exec sh -c 'yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
\ No newline at end of file
+          find pr/ -maxdepth 1 -name "*.yaml" -exec sh -c 'yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
+
+      - name: Archive Results
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: benchmark-results
+          path: |
+            pr/bench*
+            pr/build/benchmarks/*
+            pr/docs/documentation/cont-bench.md

From 14066f2e150d8c17840b84a05f0765da991a9c7b Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Wed, 9 Jul 2025 16:14:37 -0400
Subject: [PATCH 10/14] added Benchmark Documentation

---
 .github/workflows/cont-bench.yml | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cont-bench.yml b/.github/workflows/cont-bench.yml
index 6bcdf7c86..df2b30e14 100644
--- a/.github/workflows/cont-bench.yml
+++ b/.github/workflows/cont-bench.yml
@@ -51,7 +51,30 @@ jobs:
       - name: Run Benchmark Cases
         run: |
           (cd pr     && ./mfc.sh bench -o bench.yaml)
-          find pr/ -maxdepth 1 -name "*.yaml" -exec sh -c 'yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
+          find pr -maxdepth 1 -name "*.yaml" -exec sh -c 'yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
+
+      - name: Create Benchmark Documentation
+        run: |
+          mkdir -p pr/docs/documentation
+          cat > pr/docs/documentation/cont-bench.md << 'EOF'
+          # Continuous Benchmarking
+
+          ## Overview
+
+          The continuous benchmarking system automatically runs performance tests on every approved pull request and main branch commit to track performance regressions and improvements over time.
+
+          ## Benchmark Results
+
+          ### Live Dashboard
+          
+          View the interactive benchmark dashboard with historical performance data:
+          
+          **[🔗 Live Benchmark Results](https://mflowcode.github.io/MFC/benchmarks/)**
+
+          *Last updated: $(date '+%Y-%m-%d %H:%M:%S UTC')*
+          *Generated automatically by the continuous benchmarking workflow*
+          EOF
+
 
       - name: Archive Results
         uses: actions/upload-artifact@v4

From d7b8ed46cee41c0147b312d1669b38d8d40facda Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Wed, 9 Jul 2025 20:38:08 -0400
Subject: [PATCH 11/14] all files

---
 .env                                  |   2 +
 .github/workflows/bench/test.yaml     |   2 +
 .github/workflows/cont-bench.yml      |  90 ++++++++++--
 .github/workflows/mfc.sh              |   6 +
 .github/workflows/test-components.sh  |  48 ++++++
 .github/workflows/test-cont-bench.yml | 201 ++++++++++++++++++++++++++
 bench                                 | 153 ++++++++++++++++++++
 bench-google.json                     |  69 +++++++++
 bench.json                            | 195 +++++++++++++++++++++++++
 bench.yaml                            | 153 ++++++++++++++++++++
 docs/documentation/cont-bench.md      |  11 ++
 test-components.sh                    |  48 ++++++
 12 files changed, 964 insertions(+), 14 deletions(-)
 create mode 100644 .env
 create mode 100644 .github/workflows/bench/test.yaml
 create mode 100755 .github/workflows/mfc.sh
 create mode 100755 .github/workflows/test-components.sh
 create mode 100644 .github/workflows/test-cont-bench.yml
 create mode 100644 bench
 create mode 100644 bench-google.json
 create mode 100644 bench.json
 create mode 100644 bench.yaml
 create mode 100644 docs/documentation/cont-bench.md
 create mode 100755 test-components.sh

diff --git a/.env b/.env
new file mode 100644
index 000000000..88bf9f148
--- /dev/null
+++ b/.env
@@ -0,0 +1,2 @@
+TOKEN=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
+GITHUB_TOKEN=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
diff --git a/.github/workflows/bench/test.yaml b/.github/workflows/bench/test.yaml
new file mode 100644
index 000000000..1e82c56d4
--- /dev/null
+++ b/.github/workflows/bench/test.yaml
@@ -0,0 +1,2 @@
+name: test_benchmark
+time: 1.23
diff --git a/.github/workflows/cont-bench.yml b/.github/workflows/cont-bench.yml
index df2b30e14..9fe93b3d0 100644
--- a/.github/workflows/cont-bench.yml
+++ b/.github/workflows/cont-bench.yml
@@ -53,28 +53,90 @@ jobs:
           (cd pr     && ./mfc.sh bench -o bench.yaml)
           find pr -maxdepth 1 -name "*.yaml" -exec sh -c 'yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
 
-      - name: Create Benchmark Documentation
+
+      - name: Convert MFC to Google Benchmark Format
         run: |
-          mkdir -p pr/docs/documentation
-          cat > pr/docs/documentation/cont-bench.md << 'EOF'
-          # Continuous Benchmarking
+          python3 << 'EOF'
+          import json
+          from datetime import datetime
+
+          # Read the MFC benchmark data
+          with open('bench.json', 'r') as f:
+              mfc_data = json.load(f)
 
-          ## Overview
+          # Convert to Google Benchmark format
+          benchmarks = []
 
-          The continuous benchmarking system automatically runs performance tests on every approved pull request and main branch commit to track performance regressions and improvements over time.
+          for case_name, case_data in mfc_data['cases'].items():
+              output_summary = case_data['output_summary']
+              
+              # Simulation execution time
+              if 'simulation' in output_summary and 'exec' in output_summary['simulation']:
+                  benchmarks.append({
+                      "name": f"{case_name}/simulation_time",
+                      "family_index": len(benchmarks),
+                      "per_family_instance_index": 0,
+                      "run_name": f"{case_name}/simulation_time",
+                      "run_type": "iteration",
+                      "repetitions": 1,
+                      "repetition_index": 0,
+                      "threads": 1,
+                      "iterations": 1,
+                      "real_time": output_summary['simulation']['exec'] * 1e9,
+                      "cpu_time": output_summary['simulation']['exec'] * 1e9,
+                      "time_unit": "ns"
+                  })
+              
+              # Simulation grind time
+              if 'simulation' in output_summary and 'grind' in output_summary['simulation']:
+                  benchmarks.append({
+                      "name": f"{case_name}/grind_time",
+                      "family_index": len(benchmarks),
+                      "per_family_instance_index": 0,
+                      "run_name": f"{case_name}/grind_time",
+                      "run_type": "iteration",
+                      "repetitions": 1,
+                      "repetition_index": 0,
+                      "threads": 1,
+                      "iterations": 1,
+                      "real_time": output_summary['simulation']['grind'],
+                      "cpu_time": output_summary['simulation']['grind'],
+                      "time_unit": "ns"
+                  })
 
-          ## Benchmark Results
+          # Create Google Benchmark format
+          google_benchmark_data = {
+              "context": {
+                  "date": datetime.now().isoformat(),
+                  "host_name": "github-runner",
+                  "executable": "mfc_benchmark",
+                  "num_cpus": 2,
+                  "mhz_per_cpu": 2000,
+                  "cpu_scaling_enabled": False,
+                  "caches": []
+              },
+              "benchmarks": benchmarks
+          }
 
-          ### Live Dashboard
-          
-          View the interactive benchmark dashboard with historical performance data:
-          
-          **[🔗 Live Benchmark Results](https://mflowcode.github.io/MFC/benchmarks/)**
+          # Write the converted data
+          with open('bench-google.json', 'w') as f:
+              json.dump(google_benchmark_data, f, indent=2)
 
-          *Last updated: $(date '+%Y-%m-%d %H:%M:%S UTC')*
-          *Generated automatically by the continuous benchmarking workflow*
+          print(f"✓ Converted {len(benchmarks)} benchmark measurements")
           EOF
 
+      - name: Store benchmark result
+        uses: benchmark-action/github-action-benchmark@v1
+        with:
+          name: C++ Benchmark
+          tool: 'googlecpp'
+          output-file-path: bench-google.json
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          auto-push: true
+          alert-threshold: '200%'
+          comment-on-alert: true
+          fail-on-alert: true
+          alert-comment-cc-users: '@Malmahrouqi'
 
       - name: Archive Results
         uses: actions/upload-artifact@v4
diff --git a/.github/workflows/mfc.sh b/.github/workflows/mfc.sh
new file mode 100755
index 000000000..33dd401fa
--- /dev/null
+++ b/.github/workflows/mfc.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+echo "Mock benchmark running..."
+mkdir -p bench
+echo "name: test_benchmark" > bench/test.yaml
+echo "time: 1.23" >> bench/test.yaml
+echo "Mock benchmark completed"
diff --git a/.github/workflows/test-components.sh b/.github/workflows/test-components.sh
new file mode 100755
index 000000000..14fab2518
--- /dev/null
+++ b/.github/workflows/test-components.sh
@@ -0,0 +1,48 @@
+#!/bin/bash
+set -e
+
+echo "=== Testing Individual Components ==="
+
+# Test 1: Check if mfc.sh exists and is executable
+echo "1. Testing mfc.sh..."
+if [ -f "./mfc.sh" ]; then
+    chmod +x ./mfc.sh
+    echo "✓ mfc.sh found and made executable"
+else
+    echo "✗ mfc.sh not found - creating mock for testing"
+    cat > ./mfc.sh << 'MOCK'
+#!/bin/bash
+echo "Mock benchmark running..."
+mkdir -p bench
+echo "name: test_benchmark" > bench/test.yaml
+echo "time: 1.23" >> bench/test.yaml
+echo "Mock benchmark completed"
+MOCK
+    chmod +x ./mfc.sh
+fi
+
+# Test 2: Run benchmark command
+echo "2. Testing benchmark execution..."
+./mfc.sh bench -o bench || echo "Benchmark failed, continuing with mock data"
+
+# Test 3: Check yq installation and YAML to JSON conversion
+echo "3. Testing YAML to JSON conversion..."
+if ! command -v yq &> /dev/null; then
+    echo "Installing yq..."
+    sudo wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64
+    sudo chmod +x /usr/local/bin/yq
+fi
+
+# Convert any YAML files found
+find . -maxdepth 1 -name "*.yaml" -exec sh -c 'echo "Converting $1"; yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
+
+# Test 4: Check JSON output format
+echo "4. Validating JSON format..."
+for json_file in *.json; do
+    if [ -f "$json_file" ]; then
+        echo "Checking $json_file:"
+        python3 -c "import json; json.load(open('$json_file')); print('✓ Valid JSON')" || echo "✗ Invalid JSON"
+    fi
+done
+
+echo "=== Component Testing Complete ==="
diff --git a/.github/workflows/test-cont-bench.yml b/.github/workflows/test-cont-bench.yml
new file mode 100644
index 000000000..3af2985bc
--- /dev/null
+++ b/.github/workflows/test-cont-bench.yml
@@ -0,0 +1,201 @@
+name: Continuous Benchmarking
+
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: write
+  deployments: write
+  pages: write
+  id-token: write
+
+jobs:
+  self:
+    name: "Store benchmark result"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Convert MFC to Google Benchmark Format
+        run: |
+          python3 << 'EOF'
+          import json
+          from datetime import datetime
+
+          # Read the MFC benchmark data
+          with open('bench.json', 'r') as f:
+              mfc_data = json.load(f)
+
+          # Convert to Google Benchmark format
+          benchmarks = []
+
+          for case_name, case_data in mfc_data['cases'].items():
+              output_summary = case_data['output_summary']
+              
+              # Simulation execution time
+              if 'simulation' in output_summary and 'exec' in output_summary['simulation']:
+                  benchmarks.append({
+                      "name": f"{case_name}/simulation_time",
+                      "family_index": len(benchmarks),
+                      "per_family_instance_index": 0,
+                      "run_name": f"{case_name}/simulation_time",
+                      "run_type": "iteration",
+                      "repetitions": 1,
+                      "repetition_index": 0,
+                      "threads": 1,
+                      "iterations": 1,
+                      "real_time": output_summary['simulation']['exec'] * 1e9,
+                      "cpu_time": output_summary['simulation']['exec'] * 1e9,
+                      "time_unit": "ns"
+                  })
+              
+              # Simulation grind time
+              if 'simulation' in output_summary and 'grind' in output_summary['simulation']:
+                  benchmarks.append({
+                      "name": f"{case_name}/grind_time",
+                      "family_index": len(benchmarks),
+                      "per_family_instance_index": 0,
+                      "run_name": f"{case_name}/grind_time",
+                      "run_type": "iteration",
+                      "repetitions": 1,
+                      "repetition_index": 0,
+                      "threads": 1,
+                      "iterations": 1,
+                      "real_time": output_summary['simulation']['grind'],
+                      "cpu_time": output_summary['simulation']['grind'],
+                      "time_unit": "ns"
+                  })
+
+          # Create Google Benchmark format
+          google_benchmark_data = {
+              "context": {
+                  "date": datetime.now().isoformat(),
+                  "host_name": "github-runner",
+                  "executable": "mfc_benchmark",
+                  "num_cpus": 2,
+                  "mhz_per_cpu": 2000,
+                  "cpu_scaling_enabled": False,
+                  "caches": []
+              },
+              "benchmarks": benchmarks
+          }
+
+          # Write the converted data
+          with open('bench-google.json', 'w') as f:
+              json.dump(google_benchmark_data, f, indent=2)
+
+          print(f"✓ Converted {len(benchmarks)} benchmark measurements")
+          EOF
+    
+      - name: Create report generator script
+        run: |
+          cat > generate_report.py << 'SCRIPT'
+          import json
+          import os
+          from datetime import datetime
+
+          def generate_markdown_report():
+              # Read benchmark data
+              with open('bench-google.json', 'r') as f:
+                  data = json.load(f)
+
+              # Create directory
+              os.makedirs('docs/documentation', exist_ok=True)
+              
+              # Start building content
+              lines = []
+              lines.append("# Continuouscl Benchmarking Results")
+              lines.append("")
+              lines.append(f"Generated on: {datetime.now().strftime('%Y-%m-%d %H:%M:%S UTC')}")
+              lines.append("")
+              lines.append("## System Information")
+              lines.append(f"- Host: {data['context']['host_name']}")
+              lines.append(f"- CPUs: {data['context']['num_cpus']}")
+              lines.append(f"- MHz per CPU: {data['context']['mhz_per_cpu']}")
+              lines.append("")
+              lines.append("## Benchmark Results")
+              lines.append("")
+              lines.append("| Test Case | Metric | Time (seconds) | Time (nanoseconds) |")
+              lines.append("|-----------|--------|----------------|-------------------|")
+              
+              # Add benchmark data
+              for benchmark in data['benchmarks']:
+                  name_parts = benchmark['name'].split('/')
+                  case_name = name_parts[0]
+                  metric_name = name_parts[1] if len(name_parts) > 1 else 'unknown'
+                  time_seconds = benchmark['real_time'] / 1e9
+                  time_ns = benchmark['real_time']
+                  lines.append(f"| {case_name} | {metric_name} | {time_seconds:.6f} | {time_ns:.0f} |")
+              
+              lines.append("")
+              lines.append("## Raw Data")
+              lines.append("")
+              lines.append("```json")
+              lines.append(json.dumps(data, indent=2))
+              lines.append("```")
+              lines.append("")
+              lines.append("---")
+              lines.append(f"*Last updated: {datetime.now().isoformat()}*")
+              
+              # Write file
+              with open('docs/documentation/cont-bench.md', 'w') as f:
+                  f.write('\n'.join(lines))
+              
+              print("✓ Generated Markdown report at docs/documentation/cont-bench.md")
+
+          if __name__ == "__main__":
+              generate_markdown_report()
+          SCRIPT
+
+      - name: Generate Markdown Report
+        run: python3 generate_report.py
+
+      - name: Commit and Push Results
+        run: |
+          git config --local user.email "mohdsaid497566@gmail.com"
+          git config --local user.name "Malmahrouqi3"
+          
+          # Fetch latest changes from the remote branch
+          git fetch origin cont-bench || true
+          
+          # Stage the generated file
+          git add docs/documentation/cont-bench.md
+          
+          # Commit changes to have a clean working tree
+          git commit -m "Update continuous benchmarking results" || true
+          
+          # Check if we're behind the remote branch
+          if git rev-list HEAD..origin/cont-bench --count | grep -q "^[1-9]"; then
+            echo "Branch is behind remote, resolving..."
+            
+            # Save our changes to a temporary branch
+            git branch temp-benchmark-updates
+            
+            # Get up to date with the remote branch
+            git reset --hard origin/cont-bench
+            
+            # Regenerate the report with the latest code
+            python3 generate_report.py
+            
+            # Add the newly generated report
+            git add docs/documentation/cont-bench.md
+            
+            # Commit the changes
+            git commit -m "Update continuous benchmarking results" || true
+          fi
+          
+          # Push the changes, forcing if necessary
+          git push origin HEAD:cont-bench || git push -f origin HEAD:cont-bench
+                    
+      - name: Store benchmark result
+        uses: benchmark-action/github-action-benchmark@v1
+        with:
+          name: C++ Benchmark
+          tool: 'googlecpp'
+          output-file-path: bench-google.json
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          auto-push: false
+          alert-threshold: '200%'
+          comment-on-alert: true
+          fail-on-alert: true
+          alert-comment-cc-users: '@Malmahrouqi'
diff --git a/bench b/bench
new file mode 100644
index 000000000..40207a9f8
--- /dev/null
+++ b/bench
@@ -0,0 +1,153 @@
+cases:
+  5eq_rk3_weno3_hllc:
+    description:
+      args: []
+      path: /home/mohammed/Desktop/cont-bench/benchmarks/5eq_rk3_weno3_hllc/case.py
+      slug: 5eq_rk3_weno3_hllc
+    output_summary:
+      invocation:
+      - run
+      - /home/mohammed/Desktop/cont-bench/benchmarks/5eq_rk3_weno3_hllc/case.py
+      - --case-optimization
+      - --targets
+      - pre_process
+      - simulation
+      - post_process
+      - --output-summary
+      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/5eq_rk3_weno3_hllc.yaml
+      - --
+      - --gbpp
+      - '1'
+      lock:
+        debug: false
+        gcov: false
+        gpu: false
+        mpi: true
+        single: false
+        unified: false
+      post_process:
+        exec: 2.6731925
+      pre_process:
+        exec: 0.945057
+      simulation:
+        exec: 553.7461466
+        grind: 311.46590698
+      syscheck:
+        exec: 0.5911245
+  hypo_hll:
+    description:
+      args: []
+      path: /home/mohammed/Desktop/cont-bench/benchmarks/hypo_hll/case.py
+      slug: hypo_hll
+    output_summary:
+      invocation:
+      - run
+      - /home/mohammed/Desktop/cont-bench/benchmarks/hypo_hll/case.py
+      - --case-optimization
+      - --targets
+      - pre_process
+      - simulation
+      - post_process
+      - --output-summary
+      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/hypo_hll.yaml
+      - --
+      - --gbpp
+      - '1'
+      lock:
+        debug: false
+        gcov: false
+        gpu: false
+        mpi: true
+        single: false
+        unified: false
+      post_process:
+        exec: 4.6181798
+      pre_process:
+        exec: 28.0626009
+      simulation:
+        exec: 1158.0062294
+        grind: 373.3648501
+      syscheck:
+        exec: 0.5746224
+  ibm:
+    description:
+      args: []
+      path: /home/mohammed/Desktop/cont-bench/benchmarks/ibm/case.py
+      slug: ibm
+    output_summary:
+      invocation:
+      - run
+      - /home/mohammed/Desktop/cont-bench/benchmarks/ibm/case.py
+      - --case-optimization
+      - --targets
+      - pre_process
+      - simulation
+      - post_process
+      - --output-summary
+      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/ibm.yaml
+      - --
+      - --gbpp
+      - '1'
+      lock:
+        debug: false
+        gcov: false
+        gpu: false
+        mpi: true
+        single: false
+        unified: false
+      post_process:
+        exec: 2.7696633
+      pre_process:
+        exec: 0.6595922
+      simulation:
+        exec: 1560.6666524
+        grind: 1329.41865639
+      syscheck:
+        exec: 0.350557
+  viscous_weno5_sgb_acoustic:
+    description:
+      args: []
+      path: /home/mohammed/Desktop/cont-bench/benchmarks/viscous_weno5_sgb_acoustic/case.py
+      slug: viscous_weno5_sgb_acoustic
+    output_summary:
+      invocation:
+      - run
+      - /home/mohammed/Desktop/cont-bench/benchmarks/viscous_weno5_sgb_acoustic/case.py
+      - --case-optimization
+      - --targets
+      - pre_process
+      - simulation
+      - post_process
+      - --output-summary
+      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/viscous_weno5_sgb_acoustic.yaml
+      - --
+      - --gbpp
+      - '1'
+      lock:
+        debug: false
+        gcov: false
+        gpu: false
+        mpi: true
+        single: false
+        unified: false
+      post_process:
+        exec: 1.7293213
+      pre_process:
+        exec: 0.7582608
+      simulation:
+        exec: 968.760392
+        grind: 1051.98369313
+      syscheck:
+        exec: 0.6131606
+metadata:
+  invocation:
+  - bench
+  - -o
+  - bench
+  lock:
+    debug: false
+    gcov: false
+    gpu: false
+    mpi: true
+    single: false
+    unified: false
diff --git a/bench-google.json b/bench-google.json
new file mode 100644
index 000000000..258ff5933
--- /dev/null
+++ b/bench-google.json
@@ -0,0 +1,69 @@
+{
+  "context": {
+    "date": "2025-07-09T16:51:13.791064",
+    "host_name": "test",
+    "executable": "mfc_benchmark",
+    "num_cpus": 2,
+    "mhz_per_cpu": 2000,
+    "cpu_scaling_enabled": false,
+    "caches": []
+  },
+  "benchmarks": [
+    {
+      "name": "5eq_rk3_weno3_hllc/simulation_time",
+      "family_index": 0,
+      "per_family_instance_index": 0,
+      "run_name": "5eq_rk3_weno3_hllc/simulation_time",
+      "run_type": "iteration",
+      "repetitions": 1,
+      "repetition_index": 0,
+      "threads": 1,
+      "iterations": 1,
+      "real_time": 553746146600.0,
+      "cpu_time": 553746146600.0,
+      "time_unit": "ns"
+    },
+    {
+      "name": "hypo_hll/simulation_time",
+      "family_index": 1,
+      "per_family_instance_index": 0,
+      "run_name": "hypo_hll/simulation_time",
+      "run_type": "iteration",
+      "repetitions": 1,
+      "repetition_index": 0,
+      "threads": 1,
+      "iterations": 1,
+      "real_time": 1158006229400.0,
+      "cpu_time": 1158006229400.0,
+      "time_unit": "ns"
+    },
+    {
+      "name": "ibm/simulation_time",
+      "family_index": 2,
+      "per_family_instance_index": 0,
+      "run_name": "ibm/simulation_time",
+      "run_type": "iteration",
+      "repetitions": 1,
+      "repetition_index": 0,
+      "threads": 1,
+      "iterations": 1,
+      "real_time": 1560666652400.0,
+      "cpu_time": 1560666652400.0,
+      "time_unit": "ns"
+    },
+    {
+      "name": "viscous_weno5_sgb_acoustic/simulation_time",
+      "family_index": 3,
+      "per_family_instance_index": 0,
+      "run_name": "viscous_weno5_sgb_acoustic/simulation_time",
+      "run_type": "iteration",
+      "repetitions": 1,
+      "repetition_index": 0,
+      "threads": 1,
+      "iterations": 1,
+      "real_time": 968760392000.0,
+      "cpu_time": 968760392000.0,
+      "time_unit": "ns"
+    }
+  ]
+}
\ No newline at end of file
diff --git a/bench.json b/bench.json
new file mode 100644
index 000000000..51457d2dc
--- /dev/null
+++ b/bench.json
@@ -0,0 +1,195 @@
+{
+  "cases": {
+    "5eq_rk3_weno3_hllc": {
+      "description": {
+        "args": [],
+        "path": "/home/mohammed/Desktop/cont-bench/benchmarks/5eq_rk3_weno3_hllc/case.py",
+        "slug": "5eq_rk3_weno3_hllc"
+      },
+      "output_summary": {
+        "invocation": [
+          "run",
+          "/home/mohammed/Desktop/cont-bench/benchmarks/5eq_rk3_weno3_hllc/case.py",
+          "--case-optimization",
+          "--targets",
+          "pre_process",
+          "simulation",
+          "post_process",
+          "--output-summary",
+          "/home/mohammed/Desktop/cont-bench/build/benchmarks/6462/5eq_rk3_weno3_hllc.yaml",
+          "--",
+          "--gbpp",
+          "1"
+        ],
+        "lock": {
+          "debug": false,
+          "gcov": false,
+          "gpu": false,
+          "mpi": true,
+          "single": false,
+          "unified": false
+        },
+        "post_process": {
+          "exec": 2.6731925
+        },
+        "pre_process": {
+          "exec": 0.945057
+        },
+        "simulation": {
+          "exec": 553.7461466,
+          "grind": 311.46590698
+        },
+        "syscheck": {
+          "exec": 0.5911245
+        }
+      }
+    },
+    "hypo_hll": {
+      "description": {
+        "args": [],
+        "path": "/home/mohammed/Desktop/cont-bench/benchmarks/hypo_hll/case.py",
+        "slug": "hypo_hll"
+      },
+      "output_summary": {
+        "invocation": [
+          "run",
+          "/home/mohammed/Desktop/cont-bench/benchmarks/hypo_hll/case.py",
+          "--case-optimization",
+          "--targets",
+          "pre_process",
+          "simulation",
+          "post_process",
+          "--output-summary",
+          "/home/mohammed/Desktop/cont-bench/build/benchmarks/6462/hypo_hll.yaml",
+          "--",
+          "--gbpp",
+          "1"
+        ],
+        "lock": {
+          "debug": false,
+          "gcov": false,
+          "gpu": false,
+          "mpi": true,
+          "single": false,
+          "unified": false
+        },
+        "post_process": {
+          "exec": 4.6181798
+        },
+        "pre_process": {
+          "exec": 28.0626009
+        },
+        "simulation": {
+          "exec": 1158.0062294,
+          "grind": 373.3648501
+        },
+        "syscheck": {
+          "exec": 0.5746224
+        }
+      }
+    },
+    "ibm": {
+      "description": {
+        "args": [],
+        "path": "/home/mohammed/Desktop/cont-bench/benchmarks/ibm/case.py",
+        "slug": "ibm"
+      },
+      "output_summary": {
+        "invocation": [
+          "run",
+          "/home/mohammed/Desktop/cont-bench/benchmarks/ibm/case.py",
+          "--case-optimization",
+          "--targets",
+          "pre_process",
+          "simulation",
+          "post_process",
+          "--output-summary",
+          "/home/mohammed/Desktop/cont-bench/build/benchmarks/6462/ibm.yaml",
+          "--",
+          "--gbpp",
+          "1"
+        ],
+        "lock": {
+          "debug": false,
+          "gcov": false,
+          "gpu": false,
+          "mpi": true,
+          "single": false,
+          "unified": false
+        },
+        "post_process": {
+          "exec": 2.7696633
+        },
+        "pre_process": {
+          "exec": 0.6595922
+        },
+        "simulation": {
+          "exec": 1560.6666524,
+          "grind": 1329.41865639
+        },
+        "syscheck": {
+          "exec": 0.350557
+        }
+      }
+    },
+    "viscous_weno5_sgb_acoustic": {
+      "description": {
+        "args": [],
+        "path": "/home/mohammed/Desktop/cont-bench/benchmarks/viscous_weno5_sgb_acoustic/case.py",
+        "slug": "viscous_weno5_sgb_acoustic"
+      },
+      "output_summary": {
+        "invocation": [
+          "run",
+          "/home/mohammed/Desktop/cont-bench/benchmarks/viscous_weno5_sgb_acoustic/case.py",
+          "--case-optimization",
+          "--targets",
+          "pre_process",
+          "simulation",
+          "post_process",
+          "--output-summary",
+          "/home/mohammed/Desktop/cont-bench/build/benchmarks/6462/viscous_weno5_sgb_acoustic.yaml",
+          "--",
+          "--gbpp",
+          "1"
+        ],
+        "lock": {
+          "debug": false,
+          "gcov": false,
+          "gpu": false,
+          "mpi": true,
+          "single": false,
+          "unified": false
+        },
+        "post_process": {
+          "exec": 1.7293213
+        },
+        "pre_process": {
+          "exec": 0.7582608
+        },
+        "simulation": {
+          "exec": 968.760392,
+          "grind": 1051.98369313
+        },
+        "syscheck": {
+          "exec": 0.6131606
+        }
+      }
+    }
+  },
+  "metadata": {
+    "invocation": [
+      "bench",
+      "-o",
+      "bench"
+    ],
+    "lock": {
+      "debug": false,
+      "gcov": false,
+      "gpu": false,
+      "mpi": true,
+      "single": false,
+      "unified": false
+    }
+  }
+}
diff --git a/bench.yaml b/bench.yaml
new file mode 100644
index 000000000..40207a9f8
--- /dev/null
+++ b/bench.yaml
@@ -0,0 +1,153 @@
+cases:
+  5eq_rk3_weno3_hllc:
+    description:
+      args: []
+      path: /home/mohammed/Desktop/cont-bench/benchmarks/5eq_rk3_weno3_hllc/case.py
+      slug: 5eq_rk3_weno3_hllc
+    output_summary:
+      invocation:
+      - run
+      - /home/mohammed/Desktop/cont-bench/benchmarks/5eq_rk3_weno3_hllc/case.py
+      - --case-optimization
+      - --targets
+      - pre_process
+      - simulation
+      - post_process
+      - --output-summary
+      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/5eq_rk3_weno3_hllc.yaml
+      - --
+      - --gbpp
+      - '1'
+      lock:
+        debug: false
+        gcov: false
+        gpu: false
+        mpi: true
+        single: false
+        unified: false
+      post_process:
+        exec: 2.6731925
+      pre_process:
+        exec: 0.945057
+      simulation:
+        exec: 553.7461466
+        grind: 311.46590698
+      syscheck:
+        exec: 0.5911245
+  hypo_hll:
+    description:
+      args: []
+      path: /home/mohammed/Desktop/cont-bench/benchmarks/hypo_hll/case.py
+      slug: hypo_hll
+    output_summary:
+      invocation:
+      - run
+      - /home/mohammed/Desktop/cont-bench/benchmarks/hypo_hll/case.py
+      - --case-optimization
+      - --targets
+      - pre_process
+      - simulation
+      - post_process
+      - --output-summary
+      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/hypo_hll.yaml
+      - --
+      - --gbpp
+      - '1'
+      lock:
+        debug: false
+        gcov: false
+        gpu: false
+        mpi: true
+        single: false
+        unified: false
+      post_process:
+        exec: 4.6181798
+      pre_process:
+        exec: 28.0626009
+      simulation:
+        exec: 1158.0062294
+        grind: 373.3648501
+      syscheck:
+        exec: 0.5746224
+  ibm:
+    description:
+      args: []
+      path: /home/mohammed/Desktop/cont-bench/benchmarks/ibm/case.py
+      slug: ibm
+    output_summary:
+      invocation:
+      - run
+      - /home/mohammed/Desktop/cont-bench/benchmarks/ibm/case.py
+      - --case-optimization
+      - --targets
+      - pre_process
+      - simulation
+      - post_process
+      - --output-summary
+      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/ibm.yaml
+      - --
+      - --gbpp
+      - '1'
+      lock:
+        debug: false
+        gcov: false
+        gpu: false
+        mpi: true
+        single: false
+        unified: false
+      post_process:
+        exec: 2.7696633
+      pre_process:
+        exec: 0.6595922
+      simulation:
+        exec: 1560.6666524
+        grind: 1329.41865639
+      syscheck:
+        exec: 0.350557
+  viscous_weno5_sgb_acoustic:
+    description:
+      args: []
+      path: /home/mohammed/Desktop/cont-bench/benchmarks/viscous_weno5_sgb_acoustic/case.py
+      slug: viscous_weno5_sgb_acoustic
+    output_summary:
+      invocation:
+      - run
+      - /home/mohammed/Desktop/cont-bench/benchmarks/viscous_weno5_sgb_acoustic/case.py
+      - --case-optimization
+      - --targets
+      - pre_process
+      - simulation
+      - post_process
+      - --output-summary
+      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/viscous_weno5_sgb_acoustic.yaml
+      - --
+      - --gbpp
+      - '1'
+      lock:
+        debug: false
+        gcov: false
+        gpu: false
+        mpi: true
+        single: false
+        unified: false
+      post_process:
+        exec: 1.7293213
+      pre_process:
+        exec: 0.7582608
+      simulation:
+        exec: 968.760392
+        grind: 1051.98369313
+      syscheck:
+        exec: 0.6131606
+metadata:
+  invocation:
+  - bench
+  - -o
+  - bench
+  lock:
+    debug: false
+    gcov: false
+    gpu: false
+    mpi: true
+    single: false
+    unified: false
diff --git a/docs/documentation/cont-bench.md b/docs/documentation/cont-bench.md
new file mode 100644
index 000000000..e12bb3406
--- /dev/null
+++ b/docs/documentation/cont-bench.md
@@ -0,0 +1,11 @@
+# Continuous Benchmarking
+
+## Overview
+
+The continuous benchmarking framework automatically runs performance tests on select performance-critical approved pull request and main branch commit to track performance regressions and improvements over time.
+
+## Benchmark Results
+
+View historical performance data:
+
+**[Live Benchmark Results](https://mflowcode.github.io/MFC/benchmarks/)**
\ No newline at end of file
diff --git a/test-components.sh b/test-components.sh
new file mode 100755
index 000000000..14fab2518
--- /dev/null
+++ b/test-components.sh
@@ -0,0 +1,48 @@
+#!/bin/bash
+set -e
+
+echo "=== Testing Individual Components ==="
+
+# Test 1: Check if mfc.sh exists and is executable
+echo "1. Testing mfc.sh..."
+if [ -f "./mfc.sh" ]; then
+    chmod +x ./mfc.sh
+    echo "✓ mfc.sh found and made executable"
+else
+    echo "✗ mfc.sh not found - creating mock for testing"
+    cat > ./mfc.sh << 'MOCK'
+#!/bin/bash
+echo "Mock benchmark running..."
+mkdir -p bench
+echo "name: test_benchmark" > bench/test.yaml
+echo "time: 1.23" >> bench/test.yaml
+echo "Mock benchmark completed"
+MOCK
+    chmod +x ./mfc.sh
+fi
+
+# Test 2: Run benchmark command
+echo "2. Testing benchmark execution..."
+./mfc.sh bench -o bench || echo "Benchmark failed, continuing with mock data"
+
+# Test 3: Check yq installation and YAML to JSON conversion
+echo "3. Testing YAML to JSON conversion..."
+if ! command -v yq &> /dev/null; then
+    echo "Installing yq..."
+    sudo wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64
+    sudo chmod +x /usr/local/bin/yq
+fi
+
+# Convert any YAML files found
+find . -maxdepth 1 -name "*.yaml" -exec sh -c 'echo "Converting $1"; yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
+
+# Test 4: Check JSON output format
+echo "4. Validating JSON format..."
+for json_file in *.json; do
+    if [ -f "$json_file" ]; then
+        echo "Checking $json_file:"
+        python3 -c "import json; json.load(open('$json_file')); print('✓ Valid JSON')" || echo "✗ Invalid JSON"
+    fi
+done
+
+echo "=== Component Testing Complete ==="

From 433caf26f59c2259e3b7b99115c93219105a3760 Mon Sep 17 00:00:00 2001
From: Malmahrouqi3 <mohdsaid497566@gmail.com>
Date: Thu, 10 Jul 2025 00:46:19 +0000
Subject: [PATCH 12/14] Update continuous benchmarking results

---
 docs/documentation/cont-bench.md | 153 ++++++++++++++++++++++++++++++-
 1 file changed, 148 insertions(+), 5 deletions(-)

diff --git a/docs/documentation/cont-bench.md b/docs/documentation/cont-bench.md
index e12bb3406..60399103d 100644
--- a/docs/documentation/cont-bench.md
+++ b/docs/documentation/cont-bench.md
@@ -1,11 +1,154 @@
-# Continuous Benchmarking
+# Continuouscl Benchmarking Results
 
-## Overview
+Generated on: 2025-07-10 00:46:18 UTC
 
-The continuous benchmarking framework automatically runs performance tests on select performance-critical approved pull request and main branch commit to track performance regressions and improvements over time.
+## System Information
+- Host: github-runner
+- CPUs: 2
+- MHz per CPU: 2000
 
 ## Benchmark Results
 
-View historical performance data:
+| Test Case | Metric | Time (seconds) | Time (nanoseconds) |
+|-----------|--------|----------------|-------------------|
+| 5eq_rk3_weno3_hllc | simulation_time | 553.746147 | 553746146600 |
+| 5eq_rk3_weno3_hllc | grind_time | 0.000000 | 311 |
+| hypo_hll | simulation_time | 1158.006229 | 1158006229400 |
+| hypo_hll | grind_time | 0.000000 | 373 |
+| ibm | simulation_time | 1560.666652 | 1560666652400 |
+| ibm | grind_time | 0.000001 | 1329 |
+| viscous_weno5_sgb_acoustic | simulation_time | 968.760392 | 968760392000 |
+| viscous_weno5_sgb_acoustic | grind_time | 0.000001 | 1052 |
 
-**[Live Benchmark Results](https://mflowcode.github.io/MFC/benchmarks/)**
\ No newline at end of file
+## Raw Data
+
+```json
+{
+  "context": {
+    "date": "2025-07-10T00:46:18.506114",
+    "host_name": "github-runner",
+    "executable": "mfc_benchmark",
+    "num_cpus": 2,
+    "mhz_per_cpu": 2000,
+    "cpu_scaling_enabled": false,
+    "caches": []
+  },
+  "benchmarks": [
+    {
+      "name": "5eq_rk3_weno3_hllc/simulation_time",
+      "family_index": 0,
+      "per_family_instance_index": 0,
+      "run_name": "5eq_rk3_weno3_hllc/simulation_time",
+      "run_type": "iteration",
+      "repetitions": 1,
+      "repetition_index": 0,
+      "threads": 1,
+      "iterations": 1,
+      "real_time": 553746146600.0,
+      "cpu_time": 553746146600.0,
+      "time_unit": "ns"
+    },
+    {
+      "name": "5eq_rk3_weno3_hllc/grind_time",
+      "family_index": 1,
+      "per_family_instance_index": 0,
+      "run_name": "5eq_rk3_weno3_hllc/grind_time",
+      "run_type": "iteration",
+      "repetitions": 1,
+      "repetition_index": 0,
+      "threads": 1,
+      "iterations": 1,
+      "real_time": 311.46590698,
+      "cpu_time": 311.46590698,
+      "time_unit": "ns"
+    },
+    {
+      "name": "hypo_hll/simulation_time",
+      "family_index": 2,
+      "per_family_instance_index": 0,
+      "run_name": "hypo_hll/simulation_time",
+      "run_type": "iteration",
+      "repetitions": 1,
+      "repetition_index": 0,
+      "threads": 1,
+      "iterations": 1,
+      "real_time": 1158006229400.0,
+      "cpu_time": 1158006229400.0,
+      "time_unit": "ns"
+    },
+    {
+      "name": "hypo_hll/grind_time",
+      "family_index": 3,
+      "per_family_instance_index": 0,
+      "run_name": "hypo_hll/grind_time",
+      "run_type": "iteration",
+      "repetitions": 1,
+      "repetition_index": 0,
+      "threads": 1,
+      "iterations": 1,
+      "real_time": 373.3648501,
+      "cpu_time": 373.3648501,
+      "time_unit": "ns"
+    },
+    {
+      "name": "ibm/simulation_time",
+      "family_index": 4,
+      "per_family_instance_index": 0,
+      "run_name": "ibm/simulation_time",
+      "run_type": "iteration",
+      "repetitions": 1,
+      "repetition_index": 0,
+      "threads": 1,
+      "iterations": 1,
+      "real_time": 1560666652400.0,
+      "cpu_time": 1560666652400.0,
+      "time_unit": "ns"
+    },
+    {
+      "name": "ibm/grind_time",
+      "family_index": 5,
+      "per_family_instance_index": 0,
+      "run_name": "ibm/grind_time",
+      "run_type": "iteration",
+      "repetitions": 1,
+      "repetition_index": 0,
+      "threads": 1,
+      "iterations": 1,
+      "real_time": 1329.41865639,
+      "cpu_time": 1329.41865639,
+      "time_unit": "ns"
+    },
+    {
+      "name": "viscous_weno5_sgb_acoustic/simulation_time",
+      "family_index": 6,
+      "per_family_instance_index": 0,
+      "run_name": "viscous_weno5_sgb_acoustic/simulation_time",
+      "run_type": "iteration",
+      "repetitions": 1,
+      "repetition_index": 0,
+      "threads": 1,
+      "iterations": 1,
+      "real_time": 968760392000.0,
+      "cpu_time": 968760392000.0,
+      "time_unit": "ns"
+    },
+    {
+      "name": "viscous_weno5_sgb_acoustic/grind_time",
+      "family_index": 7,
+      "per_family_instance_index": 0,
+      "run_name": "viscous_weno5_sgb_acoustic/grind_time",
+      "run_type": "iteration",
+      "repetitions": 1,
+      "repetition_index": 0,
+      "threads": 1,
+      "iterations": 1,
+      "real_time": 1051.98369313,
+      "cpu_time": 1051.98369313,
+      "time_unit": "ns"
+    }
+  ]
+}
+```
+
+---
+*Last updated: 2025-07-10T00:46:18.566505*
\ No newline at end of file

From 052bb5d405f05e6b6296475d04b2d2fb5d0770b3 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Fri, 11 Jul 2025 16:10:34 -0400
Subject: [PATCH 13/14] premature version of workflow file

---
 .github/workflows/bench.yml                | 110 -----------
 .github/workflows/bench/test.yaml          |   2 -
 .github/workflows/cleanliness.yml          | 127 -------------
 .github/workflows/coverage.yml             |  48 -----
 .github/workflows/docs.yml                 |  76 --------
 .github/workflows/formatting.yml           |  19 --
 .github/workflows/frontier/bench.sh        |  16 --
 .github/workflows/frontier/build.sh        |  17 --
 .github/workflows/frontier/submit-bench.sh |  54 ------
 .github/workflows/frontier/submit.sh       |  55 ------
 .github/workflows/frontier/test.sh         |  10 -
 .github/workflows/line-count.yml           |  54 ------
 .github/workflows/lint-source.yml          |  55 ------
 .github/workflows/lint-toolchain.yml       |  17 --
 .github/workflows/mfc.sh                   |   6 -
 .github/workflows/phoenix/bench.sh         |  27 ---
 .github/workflows/phoenix/submit-bench.sh  |  64 -------
 .github/workflows/phoenix/submit.sh        |  64 -------
 .github/workflows/phoenix/test.sh          |  21 ---
 .github/workflows/pmd.yml                  | 131 --------------
 .github/workflows/spelling.yml             |  17 --
 .github/workflows/test-components.sh       |  48 -----
 .github/workflows/test-cont-bench.yml      | 201 ---------------------
 .github/workflows/test.yml                 | 131 --------------
 24 files changed, 1370 deletions(-)
 delete mode 100644 .github/workflows/bench.yml
 delete mode 100644 .github/workflows/bench/test.yaml
 delete mode 100644 .github/workflows/cleanliness.yml
 delete mode 100644 .github/workflows/coverage.yml
 delete mode 100644 .github/workflows/docs.yml
 delete mode 100644 .github/workflows/formatting.yml
 delete mode 100644 .github/workflows/frontier/bench.sh
 delete mode 100644 .github/workflows/frontier/build.sh
 delete mode 100644 .github/workflows/frontier/submit-bench.sh
 delete mode 100644 .github/workflows/frontier/submit.sh
 delete mode 100644 .github/workflows/frontier/test.sh
 delete mode 100644 .github/workflows/line-count.yml
 delete mode 100644 .github/workflows/lint-source.yml
 delete mode 100644 .github/workflows/lint-toolchain.yml
 delete mode 100755 .github/workflows/mfc.sh
 delete mode 100644 .github/workflows/phoenix/bench.sh
 delete mode 100644 .github/workflows/phoenix/submit-bench.sh
 delete mode 100644 .github/workflows/phoenix/submit.sh
 delete mode 100644 .github/workflows/phoenix/test.sh
 delete mode 100644 .github/workflows/pmd.yml
 delete mode 100644 .github/workflows/spelling.yml
 delete mode 100755 .github/workflows/test-components.sh
 delete mode 100644 .github/workflows/test-cont-bench.yml
 delete mode 100644 .github/workflows/test.yml

diff --git a/.github/workflows/bench.yml b/.github/workflows/bench.yml
deleted file mode 100644
index b5e89a2b5..000000000
--- a/.github/workflows/bench.yml
+++ /dev/null
@@ -1,110 +0,0 @@
-name: 'Benchmark'
-
-on:
-  pull_request:
-  pull_request_review:
-    types: [submitted]
-  workflow_dispatch:
-
-jobs:
-  file-changes:
-    name: Detect File Changes
-    runs-on: 'ubuntu-latest'
-    outputs: 
-      checkall: ${{ steps.changes.outputs.checkall }}
-    steps:
-      - name: Clone
-        uses: actions/checkout@v4
-
-      - name: Detect Changes
-        uses: dorny/paths-filter@v3
-        id: changes
-        with: 
-          filters: ".github/file-filter.yml"
-
-  self:
-    name: "${{ matrix.name }} (${{ matrix.device }})"
-    if: ${{ github.repository == 'MFlowCode/MFC' && needs.file-changes.outputs.checkall == 'true' && (
-             (github.event_name == 'pull_request_review' && github.event.review.state == 'approved') ||
-             (github.event_name == 'pull_request' && github.event.pull_request.user.login == 'sbryngelson')
-           ) }}
-    needs: file-changes
-    strategy:
-      fail-fast: false
-      matrix:
-        include:
-          - cluster: phoenix
-            name: Georgia Tech | Phoenix (NVHPC)
-            group: phoenix
-            labels: gt
-            flag: p
-            device: cpu
-            build_script: ""
-          - cluster: phoenix
-            name: Georgia Tech | Phoenix (NVHPC)
-            group: phoenix
-            labels: gt
-            flag: p
-            device: gpu
-            build_script: ""
-          - cluster: frontier
-            name: Oak Ridge | Frontier (CCE)
-            group: phoenix
-            labels: frontier
-            flag: f
-            device: gpu
-            build_script: "bash .github/workflows/frontier/build.sh gpu bench"
-    runs-on:
-      group: ${{ matrix.group }}
-      labels: ${{ matrix.labels }}
-    timeout-minutes: 1400
-    env:
-      ACTIONS_RUNNER_FORCE_ACTIONS_NODE_VERSION: node16
-      ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
-    steps:
-      - name: Clone - PR
-        uses: actions/checkout@v4
-        with:
-          path: pr
-
-      - name: Clone - Master
-        uses: actions/checkout@v4
-        with:
-          repository: MFlowCode/MFC
-          ref: master
-          path: master
-
-      - name: Setup & Build
-        if: matrix.build_script != ''
-        run: | 
-          (cd pr     && ${{ matrix.build_script }}) &
-          (cd master && ${{ matrix.build_script }}) &
-          wait %1 && wait %2
-
-      - name: Bench (Master v. PR)
-        run: |
-          (cd pr     && bash .github/workflows/${{ matrix.cluster }}/submit-bench.sh .github/workflows/${{ matrix.cluster }}/bench.sh ${{ matrix.device }}) &
-          (cd master && bash .github/workflows/${{ matrix.cluster }}/submit-bench.sh .github/workflows/${{ matrix.cluster }}/bench.sh ${{ matrix.device }}) &
-          wait %1 && wait %2
-
-      - name: Generate & Post Comment
-        run: |
-          (cd pr && . ./mfc.sh load -c ${{ matrix.flag }} -m g)
-          (cd pr && ./mfc.sh bench_diff ../master/bench-${{ matrix.device }}.yaml ../pr/bench-${{ matrix.device }}.yaml)
-
-      - name: Print Logs
-        if:   always()
-        run: |
-          cat pr/bench-${{ matrix.device }}.* 2>/dev/null || true
-          cat master/bench-${{ matrix.device }}.* 2>/dev/null || true
-      
-      - name: Archive Logs
-        uses: actions/upload-artifact@v4
-        if: always()
-        with:
-          name: ${{ matrix.cluster }}-${{ matrix.device }}
-          path: |
-            pr/bench-${{ matrix.device }}.*
-            pr/build/benchmarks/*
-            master/bench-${{ matrix.device }}.*
-            master/build/benchmarks/*
diff --git a/.github/workflows/bench/test.yaml b/.github/workflows/bench/test.yaml
deleted file mode 100644
index 1e82c56d4..000000000
--- a/.github/workflows/bench/test.yaml
+++ /dev/null
@@ -1,2 +0,0 @@
-name: test_benchmark
-time: 1.23
diff --git a/.github/workflows/cleanliness.yml b/.github/workflows/cleanliness.yml
deleted file mode 100644
index ec472dce9..000000000
--- a/.github/workflows/cleanliness.yml
+++ /dev/null
@@ -1,127 +0,0 @@
-name: Cleanliness
-
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  file-changes:
-    name: Detect File Changes
-    runs-on: 'ubuntu-latest'
-    outputs: 
-      checkall: ${{ steps.changes.outputs.checkall }}
-    steps:
-      - name: Clone
-        uses: actions/checkout@v4
-
-      - name: Detect Changes
-        uses: dorny/paths-filter@v3
-        id: changes
-        with: 
-          filters: ".github/file-filter.yml"
-
-  cleanliness:
-      name: Code Cleanliness Check
-      if: needs.file-changes.outputs.checkall == 'true'
-      needs: file-changes
-      runs-on: "ubuntu-latest"
-      env:
-          pr_everything: 0
-          master_everything: 0
-      steps:
-          - name: Clone - PR
-            uses: actions/checkout@v4
-            with:
-              path: pr
-          - name: Clone - Master
-            uses: actions/checkout@v4
-            with:
-              repository: MFlowCode/MFC
-              ref: master
-              path: master
-
-          - name: Setup Ubuntu
-            run: |
-              sudo apt update -y
-              sudo apt install -y tar wget make cmake gcc g++ python3 python3-dev "openmpi-*" libopenmpi-dev
-          
-          - name: Build
-            run: |
-              (cd pr && /bin/bash mfc.sh build -j $(nproc) --debug 2> ../pr.txt) 
-              (cd master && /bin/bash mfc.sh build -j $(nproc) --debug 2> ../master.txt)
-              sed -i '/\/pr\//d' pr.txt
-              sed -i '/\/master\//d' master.txt
-          
-          - name: Unused Variables Diff
-            continue-on-error: true
-            run: |
-              grep -F 'Wunused-variable' master.txt > mUnused.txt
-              grep -F 'Wunused-variable' pr.txt > prUnused.txt
-              diff prUnused.txt mUnused.txt
-          
-          - name: Unused Dummy Arguments Diff
-            continue-on-error: true
-            run: |
-              grep -F 'Wunused-dummy-argument' pr.txt > prDummy.txt 
-              grep -F 'Wunused-dummy-argument' master.txt > mDummy.txt
-              diff prDummy.txt mDummy.txt
-
-          - name: Unused Value Diff
-            continue-on-error: true
-            run: |
-              grep -F 'Wunused-value' pr.txt > prUnused_val.txt
-              grep -F 'Wunused-value' master.txt > mUnused_val.txt
-              diff prUnused_val.txt mUnused_val.txt
-
-          - name: Maybe Uninitialized Variables Diff
-            continue-on-error: true
-            run: |
-              grep -F 'Wmaybe-uninitialized' pr.txt > prMaybe.txt
-              grep -F 'Wmaybe-uninitialized' master.txt > mMaybe.txt
-              diff prMaybe.txt mMaybe.txt
-
-
-          - name: Everything Diff
-            continue-on-error: true
-            run: |
-              grep '\-W' pr.txt > pr_every.txt
-              grep '\-W' master.txt > m_every.txt
-              diff pr_every.txt m_every.txt
-
-          - name: List of Warnings
-            run: |
-              cat pr_every.txt
-              
-
-          - name: Summary
-            continue-on-error: true
-            run: |  
-              pr_variable=$(grep -c -F 'Wunused-variable' pr.txt)
-              pr_argument=$(grep -c -F 'Wunused-dummy-argument' pr.txt)
-              pr_value=$(grep -c -F 'Wunused-value' pr.txt)
-              pr_uninit=$(grep -c -F 'Wmaybe-uninitialized' pr.txt)
-              pr_everything=$(grep -c '\-W' pr.txt)
-
-              master_variable=$(grep -c -F 'Wunused-variable' master.txt)
-              master_argument=$(grep -c -F 'Wunused-dummy-argument' master.txt)
-              master_value=$(grep -c -F 'Wunused-value' master.txt)
-              master_uninit=$(grep -c -F 'Wmaybe-uninitialized' master.txt)
-              master_everything=$(grep -c '\-W' master.txt  )    
-
-              echo "pr_everything=$pr_everything" >> $GITHUB_ENV
-              echo "master_everything=$master_everything" >> $GITHUB_ENV
-
-              echo "Difference is how many warnings were added or removed from master to PR."
-              echo "Negative numbers are better since you are removing warnings." 
-              echo " "
-              echo "Unused Variable Count: $pr_variable, Difference: $((pr_variable - master_variable))"
-              echo "Unused Dummy Argument: $pr_argument, Difference: $((pr_argument - master_argument))"
-              echo "Unused Value: $pr_value, Difference: $((pr_value - master_value))"
-              echo "Maybe Uninitialized: $pr_uninit, Difference: $((pr_uninit - master_uninit))"
-              echo "Everything: $pr_everything, Difference: $((pr_everything - master_everything))"
-          
-          
-          - name: Check Differences
-            if: env.pr_everything > env.master_everything 
-            run: |
-              echo "Difference between warning count in PR is greater than in master."
-
-
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
deleted file mode 100644
index 7487d8e55..000000000
--- a/.github/workflows/coverage.yml
+++ /dev/null
@@ -1,48 +0,0 @@
-name: Coverage Check
-
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  file-changes:
-    name: Detect File Changes
-    runs-on: 'ubuntu-latest'
-    outputs: 
-      checkall: ${{ steps.changes.outputs.checkall }}
-    steps:
-      - name: Clone
-        uses: actions/checkout@v4
-
-      - name: Detect Changes
-        uses: dorny/paths-filter@v3
-        id: changes
-        with: 
-          filters: ".github/file-filter.yml"
-
-  run:
-    name: Coverage Test on CodeCov
-    if: needs.file-changes.outputs.checkall == 'true'
-    needs: file-changes
-    runs-on: "ubuntu-latest"
-    steps:
-      - name: Checkouts
-        uses: actions/checkout@v4
-
-      - name: Setup Ubuntu
-        run: |
-            sudo apt update -y
-            sudo apt install -y tar wget make cmake gcc g++ python3 python3-dev "openmpi-*" libopenmpi-dev
-
-      - name: Build
-        run: /bin/bash mfc.sh build -j $(nproc) --gcov
-
-      - name: Test
-        run: /bin/bash mfc.sh test -a -j $(nproc)
-
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v4
-        with:
-          fail_ci_if_error: false
-          verbose: true
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
deleted file mode 100644
index d161d8034..000000000
--- a/.github/workflows/docs.yml
+++ /dev/null
@@ -1,76 +0,0 @@
-name: Documentation
-
-on:
-  schedule:
-    - cron: '0 0 * * *'  # This runs every day at midnight UTC
-  workflow_dispatch:
-  push:
-  pull_request:
-
-jobs:
-  docs:
-    name:    Build & Publish
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v4
-
-    # We build doxygen from source because of
-    # https://github.com/doxygen/doxygen/issues/9016
-    - name: Build Doxygen
-      run:  |
-        sudo apt update -y
-        sudo apt install -y cmake ninja-build graphviz graphviz
-        git clone https://github.com/doxygen/doxygen.git ../doxygen
-        cd ../doxygen
-        git checkout 26b5403
-        cd -
-        cmake -S ../doxygen -B ../doxygen/build -G Ninja
-        sudo ninja -C ../doxygen/build install
-
-    - name: Build Documentation
-      run:  |
-        pip3 install fypp
-        cmake -S . -B build -G Ninja --install-prefix=$(pwd)/build/install -D MFC_DOCUMENTATION=ON
-        ninja -C build install
-
-    # From here https://github.com/cicirello/generate-sitemap
-    - name: Generate the sitemap
-      id: sitemap
-      uses: cicirello/generate-sitemap@v1
-      with:
-        base-url-path: https://mflowcode.github.io/
-        path-to-root: build/install/docs/mfc
-        include-pdf: false
-        sitemap-format: txt
-
-    - name: Output stats
-      run: |
-        echo "sitemap-path = ${{ steps.sitemap.outputs.sitemap-path }}"
-        echo "url-count = ${{ steps.sitemap.outputs.url-count }}"
-        echo "excluded-count = ${{ steps.sitemap.outputs.excluded-count }}"
-
-    - name: Linkcheck - Lychee
-      uses: lycheeverse/lychee-action@v2
-      with:
-        args: -c .lychee.toml build/install/docs/mfc/
-        fail: false
-
-    - name: Publish Documentation
-      if:   github.repository == 'MFlowCode/MFC' && github.ref == 'refs/heads/master' &&  (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' )
-      run:  |
-        set +e
-        git ls-remote "${{ secrets.DOC_PUSH_URL }}" -q
-        if [ "$?" -ne "0" ]; then exit 0; fi
-        set -e
-        git config --global user.name  'MFC Action'
-        git config --global user.email '<>'
-        git clone "${{ secrets.DOC_PUSH_URL }}" ../www
-        rm -rf ../www/*
-        mv build/install/docs/mfc/* ../www/
-        git -C ../www add -A
-        git -C ../www commit -m "Docs @ ${GITHUB_SHA::7}" || true
-        git -C ../www push
-
-# DOC_PUSH_URL should be of the format:
-# --> https://<username>:<token>@github.com/<username>/<repository>
diff --git a/.github/workflows/formatting.yml b/.github/workflows/formatting.yml
deleted file mode 100644
index 16043daa9..000000000
--- a/.github/workflows/formatting.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-name: Pretty
-
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  docs:
-    name:    Formatting
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: MFC Python setup
-      run: ./mfc.sh init
-
-    - name: Check formatting
-      run: |
-        ./mfc.sh format -j $(nproc)
-        git diff --exit-code
diff --git a/.github/workflows/frontier/bench.sh b/.github/workflows/frontier/bench.sh
deleted file mode 100644
index 31a514d45..000000000
--- a/.github/workflows/frontier/bench.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/bash
-
-n_ranks=12
-
-if [ "$job_device" = "gpu" ]; then
-    gpus=$(rocm-smi --showid | awk '{print $1}' | grep -Eo '[0-9]+' | uniq | tr '\n' ' ')
-    n_ranks=$(echo "$gpus" | wc -w)         # number of GPUs on node
-    gpu_ids=$(echo "$gpus" | tr ' ' '\n' | tr '\n' ' ' | sed 's/ $//')  # GPU IDs from rocm-smi
-    device_opts="--gpu -g $gpu_ids"
-fi
-
-if [ "$job_device" = "gpu" ]; then
-    ./mfc.sh bench --mem 12 -j $n_ranks -o "$job_slug.yaml" -- -c frontier $device_opts -n $n_ranks
-else
-    ./mfc.sh bench --mem 1 -j $(nproc) -o "$job_slug.yaml" -- -c frontier $device_opts -n $n_ranks
-fi
diff --git a/.github/workflows/frontier/build.sh b/.github/workflows/frontier/build.sh
deleted file mode 100644
index c2e189342..000000000
--- a/.github/workflows/frontier/build.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/bash
-
-build_opts=""
-if [ "$1" = "gpu" ]; then
-    build_opts="--gpu"
-fi
-
-. ./mfc.sh load -c f -m g
-
-if [ "$2" == "bench" ]; then
-    for dir in benchmarks/*/; do
-        dirname=$(basename "$dir")
-        ./mfc.sh run "$dir/case.py" --case-optimization -j 8 --dry-run $build_opts
-    done
-else
-    ./mfc.sh test --dry-run -j 8 $build_opts
-fi
diff --git a/.github/workflows/frontier/submit-bench.sh b/.github/workflows/frontier/submit-bench.sh
deleted file mode 100644
index 4e498a609..000000000
--- a/.github/workflows/frontier/submit-bench.sh
+++ /dev/null
@@ -1,54 +0,0 @@
-#!/bin/bash
-
-set -e
-
-usage() {
-    echo "Usage: $0 [script.sh] [cpu|gpu]"
-}
-
-if [ ! -z "$1" ]; then
-    sbatch_script_contents=`cat $1`
-else
-    usage
-    exit 1
-fi
-
-if [ "$2" = "cpu" ]; then
-    sbatch_device_opts="\
-#SBATCH -n 32                       # Number of cores required"
-elif [ "$2" = "gpu" ]; then
-    sbatch_device_opts="\
-#SBATCH -n 8                       # Number of cores required"
-else
-    usage; exit 1
-fi
-
-
-job_slug="`basename "$1" | sed 's/\.sh$//' | sed 's/[^a-zA-Z0-9]/-/g'`-$2"
-
-sbatch <<EOT
-#!/bin/bash
-#SBATCH -JMFC-$job_slug            # Job name
-#SBATCH -A CFD154                  # charge account
-#SBATCH -N 1                       # Number of nodes required
-$sbatch_device_opts
-#SBATCH -t 03:59:00                # Duration of the job (Ex: 15 mins)
-#SBATCH -o$job_slug.out            # Combined output and error messages file
-#SBATCH -p extended                # Extended partition for shorter queues
-#SBATCH -W                         # Do not exit until the submitted job terminates.
-
-set -e
-set -x
-
-cd "\$SLURM_SUBMIT_DIR"
-echo "Running in $(pwd):"
-
-job_slug="$job_slug"
-job_device="$2"
-
-. ./mfc.sh load -c f -m g
-
-$sbatch_script_contents
-
-EOT
-
diff --git a/.github/workflows/frontier/submit.sh b/.github/workflows/frontier/submit.sh
deleted file mode 100644
index 7c4cb059b..000000000
--- a/.github/workflows/frontier/submit.sh
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/bin/bash
-
-set -e
-
-usage() {
-    echo "Usage: $0 [script.sh] [cpu|gpu]"
-}
-
-if [ ! -z "$1" ]; then
-    sbatch_script_contents=`cat $1`
-else
-    usage
-    exit 1
-fi
-
-if [ "$2" = "cpu" ]; then
-    sbatch_device_opts="\
-#SBATCH -n 32                       # Number of cores required"
-elif [ "$2" = "gpu" ]; then
-    sbatch_device_opts="\
-#SBATCH -n 8                       # Number of cores required"
-else
-    usage
-    exit 1
-fi
-
-
-job_slug="`basename "$1" | sed 's/\.sh$//' | sed 's/[^a-zA-Z0-9]/-/g'`-$2"
-
-sbatch <<EOT
-#!/bin/bash
-#SBATCH -JMFC-$job_slug            # Job name
-#SBATCH -A CFD154                  # charge account
-#SBATCH -N 1                       # Number of nodes required
-$sbatch_device_opts
-#SBATCH -t 03:59:00                # Duration of the job (Ex: 15 mins)
-#SBATCH -o$job_slug.out            # Combined output and error messages file
-#SBATCH -p extended                # Extended partition for shorter queues
-#SBATCH -W                         # Do not exit until the submitted job terminates.
-
-set -e
-set -x
-
-cd "\$SLURM_SUBMIT_DIR"
-echo "Running in $(pwd):"
-
-job_slug="$job_slug"
-job_device="$2"
-
-. ./mfc.sh load -c f -m g
-
-$sbatch_script_contents
-
-EOT
-
diff --git a/.github/workflows/frontier/test.sh b/.github/workflows/frontier/test.sh
deleted file mode 100644
index 57481fa94..000000000
--- a/.github/workflows/frontier/test.sh
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash
-
-gpus=`rocm-smi --showid | awk '{print $1}' | grep -Eo '[0-9]+' | uniq | tr '\n' ' '`
-ngpus=`echo "$gpus" | tr -d '[:space:]' | wc -c`
-
-if [ "$job_device" = "gpu" ]; then
-    ./mfc.sh test --max-attempts 3 -j $ngpus -- -c frontier
-else
-    ./mfc.sh test --max-attempts 3 -j 32 -- -c frontier
-fi
diff --git a/.github/workflows/line-count.yml b/.github/workflows/line-count.yml
deleted file mode 100644
index 4cc6014e0..000000000
--- a/.github/workflows/line-count.yml
+++ /dev/null
@@ -1,54 +0,0 @@
-name: Lines of Code
-
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  file-changes:
-    name: Detect File Changes
-    runs-on: 'ubuntu-latest'
-    outputs: 
-      checkall: ${{ steps.changes.outputs.checkall }}
-    steps:
-      - name: Clone
-        uses: actions/checkout@v4
-
-      - name: Detect Changes
-        uses: dorny/paths-filter@v3
-        id: changes
-        with: 
-          filters: ".github/file-filter.yml"
-
-  sz:
-    name: Core MFC Line Difference
-    if: needs.file-changes.outputs.checkall == 'true'
-    needs: file-changes
-    permissions:
-      contents: read
-      pull-requests: write
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code from PR branch
-        uses: actions/checkout@v4
-        with:
-          path: pr
-
-      - name: Checkout code from MFC master
-        uses: actions/checkout@v4
-        with:
-          repository: ${{ github.event.pull_request.repository }}
-          ref:        ${{ github.event.pull_request.base.ref }}
-          path:       base
-          # repository: MFlowCode/MFC
-          # ref:        master
-          # path:       base
-
-      - name: Get Line Diff
-        run: |
-          BASE="$GITHUB_WORKSPACE/base"
-          PR="$GITHUB_WORKSPACE/pr"
-          cd $BASE
-          export MFC_PR=$PR
-          pwd
-          ./mfc.sh init &> tmp.txt
-          ./mfc.sh count_diff
-
diff --git a/.github/workflows/lint-source.yml b/.github/workflows/lint-source.yml
deleted file mode 100644
index 68c07d6c1..000000000
--- a/.github/workflows/lint-source.yml
+++ /dev/null
@@ -1,55 +0,0 @@
-name: Lint Source
-
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  file-changes:
-    name: Detect File Changes
-    runs-on: 'ubuntu-latest'
-    outputs: 
-      checkall: ${{ steps.changes.outputs.checkall }}
-    steps:
-      - name: Clone
-        uses: actions/checkout@v4
-
-      - name: Detect Changes
-        uses: dorny/paths-filter@v3
-        id: changes
-        with: 
-          filters: ".github/file-filter.yml"
-
-  lint-source:
-    name: Lint Source
-    runs-on: 'ubuntu-latest'
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: Initialize MFC
-      run: ./mfc.sh init
-
-    - name: Lint the full source
-      run: |
-        source build/venv/bin/activate
-        find ./src -type f -not -name '*nvtx*' -exec sh -c 'fortitude check "$1" | grep -v E001' _ {} \;
-        find ./src -type f -not -name '*nvtx*' -exec sh -c 'fortitude check "$1" | grep -v E001' _ {} \; | wc -l | xargs -I{} sh -c '[ {} -gt 0 ] && exit 1 || exit 0'
-
-    - name: No double precision intrinsics
-      run: |
-        ! grep -iR 'double_precision\|dsqrt\|dexp\|dlog\|dble\|dabs\|double\ precision\|real(8)\|real(4)\|dprod\|dmin\|dmax\|dfloat\|dreal\|dcos\|dsin\|dtan\|dsign\|dtanh\|dsinh\|dcosh\|d0' --exclude-dir=syscheck --exclude="*nvtx*" --exclude="*precision_select*" ./src/*
-
-    - name: Looking for junk code
-      run: |
-        ! grep -iR -e '\.\.\.' -e '\-\-\-' -e '===' ./src/*
-
-    - name: Looking for false integers
-      run: |
-        ! grep -onRP '(?<![0-9.eE\-])\b[0-9]*_wp\b' src/
-
-    - name: Looking for junk comments in examples
-      run: |
-        ! grep -R '# ===' ./benchmarks **/*.py
-        ! grep -R '# ===' ./examples/**/*.py
-        ! grep -R '==='   ./benchmarks/**/*.py
-        ! grep -R '==='   ./examples/**/*.py
-
diff --git a/.github/workflows/lint-toolchain.yml b/.github/workflows/lint-toolchain.yml
deleted file mode 100644
index 45b3604ed..000000000
--- a/.github/workflows/lint-toolchain.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-name: Lint Toolchain
-
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  lint-toolchain:
-    name:    Lint Toolchain
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v4
-
-    - name: MFC Python setup
-      run: ./mfc.sh init
-
-    - name: Lint the toolchain
-      run: ./mfc.sh lint
diff --git a/.github/workflows/mfc.sh b/.github/workflows/mfc.sh
deleted file mode 100755
index 33dd401fa..000000000
--- a/.github/workflows/mfc.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-echo "Mock benchmark running..."
-mkdir -p bench
-echo "name: test_benchmark" > bench/test.yaml
-echo "time: 1.23" >> bench/test.yaml
-echo "Mock benchmark completed"
diff --git a/.github/workflows/phoenix/bench.sh b/.github/workflows/phoenix/bench.sh
deleted file mode 100644
index f58ef4472..000000000
--- a/.github/workflows/phoenix/bench.sh
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/bin/bash
-
-n_ranks=12
-
-if [ "$job_device" = "gpu" ]; then
-    n_ranks=$(nvidia-smi -L | wc -l)        # number of GPUs on node
-    gpu_ids=$(seq -s ' ' 0 $(($n_ranks-1))) # 0,1,2,...,gpu_count-1
-    device_opts="--gpu -g $gpu_ids"
-fi
-
-tmpbuild=/storage/scratch1/6/sbryngelson3/mytmp_build
-currentdir=$tmpbuild/run-$(( RANDOM % 900 ))
-mkdir -p $tmpbuild
-mkdir -p $currentdir
-
-export TMPDIR=$currentdir
-
-if [ "$job_device" = "gpu" ]; then
-    ./mfc.sh bench --mem 12 -j $(nproc) -o "$job_slug.yaml" -- -c phoenix-bench $device_opts -n $n_ranks
-else
-    ./mfc.sh bench --mem 1 -j $(nproc) -o "$job_slug.yaml" -- -c phoenix-bench $device_opts -n $n_ranks
-fi
-
-sleep 10
-rm -rf "$currentdir" || true
-
-unset TMPDIR
diff --git a/.github/workflows/phoenix/submit-bench.sh b/.github/workflows/phoenix/submit-bench.sh
deleted file mode 100644
index e8b6dd348..000000000
--- a/.github/workflows/phoenix/submit-bench.sh
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/bin/bash
-
-set -e
-
-usage() {
-    echo "Usage: $0 [script.sh] [cpu|gpu]"
-}
-
-if [ ! -z "$1" ]; then
-    sbatch_script_contents=`cat $1`
-else
-    usage
-    exit 1
-fi
-
-sbatch_cpu_opts="\
-#SBATCH -p cpu-small               # partition
-#SBATCH --ntasks-per-node=24       # Number of cores per node required
-#SBATCH --mem-per-cpu=2G           # Memory per core\
-"
-
-sbatch_gpu_opts="\
-#SBATCH -CL40S
-#SBATCH --ntasks-per-node=4       # Number of cores per node required
-#SBATCH -G2\
-"
-
-if [ "$2" = "cpu" ]; then
-    sbatch_device_opts="$sbatch_cpu_opts"
-elif [ "$2" = "gpu" ]; then
-    sbatch_device_opts="$sbatch_gpu_opts"
-else
-    usage
-    exit 1
-fi
-
-job_slug="`basename "$1" | sed 's/\.sh$//' | sed 's/[^a-zA-Z0-9]/-/g'`-$2"
-
-sbatch <<EOT
-#!/bin/bash
-#SBATCH -Jshb-$job_slug            # Job name
-#SBATCH --account=gts-sbryngelson3 # charge account
-#SBATCH -N1                        # Number of nodes required
-$sbatch_device_opts
-#SBATCH -t 02:00:00                # Duration of the job (Ex: 15 mins)
-#SBATCH -q embers                  # QOS Name
-#SBATCH -o$job_slug.out            # Combined output and error messages file
-#SBATCH -W                         # Do not exit until the submitted job terminates.
-
-set -e
-set -x
-
-cd "\$SLURM_SUBMIT_DIR"
-echo "Running in $(pwd):"
-
-job_slug="$job_slug"
-job_device="$2"
-
-. ./mfc.sh load -c p -m $2
-
-$sbatch_script_contents
-
-EOT
-
diff --git a/.github/workflows/phoenix/submit.sh b/.github/workflows/phoenix/submit.sh
deleted file mode 100644
index 6700e38c5..000000000
--- a/.github/workflows/phoenix/submit.sh
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/bin/bash
-
-set -e
-
-usage() {
-    echo "Usage: $0 [script.sh] [cpu|gpu]"
-}
-
-if [ ! -z "$1" ]; then
-    sbatch_script_contents=`cat $1`
-else
-    usage
-    exit 1
-fi
-
-sbatch_cpu_opts="\
-#SBATCH -p cpu-small               # partition
-#SBATCH --ntasks-per-node=24       # Number of cores per node required
-#SBATCH --mem-per-cpu=2G           # Memory per core\
-"
-
-sbatch_gpu_opts="\
-#SBATCH -p gpu-v100,gpu-a100,gpu-h100,gpu-l40s
-#SBATCH --ntasks-per-node=4       # Number of cores per node required
-#SBATCH -G2\
-"
-
-if [ "$2" = "cpu" ]; then
-    sbatch_device_opts="$sbatch_cpu_opts"
-elif [ "$2" = "gpu" ]; then
-    sbatch_device_opts="$sbatch_gpu_opts"
-else
-    usage
-    exit 1
-fi
-
-job_slug="`basename "$1" | sed 's/\.sh$//' | sed 's/[^a-zA-Z0-9]/-/g'`-$2"
-
-sbatch <<EOT
-#!/bin/bash
-#SBATCH -Jshb-$job_slug            # Job name
-#SBATCH --account=gts-sbryngelson3 # charge account
-#SBATCH -N1                        # Number of nodes required
-$sbatch_device_opts
-#SBATCH -t 03:00:00                # Duration of the job (Ex: 15 mins)
-#SBATCH -q embers                  # QOS Name
-#SBATCH -o$job_slug.out            # Combined output and error messages file
-#SBATCH -W                         # Do not exit until the submitted job terminates.
-
-set -e
-set -x
-
-cd "\$SLURM_SUBMIT_DIR"
-echo "Running in $(pwd):"
-
-job_slug="$job_slug"
-job_device="$2"
-
-. ./mfc.sh load -c p -m $2
-
-$sbatch_script_contents
-
-EOT
-
diff --git a/.github/workflows/phoenix/test.sh b/.github/workflows/phoenix/test.sh
deleted file mode 100644
index 5582e9f6d..000000000
--- a/.github/workflows/phoenix/test.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/bash
-
-build_opts=""
-if [ "$job_device" = "gpu" ]; then
-    build_opts="--gpu"
-fi
-
-./mfc.sh test --dry-run -j 8 $build_opts
-
-n_test_threads=8
-
-if [ "$job_device" = "gpu" ]; then
-    gpu_count=$(nvidia-smi -L | wc -l)        # number of GPUs on node
-    gpu_ids=$(seq -s ' ' 0 $(($gpu_count-1))) # 0,1,2,...,gpu_count-1
-    device_opts="-g $gpu_ids"
-    n_test_threads=`expr $gpu_count \* 2`
-fi
-
-./mfc.sh test --max-attempts 3 -a -j $n_test_threads $device_opts -- -c phoenix
-
-
diff --git a/.github/workflows/pmd.yml b/.github/workflows/pmd.yml
deleted file mode 100644
index 24361e777..000000000
--- a/.github/workflows/pmd.yml
+++ /dev/null
@@ -1,131 +0,0 @@
-name: Source DRYness
-
-on: [push, pull_request, workflow_dispatch]
-
-jobs:    
-  pmd:
-      name: PMD
-      runs-on: "ubuntu-latest"
-      env:
-          pr_everything: 0
-      steps:
-          - name: Clone - PR
-            uses: actions/checkout@v4
-
-          - name: Set up Java
-            uses: actions/setup-java@v4
-            with:
-              distribution: temurin
-              java-version: '17'
-
-          - name: Run CPD for Fortran
-            continue-on-error: true
-            run: |
-              # Get latest PMD version from GitHub API
-              PMD_VERSION=$(curl -s https://api.github.com/repos/pmd/pmd/releases/latest | grep '"tag_name":' | cut -d'"' -f4 | sed 's/pmd_releases\///')
-              echo "Using PMD version: $PMD_VERSION"
-
-              curl -sSL -o pmd.zip \
-                "https://github.com/pmd/pmd/releases/download/pmd_releases/${PMD_VERSION}/pmd-dist-${PMD_VERSION}-bin.zip"
-              unzip -q pmd.zip
-              PMD_HOME="pmd-bin-${PMD_VERSION}"
-          
-              SOURCE_DIR="${1:-src}"
-              total_files=$(find "$SOURCE_DIR" -type f \( -name "*.f" -o -name "*.f90" -o -name "*.for" -o -name "*.fpp" -o -name "*.F" -o -name "*.F90" \) | wc -l)
-              processed=0
-
-              find "$SOURCE_DIR" -type f \( -name "*.f" -o -name "*.f90" -o -name "*.for" -o -name "*.fpp" -o -name "*.F" -o -name "*.F90" \) -print0 | 
-              while IFS= read -r -d $'\0' file; do
-                  processed=$((processed + 1))
-                  
-                  # Create a temporary file with same permissions as original
-                  TMP_FILE=$(mktemp)
-                  if [ $? -ne 0 ]; then
-                      echo -e "Failed to create temporary file for $file, skipping"
-                      continue
-                  fi
-                  
-                  # Copy permissions from original file
-                  chmod --reference="$file" "$TMP_FILE"
-                  
-                  # More comprehensive sed command to handle different Fortran comment styles:
-                  # 1. Replace lines that are entirely comments with an empty line:
-                  #    - Lines starting with '!' (free form comments)
-                  #    - Lines starting with 'c', 'C', '*', 'd', 'D' in column 1 (fixed form comments)
-                  # 2. Remove end-of-line comments (anything after '!' that isn't in a string)
-                  # 3. Preserve strings containing '!' characters                  
-                  sed -E '
-                    # First handle & continuation style (modern Fortran)
-                    :ampersand_loop
-                    /&[[:space:]]*$/ {
-                      N
-                      s/&[[:space:]]*\n[[:space:]]*(&)?/ /g
-                      tampersand_loop
-                    }
-                    
-                    # Handle fixed-form continuation (column 6 indicator)
-                    :fixed_form_loop
-                    /^[[:space:]]{0,5}[^[:space:]!&]/ {
-                      N
-                      s/\n[[:space:]]{5}[^[:space:]]/ /g
-                      tfixed_form_loop
-                    }
-                    
-                    # Remove any remaining continuation markers
-                    s/&//g
-                    
-                    # Normalize spacing - replace multiple spaces with single space
-                    s/[[:space:]]{2,}/ /g
-                    
-                    # Remove spaces around mathematical operators
-                    s/[[:space:]]*\*[[:space:]]*/*/g
-                    s/[[:space:]]*\+[[:space:]]*/+/g
-                    s/[[:space:]]*-[[:space:]]*/-/g
-                    s/[[:space:]]*\/[[:space:]]*/\//g
-                    s/[[:space:]]*\*\*[[:space:]]*/\*\*/g
-                    
-                    # Remove spaces in common Fortran constructs (array indexing, function calls)
-                    s/\([[:space:]]*([^,)[:space:]]+)[[:space:]]*,/(\1,/g      # First argument
-                    s/,[[:space:]]*([^,)[:space:]]+)[[:space:]]*,/,\1,/g       # Middle arguments
-                    s/,[[:space:]]*([^,)[:space:]]+)[[:space:]]*\)/,\1)/g      # Last argument
-                    s/\([[:space:]]*([^,)[:space:]]+)[[:space:]]*\)/(\1)/g     # Single argument
-                    
-                    # Remove spaces around brackets and parentheses
-                    s/\[[[:space:]]*/</g
-                    s/\[[[:space:]]*/>/g
-                    s/\[[[:space:]]*/</g
-                    s/[[:space:]]*\]/]/g
-                    s/\([[:space:]]*/(/g
-                    s/[[:space:]]*\)/)/g
-
-                    # Remove spaces around comparison operators
-                    s/[[:space:]]*<=[[:space:]]*/</g
-                    s/[[:space:]]*>=[[:space:]]*/>/g
-                    s/[[:space:]]*<[[:space:]]*/</g
-                    s/[[:space:]]*>[[:space:]]*/>/g
-                    s/[[:space:]]*==[[:space:]]*/==/g
-
-                    # Remove full-line comments
-                    /^\s*!/d
-                    /^[cC*dD]/d
-                    /^[ \t]*[cC*dD]/d
-                    /^[[:space:]]*$/d
-
-                    # Remove end-of-line comments, preserving quoted strings
-                    s/([^"'\''\\]*("[^"]*")?('\''[^'\'']*'\''?)?[^"'\''\\]*)[!].*$/\1/
-                  ' "$file" > "$TMP_FILE"
-
-                  if cmp -s "$file" "$TMP_FILE"; then
-                      rm "$TMP_FILE"
-                  else
-                      # Overwrite the original file with the processed content
-                      mv "$TMP_FILE" "$file"
-                  fi
-              done
-
-              "${PMD_HOME}/bin/pmd" cpd \
-                --dir src \
-                --language fortran \
-                --minimum-tokens=20 \
-                --no-fail-on-violation \
-                --no-fail-on-error
diff --git a/.github/workflows/spelling.yml b/.github/workflows/spelling.yml
deleted file mode 100644
index accdc9628..000000000
--- a/.github/workflows/spelling.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-name: Spell Check
-
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  run:
-    name: Spell Check
-    runs-on: ubuntu-latest
-    steps:
-    - name: Checkout
-      uses: actions/checkout@v4
-      
-    - name: MFC Python Setup
-      run:  ./mfc.sh init
-      
-    - name: Spell Check
-      run:  ./mfc.sh spelling
diff --git a/.github/workflows/test-components.sh b/.github/workflows/test-components.sh
deleted file mode 100755
index 14fab2518..000000000
--- a/.github/workflows/test-components.sh
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/bin/bash
-set -e
-
-echo "=== Testing Individual Components ==="
-
-# Test 1: Check if mfc.sh exists and is executable
-echo "1. Testing mfc.sh..."
-if [ -f "./mfc.sh" ]; then
-    chmod +x ./mfc.sh
-    echo "✓ mfc.sh found and made executable"
-else
-    echo "✗ mfc.sh not found - creating mock for testing"
-    cat > ./mfc.sh << 'MOCK'
-#!/bin/bash
-echo "Mock benchmark running..."
-mkdir -p bench
-echo "name: test_benchmark" > bench/test.yaml
-echo "time: 1.23" >> bench/test.yaml
-echo "Mock benchmark completed"
-MOCK
-    chmod +x ./mfc.sh
-fi
-
-# Test 2: Run benchmark command
-echo "2. Testing benchmark execution..."
-./mfc.sh bench -o bench || echo "Benchmark failed, continuing with mock data"
-
-# Test 3: Check yq installation and YAML to JSON conversion
-echo "3. Testing YAML to JSON conversion..."
-if ! command -v yq &> /dev/null; then
-    echo "Installing yq..."
-    sudo wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64
-    sudo chmod +x /usr/local/bin/yq
-fi
-
-# Convert any YAML files found
-find . -maxdepth 1 -name "*.yaml" -exec sh -c 'echo "Converting $1"; yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
-
-# Test 4: Check JSON output format
-echo "4. Validating JSON format..."
-for json_file in *.json; do
-    if [ -f "$json_file" ]; then
-        echo "Checking $json_file:"
-        python3 -c "import json; json.load(open('$json_file')); print('✓ Valid JSON')" || echo "✗ Invalid JSON"
-    fi
-done
-
-echo "=== Component Testing Complete ==="
diff --git a/.github/workflows/test-cont-bench.yml b/.github/workflows/test-cont-bench.yml
deleted file mode 100644
index 3af2985bc..000000000
--- a/.github/workflows/test-cont-bench.yml
+++ /dev/null
@@ -1,201 +0,0 @@
-name: Continuous Benchmarking
-
-on: [push, pull_request, workflow_dispatch]
-
-permissions:
-  contents: write
-  deployments: write
-  pages: write
-  id-token: write
-
-jobs:
-  self:
-    name: "Store benchmark result"
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Convert MFC to Google Benchmark Format
-        run: |
-          python3 << 'EOF'
-          import json
-          from datetime import datetime
-
-          # Read the MFC benchmark data
-          with open('bench.json', 'r') as f:
-              mfc_data = json.load(f)
-
-          # Convert to Google Benchmark format
-          benchmarks = []
-
-          for case_name, case_data in mfc_data['cases'].items():
-              output_summary = case_data['output_summary']
-              
-              # Simulation execution time
-              if 'simulation' in output_summary and 'exec' in output_summary['simulation']:
-                  benchmarks.append({
-                      "name": f"{case_name}/simulation_time",
-                      "family_index": len(benchmarks),
-                      "per_family_instance_index": 0,
-                      "run_name": f"{case_name}/simulation_time",
-                      "run_type": "iteration",
-                      "repetitions": 1,
-                      "repetition_index": 0,
-                      "threads": 1,
-                      "iterations": 1,
-                      "real_time": output_summary['simulation']['exec'] * 1e9,
-                      "cpu_time": output_summary['simulation']['exec'] * 1e9,
-                      "time_unit": "ns"
-                  })
-              
-              # Simulation grind time
-              if 'simulation' in output_summary and 'grind' in output_summary['simulation']:
-                  benchmarks.append({
-                      "name": f"{case_name}/grind_time",
-                      "family_index": len(benchmarks),
-                      "per_family_instance_index": 0,
-                      "run_name": f"{case_name}/grind_time",
-                      "run_type": "iteration",
-                      "repetitions": 1,
-                      "repetition_index": 0,
-                      "threads": 1,
-                      "iterations": 1,
-                      "real_time": output_summary['simulation']['grind'],
-                      "cpu_time": output_summary['simulation']['grind'],
-                      "time_unit": "ns"
-                  })
-
-          # Create Google Benchmark format
-          google_benchmark_data = {
-              "context": {
-                  "date": datetime.now().isoformat(),
-                  "host_name": "github-runner",
-                  "executable": "mfc_benchmark",
-                  "num_cpus": 2,
-                  "mhz_per_cpu": 2000,
-                  "cpu_scaling_enabled": False,
-                  "caches": []
-              },
-              "benchmarks": benchmarks
-          }
-
-          # Write the converted data
-          with open('bench-google.json', 'w') as f:
-              json.dump(google_benchmark_data, f, indent=2)
-
-          print(f"✓ Converted {len(benchmarks)} benchmark measurements")
-          EOF
-    
-      - name: Create report generator script
-        run: |
-          cat > generate_report.py << 'SCRIPT'
-          import json
-          import os
-          from datetime import datetime
-
-          def generate_markdown_report():
-              # Read benchmark data
-              with open('bench-google.json', 'r') as f:
-                  data = json.load(f)
-
-              # Create directory
-              os.makedirs('docs/documentation', exist_ok=True)
-              
-              # Start building content
-              lines = []
-              lines.append("# Continuouscl Benchmarking Results")
-              lines.append("")
-              lines.append(f"Generated on: {datetime.now().strftime('%Y-%m-%d %H:%M:%S UTC')}")
-              lines.append("")
-              lines.append("## System Information")
-              lines.append(f"- Host: {data['context']['host_name']}")
-              lines.append(f"- CPUs: {data['context']['num_cpus']}")
-              lines.append(f"- MHz per CPU: {data['context']['mhz_per_cpu']}")
-              lines.append("")
-              lines.append("## Benchmark Results")
-              lines.append("")
-              lines.append("| Test Case | Metric | Time (seconds) | Time (nanoseconds) |")
-              lines.append("|-----------|--------|----------------|-------------------|")
-              
-              # Add benchmark data
-              for benchmark in data['benchmarks']:
-                  name_parts = benchmark['name'].split('/')
-                  case_name = name_parts[0]
-                  metric_name = name_parts[1] if len(name_parts) > 1 else 'unknown'
-                  time_seconds = benchmark['real_time'] / 1e9
-                  time_ns = benchmark['real_time']
-                  lines.append(f"| {case_name} | {metric_name} | {time_seconds:.6f} | {time_ns:.0f} |")
-              
-              lines.append("")
-              lines.append("## Raw Data")
-              lines.append("")
-              lines.append("```json")
-              lines.append(json.dumps(data, indent=2))
-              lines.append("```")
-              lines.append("")
-              lines.append("---")
-              lines.append(f"*Last updated: {datetime.now().isoformat()}*")
-              
-              # Write file
-              with open('docs/documentation/cont-bench.md', 'w') as f:
-                  f.write('\n'.join(lines))
-              
-              print("✓ Generated Markdown report at docs/documentation/cont-bench.md")
-
-          if __name__ == "__main__":
-              generate_markdown_report()
-          SCRIPT
-
-      - name: Generate Markdown Report
-        run: python3 generate_report.py
-
-      - name: Commit and Push Results
-        run: |
-          git config --local user.email "mohdsaid497566@gmail.com"
-          git config --local user.name "Malmahrouqi3"
-          
-          # Fetch latest changes from the remote branch
-          git fetch origin cont-bench || true
-          
-          # Stage the generated file
-          git add docs/documentation/cont-bench.md
-          
-          # Commit changes to have a clean working tree
-          git commit -m "Update continuous benchmarking results" || true
-          
-          # Check if we're behind the remote branch
-          if git rev-list HEAD..origin/cont-bench --count | grep -q "^[1-9]"; then
-            echo "Branch is behind remote, resolving..."
-            
-            # Save our changes to a temporary branch
-            git branch temp-benchmark-updates
-            
-            # Get up to date with the remote branch
-            git reset --hard origin/cont-bench
-            
-            # Regenerate the report with the latest code
-            python3 generate_report.py
-            
-            # Add the newly generated report
-            git add docs/documentation/cont-bench.md
-            
-            # Commit the changes
-            git commit -m "Update continuous benchmarking results" || true
-          fi
-          
-          # Push the changes, forcing if necessary
-          git push origin HEAD:cont-bench || git push -f origin HEAD:cont-bench
-                    
-      - name: Store benchmark result
-        uses: benchmark-action/github-action-benchmark@v1
-        with:
-          name: C++ Benchmark
-          tool: 'googlecpp'
-          output-file-path: bench-google.json
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          auto-push: false
-          alert-threshold: '200%'
-          comment-on-alert: true
-          fail-on-alert: true
-          alert-comment-cc-users: '@Malmahrouqi'
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
deleted file mode 100644
index 2948b1133..000000000
--- a/.github/workflows/test.yml
+++ /dev/null
@@ -1,131 +0,0 @@
-name: 'Test Suite'
-
-on: [push, pull_request, workflow_dispatch]
-    
-jobs:
-  file-changes:
-    name: Detect File Changes
-    runs-on: 'ubuntu-latest'
-    outputs: 
-      checkall: ${{ steps.changes.outputs.checkall }}
-    steps:
-      - name: Clone
-        uses: actions/checkout@v4
-
-      - name: Detect Changes
-        uses: dorny/paths-filter@v3
-        id: changes
-        with: 
-          filters: ".github/file-filter.yml"
-
-  github:
-    name: Github
-    if: needs.file-changes.outputs.checkall == 'true'
-    needs: file-changes
-    strategy:
-      matrix:
-        os:    ['ubuntu', 'macos']
-        mpi:   ['mpi']
-        precision: ['']
-        debug: ['debug', 'no-debug']
-        intel: [true, false]
-        exclude:
-          - os:    macos
-            intel: true
-
-        include:
-          - os:    ubuntu
-            mpi:   no-mpi
-            precision: single
-            debug: no-debug
-            intel: false
-
-      fail-fast: false
-    continue-on-error: true
-    runs-on: ${{ matrix.os }}-latest
-
-    steps:
-      - name: Clone
-        uses: actions/checkout@v4
-
-      - name: Setup MacOS
-        if:   matrix.os == 'macos'
-        run:  |
-          brew update
-          brew upgrade
-          brew install coreutils python cmake fftw hdf5 gcc@15 boost open-mpi
-          echo "FC=gfortran-15" >> $GITHUB_ENV
-          echo "BOOST_INCLUDE=/opt/homebrew/include/" >> $GITHUB_ENV
-
-      - name: Setup Ubuntu
-        if:   matrix.os == 'ubuntu' && matrix.intel == false
-        run: |
-           sudo apt update -y
-           sudo apt install -y cmake gcc g++ python3 python3-dev hdf5-tools \
-                    libfftw3-dev libhdf5-dev openmpi-bin libopenmpi-dev
-
-      - name: Setup Ubuntu (Intel)
-        if:   matrix.os == 'ubuntu' && matrix.intel == true
-        run: |
-          wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-          sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-          sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"
-          sudo apt-get update
-          sudo apt-get install -y intel-oneapi-compiler-fortran intel-oneapi-mpi intel-oneapi-mpi-devel
-          source /opt/intel/oneapi/setvars.sh
-          printenv >> $GITHUB_ENV
-
-
-      - name: Build
-        run:  |
-          /bin/bash mfc.sh test --dry-run -j $(nproc) --${{ matrix.debug }} --${{ matrix.mpi }} --${{ matrix.precision }} 
-
-      - name: Test
-        run:  |
-          /bin/bash mfc.sh test --max-attempts 3 -j $(nproc) $OPT1 $OPT2
-        env:
-          OPT1: ${{ matrix.mpi == 'mpi' && '--test-all' || '' }}
-          OPT2: ${{ matrix.debug == 'debug' && '-% 20' || '' }}
-
-  self:
-    name: Self Hosted
-    if: github.repository == 'MFlowCode/MFC' && needs.file-changes.outputs.checkall == 'true'
-    needs: file-changes
-    continue-on-error: false
-    timeout-minutes: 1400
-    strategy:
-      matrix:
-        device: ['cpu', 'gpu']
-        lbl: ['gt', 'frontier']
-    runs-on:
-      group:  phoenix
-      labels: ${{ matrix.lbl }}
-    env:
-      ACTIONS_RUNNER_FORCE_ACTIONS_NODE_VERSION: node16
-      ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
-    steps:
-      - name: Clone
-        uses: actions/checkout@v4
-
-      - name: Build & Test
-        if:   matrix.lbl == 'gt'
-        run:  bash .github/workflows/phoenix/submit.sh .github/workflows/phoenix/test.sh ${{ matrix.device }}
-
-      - name: Build
-        if:   matrix.lbl == 'frontier'
-        run:  bash .github/workflows/frontier/build.sh ${{ matrix.device }}
-
-      - name: Test
-        if:   matrix.lbl == 'frontier'
-        run:  bash .github/workflows/frontier/submit.sh .github/workflows/frontier/test.sh ${{matrix.device}}
-
-      - name: Print Logs
-        if:   always()
-        run:  cat test-${{ matrix.device }}.out
-
-      - name: Archive Logs
-        uses: actions/upload-artifact@v4
-        if:   always()
-        with:
-          name: logs-${{ strategy.job-index }}-${{ matrix.device }}
-          path: test-${{ matrix.device }}.out

From 4a95eb10b9c5f0dae41b7fc25e1a8ab2c0f25174 Mon Sep 17 00:00:00 2001
From: malmahrouqi3 <malmahrouqi3@gatech.edu>
Date: Fri, 11 Jul 2025 16:54:04 -0400
Subject: [PATCH 14/14] removed junk

---
 bench                                         | 153 ----------
 bench-google.json                             |  69 -----
 bench.json                                    | 195 -------------
 bench.yaml                                    | 153 ----------
 benchmarks/5eq_rk3_weno3_hllc/case.py         | 276 ------------------
 benchmarks/hypo_hll/case.py                   | 121 --------
 benchmarks/ibm/case.py                        | 115 --------
 benchmarks/viscous_weno5_sgb_acoustic/case.py | 225 --------------
 test-components.sh                            |  48 ---
 9 files changed, 1355 deletions(-)
 delete mode 100644 bench
 delete mode 100644 bench-google.json
 delete mode 100644 bench.json
 delete mode 100644 bench.yaml
 delete mode 100644 benchmarks/5eq_rk3_weno3_hllc/case.py
 delete mode 100644 benchmarks/hypo_hll/case.py
 delete mode 100644 benchmarks/ibm/case.py
 delete mode 100644 benchmarks/viscous_weno5_sgb_acoustic/case.py
 delete mode 100755 test-components.sh

diff --git a/bench b/bench
deleted file mode 100644
index 40207a9f8..000000000
--- a/bench
+++ /dev/null
@@ -1,153 +0,0 @@
-cases:
-  5eq_rk3_weno3_hllc:
-    description:
-      args: []
-      path: /home/mohammed/Desktop/cont-bench/benchmarks/5eq_rk3_weno3_hllc/case.py
-      slug: 5eq_rk3_weno3_hllc
-    output_summary:
-      invocation:
-      - run
-      - /home/mohammed/Desktop/cont-bench/benchmarks/5eq_rk3_weno3_hllc/case.py
-      - --case-optimization
-      - --targets
-      - pre_process
-      - simulation
-      - post_process
-      - --output-summary
-      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/5eq_rk3_weno3_hllc.yaml
-      - --
-      - --gbpp
-      - '1'
-      lock:
-        debug: false
-        gcov: false
-        gpu: false
-        mpi: true
-        single: false
-        unified: false
-      post_process:
-        exec: 2.6731925
-      pre_process:
-        exec: 0.945057
-      simulation:
-        exec: 553.7461466
-        grind: 311.46590698
-      syscheck:
-        exec: 0.5911245
-  hypo_hll:
-    description:
-      args: []
-      path: /home/mohammed/Desktop/cont-bench/benchmarks/hypo_hll/case.py
-      slug: hypo_hll
-    output_summary:
-      invocation:
-      - run
-      - /home/mohammed/Desktop/cont-bench/benchmarks/hypo_hll/case.py
-      - --case-optimization
-      - --targets
-      - pre_process
-      - simulation
-      - post_process
-      - --output-summary
-      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/hypo_hll.yaml
-      - --
-      - --gbpp
-      - '1'
-      lock:
-        debug: false
-        gcov: false
-        gpu: false
-        mpi: true
-        single: false
-        unified: false
-      post_process:
-        exec: 4.6181798
-      pre_process:
-        exec: 28.0626009
-      simulation:
-        exec: 1158.0062294
-        grind: 373.3648501
-      syscheck:
-        exec: 0.5746224
-  ibm:
-    description:
-      args: []
-      path: /home/mohammed/Desktop/cont-bench/benchmarks/ibm/case.py
-      slug: ibm
-    output_summary:
-      invocation:
-      - run
-      - /home/mohammed/Desktop/cont-bench/benchmarks/ibm/case.py
-      - --case-optimization
-      - --targets
-      - pre_process
-      - simulation
-      - post_process
-      - --output-summary
-      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/ibm.yaml
-      - --
-      - --gbpp
-      - '1'
-      lock:
-        debug: false
-        gcov: false
-        gpu: false
-        mpi: true
-        single: false
-        unified: false
-      post_process:
-        exec: 2.7696633
-      pre_process:
-        exec: 0.6595922
-      simulation:
-        exec: 1560.6666524
-        grind: 1329.41865639
-      syscheck:
-        exec: 0.350557
-  viscous_weno5_sgb_acoustic:
-    description:
-      args: []
-      path: /home/mohammed/Desktop/cont-bench/benchmarks/viscous_weno5_sgb_acoustic/case.py
-      slug: viscous_weno5_sgb_acoustic
-    output_summary:
-      invocation:
-      - run
-      - /home/mohammed/Desktop/cont-bench/benchmarks/viscous_weno5_sgb_acoustic/case.py
-      - --case-optimization
-      - --targets
-      - pre_process
-      - simulation
-      - post_process
-      - --output-summary
-      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/viscous_weno5_sgb_acoustic.yaml
-      - --
-      - --gbpp
-      - '1'
-      lock:
-        debug: false
-        gcov: false
-        gpu: false
-        mpi: true
-        single: false
-        unified: false
-      post_process:
-        exec: 1.7293213
-      pre_process:
-        exec: 0.7582608
-      simulation:
-        exec: 968.760392
-        grind: 1051.98369313
-      syscheck:
-        exec: 0.6131606
-metadata:
-  invocation:
-  - bench
-  - -o
-  - bench
-  lock:
-    debug: false
-    gcov: false
-    gpu: false
-    mpi: true
-    single: false
-    unified: false
diff --git a/bench-google.json b/bench-google.json
deleted file mode 100644
index 258ff5933..000000000
--- a/bench-google.json
+++ /dev/null
@@ -1,69 +0,0 @@
-{
-  "context": {
-    "date": "2025-07-09T16:51:13.791064",
-    "host_name": "test",
-    "executable": "mfc_benchmark",
-    "num_cpus": 2,
-    "mhz_per_cpu": 2000,
-    "cpu_scaling_enabled": false,
-    "caches": []
-  },
-  "benchmarks": [
-    {
-      "name": "5eq_rk3_weno3_hllc/simulation_time",
-      "family_index": 0,
-      "per_family_instance_index": 0,
-      "run_name": "5eq_rk3_weno3_hllc/simulation_time",
-      "run_type": "iteration",
-      "repetitions": 1,
-      "repetition_index": 0,
-      "threads": 1,
-      "iterations": 1,
-      "real_time": 553746146600.0,
-      "cpu_time": 553746146600.0,
-      "time_unit": "ns"
-    },
-    {
-      "name": "hypo_hll/simulation_time",
-      "family_index": 1,
-      "per_family_instance_index": 0,
-      "run_name": "hypo_hll/simulation_time",
-      "run_type": "iteration",
-      "repetitions": 1,
-      "repetition_index": 0,
-      "threads": 1,
-      "iterations": 1,
-      "real_time": 1158006229400.0,
-      "cpu_time": 1158006229400.0,
-      "time_unit": "ns"
-    },
-    {
-      "name": "ibm/simulation_time",
-      "family_index": 2,
-      "per_family_instance_index": 0,
-      "run_name": "ibm/simulation_time",
-      "run_type": "iteration",
-      "repetitions": 1,
-      "repetition_index": 0,
-      "threads": 1,
-      "iterations": 1,
-      "real_time": 1560666652400.0,
-      "cpu_time": 1560666652400.0,
-      "time_unit": "ns"
-    },
-    {
-      "name": "viscous_weno5_sgb_acoustic/simulation_time",
-      "family_index": 3,
-      "per_family_instance_index": 0,
-      "run_name": "viscous_weno5_sgb_acoustic/simulation_time",
-      "run_type": "iteration",
-      "repetitions": 1,
-      "repetition_index": 0,
-      "threads": 1,
-      "iterations": 1,
-      "real_time": 968760392000.0,
-      "cpu_time": 968760392000.0,
-      "time_unit": "ns"
-    }
-  ]
-}
\ No newline at end of file
diff --git a/bench.json b/bench.json
deleted file mode 100644
index 51457d2dc..000000000
--- a/bench.json
+++ /dev/null
@@ -1,195 +0,0 @@
-{
-  "cases": {
-    "5eq_rk3_weno3_hllc": {
-      "description": {
-        "args": [],
-        "path": "/home/mohammed/Desktop/cont-bench/benchmarks/5eq_rk3_weno3_hllc/case.py",
-        "slug": "5eq_rk3_weno3_hllc"
-      },
-      "output_summary": {
-        "invocation": [
-          "run",
-          "/home/mohammed/Desktop/cont-bench/benchmarks/5eq_rk3_weno3_hllc/case.py",
-          "--case-optimization",
-          "--targets",
-          "pre_process",
-          "simulation",
-          "post_process",
-          "--output-summary",
-          "/home/mohammed/Desktop/cont-bench/build/benchmarks/6462/5eq_rk3_weno3_hllc.yaml",
-          "--",
-          "--gbpp",
-          "1"
-        ],
-        "lock": {
-          "debug": false,
-          "gcov": false,
-          "gpu": false,
-          "mpi": true,
-          "single": false,
-          "unified": false
-        },
-        "post_process": {
-          "exec": 2.6731925
-        },
-        "pre_process": {
-          "exec": 0.945057
-        },
-        "simulation": {
-          "exec": 553.7461466,
-          "grind": 311.46590698
-        },
-        "syscheck": {
-          "exec": 0.5911245
-        }
-      }
-    },
-    "hypo_hll": {
-      "description": {
-        "args": [],
-        "path": "/home/mohammed/Desktop/cont-bench/benchmarks/hypo_hll/case.py",
-        "slug": "hypo_hll"
-      },
-      "output_summary": {
-        "invocation": [
-          "run",
-          "/home/mohammed/Desktop/cont-bench/benchmarks/hypo_hll/case.py",
-          "--case-optimization",
-          "--targets",
-          "pre_process",
-          "simulation",
-          "post_process",
-          "--output-summary",
-          "/home/mohammed/Desktop/cont-bench/build/benchmarks/6462/hypo_hll.yaml",
-          "--",
-          "--gbpp",
-          "1"
-        ],
-        "lock": {
-          "debug": false,
-          "gcov": false,
-          "gpu": false,
-          "mpi": true,
-          "single": false,
-          "unified": false
-        },
-        "post_process": {
-          "exec": 4.6181798
-        },
-        "pre_process": {
-          "exec": 28.0626009
-        },
-        "simulation": {
-          "exec": 1158.0062294,
-          "grind": 373.3648501
-        },
-        "syscheck": {
-          "exec": 0.5746224
-        }
-      }
-    },
-    "ibm": {
-      "description": {
-        "args": [],
-        "path": "/home/mohammed/Desktop/cont-bench/benchmarks/ibm/case.py",
-        "slug": "ibm"
-      },
-      "output_summary": {
-        "invocation": [
-          "run",
-          "/home/mohammed/Desktop/cont-bench/benchmarks/ibm/case.py",
-          "--case-optimization",
-          "--targets",
-          "pre_process",
-          "simulation",
-          "post_process",
-          "--output-summary",
-          "/home/mohammed/Desktop/cont-bench/build/benchmarks/6462/ibm.yaml",
-          "--",
-          "--gbpp",
-          "1"
-        ],
-        "lock": {
-          "debug": false,
-          "gcov": false,
-          "gpu": false,
-          "mpi": true,
-          "single": false,
-          "unified": false
-        },
-        "post_process": {
-          "exec": 2.7696633
-        },
-        "pre_process": {
-          "exec": 0.6595922
-        },
-        "simulation": {
-          "exec": 1560.6666524,
-          "grind": 1329.41865639
-        },
-        "syscheck": {
-          "exec": 0.350557
-        }
-      }
-    },
-    "viscous_weno5_sgb_acoustic": {
-      "description": {
-        "args": [],
-        "path": "/home/mohammed/Desktop/cont-bench/benchmarks/viscous_weno5_sgb_acoustic/case.py",
-        "slug": "viscous_weno5_sgb_acoustic"
-      },
-      "output_summary": {
-        "invocation": [
-          "run",
-          "/home/mohammed/Desktop/cont-bench/benchmarks/viscous_weno5_sgb_acoustic/case.py",
-          "--case-optimization",
-          "--targets",
-          "pre_process",
-          "simulation",
-          "post_process",
-          "--output-summary",
-          "/home/mohammed/Desktop/cont-bench/build/benchmarks/6462/viscous_weno5_sgb_acoustic.yaml",
-          "--",
-          "--gbpp",
-          "1"
-        ],
-        "lock": {
-          "debug": false,
-          "gcov": false,
-          "gpu": false,
-          "mpi": true,
-          "single": false,
-          "unified": false
-        },
-        "post_process": {
-          "exec": 1.7293213
-        },
-        "pre_process": {
-          "exec": 0.7582608
-        },
-        "simulation": {
-          "exec": 968.760392,
-          "grind": 1051.98369313
-        },
-        "syscheck": {
-          "exec": 0.6131606
-        }
-      }
-    }
-  },
-  "metadata": {
-    "invocation": [
-      "bench",
-      "-o",
-      "bench"
-    ],
-    "lock": {
-      "debug": false,
-      "gcov": false,
-      "gpu": false,
-      "mpi": true,
-      "single": false,
-      "unified": false
-    }
-  }
-}
diff --git a/bench.yaml b/bench.yaml
deleted file mode 100644
index 40207a9f8..000000000
--- a/bench.yaml
+++ /dev/null
@@ -1,153 +0,0 @@
-cases:
-  5eq_rk3_weno3_hllc:
-    description:
-      args: []
-      path: /home/mohammed/Desktop/cont-bench/benchmarks/5eq_rk3_weno3_hllc/case.py
-      slug: 5eq_rk3_weno3_hllc
-    output_summary:
-      invocation:
-      - run
-      - /home/mohammed/Desktop/cont-bench/benchmarks/5eq_rk3_weno3_hllc/case.py
-      - --case-optimization
-      - --targets
-      - pre_process
-      - simulation
-      - post_process
-      - --output-summary
-      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/5eq_rk3_weno3_hllc.yaml
-      - --
-      - --gbpp
-      - '1'
-      lock:
-        debug: false
-        gcov: false
-        gpu: false
-        mpi: true
-        single: false
-        unified: false
-      post_process:
-        exec: 2.6731925
-      pre_process:
-        exec: 0.945057
-      simulation:
-        exec: 553.7461466
-        grind: 311.46590698
-      syscheck:
-        exec: 0.5911245
-  hypo_hll:
-    description:
-      args: []
-      path: /home/mohammed/Desktop/cont-bench/benchmarks/hypo_hll/case.py
-      slug: hypo_hll
-    output_summary:
-      invocation:
-      - run
-      - /home/mohammed/Desktop/cont-bench/benchmarks/hypo_hll/case.py
-      - --case-optimization
-      - --targets
-      - pre_process
-      - simulation
-      - post_process
-      - --output-summary
-      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/hypo_hll.yaml
-      - --
-      - --gbpp
-      - '1'
-      lock:
-        debug: false
-        gcov: false
-        gpu: false
-        mpi: true
-        single: false
-        unified: false
-      post_process:
-        exec: 4.6181798
-      pre_process:
-        exec: 28.0626009
-      simulation:
-        exec: 1158.0062294
-        grind: 373.3648501
-      syscheck:
-        exec: 0.5746224
-  ibm:
-    description:
-      args: []
-      path: /home/mohammed/Desktop/cont-bench/benchmarks/ibm/case.py
-      slug: ibm
-    output_summary:
-      invocation:
-      - run
-      - /home/mohammed/Desktop/cont-bench/benchmarks/ibm/case.py
-      - --case-optimization
-      - --targets
-      - pre_process
-      - simulation
-      - post_process
-      - --output-summary
-      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/ibm.yaml
-      - --
-      - --gbpp
-      - '1'
-      lock:
-        debug: false
-        gcov: false
-        gpu: false
-        mpi: true
-        single: false
-        unified: false
-      post_process:
-        exec: 2.7696633
-      pre_process:
-        exec: 0.6595922
-      simulation:
-        exec: 1560.6666524
-        grind: 1329.41865639
-      syscheck:
-        exec: 0.350557
-  viscous_weno5_sgb_acoustic:
-    description:
-      args: []
-      path: /home/mohammed/Desktop/cont-bench/benchmarks/viscous_weno5_sgb_acoustic/case.py
-      slug: viscous_weno5_sgb_acoustic
-    output_summary:
-      invocation:
-      - run
-      - /home/mohammed/Desktop/cont-bench/benchmarks/viscous_weno5_sgb_acoustic/case.py
-      - --case-optimization
-      - --targets
-      - pre_process
-      - simulation
-      - post_process
-      - --output-summary
-      - /home/mohammed/Desktop/cont-bench/build/benchmarks/6462/viscous_weno5_sgb_acoustic.yaml
-      - --
-      - --gbpp
-      - '1'
-      lock:
-        debug: false
-        gcov: false
-        gpu: false
-        mpi: true
-        single: false
-        unified: false
-      post_process:
-        exec: 1.7293213
-      pre_process:
-        exec: 0.7582608
-      simulation:
-        exec: 968.760392
-        grind: 1051.98369313
-      syscheck:
-        exec: 0.6131606
-metadata:
-  invocation:
-  - bench
-  - -o
-  - bench
-  lock:
-    debug: false
-    gcov: false
-    gpu: false
-    mpi: true
-    single: false
-    unified: false
diff --git a/benchmarks/5eq_rk3_weno3_hllc/case.py b/benchmarks/5eq_rk3_weno3_hllc/case.py
deleted file mode 100644
index 5233ef93f..000000000
--- a/benchmarks/5eq_rk3_weno3_hllc/case.py
+++ /dev/null
@@ -1,276 +0,0 @@
-#!/usr/bin/env python3
-# Benchmark model_equations_2_time_stepper_3_weno_order_3_riemann_solver_2
-# Additional Benchmarked Features
-# - model_equations : 2
-# - time_stepper : 3
-# - weno_order : 3
-# - riemann_solver : 2
-
-import json, math, argparse
-
-parser = argparse.ArgumentParser(prog="Benchmarking Case 1", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-
-parser.add_argument("--mfc", type=json.loads, default="{}", metavar="DICT", help="MFC's toolchain's internal state.")
-parser.add_argument("--gbpp", type=int, metavar="MEM", default=16, help="Adjusts the problem size per rank to fit into [MEM] GB of GPU memory per GPU.")
-
-ARGS = vars(parser.parse_args())
-DICT = ARGS["mfc"]
-
-size = 1 if DICT["gpu"] else 0
-
-ppg = 8000000 / 16.0
-procs = DICT["nodes"] * DICT["tasks_per_node"]
-ncells = math.floor(ppg * procs * ARGS["gbpp"])
-s = math.floor((ncells / 2.0) ** (1 / 3))
-Nx, Ny, Nz = 2 * s, s, s
-
-# athmospheric pressure - Pa (used as reference value)
-patm = 101325
-
-# Initial Droplet Diameter / Reference length - m
-D0 = 1.0e-3
-
-# cavity to droplet ratio
-CtD = 0.06
-
-# cavity relative eccentricity (distance between radii)
-ecc = 0.564
-
-# initial shock distance from the y axis. Note that the droplet center is located at y = 0. Thus, the distance from the shock to
-# the droplet is about D0/8
-ISD = 5.0 / 8 * D0
-
-## pre-shock properties - AIR
-
-# pressure - Pa
-p0a = patm
-
-# density - kg/m3
-rho0a = 1.204
-
-# gamma
-gama = 1.40
-
-# pi infinity - Pa
-pia = 0
-
-# speed of sound - M/s
-c_a = math.sqrt(gama * (p0a + pia) / rho0a)
-
-## Droplet - WATER
-
-# surface tension - N / m
-st = 0.00e0
-
-# Delta Pressure - Pa
-DP = -st * 4 / D0
-
-# initial pressure inside the droplet - Pa
-p0w = p0a - DP
-
-# density - kg/m3
-rho0w = 1000
-
-# gama
-gamw = 6.12
-
-# pi infty - Pa
-piw = 3.43e08
-
-# speed of sound - m/s
-c_w = math.sqrt(gamw * (p0w + piw) / rho0w)
-
-# Shock Mach number of interest. Note that the post-shock properties can be defined in terms of either
-# Min or psOp0a. Just comment/uncomment appropriatelly
-Min = 2.4
-
-## Pos to pre shock ratios - AIR
-
-# pressure
-psOp0a = (Min**2 - 1) * 2 * gama / (gama + 1) + 1
-# psOp0a = 4.5
-
-# density
-rhosOrho0a = (1 + (gama + 1) / (gama - 1) * psOp0a) / ((gama + 1) / (gama - 1) + psOp0a)
-
-# Mach number of the shocked region - just a checker, as it must return "Min"
-Ms = math.sqrt((gama + 1.0) / (2.0 * gama) * (psOp0a - 1.0) * (p0a / (p0a + pia)) + 1.0)
-
-# shock speed of sound - m/s
-ss = Ms * c_a
-
-## post-shock - AIR
-
-# pressure - Pa
-ps = psOp0a * p0a
-
-# density - kg / m3
-rhos = rhosOrho0a * rho0a
-
-# post shock speed of sound - m/s
-c_s = math.sqrt(gama * (ps + pia) / rhos)
-
-# velocity at the post shock - m/s
-vel = c_a / gama * (psOp0a - 1.0) * p0a / (p0a + pia) / Ms
-
-## Domain boundaries - m
-
-# x direction
-xb = -8.4707 * D0
-xe = 9.6226 * D0
-
-# xb = -10 * D0
-# xe = 10 * D0
-
-# y direction
-yb = 0 * D0
-ye = 10 * D0
-
-# y direction
-zb = 0 * D0
-ze = 10 * D0
-
-# Stretching factor, to make sure the domaing is sufficiently large after the mesh stretch
-StF = 4.0
-
-# grid delta x if mesh were uniform in x direction - m. Note that I do not need a measure for dy
-dx = (xe - xb) / Nx
-
-# I calculate tend twice; first is an estimate, second is
-# the actual value used. This is because I am getting errors in the
-# post process part every time I approximate the actual Nt by an integer
-# number (think of a smarter way).
-
-# dimensionless time
-ttilde = 1.92
-
-# auxiliary simulation physical time - s. This is not YET the total simulation time, as it will be corrected so as to avoid
-# mismatches in simulation and post_process parts. Note that I wrote it this way so I have better control over the # of autosaves
-tendA = ttilde * D0 / vel
-
-cfl = 0.1
-
-# time-step - s
-dt = dx * cfl / ss
-
-# Save Frequency. Note that the number of autosaves will be SF + 1, as th IC (0.dat) is also saved
-SF = 400
-
-## making Nt divisible by SF
-# 1 - ensure NtA goes slightly beyond tendA
-NtA = int(tendA // dt + 1)
-
-# Array of saves. It is the same as Nt/Sf = t_step_save
-AS = int(NtA // SF + 1)
-
-# Nt = total number of steps. Note that Nt >= NtA (so at least tendA is completely simulated)
-Nt = AS * SF
-
-# total simulation time - s. Note that tend >= tendA
-tend = Nt * dt
-
-# Configuring case dictionary
-print(
-    json.dumps(
-        {
-            # Logistics
-            "run_time_info": "F",
-            # Computational Domain Parameters
-            "x_domain%beg": xb,
-            "x_domain%end": xe,
-            "y_domain%beg": yb,
-            "y_domain%end": ye,
-            "z_domain%beg": zb,
-            "z_domain%end": ze,
-            "m": Nx,
-            "n": Ny,
-            "p": Nz,
-            "cyl_coord": "F",
-            "dt": dt,
-            "t_step_start": 0,
-            "t_step_stop": int(30 * (95 * size + 5)),
-            "t_step_save": int(30 * (95 * size + 5)),
-            # Simulation Algorithm Parameters
-            "num_patches": 3,
-            "model_eqns": 2,
-            "alt_soundspeed": "F",
-            "num_fluids": 2,
-            "mpp_lim": "T",
-            "mixture_err": "T",
-            "time_stepper": 3,
-            "weno_order": 3,
-            "weno_eps": 1.0e-16,
-            "weno_Re_flux": "F",
-            "weno_avg": "F",
-            "mapped_weno": "T",
-            "riemann_solver": 2,
-            "wave_speeds": 1,
-            "avg_state": 2,
-            "bc_x%beg": -6,
-            "bc_x%end": -6,
-            "bc_y%beg": -2,
-            "bc_y%end": -3,
-            "bc_z%beg": -2,
-            "bc_z%end": -3,
-            # Formatted Database Files Structure Parameters
-            "format": 1,
-            "precision": 2,
-            "prim_vars_wrt": "T",
-            "parallel_io": "T",
-            # I will use 1 for WATER properties, and 2 for AIR properties
-            # Patch 1: Background (AIR - 2)
-            "patch_icpp(1)%geometry": 9,
-            "patch_icpp(1)%x_centroid": (xb + xe) / 2 * StF,
-            "patch_icpp(1)%y_centroid": (yb + ye) / 2 * StF,
-            "patch_icpp(1)%z_centroid": (yb + ye) / 2 * StF,
-            "patch_icpp(1)%length_x": (xe - xb) * StF,
-            "patch_icpp(1)%length_y": (ye - yb) * StF,
-            "patch_icpp(1)%length_z": (ze - zb) * StF,
-            "patch_icpp(1)%vel(1)": 0.0e00,
-            "patch_icpp(1)%vel(2)": 0.0e00,
-            "patch_icpp(1)%vel(3)": 0.0e00,
-            "patch_icpp(1)%pres": p0a,
-            "patch_icpp(1)%alpha_rho(1)": 0.0e00,
-            "patch_icpp(1)%alpha_rho(2)": rho0a,
-            "patch_icpp(1)%alpha(1)": 0.0e00,
-            "patch_icpp(1)%alpha(2)": 1.0e00,
-            # Patch 2: Shocked state (AIR - 2)
-            "patch_icpp(2)%geometry": 9,
-            "patch_icpp(2)%alter_patch(1)": "T",
-            "patch_icpp(2)%x_centroid": -ISD - (xe - xb) / 2 * StF,
-            "patch_icpp(2)%y_centroid": (yb + ye) / 2 * StF,
-            "patch_icpp(2)%z_centroid": (zb + ze) / 2 * StF,
-            "patch_icpp(2)%length_x": (xe - xb) * StF,
-            "patch_icpp(2)%length_y": (ye - yb) * StF,
-            "patch_icpp(2)%length_z": (ze - zb) * StF,
-            "patch_icpp(2)%vel(1)": vel,
-            "patch_icpp(2)%vel(2)": 0.0e00,
-            "patch_icpp(2)%vel(3)": 0.0e00,
-            "patch_icpp(2)%pres": ps,
-            "patch_icpp(2)%alpha_rho(1)": 0.0e00,
-            "patch_icpp(2)%alpha_rho(2)": rhos,
-            "patch_icpp(2)%alpha(1)": 0.0e00,
-            "patch_icpp(2)%alpha(2)": 1.0e00,
-            # Patch 3: Droplet (WATER - 1)
-            "patch_icpp(3)%geometry": 8,
-            "patch_icpp(3)%x_centroid": 0.0e00,
-            "patch_icpp(3)%y_centroid": 0.0e00,
-            "patch_icpp(3)%z_centroid": 0.0e00,
-            "patch_icpp(3)%radius": D0 / 2,
-            "patch_icpp(3)%alter_patch(1)": "T",
-            "patch_icpp(3)%vel(1)": 0.0e00,
-            "patch_icpp(3)%vel(2)": 0.0e00,
-            "patch_icpp(3)%vel(3)": 0.0e00,
-            "patch_icpp(3)%pres": p0w,
-            "patch_icpp(3)%alpha_rho(1)": rho0w,
-            "patch_icpp(3)%alpha_rho(2)": 0.0e00,
-            "patch_icpp(3)%alpha(1)": 1.0e00,
-            "patch_icpp(3)%alpha(2)": 0.0e00,
-            # Fluids Physical Parameters
-            "fluid_pp(1)%gamma": 1.0e00 / (gamw - 1),
-            "fluid_pp(1)%pi_inf": gamw * piw / (gamw - 1),
-            "fluid_pp(2)%gamma": 1.0e00 / (gama - 1),
-            "fluid_pp(2)%pi_inf": gama * pia / (gama - 1),
-        }
-    )
-)
diff --git a/benchmarks/hypo_hll/case.py b/benchmarks/hypo_hll/case.py
deleted file mode 100644
index e9b4188b2..000000000
--- a/benchmarks/hypo_hll/case.py
+++ /dev/null
@@ -1,121 +0,0 @@
-#!/usr/bin/env python3
-# Benchmark hypoelasticity_T_riemann_solver_1
-# Additional Benchmarked Features
-# - hypoelasticity : T
-# - riemann_solver : 1
-
-import json, math, argparse
-
-parser = argparse.ArgumentParser(prog="Benchmarkin Case 3", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-
-parser.add_argument("--mfc", type=json.loads, default="{}", metavar="DICT", help="MFC's toolchain's internal state.")
-parser.add_argument("--gbpp", type=int, metavar="MEM", default=16, help="Adjusts the problem size per rank to fit into [MEM] GB of GPU memory per GPU.")
-
-ARGS = vars(parser.parse_args())
-DICT = ARGS["mfc"]
-
-size = 1 if DICT["gpu"] else 0
-
-ppg = 8000000 / 16.0
-procs = DICT["nodes"] * DICT["tasks_per_node"]
-ncells = math.floor(ppg * procs * ARGS["gbpp"])
-s = math.floor((ncells / 2.0) ** (1 / 3))
-Nx, Ny, Nz = 2 * s, s, s
-
-
-# Configuring case dictionary
-print(
-    json.dumps(
-        {
-            # Logistics
-            "run_time_info": "F",
-            # Computational Domain Parameters
-            "x_domain%beg": 0.0e00,
-            "x_domain%end": 1.0e00,
-            "y_domain%beg": 0.0e00,
-            "y_domain%end": 2.0e00,
-            "z_domain%beg": 0.0e00,
-            "z_domain%end": 1.0e00,
-            "m": Nx,
-            "n": Ny,
-            "p": Nz,
-            "dt": 1e-8,
-            "t_step_start": 0,
-            "t_step_stop": int(30 * (95 * size + 5)),
-            "t_step_save": int(30 * (95 * size + 5)),
-            # Simulation Algorithm Parameters
-            "num_patches": 2,
-            "model_eqns": 2,
-            "alt_soundspeed": "F",
-            "num_fluids": 2,
-            "mpp_lim": "F",
-            "mixture_err": "F",
-            "time_stepper": 3,
-            "weno_order": 3,
-            "weno_eps": 1.0e-16,
-            "weno_Re_flux": "F",
-            "weno_avg": "F",
-            "mapped_weno": "F",
-            "null_weights": "F",
-            "mp_weno": "F",
-            "riemann_solver": 1,
-            "wave_speeds": 1,
-            "avg_state": 2,
-            "bc_x%beg": -3,
-            "bc_x%end": -3,
-            "bc_y%beg": -3,
-            "bc_y%end": -3,
-            "bc_z%beg": -3,
-            "bc_z%end": -3,
-            # Turning on Hypoelasticity
-            "hypoelasticity": "T",
-            "fd_order": 4,
-            # Formatted Database Files Structure Parameters
-            "format": 1,
-            "precision": 2,
-            "prim_vars_wrt": "T",
-            "parallel_io": "F",
-            # Patch 1 L
-            "patch_icpp(1)%geometry": 9,
-            "patch_icpp(1)%x_centroid": 0.35,
-            "patch_icpp(1)%y_centroid": 1.0,
-            "patch_icpp(1)%z_centroid": 0.5,
-            "patch_icpp(1)%length_x": 0.7,
-            "patch_icpp(1)%length_y": 2,
-            "patch_icpp(1)%length_z": 1,
-            "patch_icpp(1)%vel(1)": 0.0,
-            "patch_icpp(1)%vel(2)": 0.0,
-            "patch_icpp(1)%vel(3)": 0.0,
-            "patch_icpp(1)%pres": 1e09,
-            "patch_icpp(1)%alpha_rho(1)": 1000,
-            "patch_icpp(1)%alpha_rho(2)": 0.0,
-            "patch_icpp(1)%alpha(1)": 1,
-            "patch_icpp(1)%alpha(2)": 0.0,
-            "patch_icpp(1)%tau_e(1)": 0.0,
-            # Patch 2 R
-            "patch_icpp(2)%geometry": 9,
-            "patch_icpp(2)%x_centroid": 0.85,
-            "patch_icpp(2)%y_centroid": 1.0,
-            "patch_icpp(2)%z_centroid": 0.5,
-            "patch_icpp(2)%length_x": 0.3,
-            "patch_icpp(2)%length_y": 2.0,
-            "patch_icpp(2)%length_z": 1.0,
-            "patch_icpp(2)%vel(1)": 0,
-            "patch_icpp(2)%vel(2)": 0,
-            "patch_icpp(2)%vel(3)": 0,
-            "patch_icpp(2)%pres": 1e05,
-            "patch_icpp(2)%alpha_rho(1)": 0.0,
-            "patch_icpp(2)%alpha_rho(2)": 50.0,
-            "patch_icpp(2)%alpha(1)": 0,
-            "patch_icpp(2)%alpha(2)": 1,
-            "patch_icpp(2)%tau_e(1)": 0.0,
-            # Fluids Physical Parameters
-            "fluid_pp(1)%gamma": 1.0e00 / (4.4e00 - 1.0e00),
-            "fluid_pp(1)%pi_inf": 4.4e00 * 6.0e08 / (4.4e00 - 1.0e00),
-            "fluid_pp(1)%G": 1.0e09,
-            "fluid_pp(2)%gamma": 1.0e00 / (1.4e00 - 1.0e00),
-            "fluid_pp(2)%pi_inf": 0.0,
-            "fluid_pp(2)%G": 0.0,
-        }
-    )
-)
diff --git a/benchmarks/ibm/case.py b/benchmarks/ibm/case.py
deleted file mode 100644
index ba163d949..000000000
--- a/benchmarks/ibm/case.py
+++ /dev/null
@@ -1,115 +0,0 @@
-#!/usr/bin/env python3
-# Benchmark ibm_T
-# Additional Benchmarked Features
-# - ibm : T
-
-import json, math, argparse
-
-parser = argparse.ArgumentParser(prog="Benchmarking Case 4", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-
-parser.add_argument("--mfc", type=json.loads, default="{}", metavar="DICT", help="MFC's toolchain's internal state.")
-parser.add_argument("--gbpp", type=int, metavar="MEM", default=16, help="Adjusts the problem size per rank to fit into [MEM] GB of GPU memory per GPU.")
-
-ARGS = vars(parser.parse_args())
-DICT = ARGS["mfc"]
-
-size = 1 if DICT["gpu"] else 0
-
-ppg = 8000000 / 16.0
-procs = DICT["nodes"] * DICT["tasks_per_node"]
-ncells = math.floor(ppg * procs * ARGS["gbpp"])
-s = math.floor((ncells / 2.0) ** (1 / 3))
-Nx, Ny, Nz = 2 * s, s, s
-
-dx = 1.0 / (1.0 * (Nx + 1))
-
-Tend = 1e-4
-Nt = 200
-mydt = Tend / (1.0 * Nt)
-
-# Configuring case dictionary
-print(
-    json.dumps(
-        {
-            # Logistics
-            "run_time_info": "F",
-            # Computational Domain Parameters
-            "x_domain%beg": 0.0e00,
-            "x_domain%end": 1.0e00,
-            "y_domain%beg": 0,
-            "y_domain%end": 0.5,
-            "z_domain%beg": 0.0,
-            "z_domain%end": 0.5,
-            "m": Nx,
-            "n": Ny,
-            "p": Nz,
-            "dt": mydt,
-            "t_step_start": 0,
-            "t_step_stop": int(20 * (95 * size + 5)),
-            "t_step_save": int(20 * (95 * size + 5)),
-            # Simulation Algorithm Parameters
-            "num_patches": 1,
-            "model_eqns": 2,
-            "alt_soundspeed": "F",
-            "num_fluids": 2,
-            "mpp_lim": "F",
-            "mixture_err": "F",
-            "time_stepper": 3,
-            "weno_order": 5,
-            "weno_eps": 1.0e-16,
-            "weno_Re_flux": "T",
-            "weno_avg": "T",
-            "mapped_weno": "T",
-            "null_weights": "F",
-            "mp_weno": "F",
-            "riemann_solver": 2,
-            "wave_speeds": 1,
-            "avg_state": 2,
-            "bc_x%beg": -3,
-            "bc_x%end": -3,
-            "bc_y%beg": -3,
-            "bc_y%end": -3,
-            "bc_z%beg": -3,
-            "bc_z%end": -3,
-            # Turn on IBM
-            "ib": "T",
-            "num_ibs": 1,
-            "viscous": "T",
-            # Formatted Database Files Structure Parameters
-            "format": 1,
-            "precision": 2,
-            "prim_vars_wrt": "T",
-            "parallel_io": "T",
-            # Patch 1 L
-            "patch_icpp(1)%geometry": 9,
-            "patch_icpp(1)%x_centroid": 0.5,
-            "patch_icpp(1)%y_centroid": 0.25,
-            "patch_icpp(1)%z_centroid": 0.25,
-            "patch_icpp(1)%length_x": 1.0,
-            "patch_icpp(1)%length_y": 0.5,
-            "patch_icpp(1)%length_z": 0.5,
-            "patch_icpp(1)%vel(1)": 0.1,
-            "patch_icpp(1)%vel(2)": 0,
-            "patch_icpp(1)%vel(3)": 0,
-            "patch_icpp(1)%pres": 1.0,
-            "patch_icpp(1)%alpha_rho(1)": 0.8e00,
-            "patch_icpp(1)%alpha(1)": 0.8e00,
-            "patch_icpp(1)%alpha_rho(2)": 0.2e00,
-            "patch_icpp(1)%alpha(2)": 0.2e00,
-            # Patch: Sphere Immersed Boundary
-            "patch_ib(1)%geometry": 8,
-            "patch_ib(1)%x_centroid": 0.25,
-            "patch_ib(1)%y_centroid": 0.25,
-            "patch_ib(1)%z_centroid": 0.25,
-            "patch_ib(1)%radius": 0.1,
-            # Fluids Physical Parameters
-            # Specify 2 fluids
-            "fluid_pp(1)%gamma": 1.0e00 / (1.4 - 1.0e00),
-            "fluid_pp(1)%pi_inf": 0,
-            "fluid_pp(1)%Re(1)": 54000,
-            "fluid_pp(2)%gamma": 1.0e00 / (1.4 - 1.0e00),
-            "fluid_pp(2)%pi_inf": 0,
-            "fluid_pp(2)%Re(1)": 54000,
-        }
-    )
-)
diff --git a/benchmarks/viscous_weno5_sgb_acoustic/case.py b/benchmarks/viscous_weno5_sgb_acoustic/case.py
deleted file mode 100644
index 1a85a4b28..000000000
--- a/benchmarks/viscous_weno5_sgb_acoustic/case.py
+++ /dev/null
@@ -1,225 +0,0 @@
-#!/usr/bin/env python3
-# Benchmark viscosity_weno_Re_flux_T_weno_order_5_bubbles_T_bubble_mode_3_acoustic_T
-# Additional Benchmarked Features
-# - viscosity enabled
-# - weno_Re_flux : T
-# - weno_order : 5
-# - bubbles_euler : T
-# - bubble_model : 3
-# - acoustic_source : T
-
-import json, math, argparse
-
-parser = argparse.ArgumentParser(prog="Benchmarking Case 2", description="This MFC case was created for the purposes of benchmarking MFC.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-
-parser.add_argument("--mfc", type=json.loads, default="{}", metavar="DICT", help="MFC's toolchain's internal state.")
-parser.add_argument("--gbpp", type=int, metavar="MEM", default=16, help="Adjusts the problem size per rank to fit into [MEM] GB of GPU memory per GPU.")
-
-ARGS = vars(parser.parse_args())
-DICT = ARGS["mfc"]
-
-size = 1 if DICT["gpu"] else 0
-
-ppg = 8000000 / 16.0
-procs = DICT["nodes"] * DICT["tasks_per_node"]
-ncells = math.floor(ppg * procs * ARGS["gbpp"])
-s = math.floor((ncells / 2.0) ** (1 / 3))
-Nx, Ny, Nz = 2 * s, s, s
-
-x0 = 10.0e-04
-y0 = 10.0e-04
-z0 = 10.0e-04
-p0 = 1.0
-rho0 = 1.0e03
-c0 = math.sqrt(p0 / rho0)
-patm = 1.0
-
-# water props
-n_tait = 7.1
-B_tait = 306.0e06 / p0
-mul0 = 1.002e-03  # viscosity
-ss = 0.07275  # surface tension
-pv = 2.3388e03  # vapor pressure
-
-gamma_v = 1.33
-M_v = 18.02
-mu_v = 0.8816e-05
-k_v = 0.019426
-
-# air props
-gamma_n = 1.4
-M_n = 28.97
-mu_n = 1.8e-05
-k_n = 0.02556
-
-# air props
-gamma_gas = gamma_n
-
-# reference bubble size
-R0ref = 10.0e-06
-
-pa = 0.1 * 1.0e06 / 101325.0
-
-# Characteristic velocity
-uu = math.sqrt(p0 / rho0)
-# Cavitation number
-Ca = (p0 - pv) / (rho0 * (uu**2.0))
-# Weber number
-We = rho0 * (uu**2.0) * R0ref / ss
-# Inv. bubble Reynolds number
-Re_inv = mul0 / (rho0 * uu * R0ref)
-
-# IC setup
-vf0 = 0.00004
-n0 = vf0 / (math.pi * 4.0e00 / 3.0e00)
-
-cact = 1475.0
-t0 = x0 / c0
-
-nbubbles = 1
-myr0 = R0ref
-
-cfl = 0.01
-Ldomain = 20.0e-03
-L = Ldomain / x0
-dx = L / float(Nx)
-dt = cfl * dx * c0 / cact
-Lpulse = 0.3 * Ldomain
-Tpulse = Lpulse / cact
-
-# Configuring case dictionary
-print(
-    json.dumps(
-        {
-            # Logistics
-            "run_time_info": "F",
-            # Computational Domain Parameters
-            "x_domain%beg": -10.0e-03 / x0,
-            "x_domain%end": 10.0e-03 / x0,
-            "y_domain%beg": -5.0e-03 / y0,
-            "y_domain%end": 5.0e-03 / y0,
-            "z_domain%beg": -5.0e-03 / z0,
-            "z_domain%end": 5.0e-03 / z0,
-            "stretch_x": "F",
-            "cyl_coord": "F",
-            "m": Nx,
-            "n": Ny,
-            "p": Nz,
-            "dt": dt,
-            "t_step_start": 0,
-            "t_step_stop": int(15 * (25 * size + 5)),
-            "t_step_save": int(15 * (25 * size + 5)),
-            # Simulation Algorithm Parameters
-            "num_patches": 2,
-            "model_eqns": 2,
-            "alt_soundspeed": "F",
-            "num_fluids": 1,
-            "mpp_lim": "F",
-            "mixture_err": "F",
-            "time_stepper": 3,
-            "weno_order": 5,
-            "weno_eps": 1.0e-16,
-            "weno_Re_flux": "F",
-            "weno_avg": "F",
-            "mapped_weno": "T",
-            "null_weights": "F",
-            "mp_weno": "T",
-            "riemann_solver": 2,
-            "wave_speeds": 1,
-            "avg_state": 2,
-            "bc_x%beg": -3,
-            "bc_x%end": -3,
-            "bc_y%beg": -3,
-            "bc_y%end": -3,
-            "bc_z%beg": -3,
-            "bc_z%end": -3,
-            "viscous": "T",
-            # Formatted Database Files Structure Parameters
-            "format": 1,
-            "precision": 2,
-            "prim_vars_wrt": "T",
-            "parallel_io": "T",
-            # Patch 1 _ Background
-            "patch_icpp(1)%geometry": 9,
-            "patch_icpp(1)%x_centroid": 0.0,
-            "patch_icpp(1)%y_centroid": 0.0,
-            "patch_icpp(1)%z_centroid": 0.0,
-            "patch_icpp(1)%length_x": 20.0e-03 / x0,
-            "patch_icpp(1)%length_y": 10.0e-03 / y0,
-            "patch_icpp(1)%length_z": 10.0e-03 / z0,
-            "patch_icpp(1)%vel(1)": 0.0,
-            "patch_icpp(1)%vel(2)": 0.0,
-            "patch_icpp(1)%vel(3)": 0.0,
-            "patch_icpp(1)%pres": patm,
-            "patch_icpp(1)%alpha_rho(1)": (1.0 - 1.0e-12) * 1.0e03 / rho0,
-            "patch_icpp(1)%alpha(1)": 1.0e-12,
-            "patch_icpp(1)%r0": 1.0,
-            "patch_icpp(1)%v0": 0.0e00,
-            # Patch 2 Screen
-            "patch_icpp(2)%geometry": 9,
-            "patch_icpp(2)%x_centroid": 0.0,
-            "patch_icpp(2)%y_centroid": 0.0,
-            "patch_icpp(2)%z_centroid": 0.0,
-            "patch_icpp(2)%length_x": 5.0e-03 / x0,
-            "patch_icpp(2)%length_y": 10.0e-03 / y0,
-            "patch_icpp(2)%length_z": 10.0e-03 / z0,
-            "patch_icpp(2)%alter_patch(1)": "T",
-            "patch_icpp(2)%vel(1)": 0.0,
-            "patch_icpp(2)%vel(2)": 0.0,
-            "patch_icpp(2)%vel(3)": 0.0,
-            "patch_icpp(2)%pres": patm,
-            "patch_icpp(2)%alpha_rho(1)": (1.0 - vf0) * 1.0e03 / rho0,
-            "patch_icpp(2)%alpha(1)": vf0,
-            "patch_icpp(2)%r0": 1.0,
-            "patch_icpp(2)%v0": 0.0e00,
-            # Fluids Physical Parameters
-            # Surrounding liquid
-            "fluid_pp(1)%gamma": 1.0e00 / (n_tait - 1.0e00),
-            "fluid_pp(1)%pi_inf": n_tait * B_tait / (n_tait - 1.0),
-            "fluid_pp(1)%mul0": mul0,
-            "fluid_pp(1)%ss": ss,
-            "fluid_pp(1)%pv": pv,
-            "fluid_pp(1)%gamma_v": gamma_v,
-            "fluid_pp(1)%M_v": M_v,
-            "fluid_pp(1)%mu_v": mu_v,
-            "fluid_pp(1)%k_v": k_v,
-            "fluid_pp(1)%Re(1)": 1e3,
-            # Last fluid_pp is always reserved for bubble gas state
-            # if applicable
-            "fluid_pp(2)%gamma": 1.0 / (gamma_gas - 1.0),
-            "fluid_pp(2)%pi_inf": 0.0e00,
-            "fluid_pp(2)%gamma_v": gamma_n,
-            "fluid_pp(2)%M_v": M_n,
-            "fluid_pp(2)%mu_v": mu_n,
-            "fluid_pp(2)%k_v": k_n,
-            # Non-polytropic gas compression model AND/OR Tait EOS
-            "pref": p0,
-            "rhoref": rho0,
-            # Bubbles
-            "bubbles_euler": "T",
-            "bubble_model": 3,
-            "polytropic": "T",
-            "polydisperse": "F",
-            # 'poly_sigma'                   : 0.3,
-            "thermal": 3,
-            "R0ref": myr0,
-            "nb": 1,
-            "Ca": Ca,
-            "Web": We,
-            "Re_inv": Re_inv,
-            # Acoustic source
-            "acoustic_source": "T",
-            "num_source": 1,
-            "acoustic(1)%support": 3,
-            "acoustic(1)%loc(1)": -5.0e-03 / x0,
-            "acoustic(1)%loc(2)": 0.0,
-            "acoustic(1)%length": 1.0 / x0,
-            "acoustic(1)%height": 1.0 / x0,
-            "acoustic(1)%npulse": 1,
-            "acoustic(1)%dir": 1.0,
-            "acoustic(1)%pulse": 1,
-            "acoustic(1)%mag": pa,
-            "acoustic(1)%wavelength": (1.0 / (300000.0)) * cact / x0,
-        }
-    )
-)
diff --git a/test-components.sh b/test-components.sh
deleted file mode 100755
index 14fab2518..000000000
--- a/test-components.sh
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/bin/bash
-set -e
-
-echo "=== Testing Individual Components ==="
-
-# Test 1: Check if mfc.sh exists and is executable
-echo "1. Testing mfc.sh..."
-if [ -f "./mfc.sh" ]; then
-    chmod +x ./mfc.sh
-    echo "✓ mfc.sh found and made executable"
-else
-    echo "✗ mfc.sh not found - creating mock for testing"
-    cat > ./mfc.sh << 'MOCK'
-#!/bin/bash
-echo "Mock benchmark running..."
-mkdir -p bench
-echo "name: test_benchmark" > bench/test.yaml
-echo "time: 1.23" >> bench/test.yaml
-echo "Mock benchmark completed"
-MOCK
-    chmod +x ./mfc.sh
-fi
-
-# Test 2: Run benchmark command
-echo "2. Testing benchmark execution..."
-./mfc.sh bench -o bench || echo "Benchmark failed, continuing with mock data"
-
-# Test 3: Check yq installation and YAML to JSON conversion
-echo "3. Testing YAML to JSON conversion..."
-if ! command -v yq &> /dev/null; then
-    echo "Installing yq..."
-    sudo wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64
-    sudo chmod +x /usr/local/bin/yq
-fi
-
-# Convert any YAML files found
-find . -maxdepth 1 -name "*.yaml" -exec sh -c 'echo "Converting $1"; yq eval -o=json "$1" > "${1%.yaml}.json"' _ {} \;
-
-# Test 4: Check JSON output format
-echo "4. Validating JSON format..."
-for json_file in *.json; do
-    if [ -f "$json_file" ]; then
-        echo "Checking $json_file:"
-        python3 -c "import json; json.load(open('$json_file')); print('✓ Valid JSON')" || echo "✗ Invalid JSON"
-    fi
-done
-
-echo "=== Component Testing Complete ==="