Merge remote-tracking branch 'origin/main' into perf-build

.github/workflows/build-and-publish.yml

@@ -1,11 +0,0 @@
-name: CI
-
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
-
-jobs:
-  build:
-    uses: ./.github/workflows/build-reusable.yml 

.github/workflows/build-reusable.yml

@@ -1,167 +0,0 @@
-name: Reusable Build
-
-on:
-  workflow_call:
-    inputs:
-      ref:
-        description: 'Git ref to build'
-        required: false
-        type: string
-        default: ''
-
-jobs:
-  build:
-    name: Build ${{ matrix.os }} Python ${{ matrix.python }}
-    strategy:
-      matrix:
-        include:
-          - os: ubuntu-22.04
-            python: '3.9'
-          - os: ubuntu-22.04
-            python: '3.10'
-          - os: ubuntu-22.04
-            python: '3.11'
-          - os: ubuntu-22.04
-            python: '3.12'
-          - os: ubuntu-22.04
-            python: '3.13'
-          - os: macos-latest
-            python: '3.9'
-          - os: macos-latest
-            python: '3.10'
-          - os: macos-latest
-            python: '3.11'
-          - os: macos-latest
-            python: '3.12'
-          - os: macos-latest
-            python: '3.13'
-    runs-on: ${{ matrix.os }}
-    
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          ref: ${{ inputs.ref }}
-          submodules: recursive
-      
-      - name: Setup Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python }}
-      
-      - name: Install uv
-        uses: astral-sh/setup-uv@v4
-      
-      - name: Install system dependencies (Ubuntu)
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y libomp-dev libboost-all-dev protobuf-compiler libzmq3-dev \
-            pkg-config libopenblas-dev patchelf libabsl-dev libaio-dev libprotobuf-dev
-          
-          # Install Intel MKL for DiskANN
-          wget -q https://registrationcenter-download.intel.com/akdlm/IRC_NAS/79153e0f-74d7-45af-b8c2-258941adf58a/intel-onemkl-2025.0.0.940.sh
-          sudo sh intel-onemkl-2025.0.0.940.sh -a --components intel.oneapi.lin.mkl.devel --action install --eula accept -s
-          source /opt/intel/oneapi/setvars.sh
-          echo "MKLROOT=/opt/intel/oneapi/mkl/latest" >> $GITHUB_ENV
-          echo "LD_LIBRARY_PATH=/opt/intel/oneapi/mkl/latest/lib/intel64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
-      
-      - name: Install system dependencies (macOS)
-        if: runner.os == 'macOS'
-        run: |
-          brew install llvm libomp boost protobuf zeromq
-      
-      - name: Install build dependencies
-        run: |
-          uv pip install --system scikit-build-core numpy swig Cython pybind11
-          if [[ "$RUNNER_OS" == "Linux" ]]; then
-            uv pip install --system auditwheel
-          else
-            uv pip install --system delocate
-          fi
-      
-      - name: Build packages
-        run: |
-          # Build core (platform independent)
-          if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then
-            cd packages/leann-core
-            uv build
-            cd ../..
-          fi
-          
-          # Build HNSW backend
-          cd packages/leann-backend-hnsw
-          if [ "${{ matrix.os }}" == "macos-latest" ]; then
-            CC=$(brew --prefix llvm)/bin/clang CXX=$(brew --prefix llvm)/bin/clang++ uv build --wheel --python python
-          else
-            uv build --wheel --python python
-          fi
-          cd ../..
-          
-          # Build DiskANN backend
-          cd packages/leann-backend-diskann
-          if [ "${{ matrix.os }}" == "macos-latest" ]; then
-            CC=$(brew --prefix llvm)/bin/clang CXX=$(brew --prefix llvm)/bin/clang++ uv build --wheel --python python
-          else
-            uv build --wheel --python python
-          fi
-          cd ../..
-          
-          # Build meta package (platform independent)
-          if [ "${{ matrix.os }}" == "ubuntu-latest" ]; then
-            cd packages/leann
-            uv build
-            cd ../..
-          fi
-      
-      - name: Repair wheels (Linux)
-        if: runner.os == 'Linux'
-        run: |
-          # Repair HNSW wheel
-          cd packages/leann-backend-hnsw
-          if [ -d dist ]; then
-            auditwheel repair dist/*.whl -w dist_repaired
-            rm -rf dist
-            mv dist_repaired dist
-          fi
-          cd ../..
-          
-          # Repair DiskANN wheel
-          cd packages/leann-backend-diskann
-          if [ -d dist ]; then
-            auditwheel repair dist/*.whl -w dist_repaired
-            rm -rf dist
-            mv dist_repaired dist
-          fi
-          cd ../..
-      
-      - name: Repair wheels (macOS)
-        if: runner.os == 'macOS'
-        run: |
-          # Repair HNSW wheel
-          cd packages/leann-backend-hnsw
-          if [ -d dist ]; then
-            delocate-wheel -w dist_repaired -v dist/*.whl
-            rm -rf dist
-            mv dist_repaired dist
-          fi
-          cd ../..
-          
-          # Repair DiskANN wheel
-          cd packages/leann-backend-diskann
-          if [ -d dist ]; then
-            delocate-wheel -w dist_repaired -v dist/*.whl
-            rm -rf dist
-            mv dist_repaired dist
-          fi
-          cd ../..
-      
-      - name: List built packages
-        run: |
-          echo "📦 Built packages:"
-          find packages/*/dist -name "*.whl" -o -name "*.tar.gz" | sort
-      
-      - name: Upload artifacts
-        uses: actions/upload-artifact@v4
-        with:
-          name: packages-${{ matrix.os }}-py${{ matrix.python }}
-          path: packages/*/dist/ 

.github/workflows/release-manual.yml

@@ -1,126 +0,0 @@
-name: Release
-
-on:
-  workflow_dispatch:
-    inputs:
-      version:
-        description: 'Version to release (e.g., 0.1.2)'
-        required: true
-        type: string
-
-jobs:
-  update-version:
-    name: Update Version
-    runs-on: ubuntu-latest
-    permissions:
-      contents: write
-    outputs:
-      commit-sha: ${{ steps.push.outputs.commit-sha }}
-    
-    steps:
-      - uses: actions/checkout@v4
-      
-      - name: Validate version
-        run: |
-          if ! [[ "${{ inputs.version }}" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
-            echo "❌ Invalid version format"
-            exit 1
-          fi
-          echo "✅ Version format valid"
-      
-      - name: Update versions and push
-        id: push
-        run: |
-          # Check current version
-          CURRENT_VERSION=$(grep "^version" packages/leann-core/pyproject.toml | cut -d'"' -f2)
-          echo "Current version: $CURRENT_VERSION"
-          echo "Target version: ${{ inputs.version }}"
-          
-          if [ "$CURRENT_VERSION" = "${{ inputs.version }}" ]; then
-            echo "⚠️  Version is already ${{ inputs.version }}, skipping update"
-            COMMIT_SHA=$(git rev-parse HEAD)
-          else
-            ./scripts/bump_version.sh ${{ inputs.version }}
-            git config user.name "GitHub Actions"
-            git config user.email "actions@github.com"
-            git add packages/*/pyproject.toml
-            git commit -m "chore: release v${{ inputs.version }}"
-            git push origin main
-            COMMIT_SHA=$(git rev-parse HEAD)
-            echo "✅ Pushed version update: $COMMIT_SHA"
-          fi
-          
-          echo "commit-sha=$COMMIT_SHA" >> $GITHUB_OUTPUT
-
-  build-packages:
-    name: Build packages
-    needs: update-version
-    uses: ./.github/workflows/build-reusable.yml
-    with:
-      ref: ${{ needs.update-version.outputs.commit-sha }}
-
-  publish:
-    name: Publish and Release
-    needs: [update-version, build-packages]
-    if: always() && needs.update-version.result == 'success' && needs.build-packages.result == 'success'
-    runs-on: ubuntu-latest
-    permissions:
-      contents: write
-    
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          ref: ${{ needs.update-version.outputs.commit-sha }}
-      
-      - name: Download all artifacts
-        uses: actions/download-artifact@v4
-        with:
-          path: dist-artifacts
-      
-      - name: Collect packages
-        run: |
-          mkdir -p dist
-          find dist-artifacts -name "*.whl" -exec cp {} dist/ \;
-          find dist-artifacts -name "*.tar.gz" -exec cp {} dist/ \;
-          
-          echo "📦 Packages to publish:"
-          ls -la dist/
-      
-      - name: Publish to PyPI
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
-        run: |
-          if [ -z "$TWINE_PASSWORD" ]; then
-            echo "❌ PYPI_API_TOKEN not configured!"
-            exit 1
-          fi
-          
-          pip install twine
-          twine upload dist/* --skip-existing --verbose
-          
-          echo "✅ Published to PyPI!"
-      
-      - name: Create release
-        run: |
-          # Check if tag already exists
-          if git rev-parse "v${{ inputs.version }}" >/dev/null 2>&1; then
-            echo "⚠️  Tag v${{ inputs.version }} already exists, skipping tag creation"
-          else
-            git tag "v${{ inputs.version }}"
-            git push origin "v${{ inputs.version }}"
-            echo "✅ Created and pushed tag v${{ inputs.version }}"
-          fi
-          
-          # Check if release already exists
-          if gh release view "v${{ inputs.version }}" >/dev/null 2>&1; then
-            echo "⚠️  Release v${{ inputs.version }} already exists, skipping release creation"
-          else
-            gh release create "v${{ inputs.version }}" \
-              --title "Release v${{ inputs.version }}" \
-              --notes "🚀 Released to PyPI: https://pypi.org/project/leann/${{ inputs.version }}/" \
-              --latest
-            echo "✅ Created GitHub release v${{ inputs.version }}"
-          fi
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -12,6 +12,7 @@ outputs/
 *.idx 
 *.map
 .history/
+scripts/
 lm_eval.egg-info/
 demo/experiment_results/**/*.json
 *.jsonl
@@ -83,6 +84,4 @@ test_*.py
 packages/leann-backend-diskann/third_party/DiskANN/_deps/
 
 *.meta.json
-*.passages.json
-
-batchtest.py
+*.passages.json

.vscode/extensions.json

@@ -0,0 +1,9 @@
+{
+    "recommendations": [
+        "llvm-vs-code-extensions.vscode-clangd",
+        "ms-python.python",
+        "ms-vscode.cmake-tools",
+        "vadimcn.vscode-lldb",
+        "eamodio.gitlens",
+    ]
+}

.vscode/launch.json

@@ -0,0 +1,283 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        // new emdedder
+        {
+            "name": "New Embedder",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "demo/main.py",
+            "console": "integratedTerminal",
+            "args": [
+                "--search",
+                "--use-original",
+                "--domain",
+                "dpr",
+                "--nprobe",
+                "5000",
+                "--load",
+                "flat",
+                "--embedder",
+                "intfloat/multilingual-e5-small"
+            ]
+        }
+        //python /home/ubuntu/Power-RAG/faiss/demo/simple_build.py
+        {
+            "name": "main.py",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "demo/main.py",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+            "args": [
+                "--query",
+                "1000",
+                "--load",
+                "bm25"
+            ]
+        },
+        {
+            "name": "Simple Build",
+            "type": "lldb",
+            "request": "launch",
+            "program": "${workspaceFolder}/.venv/bin/python",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+            "args": [
+                "faiss/demo/simple_build.py"
+            ],
+            "env": {
+                "LD_PRELOAD": "/lib/x86_64-linux-gnu/libmkl_core.so:/lib/x86_64-linux-gnu/libmkl_intel_thread.so:/lib/x86_64-linux-gnu/libmkl_intel_lp64.so:/lib/x86_64-linux-gnu/libiomp5.so"
+            }
+        },
+        //# Fix for Intel MKL error
+        //export LD_PRELOAD=/lib/x86_64-linux-gnu/libmkl_core.so:/lib/x86_64-linux-gnu/libmkl_intel_thread.so:/lib/x86_64-linux-gnu/libmkl_intel_lp64.so:/lib/x86_64-linux-gnu/libiomp5.so
+        //python faiss/demo/build_demo.py
+        {
+            "name": "Build Demo",
+            "type": "lldb",
+            "request": "launch",
+            "program": "${workspaceFolder}/.venv/bin/python",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+            "args": [
+                "faiss/demo/build_demo.py"
+            ],
+            "env": {
+                "LD_PRELOAD": "/lib/x86_64-linux-gnu/libmkl_core.so:/lib/x86_64-linux-gnu/libmkl_intel_thread.so:/lib/x86_64-linux-gnu/libmkl_intel_lp64.so:/lib/x86_64-linux-gnu/libiomp5.so"
+            }
+        },
+        {
+            "name": "DiskANN Serve",
+            "type": "lldb",
+            "request": "launch",
+            "program": "${workspaceFolder}/.venv/bin/python",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+            "args": [
+                "demo/main.py",
+                "--mode",
+                "serve",
+                "--engine",
+                "sglang",
+                "--load-indices",
+                "diskann",
+                "--domain",
+                "rpj_wiki",
+                "--lazy-load",
+                "--recompute-beighbor-embeddings",
+                "--port",
+                "8082",
+                "--diskann-search-memory-maximum",
+                "2",
+                "--diskann-graph",
+                "240",
+                "--search-only"
+            ],
+            "env": {
+                "PYTHONPATH": "${workspaceFolder}/faiss_repo/build/faiss/python:$PYTHONPATH"
+            },
+            "preLaunchTask": "CMake: build",
+        },
+        {
+            "name": "DiskANN Serve MAC",
+            "type": "lldb",
+            "request": "launch",
+            "program": "${workspaceFolder}/.venv/bin/python",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+            "args": [
+                "demo/main.py",
+                "--mode",
+                "serve",
+                "--engine",
+                "ollama",
+                "--load-indices",
+                "diskann",
+                "--domain",
+                "rpj_wiki",
+                "--lazy-load",
+                "--recompute-beighbor-embeddings"
+            ],
+            "preLaunchTask": "CMake: build",
+            "env": {
+                "KMP_DUPLICATE_LIB_OK": "TRUE",
+                "OMP_NUM_THREADS": "1",
+                "MKL_NUM_THREADS": "1",
+                "DYLD_INSERT_LIBRARIES": "/Users/ec2-user/Power-RAG/.venv/lib/python3.10/site-packages/torch/lib/libomp.dylib",
+                "KMP_BLOCKTIME": "0"
+            }
+        },
+        {
+            "name": "Python Debugger: Current File with Arguments",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "ric/main_ric.py",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+            "args": [
+                "--config-name",
+                "${input:configSelection}"
+            ],
+            "justMyCode": false
+        },
+        //python ./demo/validate_equivalence.py sglang
+        {
+            "name": "Validate Equivalence",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "demo/validate_equivalence.py",
+            "console": "integratedTerminal",
+            "args": [
+                "sglang"
+            ],
+        },
+        //python demo/retrieval_demo.py --engine sglang  --skip-embeddings --domain dpr --load-indices flat ivf_flat
+        {
+            "name": "Retrieval Demo",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "demo/retrieval_demo.py",
+            "console": "integratedTerminal",
+            "args": [
+                "--engine",
+                "vllm",
+                "--skip-embeddings",
+                "--domain",
+                "dpr",
+                "--load-indices",
+                // "flat",
+                "ivf_flat"
+            ],
+        },
+        //python demo/retrieval_demo.py --engine sglang  --skip-embeddings --domain dpr  --load-indices  diskann --hnsw-M 64 --hnsw-efConstruction 150 --hnsw-efSearch 128  --hnsw-sq-bits 8 
+        {
+            "name": "Retrieval Demo DiskANN",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "demo/retrieval_demo.py",
+            "console": "integratedTerminal",
+            "args": [
+                "--engine",
+                "sglang",
+                "--skip-embeddings",
+                "--domain",
+                "dpr",
+                "--load-indices",
+                "diskann",
+                "--hnsw-M",
+                "64",
+                "--hnsw-efConstruction",
+                "150",
+                "--hnsw-efSearch",
+                "128",
+                "--hnsw-sq-bits",
+                "8"
+            ],
+        },
+        {
+            "name": "Find Probe",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "find_probe.py",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+        },
+        {
+            "name": "Python: Attach",
+            "type": "debugpy",
+            "request": "attach",
+            "processId": "${command:pickProcess}",
+            "justMyCode": true
+        },
+        {
+            "name": "Edge RAG",
+            "type": "lldb",
+            "request": "launch",
+            "program": "${workspaceFolder}/.venv/bin/python",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+            "args": [
+                "edgerag_demo.py"
+            ],
+            "env": {
+                "LD_PRELOAD": "/lib/x86_64-linux-gnu/libiomp5.so /lib/x86_64-linux-gnu/libmkl_core.so /lib/x86_64-linux-gnu/libmkl_intel_lp64.so /lib/x86_64-linux-gnu/libmkl_intel_thread.so",
+                "MKL_NUM_THREADS": "1",
+                "OMP_NUM_THREADS": "1",
+            }
+        },
+        {
+            "name": "Launch Embedding Server",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "demo/embedding_server.py",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+            "args": [
+                "--domain",
+                "rpj_wiki",
+                "--zmq-port",
+                "5556",
+            ]
+        },
+        {
+            "name": "HNSW Serve",
+            "type": "lldb",
+            "request": "launch",
+            "program": "${workspaceFolder}/.venv/bin/python",
+            "console": "integratedTerminal",
+            "cwd": "${workspaceFolder}",
+            "args": [
+                "demo/main.py",
+                "--domain",
+                "rpj_wiki",
+                "--load",
+                "hnsw",
+                "--mode",
+                "serve",
+                "--search",
+                "--skip-pa",
+                "--recompute",
+                "--hnsw-old"
+            ],
+            "env": {
+                "LD_PRELOAD": "/lib/x86_64-linux-gnu/libmkl_core.so:/lib/x86_64-linux-gnu/libmkl_intel_thread.so:/lib/x86_64-linux-gnu/libmkl_intel_lp64.so:/lib/x86_64-linux-gnu/libiomp5.so"
+            }
+        },
+    ],
+    "inputs": [
+        {
+            "id": "configSelection",
+            "type": "pickString",
+            "description": "Select a configuration",
+            "options": [
+                "example_config",
+                "vllm_gritlm"
+            ],
+            "default": "example_config"
+        }
+    ],
+}

.vscode/settings.json

@@ -0,0 +1,43 @@
+{
+    "python.analysis.extraPaths": [
+        "./sglang_repo/python"
+    ],
+    "cmake.sourceDirectory": "${workspaceFolder}/DiskANN",
+    "cmake.configureArgs": [
+        "-DPYBIND=True",
+        "-DUPDATE_EDITABLE_INSTALL=ON",
+    ],
+    "cmake.environment": {
+        "PATH": "/Users/ec2-user/Power-RAG/.venv/bin:${env:PATH}"
+    },
+    "cmake.buildDirectory": "${workspaceFolder}/build",
+    "files.associations": {
+        "*.tcc": "cpp",
+        "deque": "cpp",
+        "string": "cpp",
+        "unordered_map": "cpp",
+        "vector": "cpp",
+        "map": "cpp",
+        "unordered_set": "cpp",
+        "atomic": "cpp",
+        "inplace_vector": "cpp",
+        "*.ipp": "cpp",
+        "forward_list": "cpp",
+        "list": "cpp",
+        "any": "cpp",
+        "system_error": "cpp",
+        "__hash_table": "cpp",
+        "__split_buffer": "cpp",
+        "__tree": "cpp",
+        "ios": "cpp",
+        "set": "cpp",
+        "__string": "cpp",
+        "string_view": "cpp",
+        "ranges": "cpp",
+        "iosfwd": "cpp"
+    },
+    "lldb.displayFormat": "auto",
+    "lldb.showDisassembly": "auto",
+    "lldb.dereferencePointers": true,
+    "lldb.consoleMode": "commands",
+}

.vscode/tasks.json

@@ -0,0 +1,16 @@
+{
+	"version": "2.0.0",
+	"tasks": [
+		{
+			"type": "cmake",
+			"label": "CMake: build",
+			"command": "build",
+			"targets": [
+				"all"
+			],
+			"group": "build",
+			"problemMatcher": [],
+			"detail": "CMake template build task"
+		}
+	]
+}

README.md

@@ -12,11 +12,11 @@
     The smallest vector index in the world. RAG Everything with LEANN!
 </h2>
 
-LEANN is a revolutionary vector database that democratizes personal AI. Transform your laptop into a powerful RAG system that can index and search through millions of documents while using **97% less storage** than traditional solutions **without accuracy loss**.
+LEANN is a revolutionary vector database that democratizes personal AI. Transform your laptop into a powerful RAG system that can index and search through millions of documents while using **[97% less storage]** than traditional solutions **without accuracy loss**.
 
-LEANN achieves this through *graph-based selective recomputation* with *high-degree preserving pruning*, computing embeddings on-demand instead of storing them all. [Illustration Fig →](#️-architecture--how-it-works) | [Paper →](https://arxiv.org/abs/2506.08276)
+LEANN achieves this through *graph-based selective recomputation* with *high-degree preserving pruning*, computing embeddings on-demand instead of storing them all. [Illustration →](#️-architecture--how-it-works) | [Paper →](https://arxiv.org/abs/2506.08276)
 
-**Ready to RAG Everything?** Transform your laptop into a personal AI assistant that can search your **[file system](#-personal-data-manager-process-any-documents-pdf-txt-md)**, **[emails](#-your-personal-email-secretary-rag-on-apple-mail)**, **[browser history](#-time-machine-for-the-web-rag-your-entire-browser-history)**, **[chat history](#-wechat-detective-unlock-your-golden-memories)**, or external knowledge bases (i.e., 60M documents) - all on your laptop, with zero cloud costs and complete privacy.
+**Ready to RAG Everything?** Transform your laptop into a personal AI assistant that can search your **[file system](#process-any-documents-pdf-txt-md)**, **[emails](#search-your-entire-life)**, **[browser history](#time-machine-for-the-web)**, **[chat history](#wechat-detective)**, or external knowledge bases (i.e., 60M documents) - all on your laptop, with zero cloud costs and complete privacy.
 
 
 
@@ -26,8 +26,9 @@ LEANN achieves this through *graph-based selective recomputation* with *high-deg
   <img src="assets/effects.png" alt="LEANN vs Traditional Vector DB Storage Comparison" width="70%">
 </p>
 
-> **The numbers speak for themselves:** Index 60 million Wikipedia chunks in just 6GB instead of 201GB. From emails to browser history, everything fits on your laptop. [See detailed benchmarks for different applications below ↓](#storage-comparison)
+**The numbers speak for themselves:** Index 60 million Wikipedia articles in just 6GB instead of 201GB. From emails to browser history, everything fits on your laptop. [See detailed benchmarks below ↓](#storage-usage-comparison)
 
+## Why This Matters
 
 🔒 **Privacy:** Your data never leaves your laptop. No OpenAI, no cloud, no "terms of service".
 
@@ -37,8 +38,8 @@ LEANN achieves this through *graph-based selective recomputation* with *high-deg
 
 ✨ **No Accuracy Loss:** Maintain the same search quality as heavyweight solutions while using 97% less storage.
 
-## Installation
-> `pip leann` coming soon!
+## Quick Start in 1 minute
+
 ```bash
 git clone git@github.com:yichuan-w/LEANN.git leann
 cd leann
@@ -47,30 +48,33 @@ git submodule update --init --recursive
 
 **macOS:**
 ```bash
-brew install llvm libomp boost protobuf zeromq pkgconf
+brew install llvm libomp boost protobuf zeromq
+export CC=$(brew --prefix llvm)/bin/clang
+export CXX=$(brew --prefix llvm)/bin/clang++
 
 # Install with HNSW backend (default, recommended for most users)
-# Install uv first if you don't have it:
-# curl -LsSf https://astral.sh/uv/install.sh | sh
-# See: https://docs.astral.sh/uv/getting-started/installation/#installation-methods
-CC=$(brew --prefix llvm)/bin/clang CXX=$(brew --prefix llvm)/bin/clang++ uv sync
+uv sync
+
+# Or add DiskANN backend if you want to test more options
+uv sync --extra diskann
 ```
 
-**Linux:**
+**Linux (Ubuntu/Debian):**
 ```bash
 sudo apt-get install libomp-dev libboost-all-dev protobuf-compiler libabsl-dev libmkl-full-dev libaio-dev libzmq3-dev
 
 # Install with HNSW backend (default, recommended for most users)
 uv sync
+
+# Or add DiskANN backend if you want to test more options
+uv sync --extra diskann
 ```
 
+**Ollama Setup (Optional for Local LLM):**
 
-**Ollama Setup (Recommended for full privacy):**
+*We support both hf-transformers and Ollama for local LLMs. Ollama is recommended for faster performance.*
 
-> *You can skip this installation if you only want to use OpenAI API for generation.*
-
-
-**macOS:**
+*macOS:*
 
 First, [download Ollama for macOS](https://ollama.com/download/mac).
 
@@ -79,7 +83,7 @@ First, [download Ollama for macOS](https://ollama.com/download/mac).
 ollama pull llama3.2:1b
 ```
 
-**Linux:**
+*Linux:*
 ```bash
 # Install Ollama
 curl -fsSL https://ollama.ai/install.sh | sh
@@ -91,78 +95,62 @@ ollama serve &
 ollama pull llama3.2:1b
 ```
 
-## Quick Start in 30s
+You can also replace `llama3.2:1b` to `deepseek-r1:1.5b` or `qwen3:4b` for better performance but higher memory usage.
 
-Our declarative API makes RAG as easy as writing a config file.
-[Try in this ipynb file →](demo.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/yichuan-w/LEANN/blob/main/demo.ipynb)
+## Dead Simple API
+
+Just 3 lines of code. Our declarative API makes RAG as easy as writing a config file:
 
 ```python
-from leann.api import LeannBuilder, LeannSearcher, LeannChat
+from leann.api import LeannBuilder, LeannSearcher
 
-# 1. Build the index (no embeddings stored!)
+# 1. Build index (no embeddings stored!)
 builder = LeannBuilder(backend_name="hnsw")
 builder.add_text("C# is a powerful programming language")
-builder.add_text("Python is a powerful programming language and it is very popular")
-builder.add_text("Machine learning transforms industries")
+builder.add_text("Python is a powerful programming language")
+builder.add_text("Machine learning transforms industries")  
 builder.add_text("Neural networks process complex data")
-builder.add_text("Leann is a great storage saving engine for RAG on your MacBook")
+builder.add_text("Leann is a great storage saving engine for RAG on your macbook")
 builder.build_index("knowledge.leann")
 
 # 2. Search with real-time embeddings
 searcher = LeannSearcher("knowledge.leann")
-results = searcher.search("programming languages", top_k=2)
-
-# 3. Chat with LEANN using retrieved results
-llm_config = {
-    "type": "ollama",
-    "model": "llama3.2:1b"
-}
-
-chat = LeannChat(index_path="knowledge.leann", llm_config=llm_config)
-response = chat.ask(
-    "Compare the two retrieved programming languages and say which one is more popular today.",
-    top_k=2,
-)
+results = searcher.search("C++ programming languages", top_k=2, recompute_beighbor_embeddings=True)
+print(results)
 ```
 
-## RAG on Everything!
+**That's it.** No cloud setup, no API keys, no "fine-tuning". Just your data, your questions, your laptop.
 
-LEANN supports RAG on various data sources including documents (.pdf, .txt, .md), Apple Mail, Google Search History, WeChat, and more.
+[Try the interactive demo →](demo.ipynb)
 
-### 📄 Personal Data Manager: Process Any Documents (.pdf, .txt, .md)!
+## Wild Things You Can Do
 
-Ask questions directly about your personal PDFs, documents, and any directory containing your files!
+LEANN supports RAGing a lot of data sources, like .pdf, .txt, .md, and also supports RAGing your WeChat, Google Search History, and more.
 
-<p align="center">
-  <img src="videos/paper_clear.gif" alt="LEANN Document Search Demo" width="600">
-</p>
+### Process Any Documents (.pdf, .txt, .md)
 
-The example below asks a question about summarizing two papers (uses default data in `examples/data`):
+Above we showed the Python API, while this CLI script demonstrates the same concepts while directly processing PDFs and documents.
 
 ```bash
 # Drop your PDFs, .txt, .md files into examples/data/
 uv run ./examples/main_cli_example.py
-```
 
-```
 # Or use python directly
 source .venv/bin/activate
 python ./examples/main_cli_example.py
 ```
 
+Uses Ollama `qwen3:8b` by default. For other models: `--llm openai --model gpt-4o` (requires `OPENAI_API_KEY` environment variable) or `--llm hf --model Qwen/Qwen3-4B`.
 
+**Works with any text format** - research papers, personal notes, presentations. Built with LlamaIndex for document parsing.
 
-### 📧 Your Personal Email Secretary: RAG on Apple Mail!
-
-<p align="center">
-  <img src="videos/mail_clear.gif" alt="LEANN Email Search Demo" width="600">
-</p>
-
-**Note:** You need to grant full disk access to your terminal/VS Code in System Preferences → Privacy & Security → Full Disk Access.
+### Search Your Entire Life
 ```bash
-python examples/mail_reader_leann.py --query "What's the food I ordered by doordash or Uber eat mostly?"
+python examples/mail_reader_leann.py
+# "What did my boss say about the Christmas party last year?"
+# "Find all emails from my mom about birthday plans"
 ```
-**780K email chunks → 78MB storage** Finally, search your email like you search Google.
+**90K emails → 14MB.** Finally, search your email like you search Google.
 
 <details>
 <summary><strong>📋 Click to expand: Command Examples</strong></summary>
@@ -195,16 +183,13 @@ Once the index is built, you can ask questions like:
 - "Show me emails about travel expenses"
 </details>
 
-### 🔍 Time Machine for the Web: RAG Your Entire Google Browser History!
-
-<p align="center">
-  <img src="videos/google_clear.gif" alt="LEANN Browser History Search Demo" width="600">
-</p>
-
+### Time Machine for the Web  
 ```bash
-python examples/google_history_reader_leann.py --query "Tell me my browser history about machine learning?"
+python examples/google_history_reader_leann.py
+# "What was that AI paper I read last month?"
+# "Show me all the cooking videos I watched"
 ```
-**38K browser entries → 6MB storage.** Your browser history becomes your personal search engine.
+**38K browser entries → 6MB.** Your browser history becomes your personal search engine.
 
 <details>
 <summary><strong>📋 Click to expand: Command Examples</strong></summary>
@@ -253,17 +238,13 @@ Once the index is built, you can ask questions like:
 
 </details>
 
-### 💬 WeChat Detective: Unlock Your Golden Memories!
-
-<p align="center">
-  <img src="videos/wechat_clear.gif" alt="LEANN WeChat Search Demo" width="600">
-</p>
+### WeChat Detective
 
 ```bash
-python examples/wechat_history_reader_leann.py --query "Show me all group chats about weekend plans"
+python examples/wechat_history_reader_leann.py
+# "Show me all group chats about weekend plans"
 ```
-**400K messages → 64MB storage** Search years of chat history in any language.
-
+**400K messages → 64MB.** Search years of chat history in any language.
 
 <details>
 <summary><strong>🔧 Click to expand: Installation Requirements</strong></summary>
@@ -274,13 +255,7 @@ First, you need to install the WeChat exporter:
 sudo packages/wechat-exporter/wechattweak-cli install
 ```
 
-**Troubleshooting:**
-- **Installation issues**: Check the [WeChatTweak-CLI issues page](https://github.com/sunnyyoung/WeChatTweak-CLI/issues/41)
-- **Export errors**: If you encounter the error below, try restarting WeChat
-```
-Failed to export WeChat data. Please ensure WeChat is running and WeChatTweak is installed.
-Failed to find or export WeChat data. Exiting.
-```
+**Troubleshooting**: If you encounter installation issues, check the [WeChatTweak-CLI issues page](https://github.com/sunnyyoung/WeChatTweak-CLI/issues/41).
 </details>
 
 <details>
@@ -315,73 +290,6 @@ Once the index is built, you can ask questions like:
 </details>
 
 
-
-## 🖥️ Command Line Interface
-
-LEANN includes a powerful CLI for document processing and search. Perfect for quick document indexing and interactive chat.
-
-```bash
-# Build an index from documents
-leann build my-docs --docs ./documents
-
-# Search your documents  
-leann search my-docs "machine learning concepts"
-
-# Interactive chat with your documents
-leann ask my-docs --interactive
-
-# List all your indexes
-leann list
-```
-
-**Key CLI features:**
-- Auto-detects document formats (PDF, TXT, MD, DOCX)
-- Smart text chunking with overlap
-- Multiple LLM providers (Ollama, OpenAI, HuggingFace)
-- Organized index storage in `~/.leann/indexes/`
-- Support for advanced search parameters
-
-<details>
-<summary><strong>📋 Click to expand: Complete CLI Reference</strong></summary>
-
-**Build Command:**
-```bash
-leann build INDEX_NAME --docs DIRECTORY [OPTIONS]
-
-Options:
-  --backend {hnsw,diskann}     Backend to use (default: hnsw)
-  --embedding-model MODEL      Embedding model (default: facebook/contriever)
-  --graph-degree N            Graph degree (default: 32)
-  --complexity N              Build complexity (default: 64)
-  --force                     Force rebuild existing index
-  --compact                   Use compact storage (default: true)
-  --recompute                 Enable recomputation (default: true)
-```
-
-**Search Command:**
-```bash
-leann search INDEX_NAME QUERY [OPTIONS]
-
-Options:
-  --top-k N                   Number of results (default: 5)
-  --complexity N              Search complexity (default: 64)
-  --recompute-embeddings      Use recomputation for highest accuracy
-  --pruning-strategy {global,local,proportional}
-```
-
-**Ask Command:**
-```bash
-leann ask INDEX_NAME [OPTIONS]
-
-Options:
-  --llm {ollama,openai,hf}    LLM provider (default: ollama)
-  --model MODEL               Model name (default: qwen3:8b)
-  --interactive              Interactive chat mode
-  --top-k N                  Retrieval count (default: 20)
-```
-
-</details>
-
 ## 🏗️ Architecture & How It Works
 
 <p align="center">
@@ -400,17 +308,18 @@ Options:
 
 ## Benchmarks
 
+Run the comparison yourself:
+```bash
+python examples/compare_faiss_vs_leann.py
+```
 
-📊 **[Simple Example: Compare LEANN vs FAISS →](examples/compare_faiss_vs_leann.py)**
-### Storage Comparison
-
-| System | DPR (2.1M) | Wiki (60M) | Chat (400K) | Email (780K) | Browser (38K) |
-|--------|-------------|------------|-------------|--------------|---------------|
-| Traditional vector database (e.g., FAISS) | 3.8 GB      | 201 GB     | 1.8 GB     | 2.4 GB      | 130 MB        |
-| LEANN  | 324 MB      | 6 GB       | 64 MB       | 79 MB       | 6.4 MB        |
-| Savings| 91%         | 97%        | 97%         | 97%         | 95%           |
-
+| System | Storage | 
+|--------|---------|
+| FAISS HNSW | 5.5 MB |
+| LEANN | 0.5 MB |
+| **Savings** | **91%** |
 
+Same dataset, same hardware, same embedding model. LEANN just works better.
 
 ## Reproduce Our Results
 
@@ -420,7 +329,33 @@ python examples/run_evaluation.py data/indices/dpr/dpr_diskann      # DPR datase
 python examples/run_evaluation.py data/indices/rpj_wiki/rpj_wiki.index  # Wikipedia
 ```
 
-The evaluation script downloads data automatically on first run. The last three results were tested with partial personal data, and you can reproduce them with your own data!
+The evaluation script downloads data automatically on first run.
+
+### Storage Usage Comparison
+
+| System                | DPR (2.1M chunks) | RPJ-wiki (60M chunks) | Chat history (400K messages) | Apple emails (90K messages chunks) |Google Search History (38K entries)
+|-----------------------|------------------|------------------------|-----------------------------|------------------------------|------------------------------|
+| Traditional Vector DB(FAISS) | 3.8 GB           | 201 GB                 | 1.8G                     | 305.8 MB                     |130.4 MB                     |
+| **LEANN**             | **324 MB**       | **6 GB**               | **64 MB**                 | **14.8 MB**                  |**6.4MB**                  |
+| **Reduction**         | **91% smaller**  | **97% smaller**        | **97% smaller**             | **95% smaller**              |**95% smaller**              |
+
+<!-- ### Memory Usage Comparison
+
+| System          j      | DPR(2M docs)     | RPJ-wiki(60M docs)    | Chat history()   |
+| --------------------- | ---------------- | ---------------- | ---------------- |
+| Traditional Vector DB(LLamaindex faiss) | x GB           | x GB            | x GB           |
+| **Leann**       | **xx MB** | **x GB** | **x GB** |
+| **Reduction**   | **x%**  | **x%**  | **x%**  |
+
+### Query Performance of LEANN
+
+| Backend             | Index Size | Query Time | Recall@3 |
+| ------------------- | ---------- | ---------- | --------- |
+| DiskANN             | 1M docs    | xms       | 0.95      |
+| HNSW                | 1M docs    | xms        | 0.95      | -->
+
+*Benchmarks run on Apple M3 Pro 36 GB*
+
 ## 🔬 Paper
 
 If you find Leann useful, please cite:
@@ -439,15 +374,87 @@ If you find Leann useful, please cite:
 }
 ```
 
-## ✨ [Detailed Features →](docs/features.md)
+## ✨ Features
 
-## 🤝 [Contributing →](docs/contributing.md)
+### 🔥 Core Features
+
+- **🔄 Real-time Embeddings** - Eliminate heavy embedding storage with dynamic computation using optimized ZMQ servers and highly optimized search paradigm (overlapping and batching) with highly optimized embedding engine
+- **📈 Scalable Architecture** - Handles millions of documents on consumer hardware; the larger your dataset, the more LEANN can save
+- **🎯 Graph Pruning** - Advanced techniques to minimize the storage overhead of vector search to a limited footprint
+- **🏗️ Pluggable Backends** - DiskANN, HNSW/FAISS with unified API
+
+### 🛠️ Technical Highlights
+- **🔄 Recompute Mode** - Highest accuracy scenarios while eliminating vector storage overhead
+- **⚡ Zero-copy Operations** - Minimize IPC overhead by transferring distances instead of embeddings
+- **🚀 High-throughput Embedding Pipeline** - Optimized batched processing for maximum efficiency
+- **🎯 Two-level Search** - Novel coarse-to-fine search overlap for accelerated query processing (optional)
+- **💾 Memory-mapped Indices** - Fast startup with raw text mapping to reduce memory overhead
+- **🚀 MLX Support** - Ultra-fast recompute/build with quantized embedding models, accelerating building and search ([minimal example](test/build_mlx_index.py))
+
+### 🎨 Developer Experience
+
+- **Simple Python API** - Get started in minutes
+- **Extensible backend system** - Easy to add new algorithms
+- **Comprehensive examples** - From basic usage to production deployment
+
+## 🤝 Contributing
+
+We welcome contributions! Leann is built by the community, for the community.
+
+### Ways to Contribute
+
+- 🐛 **Bug Reports**: Found an issue? Let us know!
+- 💡 **Feature Requests**: Have an idea? We'd love to hear it!
+- 🔧 **Code Contributions**: PRs welcome for all skill levels
+- 📖 **Documentation**: Help make Leann more accessible
+- 🧪 **Benchmarks**: Share your performance results
 
 
-## [FAQ →](docs/faq.md)
+<!-- ## ❓ FAQ
+
+### Common Issues
+
+#### NCCL Topology Error
+
+**Problem**: You encounter `ncclTopoComputePaths` error during document processing:
+
+```
+ncclTopoComputePaths (system=<optimized out>, comm=comm@entry=0x5555a82fa3c0) at graph/paths.cc:688
+```
+
+**Solution**: Set these environment variables before running your script:
+
+```bash
+export NCCL_TOPO_DUMP_FILE=/tmp/nccl_topo.xml
+export NCCL_DEBUG=INFO
+export NCCL_DEBUG_SUBSYS=INIT,GRAPH
+export NCCL_IB_DISABLE=1
+export NCCL_NET_PLUGIN=none
+export NCCL_SOCKET_IFNAME=ens5
+``` -->
+
+## 📈 Roadmap
+
+### 🎯 Q2 2025
+
+- [X] DiskANN backend with MIPS/L2/Cosine support
+- [X] HNSW backend integration
+- [X] Real-time embedding pipeline
+- [X] Memory-efficient graph pruning
+
+### 🚀 Q3 2025
 
 
-## 📈 [Roadmap →](docs/roadmap.md)
+- [ ] Advanced caching strategies
+- [ ] Add contextual-retrieval https://www.anthropic.com/news/contextual-retrieval
+- [ ] Add sleep-time-compute and summarize agent! to summarilze the file on computer!
+- [ ] Add OpenAI recompute API
+
+### 🌟 Q4 2025
+
+- [ ] Integration with LangChain/LlamaIndex
+- [ ] Visual similarity search
+- [ ] Query rewrtiting, rerank and expansion
 
 ## 📄 License
 
@@ -455,7 +462,11 @@ MIT License - see [LICENSE](LICENSE) for details.
 
 ## 🙏 Acknowledgments
 
-This work is done at [**Berkeley Sky Computing Lab**](https://sky.cs.berkeley.edu/)
+- **Microsoft Research** for the DiskANN algorithm
+- **Meta AI** for FAISS and optimization insights
+- **HuggingFace** for the transformer ecosystem
+- **Our amazing contributors** who make this possible
+
 ---
 
 <p align="center">

demo.ipynb

@@ -1,321 +1,35 @@
 {
  "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Quick Start in 30s"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "# install this if you areusing colab\n",
-    "! pip install leann"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Build the index"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "INFO: Registering backend 'hnsw'\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/yichuan/Desktop/code/LEANN/leann/.venv/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
-      "  from .autonotebook import tqdm as notebook_tqdm\n",
-      "INFO:sentence_transformers.SentenceTransformer:Load pretrained SentenceTransformer: facebook/contriever\n",
-      "WARNING:sentence_transformers.SentenceTransformer:No sentence-transformers model found with name facebook/contriever. Creating a new one with mean pooling.\n",
-      "Writing passages: 100%|██████████| 5/5 [00:00<00:00, 27887.66chunk/s]\n",
-      "Batches: 100%|██████████| 1/1 [00:00<00:00, 13.51it/s]\n",
-      "WARNING:leann_backend_hnsw.hnsw_backend:Converting data to float32, shape: (5, 768)\n",
-      "INFO:leann_backend_hnsw.hnsw_backend:INFO: Converting HNSW index to CSR-pruned format...\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "M: 64 for level: 0\n",
-      "Starting conversion: knowledge.index -> knowledge.csr.tmp\n",
-      "[0.00s] Reading Index HNSW header...\n",
-      "[0.00s]   Header read: d=768, ntotal=5\n",
-      "[0.00s] Reading HNSW struct vectors...\n",
-      "  Reading vector (dtype=<class 'numpy.float64'>, fmt='d')... Count=6, Bytes=48\n",
-      "[0.00s]   Read assign_probas (6)\n",
-      "  Reading vector (dtype=<class 'numpy.int32'>, fmt='i')... Count=7, Bytes=28\n",
-      "[0.11s]   Read cum_nneighbor_per_level (7)\n",
-      "  Reading vector (dtype=<class 'numpy.int32'>, fmt='i')... Count=5, Bytes=20\n",
-      "[0.21s]   Read levels (5)\n",
-      "[0.30s]   Probing for compact storage flag...\n",
-      "[0.30s]   Found compact flag: False\n",
-      "[0.30s]   Compact flag is False, reading original format...\n",
-      "[0.30s]   Probing for potential extra byte before non-compact offsets...\n",
-      "[0.30s]   Found and consumed an unexpected 0x00 byte.\n",
-      "  Reading vector (dtype=<class 'numpy.uint64'>, fmt='Q')... Count=6, Bytes=48\n",
-      "[0.30s]   Read offsets (6)\n",
-      "[0.40s]   Attempting to read neighbors vector...\n",
-      "  Reading vector (dtype=<class 'numpy.int32'>, fmt='i')... Count=320, Bytes=1280\n",
-      "[0.40s]   Read neighbors (320)\n",
-      "[0.50s]   Read scalar params (ep=4, max_lvl=0)\n",
-      "[0.50s] Checking for storage data...\n",
-      "[0.50s]   Found storage fourcc: 49467849.\n",
-      "[0.50s] Converting to CSR format...\n",
-      "[0.50s]   Conversion loop finished.                        \n",
-      "[0.50s] Running validation checks...\n",
-      "    Checking total valid neighbor count...\n",
-      "    OK: Total valid neighbors = 20\n",
-      "    Checking final pointer indices...\n",
-      "    OK: Final pointers match data size.\n",
-      "[0.50s] Deleting original neighbors and offsets arrays...\n",
-      "    CSR Stats: |data|=20, |level_ptr|=10\n",
-      "[0.59s] Writing CSR HNSW graph data in FAISS-compatible order...\n",
-      "   Pruning embeddings: Writing NULL storage marker.\n",
-      "[0.69s] Conversion complete.\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "INFO:leann_backend_hnsw.hnsw_backend:✅ CSR conversion successful.\n",
-      "INFO:leann_backend_hnsw.hnsw_backend:INFO: Replaced original index with CSR-pruned version at 'knowledge.index'\n"
-     ]
-    }
-   ],
-   "source": [
-    "from leann.api import LeannBuilder\n",
-    "\n",
+    "from leann.api import LeannBuilder, LeannSearcher, LeannChat\n",
+    "# 1. Build index (no embeddings stored!)\n",
     "builder = LeannBuilder(backend_name=\"hnsw\")\n",
-    "builder.add_text(\"C# is a powerful programming language and it is good at game development\")\n",
-    "builder.add_text(\"Python is a powerful programming language and it is good at machine learning tasks\")\n",
-    "builder.add_text(\"Machine learning transforms industries\")\n",
+    "builder.add_text(\"C# is a powerful programming language but it is not very popular\")\n",
+    "builder.add_text(\"Python is a powerful programming language and it is very popular\")\n",
+    "builder.add_text(\"Machine learning transforms industries\")  \n",
     "builder.add_text(\"Neural networks process complex data\")\n",
-    "builder.add_text(\"Leann is a great storage saving engine for RAG on your MacBook\")\n",
-    "builder.build_index(\"knowledge.leann\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Search with real-time embeddings"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "INFO:leann.api:🔍 LeannSearcher.search() called:\n",
-      "INFO:leann.api:  Query: 'programming languages'\n",
-      "INFO:leann.api:  Top_k: 2\n",
-      "INFO:leann.api:  Additional kwargs: {}\n",
-      "INFO:leann.embedding_server_manager:Port 5557 has incompatible server, trying next port...\n",
-      "INFO:leann.embedding_server_manager:Port 5558 has incompatible server, trying next port...\n",
-      "INFO:leann.embedding_server_manager:Port 5559 has incompatible server, trying next port...\n",
-      "INFO:leann.embedding_server_manager:Using port 5560 instead of 5557\n",
-      "INFO:leann.embedding_server_manager:Starting embedding server on port 5560...\n",
-      "INFO:leann.embedding_server_manager:Command: /Users/yichuan/Desktop/code/LEANN/leann/.venv/bin/python -m leann_backend_hnsw.hnsw_embedding_server --zmq-port 5560 --model-name facebook/contriever --passages-file knowledge.leann.meta.json\n",
-      "huggingface/tokenizers: The current process just got forked, after parallelism has already been used. Disabling parallelism to avoid deadlocks...\n",
-      "To disable this warning, you can either:\n",
-      "\t- Avoid using `tokenizers` before the fork if possible\n",
-      "\t- Explicitly set the environment variable TOKENIZERS_PARALLELISM=(true | false)\n",
-      "INFO:leann.embedding_server_manager:Server process started with PID: 4574\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[read_HNSW - CSR NL v4] Reading metadata & CSR indices (manual offset)...\n",
-      "[read_HNSW NL v4] Read levels vector, size: 5\n",
-      "[read_HNSW NL v4] Reading Compact Storage format indices...\n",
-      "[read_HNSW NL v4] Read compact_level_ptr, size: 10\n",
-      "[read_HNSW NL v4] Read compact_node_offsets, size: 6\n",
-      "[read_HNSW NL v4] Read entry_point: 4, max_level: 0\n",
-      "[read_HNSW NL v4] Read storage fourcc: 0x6c6c756e\n",
-      "[read_HNSW NL v4 FIX] Detected FileIOReader. Neighbors size field offset: 326\n",
-      "[read_HNSW NL v4] Reading neighbors data into memory.\n",
-      "[read_HNSW NL v4] Read neighbors data, size: 20\n",
-      "[read_HNSW NL v4] Finished reading metadata and CSR indices.\n",
-      "INFO: Skipping external storage loading, since is_recompute is true.\n",
-      "INFO: Registering backend 'hnsw'\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "INFO:leann.embedding_server_manager:Embedding server is ready!\n",
-      "INFO:leann.api:  Launching server time: 1.078078269958496 seconds\n",
-      "INFO:leann.embedding_server_manager:Existing server process (PID 4574) is compatible\n",
-      "INFO:sentence_transformers.SentenceTransformer:Load pretrained SentenceTransformer: facebook/contriever\n",
-      "WARNING:sentence_transformers.SentenceTransformer:No sentence-transformers model found with name facebook/contriever. Creating a new one with mean pooling.\n",
-      "INFO:leann.api:  Generated embedding shape: (1, 768)\n",
-      "INFO:leann.api:  Embedding time: 2.9307072162628174 seconds\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "ZmqDistanceComputer initialized: d=768, metric=0\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "INFO:leann.api:  Search time: 0.27327895164489746 seconds\n",
-      "INFO:leann.api:  Backend returned: labels=2 results\n",
-      "INFO:leann.api:  Processing 2 passage IDs:\n",
-      "INFO:leann.api:    1. passage_id='0' -> SUCCESS: C# is a powerful programming language and it is good at game development...\n",
-      "INFO:leann.api:    2. passage_id='1' -> SUCCESS: Python is a powerful programming language and it is good at machine learning tasks...\n",
-      "INFO:leann.api:  Final enriched results: 2 passages\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "[SearchResult(id='0', score=np.float32(0.9874103), text='C# is a powerful programming language and it is good at game development', metadata={}),\n",
-       " SearchResult(id='1', score=np.float32(0.8922168), text='Python is a powerful programming language and it is good at machine learning tasks', metadata={})]"
-      ]
-     },
-     "execution_count": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "from leann.api import LeannSearcher\n",
-    "\n",
+    "builder.add_text(\"Leann is a great storage saving engine for RAG on your macbook\")\n",
+    "builder.build_index(\"knowledge.leann\")\n",
+    "# 2. Search with real-time embeddings\n",
     "searcher = LeannSearcher(\"knowledge.leann\")\n",
-    "results = searcher.search(\"programming languages\", top_k=2)\n",
-    "results"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Chat with LEANN using retrieved results"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "INFO:leann.chat:Attempting to create LLM of type='hf' with model='Qwen/Qwen3-0.6B'\n",
-      "INFO:leann.chat:Initializing HFChat with model='Qwen/Qwen3-0.6B'\n",
-      "INFO:leann.chat:MPS is available. Using Apple Silicon GPU.\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[read_HNSW - CSR NL v4] Reading metadata & CSR indices (manual offset)...\n",
-      "[read_HNSW NL v4] Read levels vector, size: 5\n",
-      "[read_HNSW NL v4] Reading Compact Storage format indices...\n",
-      "[read_HNSW NL v4] Read compact_level_ptr, size: 10\n",
-      "[read_HNSW NL v4] Read compact_node_offsets, size: 6\n",
-      "[read_HNSW NL v4] Read entry_point: 4, max_level: 0\n",
-      "[read_HNSW NL v4] Read storage fourcc: 0x6c6c756e\n",
-      "[read_HNSW NL v4 FIX] Detected FileIOReader. Neighbors size field offset: 326\n",
-      "[read_HNSW NL v4] Reading neighbors data into memory.\n",
-      "[read_HNSW NL v4] Read neighbors data, size: 20\n",
-      "[read_HNSW NL v4] Finished reading metadata and CSR indices.\n",
-      "INFO: Skipping external storage loading, since is_recompute is true.\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "INFO:leann.api:🔍 LeannSearcher.search() called:\n",
-      "INFO:leann.api:  Query: 'Compare the two retrieved programming languages and tell me their advantages.'\n",
-      "INFO:leann.api:  Top_k: 2\n",
-      "INFO:leann.api:  Additional kwargs: {}\n",
-      "INFO:leann.embedding_server_manager:Port 5557 has incompatible server, trying next port...\n",
-      "INFO:leann.embedding_server_manager:Port 5558 has incompatible server, trying next port...\n",
-      "INFO:leann.embedding_server_manager:Port 5559 has incompatible server, trying next port...\n",
-      "INFO:leann.embedding_server_manager:Found compatible server on port 5560\n",
-      "INFO:leann.embedding_server_manager:Using existing compatible server on port 5560\n",
-      "INFO:leann.api:  Launching server time: 0.04932403564453125 seconds\n",
-      "INFO:leann.embedding_server_manager:Found compatible server on port 5560\n",
-      "INFO:leann.embedding_server_manager:Using existing compatible server on port 5560\n",
-      "INFO:leann.api:  Generated embedding shape: (1, 768)\n",
-      "INFO:leann.api:  Embedding time: 0.06902289390563965 seconds\n",
-      "INFO:leann.api:  Search time: 0.026793241500854492 seconds\n",
-      "INFO:leann.api:  Backend returned: labels=2 results\n",
-      "INFO:leann.api:  Processing 2 passage IDs:\n",
-      "INFO:leann.api:    1. passage_id='0' -> SUCCESS: C# is a powerful programming language and it is good at game development...\n",
-      "INFO:leann.api:    2. passage_id='1' -> SUCCESS: Python is a powerful programming language and it is good at machine learning tasks...\n",
-      "INFO:leann.api:  Final enriched results: 2 passages\n",
-      "INFO:leann.chat:Generating with HuggingFace model, config: {'max_new_tokens': 128, 'temperature': 0.7, 'top_p': 0.9, 'do_sample': True, 'pad_token_id': 151645, 'eos_token_id': 151645}\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "ZmqDistanceComputer initialized: d=768, metric=0\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "\"<think>\\n\\n</think>\\n\\nBased on the context provided, here's a comparison of the two retrieved programming languages:\\n\\n**C#** is known for being a powerful programming language and is well-suited for game development. It is often used in game development and is popular among developers working on Windows applications.\\n\\n**Python**, on the other hand, is also a powerful language and is well-suited for machine learning tasks. It is widely used for data analysis, scientific computing, and other applications that require handling large datasets or performing complex calculations.\\n\\n**Advantages**:\\n- C#: Strong for game development and cross-platform compatibility.\\n- Python: Strong for\""
-      ]
-     },
-     "execution_count": 8,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "from leann.api import LeannChat\n",
+    "results = searcher.search(\"programming languages\", top_k=2, recompute_beighbor_embeddings=True)\n",
+    "print(results)\n",
     "\n",
-    "llm_config = {\n",
-    "    \"type\": \"hf\",\n",
-    "    \"model\": \"Qwen/Qwen3-0.6B\",\n",
-    "}\n",
+    "llm_config = {\"type\": \"ollama\", \"model\": \"qwen3:8b\"}\n",
     "\n",
     "chat = LeannChat(index_path=\"knowledge.leann\", llm_config=llm_config)\n",
+    "\n",
     "response = chat.ask(\n",
-    "    \"Compare the two retrieved programming languages and tell me their advantages.\",\n",
+    "    \"Compare the two retrieved programming languages and say which one is more popular today. Respond in a single well-formed sentence.\",\n",
     "    top_k=2,\n",
-    "    llm_kwargs={\"max_tokens\": 128}\n",
+    "    recompute_beighbor_embeddings=True,\n",
     ")\n",
-    "response"
+    "print(response)"
    ]
   }
  ],

docs/RELEASE.md

@@ -1,22 +0,0 @@
-# Release Guide
-
-## Setup (One-time)
-
-Add `PYPI_API_TOKEN` to GitHub Secrets:
-1. Get token: https://pypi.org/manage/account/token/
-2. Add to secrets: Settings → Secrets → Actions → `PYPI_API_TOKEN`
-
-## Release (One-click)
-
-1. Go to: https://github.com/yichuan-w/LEANN/actions/workflows/release-manual.yml
-2. Click "Run workflow"
-3. Enter version: `0.1.2`
-4. Click green "Run workflow" button
-
-That's it! The workflow will automatically:
-- ✅ Update version in all packages
-- ✅ Build all packages
-- ✅ Publish to PyPI
-- ✅ Create GitHub tag and release
-
-Check progress: https://github.com/yichuan-w/LEANN/actions 

docs/contributing.md

@@ -1,11 +0,0 @@
-# 🤝 Contributing
-
-We welcome contributions! Leann is built by the community, for the community.
-
-## Ways to Contribute
-
-- 🐛 **Bug Reports**: Found an issue? Let us know!
-- 💡 **Feature Requests**: Have an idea? We'd love to hear it!
-- 🔧 **Code Contributions**: PRs welcome for all skill levels
-- 📖 **Documentation**: Help make Leann more accessible
-- 🧪 **Benchmarks**: Share your performance results 

docs/faq.md

@@ -1,10 +0,0 @@
-# FAQ
-
-## 1. My building time seems long
-
-You can speed up the process by using a lightweight embedding model. Add this to your arguments:
-
-```bash
---embedding-model sentence-transformers/all-MiniLM-L6-v2
-```
-**Model sizes:** `all-MiniLM-L6-v2` (30M parameters), `facebook/contriever` (~100M parameters), `Qwen3-0.6B` (600M parameters) 

docs/features.md

@@ -1,22 +0,0 @@
-# ✨ Detailed Features
-
-## 🔥 Core Features
-
-- **🔄 Real-time Embeddings** - Eliminate heavy embedding storage with dynamic computation using optimized ZMQ servers and highly optimized search paradigm (overlapping and batching) with highly optimized embedding engine
-- **📈 Scalable Architecture** - Handles millions of documents on consumer hardware; the larger your dataset, the more LEANN can save
-- **🎯 Graph Pruning** - Advanced techniques to minimize the storage overhead of vector search to a limited footprint
-- **🏗️ Pluggable Backends** - DiskANN, HNSW/FAISS with unified API
-
-## 🛠️ Technical Highlights
-- **🔄 Recompute Mode** - Highest accuracy scenarios while eliminating vector storage overhead
-- **⚡ Zero-copy Operations** - Minimize IPC overhead by transferring distances instead of embeddings
-- **🚀 High-throughput Embedding Pipeline** - Optimized batched processing for maximum efficiency
-- **🎯 Two-level Search** - Novel coarse-to-fine search overlap for accelerated query processing (optional)
-- **💾 Memory-mapped Indices** - Fast startup with raw text mapping to reduce memory overhead
-- **🚀 MLX Support** - Ultra-fast recompute/build with quantized embedding models, accelerating building and search ([minimal example](test/build_mlx_index.py))
-
-## 🎨 Developer Experience
-
-- **Simple Python API** - Get started in minutes
-- **Extensible backend system** - Easy to add new algorithms
-- **Comprehensive examples** - From basic usage to production deployment 

docs/roadmap.md

@@ -1,21 +0,0 @@
-# 📈 Roadmap
-
-## 🎯 Q2 2025
-
-- [X] DiskANN backend with MIPS/L2/Cosine support
-- [X] HNSW backend integration
-- [X] Real-time embedding pipeline
-- [X] Memory-efficient graph pruning
-
-## 🚀 Q3 2025
-
-- [ ] Advanced caching strategies
-- [ ] Add contextual-retrieval https://www.anthropic.com/news/contextual-retrieval
-- [ ] Add sleep-time-compute and summarize agent! to summarilze the file on computer!
-- [ ] Add OpenAI recompute API
-
-## 🌟 Q4 2025
-
-- [ ] Integration with LangChain/LlamaIndex
-- [ ] Visual similarity search
-- [ ] Query rewrtiting, rerank and expansion 

examples/compare_faiss_vs_leann.py

@@ -135,7 +135,6 @@ def test_leann_hnsw():
         nodes = node_parser.get_nodes_from_documents([doc])
         for node in nodes:
             all_texts.append(node.get_content())
-    print(f"Total number of chunks: {len(all_texts)}")
 
     tracker.checkpoint("After text chunking")
 

examples/email_data/LEANN_email_reader.py

@@ -96,12 +96,14 @@ class EmlxReader(BaseReader):
                                 
                                 # Create document content with metadata embedded in text
                                 doc_content = f"""
-[File]: {filename}
-[From]: {from_addr}
-[To]: {to_addr}
-[Subject]: {subject}
-[Date]: {date}
-[EMAIL BODY Start]:
+[EMAIL METADATA]
+File: {filename}
+From: {from_addr}
+To: {to_addr}
+Subject: {subject}
+Date: {date}
+[END METADATA]
+
 {body}
 """
                                 

examples/faiss_only.py

@@ -37,7 +37,7 @@ def main():
         import faiss
     except ImportError:
         print("Faiss is not installed.")
-        print("Please install it with `uv pip install faiss-cpu` and you can  then run this script again")
+        print("Please install it with `uv pip install faiss-cpu`")
         sys.exit(1)
 
     from llama_index.core import (

examples/google_history_reader_leann.py

@@ -65,14 +65,12 @@ def create_leann_index_from_multiple_chrome_profiles(profile_dirs: List[Path], i
         
         if not all_documents:
             print("No documents loaded from any source. Exiting.")
-            # highlight info that you need to close all chrome browser before running this script and high light the instruction!!
-            print("\033[91mYou need to close or quit all chrome browser before running this script\033[0m")
             return None
         
         print(f"\nTotal loaded {len(all_documents)} history documents from {len(profile_dirs)} profiles")
         
         # Create text splitter with 256 chunk size
-        text_splitter = SentenceSplitter(chunk_size=256, chunk_overlap=128)
+        text_splitter = SentenceSplitter(chunk_size=256, chunk_overlap=25)
         
         # Convert Documents to text strings and chunk them
         all_texts = []
@@ -80,9 +78,7 @@ def create_leann_index_from_multiple_chrome_profiles(profile_dirs: List[Path], i
             # Split the document into chunks
             nodes = text_splitter.get_nodes_from_documents([doc])
             for node in nodes:
-                text = node.get_content()
-                # text = '[Title] ' + doc.metadata["title"] + '\n' + text
-                all_texts.append(text)
+                all_texts.append(node.get_content())
         
         print(f"Created {len(all_texts)} text chunks from {len(all_documents)} documents")
         
@@ -222,15 +218,14 @@ async def query_leann_index(index_path: str, query: str):
             "max_tokens": 1000
         }
     )
-
-    print(f"Leann chat response: \033[36m{chat_response}\033[0m")
+    print(f"Leann: {chat_response}")
 
 async def main():
     # Parse command line arguments
     parser = argparse.ArgumentParser(description='LEANN Chrome History Reader - Create and query browser history index')
     parser.add_argument('--chrome-profile', type=str, default=DEFAULT_CHROME_PROFILE,
                        help=f'Path to Chrome profile directory (default: {DEFAULT_CHROME_PROFILE}), usually you dont need to change this')
-    parser.add_argument('--index-dir', type=str, default="./google_history_index",
+    parser.add_argument('--index-dir', type=str, default="./chrome_history_index_leann_test",
                        help='Directory to store the LEANN index (default: ./chrome_history_index_leann_test)')
     parser.add_argument('--max-entries', type=int, default=1000,
                        help='Maximum number of history entries to process (default: 1000)')

examples/history_data/history.py

@@ -74,17 +74,22 @@ class ChromeHistoryReader(BaseReader):
                 
                 # Create document content with metadata embedded in text
                 doc_content = f"""
-[Title]: {title}
-[URL of the page]: {url}
-[Last visited time]: {last_visit}
-[Visit times]: {visit_count}
-[Typed times]: {typed_count}
+[BROWSING HISTORY METADATA]
+URL: {url}
+Title: {title}
+Last Visit: {last_visit}
+Visit Count: {visit_count}
+Typed Count: {typed_count}
+Hidden: {hidden}
+[END METADATA]
+
+Title: {title}
+URL: {url}
+Last visited: {last_visit}
 """
                 
                 # Create document with embedded metadata
-                doc = Document(text=doc_content, metadata={ "title": title[0:150]})
-                # if len(title) > 150:
-                #     print(f"Title is too long: {title}")
+                doc = Document(text=doc_content, metadata={})
                 docs.append(doc)
                 count += 1
             

examples/history_data/wechat_history.py

@@ -335,15 +335,14 @@ class WeChatHistoryReader(BaseReader):
             if create_time:
                 try:
                     timestamp = datetime.fromtimestamp(create_time)
-                    # change to YYYY-MM-DD HH:MM:SS
-                    time_str = timestamp.strftime('%Y-%m-%d %H:%M:%S')
+                    time_str = timestamp.strftime('%H:%M:%S')
                 except:
                     time_str = str(create_time)
             else:
                 time_str = "Unknown"
             
-            sender = "[Me]" if is_sent_from_self else "[Contact]"
-            message_parts.append(f"({time_str}) {sender}: {readable_text}")
+            sender = "Me" if is_sent_from_self else "Contact"
+            message_parts.append(f"[{time_str}] {sender}: {readable_text}")
         
         concatenated_text = "\n".join(message_parts)
         
@@ -355,11 +354,13 @@ Messages ({len(messages)} messages, {message_group['total_length']} chars):
 
 {concatenated_text}
 """
-        # TODO @yichuan give better format and rich info here!    
+        
         doc_content = f"""
+Contact: {contact_name}
+
 {concatenated_text}
 """
-        return doc_content, contact_name
+        return doc_content
     
     def load_data(self, input_dir: str = None, **load_kwargs: Any) -> List[Document]:
         """
@@ -440,8 +441,8 @@ Messages ({len(messages)} messages, {message_group['total_length']} chars):
                             if count >= max_count and max_count > 0:
                                 break
                             
-                            doc_content, contact_name  = self._create_concatenated_content(message_group, contact_name)
-                            doc = Document(text=doc_content, metadata={"contact_name": contact_name})
+                            doc_content = self._create_concatenated_content(message_group, contact_name)
+                            doc = Document(text=doc_content, metadata={})
                             docs.append(doc)
                             count += 1
                         

examples/mail_reader_leann.py

@@ -22,7 +22,7 @@ def get_mail_path():
     return os.path.join(home_dir, "Library", "Mail")
 
 # Default mail path for macOS
-DEFAULT_MAIL_PATH = "/Users/yichuan/Library/Mail/V10/0FCA0879-FD8C-4B7E-83BF-FDDA930791C5/[Gmail].mbox/All Mail.mbox/78BA5BE1-8819-4F9A-9613-EB63772F1DD0/Data"
+# DEFAULT_MAIL_PATH = "/Users/yichuan/Library/Mail/V10/0FCA0879-FD8C-4B7E-83BF-FDDA930791C5/[Gmail].mbox/All Mail.mbox/78BA5BE1-8819-4F9A-9613-EB63772F1DD0/Data"
 
 def create_leann_index_from_multiple_sources(messages_dirs: List[Path], index_path: str = "mail_index.leann", max_count: int = -1, include_html: bool = False, embedding_model: str = "facebook/contriever"):
     """
@@ -74,7 +74,7 @@ def create_leann_index_from_multiple_sources(messages_dirs: List[Path], index_pa
             print("No documents loaded from any source. Exiting.")
             return None
         
-        print(f"\nTotal loaded {len(all_documents)} email documents from {len(messages_dirs)} directories and starting to split them into chunks")
+        print(f"\nTotal loaded {len(all_documents)} email documents from {len(messages_dirs)} directories")
         
         # Create text splitter with 256 chunk size
         text_splitter = SentenceSplitter(chunk_size=256, chunk_overlap=25)
@@ -85,11 +85,9 @@ def create_leann_index_from_multiple_sources(messages_dirs: List[Path], index_pa
             # Split the document into chunks
             nodes = text_splitter.get_nodes_from_documents([doc])
             for node in nodes:
-                text = node.get_content()
-                # text = '[subject] ' + doc.metadata["subject"] + '\n' + text
-                all_texts.append(text)
+                all_texts.append(node.get_content())
         
-        print(f"Finished splitting {len(all_documents)} documents into {len(all_texts)} text chunks")
+        print(f"Created {len(all_texts)} text chunks from {len(all_documents)} documents")
         
         # Create LEANN index directory
 
@@ -158,7 +156,7 @@ def create_leann_index(mail_path: str, index_path: str = "mail_index.leann", max
         print(f"Loaded {len(documents)} email documents")
         
         # Create text splitter with 256 chunk size
-        text_splitter = SentenceSplitter(chunk_size=256, chunk_overlap=128)
+        text_splitter = SentenceSplitter(chunk_size=256, chunk_overlap=25)
         
         # Convert Documents to text strings and chunk them
         all_texts = []
@@ -218,22 +216,22 @@ async def query_leann_index(index_path: str, query: str):
     start_time = time.time()
     chat_response = chat.ask(
         query, 
-        top_k=20, 
+        top_k=10, 
         recompute_beighbor_embeddings=True,
-        complexity=32,
+        complexity=12,
         beam_width=1,
+        
     )
     end_time = time.time()
-    # print(f"Time taken: {end_time - start_time} seconds")
-    # highlight the answer
-    print(f"Leann chat response: \033[36m{chat_response}\033[0m")
+    print(f"Time taken: {end_time - start_time} seconds")
+    print(f"Leann: {chat_response}")
 
 async def main():
     # Parse command line arguments
     parser = argparse.ArgumentParser(description='LEANN Mail Reader - Create and query email index')
     # Remove --mail-path argument and auto-detect all Messages directories
     # Remove DEFAULT_MAIL_PATH
-    parser.add_argument('--index-dir', type=str, default="./mail_index",
+    parser.add_argument('--index-dir', type=str, default="./mail_index_leann_raw_text_all_dicts",
                        help='Directory to store the LEANN index (default: ./mail_index_leann_raw_text_all_dicts)')
     parser.add_argument('--max-emails', type=int, default=1000,
                        help='Maximum number of emails to process (-1 means all)')
@@ -253,9 +251,6 @@ async def main():
     mail_path = get_mail_path()
     print(f"Searching for email data in: {mail_path}")
     messages_dirs = find_all_messages_directories(mail_path)
-    # messages_dirs = find_all_messages_directories(DEFAULT_MAIL_PATH)
-    # messages_dirs = [DEFAULT_MAIL_PATH]
-    # messages_dirs = messages_dirs[:1]
     
     print('len(messages_dirs): ', len(messages_dirs))
     

examples/main_cli_example.py

@@ -1,40 +1,40 @@
 import argparse
-from llama_index.core import SimpleDirectoryReader
+from llama_index.core import SimpleDirectoryReader, Settings
 from llama_index.core.node_parser import SentenceSplitter
 import asyncio
 import dotenv
-from leann.api import LeannBuilder, LeannChat
+from leann.api import LeannBuilder, LeannSearcher, LeannChat
+import shutil
 from pathlib import Path
 
 dotenv.load_dotenv()
 
+node_parser = SentenceSplitter(
+    chunk_size=256, chunk_overlap=128, separator=" ", paragraph_separator="\n\n"
+)
+print("Loading documents...")
+documents = SimpleDirectoryReader(
+    "examples/data",
+    recursive=True,
+    encoding="utf-8",
+    required_exts=[".pdf", ".txt", ".md"],
+).load_data(show_progress=True)
+print("Documents loaded.")
+all_texts = []
+for doc in documents:
+    nodes = node_parser.get_nodes_from_documents([doc])
+    for node in nodes:
+        all_texts.append(node.get_content())
+
 
 async def main(args):
     INDEX_DIR = Path(args.index_dir)
     INDEX_PATH = str(INDEX_DIR / "pdf_documents.leann")
 
     if not INDEX_DIR.exists():
-        node_parser = SentenceSplitter(
-            chunk_size=256, chunk_overlap=128, separator=" ", paragraph_separator="\n\n"
-        )
+        print(f"--- Index directory not found, building new index ---")
 
-        print("Loading documents...")
-        documents = SimpleDirectoryReader(
-            args.data_dir,
-            recursive=True,
-            encoding="utf-8",
-            required_exts=[".pdf", ".txt", ".md"],
-        ).load_data(show_progress=True)
-        print("Documents loaded.")
-        all_texts = []
-        for doc in documents:
-            nodes = node_parser.get_nodes_from_documents([doc])
-            for node in nodes:
-                all_texts.append(node.get_content())
-
-        print("--- Index directory not found, building new index ---")
-
-        print("\n[PHASE 1] Building Leann index...")
+        print(f"\n[PHASE 1] Building Leann index...")
 
         # Use HNSW backend for better macOS compatibility
         builder = LeannBuilder(
@@ -58,19 +58,22 @@ async def main(args):
 
     print(f"\n[PHASE 2] Starting Leann chat session...")
 
-    llm_config = {"type": "hf", "model": "Qwen/Qwen3-4B"}
+    # llm_config = {"type": "hf", "model": "Qwen/Qwen3-4B"}
     llm_config = {"type": "ollama", "model": "qwen3:8b"}
-    llm_config = {"type": "openai", "model": "gpt-4o"}
 
     chat = LeannChat(index_path=INDEX_PATH, llm_config=llm_config)
+
+    query = "Based on the paper, what are the main techniques LEANN explores to reduce the storage overhead and DLPM explore to achieve Fairness and Efiiciency trade-off?"
+
     # query = (
     #     "什么是盘古大模型以及盘古开发过程中遇到了什么阴暗面，任务令一般在什么城市颁发"
     # )
-    query = args.query
 
     print(f"You: {query}")
-    chat_response = chat.ask(query, top_k=20, recompute_embeddings=True, complexity=32)
-    print(f"Leann chat response: \033[36m{chat_response}\033[0m")
+    chat_response = chat.ask(
+        query, top_k=20, recompute_beighbor_embeddings=True, complexity=32
+    )
+    print(f"Leann: {chat_response}")
 
 
 if __name__ == "__main__":
@@ -102,18 +105,6 @@ if __name__ == "__main__":
         default="./test_doc_files",
         help="Directory where the Leann index will be stored.",
     )
-    parser.add_argument(
-        "--data-dir",
-        type=str,
-        default="examples/data",
-        help="Directory containing documents to index (PDF, TXT, MD files).",
-    )
-    parser.add_argument(
-        "--query",
-        type=str,
-        default="Based on the paper, what are the main techniques LEANN explores to reduce the storage overhead and DLPM explore to achieve Fairness and Efiiciency trade-off?",
-        help="The query to ask the Leann chat system.",
-    )
     args = parser.parse_args()
 
     asyncio.run(main(args))

examples/wechat_history_reader_leann.py

@@ -52,7 +52,7 @@ def create_leann_index_from_multiple_wechat_exports(
                 documents = reader.load_data(
                     wechat_export_dir=str(export_dir),
                     max_count=max_count,
-                    concatenate_messages=True,  # Disable concatenation - one message per document
+                    concatenate_messages=False,  # Disable concatenation - one message per document
                 )
                 if documents:
                     print(f"Loaded {len(documents)} chat documents from {export_dir}")
@@ -74,11 +74,11 @@ def create_leann_index_from_multiple_wechat_exports(
             return None
 
         print(
-            f"\nTotal loaded {len(all_documents)} chat documents from {len(export_dirs)} exports and starting to split them into chunks"
+            f"\nTotal loaded {len(all_documents)} chat documents from {len(export_dirs)} exports"
         )
 
         # Create text splitter with 256 chunk size
-        text_splitter = SentenceSplitter(chunk_size=192, chunk_overlap=64)
+        text_splitter = SentenceSplitter(chunk_size=128, chunk_overlap=64)
 
         # Convert Documents to text strings and chunk them
         all_texts = []
@@ -86,11 +86,10 @@ def create_leann_index_from_multiple_wechat_exports(
             # Split the document into chunks
             nodes = text_splitter.get_nodes_from_documents([doc])
             for node in nodes:
-                text = '[Contact] means the message is from: ' + doc.metadata["contact_name"] + '\n' + node.get_content()
-                all_texts.append(text)
+                all_texts.append(node.get_content())
 
         print(
-            f"Finished splitting {len(all_documents)} documents into {len(all_texts)} text chunks"
+            f"Created {len(all_texts)} text chunks from {len(all_documents)} documents"
         )
 
         # Create LEANN index directory
@@ -225,7 +224,7 @@ async def query_leann_index(index_path: str, query: str):
         query,
         top_k=20,
         recompute_beighbor_embeddings=True,
-        complexity=16,
+        complexity=128,
         beam_width=1,
         llm_config={
             "type": "openai",
@@ -234,7 +233,7 @@ async def query_leann_index(index_path: str, query: str):
         },
         llm_kwargs={"temperature": 0.0, "max_tokens": 1000},
     )
-    print(f"Leann chat response: \033[36m{chat_response}\033[0m")
+    print(f"Leann: {chat_response}")
 
 
 async def main():
@@ -253,13 +252,13 @@ async def main():
     parser.add_argument(
         "--index-dir",
         type=str,
-        default="./wechat_history_magic_test_11Debug_new",
+        default="./wechat_history_june19_test",
         help="Directory to store the LEANN index (default: ./wechat_history_index_leann_test)",
     )
     parser.add_argument(
         "--max-entries",
         type=int,
-        default=50,
+        default=5000,
         help="Maximum number of chat entries to process (default: 5000)",
     )
     parser.add_argument(

packages/leann-backend-diskann/leann_backend_diskann/diskann_backend.py

@@ -1,12 +1,10 @@
 import numpy as np
 import os
 import struct
-import sys
 from pathlib import Path
-from typing import Dict, Any, List, Literal, Optional
+from typing import Dict, Any, List, Literal
 import contextlib
-
-import logging
+import pickle
 
 from leann.searcher_base import BaseSearcher
 from leann.registry import register_backend
@@ -16,46 +14,6 @@ from leann.interface import (
     LeannBackendSearcherInterface,
 )
 
-logger = logging.getLogger(__name__)
-
-
-@contextlib.contextmanager
-def suppress_cpp_output_if_needed():
-    """Suppress C++ stdout/stderr based on LEANN_LOG_LEVEL"""
-    log_level = os.getenv("LEANN_LOG_LEVEL", "WARNING").upper()
-
-    # Only suppress if log level is WARNING or higher (ERROR, CRITICAL)
-    should_suppress = log_level in ["WARNING", "ERROR", "CRITICAL"]
-
-    if not should_suppress:
-        # Don't suppress, just yield
-        yield
-        return
-
-    # Save original file descriptors
-    stdout_fd = sys.stdout.fileno()
-    stderr_fd = sys.stderr.fileno()
-
-    # Save original stdout/stderr
-    stdout_dup = os.dup(stdout_fd)
-    stderr_dup = os.dup(stderr_fd)
-
-    try:
-        # Redirect to /dev/null
-        devnull = os.open(os.devnull, os.O_WRONLY)
-        os.dup2(devnull, stdout_fd)
-        os.dup2(devnull, stderr_fd)
-        os.close(devnull)
-
-        yield
-
-    finally:
-        # Restore original file descriptors
-        os.dup2(stdout_dup, stdout_fd)
-        os.dup2(stderr_dup, stderr_fd)
-        os.close(stdout_dup)
-        os.close(stderr_dup)
-
 
 def _get_diskann_metrics():
     from . import _diskannpy as diskannpy  # type: ignore
@@ -107,20 +65,18 @@ class DiskannBuilder(LeannBackendBuilderInterface):
         index_dir.mkdir(parents=True, exist_ok=True)
 
         if data.dtype != np.float32:
-            logger.warning(f"Converting data to float32, shape: {data.shape}")
             data = data.astype(np.float32)
 
         data_filename = f"{index_prefix}_data.bin"
         _write_vectors_to_bin(data, index_dir / data_filename)
 
+
         build_kwargs = {**self.build_params, **kwargs}
         metric_enum = _get_diskann_metrics().get(
             build_kwargs.get("distance_metric", "mips").lower()
         )
         if metric_enum is None:
-            raise ValueError(
-                f"Unsupported distance_metric '{build_kwargs.get('distance_metric', 'unknown')}'."
-            )
+            raise ValueError("Unsupported distance_metric.")
 
         try:
             from . import _diskannpy as diskannpy  # type: ignore
@@ -142,40 +98,36 @@ class DiskannBuilder(LeannBackendBuilderInterface):
             temp_data_file = index_dir / data_filename
             if temp_data_file.exists():
                 os.remove(temp_data_file)
-                logger.debug(f"Cleaned up temporary data file: {temp_data_file}")
 
 
 class DiskannSearcher(BaseSearcher):
     def __init__(self, index_path: str, **kwargs):
         super().__init__(
             index_path,
-            backend_module_name="leann_backend_diskann.diskann_embedding_server",
+            backend_module_name="leann_backend_diskann.embedding_server",
             **kwargs,
         )
+        from . import _diskannpy as diskannpy  # type: ignore
 
-        # Initialize DiskANN index with suppressed C++ output based on log level
-        with suppress_cpp_output_if_needed():
-            from . import _diskannpy as diskannpy  # type: ignore
+        distance_metric = kwargs.get("distance_metric", "mips").lower()
+        metric_enum = _get_diskann_metrics().get(distance_metric)
+        if metric_enum is None:
+            raise ValueError(f"Unsupported distance_metric '{distance_metric}'.")
 
-            distance_metric = kwargs.get("distance_metric", "mips").lower()
-            metric_enum = _get_diskann_metrics().get(distance_metric)
-            if metric_enum is None:
-                raise ValueError(f"Unsupported distance_metric '{distance_metric}'.")
+        self.num_threads = kwargs.get("num_threads", 8)
+        self.zmq_port = kwargs.get("zmq_port", 6666)
 
-            self.num_threads = kwargs.get("num_threads", 8)
-
-            fake_zmq_port = 6666
-            full_index_prefix = str(self.index_dir / self.index_path.stem)
-            self._index = diskannpy.StaticDiskFloatIndex(
-                metric_enum,
-                full_index_prefix,
-                self.num_threads,
-                kwargs.get("num_nodes_to_cache", 0),
-                1,
-                fake_zmq_port,  # Initial port, can be updated at runtime
-                "",
-                "",
-            )
+        full_index_prefix = str(self.index_dir / self.index_path.stem)
+        self._index = diskannpy.StaticDiskFloatIndex(
+            metric_enum,
+            full_index_prefix,
+            self.num_threads,
+            kwargs.get("num_nodes_to_cache", 0),
+            1,
+            self.zmq_port,
+            "",
+            "",
+        )
 
     def search(
         self,
@@ -186,7 +138,7 @@ class DiskannSearcher(BaseSearcher):
         prune_ratio: float = 0.0,
         recompute_embeddings: bool = False,
         pruning_strategy: Literal["global", "local", "proportional"] = "global",
-        zmq_port: Optional[int] = None,
+        zmq_port: int = 5557,
         batch_recompute: bool = False,
         dedup_node_dis: bool = False,
         **kwargs,
@@ -205,7 +157,7 @@ class DiskannSearcher(BaseSearcher):
                 - "global": Use global pruning strategy (default)
                 - "local": Use local pruning strategy
                 - "proportional": Not supported in DiskANN, falls back to global
-            zmq_port: ZMQ port for embedding server communication. Must be provided if recompute_embeddings is True.
+            zmq_port: ZMQ port for embedding server
             batch_recompute: Whether to batch neighbor recomputation (DiskANN-specific)
             dedup_node_dis: Whether to cache and reuse distance computations (DiskANN-specific)
             **kwargs: Additional DiskANN-specific parameters (for legacy compatibility)
@@ -213,25 +165,22 @@ class DiskannSearcher(BaseSearcher):
         Returns:
             Dict with 'labels' (list of lists) and 'distances' (ndarray)
         """
-        # Handle zmq_port compatibility: DiskANN can now update port at runtime
-        if recompute_embeddings:
-            if zmq_port is None:
-                raise ValueError(
-                    "zmq_port must be provided if recompute_embeddings is True"
-                )
-            current_port = self._index.get_zmq_port()
-            if zmq_port != current_port:
-                logger.debug(
-                    f"Updating DiskANN zmq_port from {current_port} to {zmq_port}"
-                )
-                self._index.set_zmq_port(zmq_port)
-
         # DiskANN doesn't support "proportional" strategy
         if pruning_strategy == "proportional":
             raise NotImplementedError(
                 "DiskANN backend does not support 'proportional' pruning strategy. Use 'global' or 'local' instead."
             )
 
+        # Use recompute_embeddings parameter
+        use_recompute = recompute_embeddings
+        if use_recompute:
+            meta_file_path = self.index_dir / f"{self.index_path.name}.meta.json"
+            if not meta_file_path.exists():
+                raise RuntimeError(
+                    f"FATAL: Recompute enabled but metadata file not found: {meta_file_path}"
+                )
+            self._ensure_server_running(str(meta_file_path), port=zmq_port, **kwargs)
+
         if query.dtype != np.float32:
             query = query.astype(np.float32)
 
@@ -241,26 +190,25 @@ class DiskannSearcher(BaseSearcher):
         else:  # "global"
             use_global_pruning = True
 
-        # Perform search with suppressed C++ output based on log level
-        with suppress_cpp_output_if_needed():
-            labels, distances = self._index.batch_search(
-                query,
-                query.shape[0],
-                top_k,
-                complexity,
-                beam_width,
-                self.num_threads,
-                kwargs.get("USE_DEFERRED_FETCH", False),
-                kwargs.get("skip_search_reorder", False),
-                recompute_embeddings,
-                dedup_node_dis,
-                prune_ratio,
-                batch_recompute,
-                use_global_pruning,
-            )
+        labels, distances = self._index.batch_search(
+            query,
+            query.shape[0],
+            top_k,
+            complexity,
+            beam_width,
+            self.num_threads,
+            kwargs.get("USE_DEFERRED_FETCH", False),
+            kwargs.get("skip_search_reorder", False),
+            use_recompute,
+            dedup_node_dis,
+            prune_ratio,
+            batch_recompute,
+            use_global_pruning,
+        )
 
         string_labels = [
-            [str(int_label) for int_label in batch_labels] for batch_labels in labels
+            [str(int_label) for int_label in batch_labels]
+            for batch_labels in labels
         ]
 
         return {"labels": string_labels, "distances": distances}

packages/leann-backend-diskann/leann_backend_diskann/diskann_embedding_server.py

@@ -1,283 +0,0 @@
-"""
-DiskANN-specific embedding server
-"""
-
-import argparse
-import threading
-import time
-import os
-import zmq
-import numpy as np
-import json
-from pathlib import Path
-from typing import Optional
-import sys
-import logging
-
-# Set up logging based on environment variable
-LOG_LEVEL = os.getenv("LEANN_LOG_LEVEL", "WARNING").upper()
-logger = logging.getLogger(__name__)
-
-# Force set logger level (don't rely on basicConfig in subprocess)
-log_level = getattr(logging, LOG_LEVEL, logging.WARNING)
-logger.setLevel(log_level)
-
-# Ensure we have a handler if none exists
-if not logger.handlers:
-    handler = logging.StreamHandler()
-    formatter = logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
-    handler.setFormatter(formatter)
-    logger.addHandler(handler)
-    logger.propagate = False
-
-
-def create_diskann_embedding_server(
-    passages_file: Optional[str] = None,
-    zmq_port: int = 5555,
-    model_name: str = "sentence-transformers/all-mpnet-base-v2",
-    embedding_mode: str = "sentence-transformers",
-):
-    """
-    Create and start a ZMQ-based embedding server for DiskANN backend.
-    Uses ROUTER socket and protobuf communication as required by DiskANN C++ implementation.
-    """
-    logger.info(f"Starting DiskANN server on port {zmq_port} with model {model_name}")
-    logger.info(f"Using embedding mode: {embedding_mode}")
-
-    # Add leann-core to path for unified embedding computation
-    current_dir = Path(__file__).parent
-    leann_core_path = current_dir.parent.parent / "leann-core" / "src"
-    sys.path.insert(0, str(leann_core_path))
-
-    try:
-        from leann.embedding_compute import compute_embeddings
-        from leann.api import PassageManager
-
-        logger.info("Successfully imported unified embedding computation module")
-    except ImportError as e:
-        logger.error(f"Failed to import embedding computation module: {e}")
-        return
-    finally:
-        sys.path.pop(0)
-
-    # Check port availability
-    import socket
-
-    def check_port(port):
-        with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
-            return s.connect_ex(("localhost", port)) == 0
-
-    if check_port(zmq_port):
-        logger.error(f"Port {zmq_port} is already in use")
-        return
-
-    # Only support metadata file, fail fast for everything else
-    if not passages_file or not passages_file.endswith(".meta.json"):
-        raise ValueError("Only metadata files (.meta.json) are supported")
-
-    # Load metadata to get passage sources
-    with open(passages_file, "r") as f:
-        meta = json.load(f)
-
-    passages = PassageManager(meta["passage_sources"])
-    logger.info(
-        f"Loaded PassageManager with {len(passages.global_offset_map)} passages from metadata"
-    )
-
-    # Import protobuf after ensuring the path is correct
-    try:
-        from . import embedding_pb2
-    except ImportError as e:
-        logger.error(f"Failed to import protobuf module: {e}")
-        return
-
-    def zmq_server_thread():
-        """ZMQ server thread using REP socket for universal compatibility"""
-        context = zmq.Context()
-        socket = context.socket(
-            zmq.REP
-        )  # REP socket for both BaseSearcher and DiskANN C++ REQ clients
-        socket.bind(f"tcp://*:{zmq_port}")
-        logger.info(f"DiskANN ZMQ REP server listening on port {zmq_port}")
-
-        socket.setsockopt(zmq.RCVTIMEO, 300000)
-        socket.setsockopt(zmq.SNDTIMEO, 300000)
-
-        while True:
-            try:
-                # REP socket receives single-part messages
-                message = socket.recv()
-
-                # Check for empty messages - REP socket requires response to every request
-                if len(message) == 0:
-                    logger.debug("Received empty message, sending empty response")
-                    socket.send(b"")  # REP socket must respond to every request
-                    continue
-
-                logger.debug(f"Received ZMQ request of size {len(message)} bytes")
-                logger.debug(f"Message preview: {message[:50]}")  # Show first 50 bytes
-
-                e2e_start = time.time()
-
-                # Try protobuf first (for DiskANN C++ node_ids requests - primary use case)
-                texts = []
-                node_ids = []
-                is_text_request = False
-
-                try:
-                    req_proto = embedding_pb2.NodeEmbeddingRequest()
-                    req_proto.ParseFromString(message)
-                    node_ids = list(req_proto.node_ids)
-
-                    if not node_ids:
-                        raise RuntimeError(
-                            f"PROTOBUF: Received empty node_ids! Message size: {len(message)}"
-                        )
-
-                    logger.info(
-                        f"✅ PROTOBUF: Node ID request for {len(node_ids)} node embeddings: {node_ids[:10]}"
-                    )
-                except Exception as protobuf_error:
-                    logger.debug(f"Protobuf parsing failed: {protobuf_error}")
-                    # Fallback to msgpack (for BaseSearcher direct text requests)
-                    try:
-                        import msgpack
-
-                        request = msgpack.unpackb(message)
-                        # For BaseSearcher compatibility, request is a list of texts directly
-                        if isinstance(request, list) and all(
-                            isinstance(item, str) for item in request
-                        ):
-                            texts = request
-                            is_text_request = True
-                            logger.info(
-                                f"✅ MSGPACK: Direct text request for {len(texts)} texts"
-                            )
-                        else:
-                            raise ValueError("Not a valid msgpack text request")
-                    except Exception as msgpack_error:
-                        raise RuntimeError(
-                            f"Both protobuf and msgpack parsing failed! Protobuf: {protobuf_error}, Msgpack: {msgpack_error}"
-                        )
-
-                # Look up texts by node IDs (only if not direct text request)
-                if not is_text_request:
-                    for nid in node_ids:
-                        try:
-                            passage_data = passages.get_passage(str(nid))
-                            txt = passage_data["text"]
-                            if not txt:
-                                raise RuntimeError(
-                                    f"FATAL: Empty text for passage ID {nid}"
-                                )
-                            texts.append(txt)
-                        except KeyError as e:
-                            logger.error(f"Passage ID {nid} not found: {e}")
-                            raise e
-                        except Exception as e:
-                            logger.error(f"Exception looking up passage ID {nid}: {e}")
-                            raise
-
-                    # Debug logging
-                    logger.debug(f"Processing {len(texts)} texts")
-                    logger.debug(
-                        f"Text lengths: {[len(t) for t in texts[:5]]}"
-                    )  # Show first 5
-
-                # Process embeddings using unified computation
-                embeddings = compute_embeddings(texts, model_name, mode=embedding_mode)
-                logger.info(
-                    f"Computed embeddings for {len(texts)} texts, shape: {embeddings.shape}"
-                )
-
-                # Prepare response based on request type
-                if is_text_request:
-                    # For BaseSearcher compatibility: return msgpack format
-                    import msgpack
-
-                    response_data = msgpack.packb(embeddings.tolist())
-                else:
-                    # For DiskANN C++ compatibility: return protobuf format
-                    resp_proto = embedding_pb2.NodeEmbeddingResponse()
-                    hidden_contiguous = np.ascontiguousarray(
-                        embeddings, dtype=np.float32
-                    )
-
-                    # Serialize embeddings data
-                    resp_proto.embeddings_data = hidden_contiguous.tobytes()
-                    resp_proto.dimensions.append(hidden_contiguous.shape[0])
-                    resp_proto.dimensions.append(hidden_contiguous.shape[1])
-
-                    response_data = resp_proto.SerializeToString()
-
-                # Send response back to the client
-                socket.send(response_data)
-
-                e2e_end = time.time()
-                logger.info(f"⏱️  ZMQ E2E time: {e2e_end - e2e_start:.6f}s")
-
-            except zmq.Again:
-                logger.debug("ZMQ socket timeout, continuing to listen")
-                continue
-            except Exception as e:
-                logger.error(f"Error in ZMQ server loop: {e}")
-                import traceback
-
-                traceback.print_exc()
-                raise
-
-    zmq_thread = threading.Thread(target=zmq_server_thread, daemon=True)
-    zmq_thread.start()
-    logger.info(f"Started DiskANN ZMQ server thread on port {zmq_port}")
-
-    # Keep the main thread alive
-    try:
-        while True:
-            time.sleep(1)
-    except KeyboardInterrupt:
-        logger.info("DiskANN Server shutting down...")
-        return
-
-
-if __name__ == "__main__":
-    import signal
-    import sys
-
-    def signal_handler(sig, frame):
-        logger.info(f"Received signal {sig}, shutting down gracefully...")
-        sys.exit(0)
-
-    # Register signal handlers for graceful shutdown
-    signal.signal(signal.SIGTERM, signal_handler)
-    signal.signal(signal.SIGINT, signal_handler)
-
-    parser = argparse.ArgumentParser(description="DiskANN Embedding service")
-    parser.add_argument("--zmq-port", type=int, default=5555, help="ZMQ port to run on")
-    parser.add_argument(
-        "--passages-file",
-        type=str,
-        help="Metadata JSON file containing passage sources",
-    )
-    parser.add_argument(
-        "--model-name",
-        type=str,
-        default="sentence-transformers/all-mpnet-base-v2",
-        help="Embedding model name",
-    )
-    parser.add_argument(
-        "--embedding-mode",
-        type=str,
-        default="sentence-transformers",
-        choices=["sentence-transformers", "openai", "mlx"],
-        help="Embedding backend mode",
-    )
-
-    args = parser.parse_args()
-
-    # Create and start the DiskANN embedding server
-    create_diskann_embedding_server(
-        passages_file=args.passages_file,
-        zmq_port=args.zmq_port,
-        model_name=args.model_name,
-        embedding_mode=args.embedding_mode,
-    )

packages/leann-backend-diskann/leann_backend_diskann/embedding_server.py

@@ -0,0 +1,705 @@
+#!/usr/bin/env python3
+"""
+Embedding server for leann-backend-diskann - Fixed ZMQ REQ-REP pattern
+"""
+
+import pickle
+import argparse
+import time
+import json
+from typing import Dict, Any, Optional, Union
+
+from transformers import AutoTokenizer, AutoModel
+import os
+from contextlib import contextmanager
+import zmq
+import numpy as np
+import msgpack
+from pathlib import Path
+import logging
+
+RED = "\033[91m"
+
+# Set up logging based on environment variable
+LOG_LEVEL = os.getenv('LEANN_LOG_LEVEL', 'INFO').upper()
+logging.basicConfig(
+    level=getattr(logging, LOG_LEVEL, logging.INFO),
+    format='%(asctime)s - %(levelname)s - %(message)s'
+)
+logger = logging.getLogger(__name__)
+RESET = "\033[0m"
+
+# --- New Passage Loader from HNSW backend ---
+class SimplePassageLoader:
+    """
+    Simple passage loader that replaces config.py dependencies
+    """
+    def __init__(self, passages_data: Optional[Dict[str, Any]] = None):
+        self.passages_data = passages_data or {}
+        self._meta_path = ''
+    
+    def __getitem__(self, passage_id: Union[str, int]) -> Dict[str, str]:
+        """Get passage by ID"""
+        str_id = str(passage_id)
+        if str_id in self.passages_data:
+            return {"text": self.passages_data[str_id]}
+        else:
+            # Return empty text for missing passages
+            return {"text": ""}
+    
+    def __len__(self) -> int:
+        return len(self.passages_data)
+    
+    def keys(self):
+        return self.passages_data.keys()
+
+def load_passages_from_metadata(meta_file: str) -> SimplePassageLoader:
+    """
+    Load passages using metadata file with PassageManager for lazy loading
+    """
+    # Load metadata to get passage sources
+    with open(meta_file, 'r') as f:
+        meta = json.load(f)
+    
+    # Import PassageManager dynamically to avoid circular imports
+    import sys
+    from pathlib import Path
+    
+    # Find the leann package directory relative to this file
+    current_dir = Path(__file__).parent
+    leann_core_path = current_dir.parent.parent / "leann-core" / "src"
+    sys.path.insert(0, str(leann_core_path))
+    
+    try:
+        from leann.api import PassageManager
+        passage_manager = PassageManager(meta['passage_sources'])
+    finally:
+        sys.path.pop(0)
+    
+    print(f"Initialized lazy passage loading for {len(passage_manager.global_offset_map)} passages")
+    
+    class LazyPassageLoader(SimplePassageLoader):
+        def __init__(self, passage_manager):
+            self.passage_manager = passage_manager
+            # Initialize parent with empty data
+            super().__init__({})
+        
+        def __getitem__(self, passage_id: Union[str, int]) -> Dict[str, str]:
+            """Get passage by ID with lazy loading"""
+            try:
+                int_id = int(passage_id)
+                string_id = str(int_id)
+                passage_data = self.passage_manager.get_passage(string_id)
+                if passage_data and passage_data.get("text"):
+                    return {"text": passage_data["text"]}
+                else:
+                    raise RuntimeError(f"FATAL: Empty text for ID {int_id} -> {string_id}")
+            except Exception as e:
+                raise RuntimeError(f"FATAL: Exception getting passage {passage_id}: {e}")
+        
+        def __len__(self) -> int:
+            return len(self.passage_manager.global_offset_map)
+        
+        def keys(self):
+            return self.passage_manager.global_offset_map.keys()
+    
+    loader = LazyPassageLoader(passage_manager)
+    loader._meta_path = meta_file
+    return loader
+
+def load_passages_from_file(passages_file: str) -> SimplePassageLoader:
+    """
+    Load passages from a JSONL file with label map support
+    Expected format: {"id": "passage_id", "text": "passage_text", "metadata": {...}} (one per line)
+    """
+    
+    if not os.path.exists(passages_file):
+        raise FileNotFoundError(f"Passages file {passages_file} not found.")
+    
+    if not passages_file.endswith('.jsonl'):
+        raise ValueError(f"Expected .jsonl file format, got: {passages_file}")
+    
+    # Load passages directly by their sequential IDs
+    passages_data = {}
+    with open(passages_file, 'r', encoding='utf-8') as f:
+        for line in f:
+            if line.strip():
+                passage = json.loads(line)
+                passages_data[passage['id']] = passage['text']
+    
+    print(f"Loaded {len(passages_data)} passages from JSONL file {passages_file}")
+    return SimplePassageLoader(passages_data)
+
+def create_embedding_server_thread(
+    zmq_port=5555,
+    model_name="sentence-transformers/all-mpnet-base-v2",
+    max_batch_size=128,
+    passages_file: Optional[str] = None,
+    embedding_mode: str = "sentence-transformers",
+    enable_warmup: bool = False,
+):
+    """
+    Create and run embedding server in the current thread
+    This function is designed to be called in a separate thread
+    """
+    logger.info(f"Initializing embedding server thread on port {zmq_port}")
+    
+    try:
+        # Check if port is already occupied
+        import socket
+        def check_port(port):
+            with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+                return s.connect_ex(('localhost', port)) == 0
+
+        if check_port(zmq_port):
+            print(f"{RED}Port {zmq_port} is already in use{RESET}")
+            return
+
+        # Auto-detect mode based on model name if not explicitly set
+        if embedding_mode == "sentence-transformers" and model_name.startswith("text-embedding-"):
+            embedding_mode = "openai"
+        
+        if embedding_mode == "mlx":
+            from leann.api import compute_embeddings_mlx
+            import torch
+            logger.info("Using MLX for embeddings")
+            # Set device to CPU for compatibility with DeviceTimer class
+            device = torch.device("cpu")
+            cuda_available = False
+            mps_available = False
+        elif embedding_mode == "openai":
+            from leann.api import compute_embeddings_openai
+            import torch
+            logger.info("Using OpenAI API for embeddings")
+            # Set device to CPU for compatibility with DeviceTimer class
+            device = torch.device("cpu")
+            cuda_available = False
+            mps_available = False
+        elif embedding_mode == "sentence-transformers":
+            # Initialize model
+            tokenizer = AutoTokenizer.from_pretrained(model_name, use_fast=True)
+            import torch
+
+            # Select device
+            mps_available = hasattr(torch.backends, 'mps') and torch.backends.mps.is_available()
+            cuda_available = torch.cuda.is_available()
+            
+            if cuda_available:
+                device = torch.device("cuda")
+                logger.info("Using CUDA device")
+            elif mps_available:
+                device = torch.device("mps")
+                logger.info("Using MPS device (Apple Silicon)")
+            else:
+                device = torch.device("cpu")
+                logger.info("Using CPU device")
+            
+            # Load model
+            logger.info(f"Loading model {model_name}")
+            model = AutoModel.from_pretrained(model_name).to(device).eval()
+
+            # Optimize model
+            if cuda_available or mps_available:
+                try:
+                    model = model.half()
+                    model = torch.compile(model)
+                    logger.info(f"Using FP16 precision with model: {model_name}")
+                except Exception as e:
+                    print(f"WARNING: Model optimization failed: {e}")
+        else:
+            raise ValueError(f"Unsupported embedding mode: {embedding_mode}. Supported modes: sentence-transformers, mlx, openai")
+
+        # Load passages from file if provided
+        if passages_file and os.path.exists(passages_file):
+            # Check if it's a metadata file or a single passages file
+            if passages_file.endswith('.meta.json'):
+                passages = load_passages_from_metadata(passages_file)
+            else:
+                # Try to find metadata file in same directory
+                passages_dir = Path(passages_file).parent
+                meta_files = list(passages_dir.glob("*.meta.json"))
+                if meta_files:
+                    print(f"Found metadata file: {meta_files[0]}, using lazy loading")
+                    passages = load_passages_from_metadata(str(meta_files[0]))
+                else:
+                    # Fallback to original single file loading (will cause warnings)
+                    print("WARNING: No metadata file found, using single file loading (may cause missing passage warnings)")
+                    passages = load_passages_from_file(passages_file)
+        else:
+            print("WARNING: No passages file provided or file not found. Using an empty passage loader.")
+            passages = SimplePassageLoader()
+
+        logger.info(f"Loaded {len(passages)} passages.")
+
+        def client_warmup(zmq_port):
+            """Perform client-side warmup for DiskANN server"""
+            time.sleep(2)
+            print(f"Performing client-side warmup with model {model_name}...")
+            
+            # Get actual passage IDs from the loaded passages
+            sample_ids = []
+            if hasattr(passages, 'keys') and len(passages) > 0:
+                available_ids = list(passages.keys())
+                # Take up to 5 actual IDs, but at least 1
+                sample_ids = available_ids[:min(5, len(available_ids))]
+                print(f"Using actual passage IDs for warmup: {sample_ids}")
+            else:
+                print("No passages available for warmup, skipping warmup...")
+                return
+
+            try:
+                context = zmq.Context()
+                socket = context.socket(zmq.REQ)
+                socket.connect(f"tcp://localhost:{zmq_port}")
+                socket.setsockopt(zmq.RCVTIMEO, 30000)
+                socket.setsockopt(zmq.SNDTIMEO, 30000)
+
+                try:
+                    ids_to_send = [int(x) for x in sample_ids]
+                except ValueError:
+                    print("Warning: Could not convert sample IDs to integers, skipping warmup")
+                    return
+
+                if not ids_to_send:
+                    print("Skipping warmup send.")
+                    return
+
+                # Use protobuf format for warmup
+                from . import embedding_pb2
+                req_proto = embedding_pb2.NodeEmbeddingRequest()
+                req_proto.node_ids.extend(ids_to_send)
+                request_bytes = req_proto.SerializeToString()
+
+                for i in range(3):
+                    print(f"Sending warmup request {i + 1}/3 via ZMQ (Protobuf)...")
+                    socket.send(request_bytes)
+                    response_bytes = socket.recv()
+                    
+                    resp_proto = embedding_pb2.NodeEmbeddingResponse()
+                    resp_proto.ParseFromString(response_bytes)
+                    embeddings_count = resp_proto.dimensions[0] if resp_proto.dimensions else 0
+                    print(f"Warmup request {i + 1}/3 successful, received {embeddings_count} embeddings")
+                    time.sleep(0.1)
+
+                print("Client-side Protobuf ZMQ warmup complete")
+                socket.close()
+                context.term()
+            except Exception as e:
+                print(f"Error during Protobuf ZMQ warmup: {e}")
+
+        class DeviceTimer:
+            """Device timer"""
+            def __init__(self, name="", device=device):
+                self.name = name
+                self.device = device
+                self.start_time = 0
+                self.end_time = 0
+                
+                if embedding_mode == "sentence-transformers" and torch.cuda.is_available():
+                    self.start_event = torch.cuda.Event(enable_timing=True)
+                    self.end_event = torch.cuda.Event(enable_timing=True)
+                else:
+                    self.start_event = None
+                    self.end_event = None
+
+            @contextmanager
+            def timing(self):
+                self.start()
+                yield
+                self.end()
+
+            def start(self):
+                if embedding_mode == "sentence-transformers" and torch.cuda.is_available():
+                    torch.cuda.synchronize()
+                    self.start_event.record()
+                else:
+                    if embedding_mode == "sentence-transformers" and self.device.type == "mps":
+                        torch.mps.synchronize()
+                    self.start_time = time.time()
+
+            def end(self):
+                if embedding_mode == "sentence-transformers" and torch.cuda.is_available():
+                    self.end_event.record()
+                    torch.cuda.synchronize()
+                else:
+                    if embedding_mode == "sentence-transformers" and self.device.type == "mps":
+                        torch.mps.synchronize()
+                    self.end_time = time.time()
+
+            def elapsed_time(self):
+                if embedding_mode == "sentence-transformers" and torch.cuda.is_available():
+                    return self.start_event.elapsed_time(self.end_event) / 1000.0
+                else:
+                    return self.end_time - self.start_time
+
+            def print_elapsed(self):
+                elapsed = self.elapsed_time()
+                print(f"[{self.name}] Elapsed time: {elapsed:.3f}s")
+
+        def process_batch_pytorch(texts_batch, ids_batch, missing_ids):
+            """Process text batch"""
+            if not texts_batch:
+                return np.array([])
+
+            # Filter out empty texts and their corresponding IDs
+            valid_texts = []
+            valid_ids = []
+            for i, text in enumerate(texts_batch):
+                if text.strip():  # Only include non-empty texts
+                    valid_texts.append(text)
+                    valid_ids.append(ids_batch[i])
+
+            if not valid_texts:
+                print("WARNING: No valid texts in batch")
+                return np.array([])
+
+            # Tokenize
+            token_timer = DeviceTimer("tokenization")
+            with token_timer.timing():
+                inputs = tokenizer(
+                    valid_texts,
+                    padding=True,
+                    truncation=True,
+                    max_length=512,
+                    return_tensors="pt"
+                ).to(device)
+
+            # Compute embeddings
+            embed_timer = DeviceTimer("embedding computation")
+            with embed_timer.timing():
+                with torch.no_grad():
+                    outputs = model(**inputs)
+                    hidden_states = outputs.last_hidden_state
+                    
+                    # Mean pooling
+                    attention_mask = inputs['attention_mask']
+                    mask_expanded = attention_mask.unsqueeze(-1).expand(hidden_states.size()).float()
+                    sum_embeddings = torch.sum(hidden_states * mask_expanded, 1)
+                    sum_mask = torch.clamp(mask_expanded.sum(1), min=1e-9)
+                    batch_embeddings = sum_embeddings / sum_mask
+                embed_timer.print_elapsed()
+
+            return batch_embeddings.cpu().numpy()
+
+        # ZMQ server main loop - modified to use REP socket
+        context = zmq.Context()
+        socket = context.socket(zmq.ROUTER)  # Changed to REP socket
+        socket.bind(f"tcp://127.0.0.1:{zmq_port}")
+        print(f"INFO: ZMQ ROUTER server listening on port {zmq_port}")
+
+        # Set timeouts
+        socket.setsockopt(zmq.RCVTIMEO, 5000)  # 5 second receive timeout
+        socket.setsockopt(zmq.SNDTIMEO, 300000)  # 300 second send timeout
+
+        from . import embedding_pb2
+
+        print(f"INFO: Embedding server ready to serve requests")
+
+        # Start warmup thread if enabled
+        if enable_warmup and len(passages) > 0:
+            import threading
+            print(f"Warmup enabled: starting warmup thread")
+            warmup_thread = threading.Thread(target=client_warmup, args=(zmq_port,))
+            warmup_thread.daemon = True
+            warmup_thread.start()
+        else:
+            print(f"Warmup disabled or no passages available (enable_warmup={enable_warmup}, passages={len(passages)})")
+
+        while True:
+            try:
+                parts = socket.recv_multipart()
+
+                # --- Restore robust message format detection ---
+                # Must check parts length to avoid IndexError
+                if len(parts) >= 3:
+                    identity = parts[0]
+                    # empty = parts[1]  # We usually don't care about the middle empty frame
+                    message = parts[2]
+                elif len(parts) == 2:
+                    # Can also handle cases without empty frame
+                    identity = parts[0]
+                    message = parts[1]
+                else:
+                    # If received message format is wrong, print warning and ignore it instead of crashing
+                    print(f"WARNING: Received unexpected message format with {len(parts)} parts. Ignoring.")
+                    continue
+                print(f"INFO: Received ZMQ request from client {identity.hex()[:8]}, size {len(message)} bytes")
+
+                # Handle control messages (MessagePack format)
+                try:
+                    request_payload = msgpack.unpackb(message)
+                    if isinstance(request_payload, list) and len(request_payload) >= 1:
+                        if request_payload[0] == "__QUERY_META_PATH__":
+                            # Return the current meta path being used by the server
+                            current_meta_path = getattr(passages, '_meta_path', '') if hasattr(passages, '_meta_path') else ''
+                            response = [current_meta_path]
+                            socket.send_multipart([identity, b'', msgpack.packb(response)])
+                            continue
+                            
+                        elif request_payload[0] == "__UPDATE_META_PATH__" and len(request_payload) >= 2:
+                            # Update the server's meta path and reload passages
+                            new_meta_path = request_payload[1]
+                            try:
+                                print(f"INFO: Updating server meta path to: {new_meta_path}")
+                                # Reload passages from the new meta file
+                                passages = load_passages_from_metadata(new_meta_path)
+                                # Store the meta path for future queries
+                                passages._meta_path = new_meta_path
+                                response = ["SUCCESS"]
+                                print(f"INFO: Successfully updated meta path and reloaded {len(passages)} passages")
+                            except Exception as e:
+                                print(f"ERROR: Failed to update meta path: {e}")
+                                response = ["FAILED", str(e)]
+                            socket.send_multipart([identity, b'', msgpack.packb(response)])
+                            continue
+                            
+                        elif request_payload[0] == "__QUERY_MODEL__":
+                            # Return the current model being used by the server
+                            response = [model_name]
+                            socket.send_multipart([identity, b'', msgpack.packb(response)])
+                            continue
+                            
+                        elif request_payload[0] == "__UPDATE_MODEL__" and len(request_payload) >= 2:
+                            # Update the server's embedding model
+                            new_model_name = request_payload[1]
+                            try:
+                                print(f"INFO: Updating server model from {model_name} to: {new_model_name}")
+                                
+                                # Clean up old model to free memory
+                                if not use_mlx:
+                                    print("INFO: Releasing old model from memory...")
+                                    old_model = model
+                                    old_tokenizer = tokenizer
+                                    
+                                    # Load new tokenizer first
+                                    print(f"Loading new tokenizer for {new_model_name}...")
+                                    tokenizer = AutoTokenizer.from_pretrained(new_model_name, use_fast=True)
+                                    
+                                    # Load new model
+                                    print(f"Loading new model {new_model_name}...")
+                                    model = AutoModel.from_pretrained(new_model_name).to(device).eval()
+                                    
+                                    # Optimize new model
+                                    if cuda_available or mps_available:
+                                        try:
+                                            model = model.half()
+                                            model = torch.compile(model)
+                                            print(f"INFO: Using FP16 precision with model: {new_model_name}")
+                                        except Exception as e:
+                                            print(f"WARNING: Model optimization failed: {e}")
+                                    
+                                    # Now safely delete old model after new one is loaded
+                                    del old_model
+                                    del old_tokenizer
+                                    
+                                    # Clear GPU cache if available
+                                    if device.type == "cuda":
+                                        torch.cuda.empty_cache()
+                                        print("INFO: Cleared CUDA cache")
+                                    elif device.type == "mps":
+                                        torch.mps.empty_cache()
+                                        print("INFO: Cleared MPS cache")
+                                    
+                                    # Force garbage collection
+                                    import gc
+                                    gc.collect()
+                                    print("INFO: Memory cleanup completed")
+                                
+                                # Update model name
+                                model_name = new_model_name
+                                
+                                response = ["SUCCESS"]
+                                print(f"INFO: Successfully updated model to: {new_model_name}")
+                            except Exception as e:
+                                print(f"ERROR: Failed to update model: {e}")
+                                response = ["FAILED", str(e)]
+                            socket.send_multipart([identity, b'', msgpack.packb(response)])
+                            continue
+                except:
+                    # Not a control message, continue with normal protobuf processing
+                    pass
+
+                e2e_start = time.time()
+                lookup_timer = DeviceTimer("text lookup")
+
+                # Parse request
+                req_proto = embedding_pb2.NodeEmbeddingRequest()
+                req_proto.ParseFromString(message)
+                node_ids = req_proto.node_ids
+                print(f"INFO: Request for {len(node_ids)} node embeddings: {list(node_ids)}")
+
+                # Add debug information
+                if len(node_ids) > 0:
+                    print(f"DEBUG: Node ID range: {min(node_ids)} to {max(node_ids)}")
+                
+                # Look up texts
+                texts = []
+                missing_ids = []
+                with lookup_timer.timing():
+                    for nid in node_ids:
+                        txtinfo = passages[nid]
+                        txt = txtinfo["text"]
+                        if txt:
+                            texts.append(txt)
+                        else:
+                            # If text is empty, we still need a placeholder for batch processing,
+                            # but record its ID as missing
+                            texts.append("") 
+                            missing_ids.append(nid)
+                lookup_timer.print_elapsed()
+
+                if missing_ids:
+                    print(f"WARNING: Missing passages for IDs: {missing_ids}")
+
+                # Process batch
+                total_size = len(texts)
+                print(f"INFO: Total batch size: {total_size}, max_batch_size: {max_batch_size}")
+                
+                all_embeddings = []
+                
+                if total_size > max_batch_size:
+                    print(f"INFO: Splitting batch of size {total_size} into chunks of {max_batch_size}")
+                    for i in range(0, total_size, max_batch_size):
+                        end_idx = min(i + max_batch_size, total_size)
+                        print(f"INFO: Processing chunk {i//max_batch_size + 1}/{(total_size + max_batch_size - 1)//max_batch_size}: items {i} to {end_idx-1}")
+                        
+                        chunk_texts = texts[i:end_idx]
+                        chunk_ids = node_ids[i:end_idx]
+                        
+                        if embedding_mode == "mlx":
+                            embeddings_chunk = compute_embeddings_mlx(chunk_texts, model_name, batch_size=16)
+                        elif embedding_mode == "openai":
+                            embeddings_chunk = compute_embeddings_openai(chunk_texts, model_name)
+                        else:  # sentence-transformers
+                            embeddings_chunk = process_batch_pytorch(chunk_texts, chunk_ids, missing_ids)
+                        all_embeddings.append(embeddings_chunk)
+                        
+                        if embedding_mode == "sentence-transformers":
+                            if cuda_available:
+                                torch.cuda.empty_cache()
+                            elif device.type == "mps":
+                                torch.mps.empty_cache()
+                            
+                    hidden = np.vstack(all_embeddings)
+                    print(f"INFO: Combined embeddings shape: {hidden.shape}")
+                else:
+                    if embedding_mode == "mlx":
+                        hidden = compute_embeddings_mlx(texts, model_name, batch_size=16)
+                    elif embedding_mode == "openai":
+                        hidden = compute_embeddings_openai(texts, model_name)
+                    else:  # sentence-transformers
+                        hidden = process_batch_pytorch(texts, node_ids, missing_ids)
+
+                # Serialize response
+                ser_start = time.time()
+
+                resp_proto = embedding_pb2.NodeEmbeddingResponse()
+                hidden_contiguous = np.ascontiguousarray(hidden, dtype=np.float32)
+                resp_proto.embeddings_data = hidden_contiguous.tobytes()
+                resp_proto.dimensions.append(hidden_contiguous.shape[0])
+                resp_proto.dimensions.append(hidden_contiguous.shape[1])
+                resp_proto.missing_ids.extend(missing_ids)
+
+                response_data = resp_proto.SerializeToString()
+                
+                # REP socket sends a single response
+                socket.send_multipart([identity, b'', response_data])
+
+                ser_end = time.time()
+
+                print(f"INFO: Serialize time: {ser_end - ser_start:.6f} seconds")
+
+                if embedding_mode == "sentence-transformers":
+                    if device.type == "cuda":
+                        torch.cuda.synchronize()
+                    elif device.type == "mps":
+                        torch.mps.synchronize()
+                e2e_end = time.time()
+                print(f"INFO: ZMQ E2E time: {e2e_end - e2e_start:.6f} seconds")
+
+            except zmq.Again:
+                print("INFO: ZMQ socket timeout, continuing to listen")
+                continue
+            except Exception as e:
+                print(f"ERROR: Error in ZMQ server: {e}")
+                try:
+                    # Send empty response to maintain REQ-REP state
+                    empty_resp = embedding_pb2.NodeEmbeddingResponse()
+                    socket.send(empty_resp.SerializeToString())
+                except:
+                    # If sending fails, recreate socket
+                    socket.close()
+                    socket = context.socket(zmq.REP)
+                    socket.bind(f"tcp://127.0.0.1:{zmq_port}")
+                    socket.setsockopt(zmq.RCVTIMEO, 5000)
+                    socket.setsockopt(zmq.SNDTIMEO, 300000)
+                    print("INFO: ZMQ socket recreated after error")
+
+    except Exception as e:
+        print(f"ERROR: Failed to start embedding server: {e}")
+        raise
+
+
+def create_embedding_server(
+    domain="demo",
+    load_passages=True,
+    load_embeddings=False,
+    use_fp16=True,
+    use_int8=False,
+    use_cuda_graphs=False,
+    zmq_port=5555,
+    max_batch_size=128,
+    lazy_load_passages=False,
+    model_name="sentence-transformers/all-mpnet-base-v2",
+    passages_file: Optional[str] = None,
+    embedding_mode: str = "sentence-transformers",
+    enable_warmup: bool = False,
+):
+    """
+    原有的 create_embedding_server 函数保持不变
+    这个是阻塞版本，用于直接运行
+    """
+    create_embedding_server_thread(zmq_port, model_name, max_batch_size, passages_file, embedding_mode, enable_warmup)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Embedding service")
+    parser.add_argument("--zmq-port", type=int, default=5555, help="ZMQ port to run on")
+    parser.add_argument("--domain", type=str, default="demo", help="Domain name")
+    parser.add_argument("--passages-file", type=str, help="JSON file containing passage ID to text mapping")
+    parser.add_argument("--load-passages", action="store_true", default=True)
+    parser.add_argument("--load-embeddings", action="store_true", default=False)
+    parser.add_argument("--use-fp16", action="store_true", default=False)
+    parser.add_argument("--use-int8", action="store_true", default=False)
+    parser.add_argument("--use-cuda-graphs", action="store_true", default=False)
+    parser.add_argument("--max-batch-size", type=int, default=128, help="Maximum batch size before splitting")
+    parser.add_argument("--lazy-load-passages", action="store_true", default=True)
+    parser.add_argument("--model-name", type=str, default="sentence-transformers/all-mpnet-base-v2", 
+                        help="Embedding model name")
+    parser.add_argument("--embedding-mode", type=str, default="sentence-transformers", 
+                        choices=["sentence-transformers", "mlx", "openai"],
+                        help="Embedding backend mode")
+    parser.add_argument("--use-mlx", action="store_true", default=False, help="Use MLX backend for embeddings (deprecated: use --embedding-mode mlx)")
+    parser.add_argument("--disable-warmup", action="store_true", default=False, help="Disable warmup requests on server start")
+    args = parser.parse_args()
+    
+    # Handle backward compatibility with use_mlx
+    embedding_mode = args.embedding_mode
+    if args.use_mlx:
+        embedding_mode = "mlx"
+
+    create_embedding_server(
+        domain=args.domain,
+        load_passages=args.load_passages,
+        load_embeddings=args.load_embeddings,
+        use_fp16=args.use_fp16,
+        use_int8=args.use_int8,
+        use_cuda_graphs=args.use_cuda_graphs,
+        zmq_port=args.zmq_port,
+        max_batch_size=args.max_batch_size,
+        lazy_load_passages=args.lazy_load_passages,
+        model_name=args.model_name,
+        passages_file=args.passages_file,
+        embedding_mode=embedding_mode,
+        enable_warmup=not args.disable_warmup,
+    )

packages/leann-backend-diskann/pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "leann-backend-diskann"
-version = "0.1.9"
-dependencies = ["leann-core==0.1.9", "numpy"]
+version = "0.1.0"
+dependencies = ["leann-core==0.1.0", "numpy"]
 
 [tool.scikit-build]
 # Key: simplified CMake path

packages/leann-backend-hnsw/leann_backend_hnsw/hnsw_backend.py

@@ -1,9 +1,10 @@
 import numpy as np
 import os
 from pathlib import Path
-from typing import Dict, Any, List, Literal, Optional
+from typing import Dict, Any, List, Literal
+import pickle
 import shutil
-import logging
+import time
 
 from leann.searcher_base import BaseSearcher
 from .convert_to_csr import convert_hnsw_graph_to_csr
@@ -15,8 +16,6 @@ from leann.interface import (
     LeannBackendSearcherInterface,
 )
 
-logger = logging.getLogger(__name__)
-
 
 def get_metric_map():
     from . import faiss  # type: ignore
@@ -58,9 +57,9 @@ class HNSWBuilder(LeannBackendBuilderInterface):
         index_dir.mkdir(parents=True, exist_ok=True)
 
         if data.dtype != np.float32:
-            logger.warning(f"Converting data to float32, shape: {data.shape}")
             data = data.astype(np.float32)
 
+
         metric_enum = get_metric_map().get(self.distance_metric.lower())
         if metric_enum is None:
             raise ValueError(f"Unsupported distance_metric '{self.distance_metric}'.")
@@ -82,7 +81,7 @@ class HNSWBuilder(LeannBackendBuilderInterface):
     def _convert_to_csr(self, index_file: Path):
         """Convert built index to CSR format"""
         mode_str = "CSR-pruned" if self.is_recompute else "CSR-standard"
-        logger.info(f"INFO: Converting HNSW index to {mode_str} format...")
+        print(f"INFO: Converting HNSW index to {mode_str} format...")
 
         csr_temp_file = index_file.with_suffix(".csr.tmp")
 
@@ -91,11 +90,11 @@ class HNSWBuilder(LeannBackendBuilderInterface):
         )
 
         if success:
-            logger.info("✅ CSR conversion successful.")
-            # index_file_old = index_file.with_suffix(".old")
-            # shutil.move(str(index_file), str(index_file_old))
+            print("✅ CSR conversion successful.")
+            index_file_old = index_file.with_suffix(".old")
+            shutil.move(str(index_file), str(index_file_old))
             shutil.move(str(csr_temp_file), str(index_file))
-            logger.info(
+            print(
                 f"INFO: Replaced original index with {mode_str} version at '{index_file}'"
             )
         else:
@@ -132,22 +131,24 @@ class HNSWSearcher(BaseSearcher):
 
         hnsw_config = faiss.HNSWIndexConfig()
         hnsw_config.is_compact = self.is_compact
-        hnsw_config.is_recompute = (
-            self.is_pruned
-        )  # In C++ code, it's called is_recompute, but it's only for loading IIUC.
+        hnsw_config.is_recompute = self.is_pruned or kwargs.get("is_recompute", False)
+
+        if self.is_pruned and not hnsw_config.is_recompute:
+            raise RuntimeError("Index is pruned but recompute is disabled.")
 
         self._index = faiss.read_index(str(index_file), faiss.IO_FLAG_MMAP, hnsw_config)
+        
 
     def search(
         self,
         query: np.ndarray,
         top_k: int,
-        zmq_port: Optional[int] = None,
         complexity: int = 64,
         beam_width: int = 1,
         prune_ratio: float = 0.0,
-        recompute_embeddings: bool = True,
+        recompute_embeddings: bool = False,
         pruning_strategy: Literal["global", "local", "proportional"] = "global",
+        zmq_port: int = 5557,
         batch_size: int = 0,
         **kwargs,
     ) -> Dict[str, Any]:
@@ -165,7 +166,7 @@ class HNSWSearcher(BaseSearcher):
                 - "global": Use global PQ queue size for selection (default)
                 - "local": Local pruning, sort and select best candidates
                 - "proportional": Base selection on new neighbor count ratio
-            zmq_port: ZMQ port for embedding server communication. Must be provided if recompute_embeddings is True.
+            zmq_port: ZMQ port for embedding server
             batch_size: Neighbor processing batch size, 0=disabled (HNSW-specific)
             **kwargs: Additional HNSW-specific parameters (for legacy compatibility)
 
@@ -174,14 +175,15 @@ class HNSWSearcher(BaseSearcher):
         """
         from . import faiss  # type: ignore
 
-        if not recompute_embeddings:
-            if self.is_pruned:
-                raise RuntimeError("Recompute is required for pruned index.")
-        if recompute_embeddings:
-            if zmq_port is None:
-                raise ValueError(
-                    "zmq_port must be provided if recompute_embeddings is True"
+        # Use recompute_embeddings parameter
+        use_recompute = recompute_embeddings or self.is_pruned
+        if use_recompute:
+            meta_file_path = self.index_dir / f"{self.index_path.name}.meta.json"
+            if not meta_file_path.exists():
+                raise RuntimeError(
+                    f"FATAL: Recompute enabled but metadata file not found: {meta_file_path}"
                 )
+            self._ensure_server_running(str(meta_file_path), port=zmq_port, **kwargs)
 
         if query.dtype != np.float32:
             query = query.astype(np.float32)
@@ -189,10 +191,7 @@ class HNSWSearcher(BaseSearcher):
             faiss.normalize_L2(query)
 
         params = faiss.SearchParametersHNSW()
-        if zmq_port is not None:
-            params.zmq_port = (
-                zmq_port  # C++ code won't use this if recompute_embeddings is False
-            )
+        params.zmq_port = zmq_port
         params.efSearch = complexity
         params.beam_size = beam_width
 
@@ -229,7 +228,8 @@ class HNSWSearcher(BaseSearcher):
         )
 
         string_labels = [
-            [str(int_label) for int_label in batch_labels] for batch_labels in labels
+            [str(int_label) for int_label in batch_labels]
+            for batch_labels in labels
         ]
 
         return {"labels": string_labels, "distances": distances}

packages/leann-backend-hnsw/leann_backend_hnsw/hnsw_embedding_server.py

@@ -11,29 +11,25 @@ import numpy as np
 import msgpack
 import json
 from pathlib import Path
-from typing import Optional
+from typing import Dict, Any, Optional, Union
 import sys
 import logging
 
+RED = "\033[91m"
+RESET = "\033[0m"
+
 # Set up logging based on environment variable
-LOG_LEVEL = os.getenv("LEANN_LOG_LEVEL", "WARNING").upper()
+LOG_LEVEL = os.getenv("LEANN_LOG_LEVEL", "INFO").upper()
+logging.basicConfig(
+    level=getattr(logging, LOG_LEVEL, logging.INFO),
+    format="%(asctime)s - %(levelname)s - %(message)s",
+)
 logger = logging.getLogger(__name__)
 
-# Force set logger level (don't rely on basicConfig in subprocess)
-log_level = getattr(logging, LOG_LEVEL, logging.WARNING)
-logger.setLevel(log_level)
-
-# Ensure we have a handler if none exists
-if not logger.handlers:
-    handler = logging.StreamHandler()
-    formatter = logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
-    handler.setFormatter(formatter)
-    logger.addHandler(handler)
-    logger.propagate = False
-
 
 def create_hnsw_embedding_server(
     passages_file: Optional[str] = None,
+    passages_data: Optional[Dict[str, str]] = None,
     zmq_port: int = 5555,
     model_name: str = "sentence-transformers/all-mpnet-base-v2",
     distance_metric: str = "mips",
@@ -43,8 +39,14 @@ def create_hnsw_embedding_server(
     Create and start a ZMQ-based embedding server for HNSW backend.
     Simplified version using unified embedding computation module.
     """
-    logger.info(f"Starting HNSW server on port {zmq_port} with model {model_name}")
-    logger.info(f"Using embedding mode: {embedding_mode}")
+    # Auto-detect mode based on model name if not explicitly set
+    if embedding_mode == "sentence-transformers" and model_name.startswith(
+        "text-embedding-"
+    ):
+        embedding_mode = "openai"
+
+    print(f"Starting HNSW server on port {zmq_port} with model {model_name}")
+    print(f"Using embedding mode: {embedding_mode}")
 
     # Add leann-core to path for unified embedding computation
     current_dir = Path(__file__).parent
@@ -55,9 +57,9 @@ def create_hnsw_embedding_server(
         from leann.embedding_compute import compute_embeddings
         from leann.api import PassageManager
 
-        logger.info("Successfully imported unified embedding computation module")
+        print("Successfully imported unified embedding computation module")
     except ImportError as e:
-        logger.error(f"Failed to import embedding computation module: {e}")
+        print(f"ERROR: Failed to import embedding computation module: {e}")
         return
     finally:
         sys.path.pop(0)
@@ -70,28 +72,26 @@ def create_hnsw_embedding_server(
             return s.connect_ex(("localhost", port)) == 0
 
     if check_port(zmq_port):
-        logger.error(f"Port {zmq_port} is already in use")
+        print(f"{RED}Port {zmq_port} is already in use{RESET}")
         return
 
     # Only support metadata file, fail fast for everything else
     if not passages_file or not passages_file.endswith(".meta.json"):
         raise ValueError("Only metadata files (.meta.json) are supported")
-
+    
     # Load metadata to get passage sources
     with open(passages_file, "r") as f:
         meta = json.load(f)
-
+    
     passages = PassageManager(meta["passage_sources"])
-    logger.info(
-        f"Loaded PassageManager with {len(passages.global_offset_map)} passages from metadata"
-    )
+    print(f"Loaded PassageManager with {len(passages.global_offset_map)} passages from metadata")
 
     def zmq_server_thread():
         """ZMQ server thread"""
         context = zmq.Context()
         socket = context.socket(zmq.REP)
         socket.bind(f"tcp://*:{zmq_port}")
-        logger.info(f"HNSW ZMQ server listening on port {zmq_port}")
+        print(f"HNSW ZMQ server listening on port {zmq_port}")
 
         socket.setsockopt(zmq.RCVTIMEO, 300000)
         socket.setsockopt(zmq.SNDTIMEO, 300000)
@@ -99,12 +99,12 @@ def create_hnsw_embedding_server(
         while True:
             try:
                 message_bytes = socket.recv()
-                logger.debug(f"Received ZMQ request of size {len(message_bytes)} bytes")
+                print(f"Received ZMQ request of size {len(message_bytes)} bytes")
 
                 e2e_start = time.time()
                 request_payload = msgpack.unpackb(message_bytes)
 
-                # Handle direct text embedding request
+                # Handle direct text embedding request (for OpenAI and sentence-transformers)
                 if isinstance(request_payload, list) and len(request_payload) > 0:
                     # Check if this is a direct text request (list of strings)
                     if all(isinstance(item, str) for item in request_payload):
@@ -112,7 +112,7 @@ def create_hnsw_embedding_server(
                             f"Processing direct text embedding request for {len(request_payload)} texts in {embedding_mode} mode"
                         )
 
-                        # Use unified embedding computation (now with model caching)
+                        # Use unified embedding computation
                         embeddings = compute_embeddings(
                             request_payload, model_name, mode=embedding_mode
                         )
@@ -136,8 +136,8 @@ def create_hnsw_embedding_server(
                     query_vector = np.array(request_payload[1], dtype=np.float32)
 
                     logger.debug("Distance calculation request received")
-                    logger.debug(f"    Node IDs: {node_ids}")
-                    logger.debug(f"    Query vector dim: {len(query_vector)}")
+                    print(f"    Node IDs: {node_ids}")
+                    print(f"    Query vector dim: {len(query_vector)}")
 
                     # Get embeddings for node IDs
                     texts = []
@@ -147,20 +147,18 @@ def create_hnsw_embedding_server(
                             txt = passage_data["text"]
                             texts.append(txt)
                         except KeyError:
-                            logger.error(f"Passage ID {nid} not found")
-                            raise RuntimeError(
-                                f"FATAL: Passage with ID {nid} not found"
-                            )
+                            print(f"ERROR: Passage ID {nid} not found")
+                            raise RuntimeError(f"FATAL: Passage with ID {nid} not found")
                         except Exception as e:
-                            logger.error(f"Exception looking up passage ID {nid}: {e}")
+                            print(f"ERROR: Exception looking up passage ID {nid}: {e}")
                             raise
 
                     # Process embeddings
                     embeddings = compute_embeddings(
                         texts, model_name, mode=embedding_mode
                     )
-                    logger.info(
-                        f"Computed embeddings for {len(texts)} texts, shape: {embeddings.shape}"
+                    print(
+                        f"INFO: Computed embeddings for {len(texts)} texts, shape: {embeddings.shape}"
                     )
 
                     # Calculate distances
@@ -175,9 +173,7 @@ def create_hnsw_embedding_server(
                     response_bytes = msgpack.packb(
                         [response_payload], use_single_float=True
                     )
-                    logger.debug(
-                        f"Sending distance response with {len(distances)} distances"
-                    )
+                    print(f"Sending distance response with {len(distances)} distances")
 
                     socket.send(response_bytes)
                     e2e_end = time.time()
@@ -192,14 +188,14 @@ def create_hnsw_embedding_server(
                     or len(request_payload) != 1
                     or not isinstance(request_payload[0], list)
                 ):
-                    logger.error(
-                        f"Invalid MessagePack request format. Expected [[ids...]] or [texts...], got: {type(request_payload)}"
+                    print(
+                        f"Error: Invalid MessagePack request format. Expected [[ids...]] or [texts...], got: {type(request_payload)}"
                     )
                     socket.send(msgpack.packb([[], []]))
                     continue
 
                 node_ids = request_payload[0]
-                logger.debug(f"Request for {len(node_ids)} node embeddings")
+                print(f"Request for {len(node_ids)} node embeddings")
 
                 # Look up texts by node IDs
                 texts = []
@@ -208,26 +204,24 @@ def create_hnsw_embedding_server(
                         passage_data = passages.get_passage(str(nid))
                         txt = passage_data["text"]
                         if not txt:
-                            raise RuntimeError(
-                                f"FATAL: Empty text for passage ID {nid}"
-                            )
+                            raise RuntimeError(f"FATAL: Empty text for passage ID {nid}")
                         texts.append(txt)
                     except KeyError:
                         raise RuntimeError(f"FATAL: Passage with ID {nid} not found")
                     except Exception as e:
-                        logger.error(f"Exception looking up passage ID {nid}: {e}")
+                        print(f"ERROR: Exception looking up passage ID {nid}: {e}")
                         raise
 
                 # Process embeddings
                 embeddings = compute_embeddings(texts, model_name, mode=embedding_mode)
-                logger.info(
-                    f"Computed embeddings for {len(texts)} texts, shape: {embeddings.shape}"
+                print(
+                    f"INFO: Computed embeddings for {len(texts)} texts, shape: {embeddings.shape}"
                 )
 
                 # Serialization and response
                 if np.isnan(embeddings).any() or np.isinf(embeddings).any():
-                    logger.error(
-                        f"NaN or Inf detected in embeddings! Requested IDs: {node_ids[:5]}..."
+                    print(
+                        f"{RED}!!! ERROR: NaN or Inf detected in embeddings! Requested IDs: {node_ids[:5]}...{RESET}"
                     )
                     assert False
 
@@ -248,7 +242,7 @@ def create_hnsw_embedding_server(
                 logger.debug("ZMQ socket timeout, continuing to listen")
                 continue
             except Exception as e:
-                logger.error(f"Error in ZMQ server loop: {e}")
+                print(f"Error in ZMQ server loop: {e}")
                 import traceback
 
                 traceback.print_exc()
@@ -256,29 +250,18 @@ def create_hnsw_embedding_server(
 
     zmq_thread = threading.Thread(target=zmq_server_thread, daemon=True)
     zmq_thread.start()
-    logger.info(f"Started HNSW ZMQ server thread on port {zmq_port}")
+    print(f"Started HNSW ZMQ server thread on port {zmq_port}")
 
     # Keep the main thread alive
     try:
         while True:
             time.sleep(1)
     except KeyboardInterrupt:
-        logger.info("HNSW Server shutting down...")
+        print("HNSW Server shutting down...")
         return
 
 
 if __name__ == "__main__":
-    import signal
-    import sys
-    
-    def signal_handler(sig, frame):
-        logger.info(f"Received signal {sig}, shutting down gracefully...")
-        sys.exit(0)
-    
-    # Register signal handlers for graceful shutdown
-    signal.signal(signal.SIGTERM, signal_handler)
-    signal.signal(signal.SIGINT, signal_handler)
-    
     parser = argparse.ArgumentParser(description="HNSW Embedding service")
     parser.add_argument("--zmq-port", type=int, default=5555, help="ZMQ port to run on")
     parser.add_argument(
@@ -299,7 +282,7 @@ if __name__ == "__main__":
         "--embedding-mode",
         type=str,
         default="sentence-transformers",
-        choices=["sentence-transformers", "openai", "mlx"],
+        choices=["sentence-transformers", "openai"],
         help="Embedding backend mode",
     )
 

packages/leann-backend-hnsw/pyproject.toml

@@ -6,14 +6,9 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "leann-backend-hnsw"
-version = "0.1.9"
+version = "0.1.0"
 description = "Custom-built HNSW (Faiss) backend for the Leann toolkit."
-dependencies = [
-    "leann-core==0.1.9", 
-    "numpy",
-    "pyzmq>=23.0.0",
-    "msgpack>=1.0.0",
-]
+dependencies = ["leann-core==0.1.0", "numpy"]
 
 [tool.scikit-build]
 wheel.packages = ["leann_backend_hnsw"]

packages/leann-core/pyproject.toml

@@ -4,23 +4,15 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "leann-core"
-version = "0.1.9"
-description = "Core API and plugin system for LEANN"
+version = "0.1.0"
+description = "Core API and plugin system for Leann."
 readme = "README.md"
 requires-python = ">=3.9"
 license = { text = "MIT" }
 
-# All required dependencies included
 dependencies = [
     "numpy>=1.20.0",
-    "tqdm>=4.60.0",
-    "psutil>=5.8.0",
-    "pyzmq>=23.0.0",
-    "msgpack>=1.0.0",
-    "torch>=2.0.0",
-    "sentence-transformers>=2.2.0",
-    "llama-index-core>=0.12.0",
-    "python-dotenv>=1.0.0",
+    "tqdm>=4.60.0"
 ]
 
 [project.scripts]

packages/leann-core/src/leann/api.py

@@ -5,18 +5,13 @@ with the correct, original embedding logic from the user's reference code.
 
 import json
 import pickle
-from leann.interface import LeannBackendSearcherInterface
 import numpy as np
-import time
 from pathlib import Path
 from typing import List, Dict, Any, Optional, Literal
 from dataclasses import dataclass, field
 from .registry import BACKEND_REGISTRY
 from .interface import LeannBackendFactoryInterface
 from .chat import get_llm
-import logging
-
-logger = logging.getLogger(__name__)
 
 
 def compute_embeddings(
@@ -24,8 +19,7 @@ def compute_embeddings(
     model_name: str,
     mode: str = "sentence-transformers",
     use_server: bool = True,
-    port: Optional[int] = None,
-    is_build=False,
+    port: int = 5557,
 ) -> np.ndarray:
     """
     Computes embeddings using different backends.
@@ -44,8 +38,6 @@ def compute_embeddings(
     """
     if use_server:
         # Use embedding server (for search/query)
-        if port is None:
-            raise ValueError("port is required when use_server is True")
         return compute_embeddings_via_server(chunks, model_name, port=port)
     else:
         # Use direct computation (for build_index)
@@ -57,7 +49,6 @@ def compute_embeddings(
             chunks,
             model_name,
             mode=mode,
-            is_build=is_build,
         )
 
 
@@ -70,8 +61,8 @@ def compute_embeddings_via_server(
         chunks: List of text chunks to embed
         model_name: Name of the sentence transformer model
     """
-    logger.info(
-        f"Computing embeddings for {len(chunks)} chunks using SentenceTransformer model '{model_name}' (via embedding server)..."
+    print(
+        f"INFO: Computing embeddings for {len(chunks)} chunks using SentenceTransformer model '{model_name}' (via embedding server)..."
     )
     import zmq
     import msgpack
@@ -114,24 +105,25 @@ class PassageManager:
         self.global_offset_map = {}  # Combined map for fast lookup
 
         for source in passage_sources:
-            assert source["type"] == "jsonl", "only jsonl is supported"
-            passage_file = source["path"]
-            index_file = source["index_path"]  # .idx file
-            if not Path(index_file).exists():
-                raise FileNotFoundError(f"Passage index file not found: {index_file}")
-            with open(index_file, "rb") as f:
-                offset_map = pickle.load(f)
-                self.offset_maps[passage_file] = offset_map
-                self.passage_files[passage_file] = passage_file
+            if source["type"] == "jsonl":
+                passage_file = source["path"]
+                index_file = source["index_path"]
+                if not Path(index_file).exists():
+                    raise FileNotFoundError(
+                        f"Passage index file not found: {index_file}"
+                    )
+                with open(index_file, "rb") as f:
+                    offset_map = pickle.load(f)
+                    self.offset_maps[passage_file] = offset_map
+                    self.passage_files[passage_file] = passage_file
 
-                # Build global map for O(1) lookup
-                for passage_id, offset in offset_map.items():
-                    self.global_offset_map[passage_id] = (passage_file, offset)
+                    # Build global map for O(1) lookup
+                    for passage_id, offset in offset_map.items():
+                        self.global_offset_map[passage_id] = (passage_file, offset)
 
     def get_passage(self, passage_id: str) -> Dict[str, Any]:
         if passage_id in self.global_offset_map:
             passage_file, offset = self.global_offset_map[passage_id]
-            # Lazy file opening - only open when needed
             with open(passage_file, "r", encoding="utf-8") as f:
                 f.seek(offset)
                 return json.loads(f.readline())
@@ -142,7 +134,7 @@ class LeannBuilder:
     def __init__(
         self,
         backend_name: str,
-        embedding_model: str = "facebook/contriever",
+        embedding_model: str = "facebook/contriever-msmarco",
         dimensions: Optional[int] = None,
         embedding_mode: str = "sentence-transformers",
         **backend_kwargs,
@@ -217,7 +209,7 @@ class LeannBuilder:
             self.embedding_model,
             self.embedding_mode,
             use_server=False,
-            is_build=True,
+            port=5557,
         )
         string_ids = [chunk["id"] for chunk in self.chunks]
         current_backend_kwargs = {**self.backend_kwargs, "dimensions": self.dimensions}
@@ -291,7 +283,7 @@ class LeannBuilder:
                 f"Dimension mismatch: expected {self.dimensions}, got {embedding_dim}"
             )
 
-        logger.info(
+        print(
             f"Building index from precomputed embeddings: {len(ids)} items, {embedding_dim} dimensions"
         )
 
@@ -299,7 +291,7 @@ class LeannBuilder:
         if len(self.chunks) != len(ids):
             # If no text chunks provided, create placeholder text entries
             if not self.chunks:
-                logger.info("No text chunks provided, creating placeholder entries...")
+                print("No text chunks provided, creating placeholder entries...")
                 for id_val in ids:
                     self.add_text(
                         f"Document {id_val}",
@@ -374,19 +366,15 @@ class LeannBuilder:
         with open(leann_meta_path, "w", encoding="utf-8") as f:
             json.dump(meta_data, f, indent=2)
 
-        logger.info(
-            f"Index built successfully from precomputed embeddings: {index_path}"
-        )
+        print(f"Index built successfully from precomputed embeddings: {index_path}")
 
 
 class LeannSearcher:
     def __init__(self, index_path: str, enable_warmup: bool = False, **backend_kwargs):
-        self.meta_path_str = f"{index_path}.meta.json"
-        if not Path(self.meta_path_str).exists():
-            raise FileNotFoundError(
-                f"Leann metadata file not found at {self.meta_path_str}"
-            )
-        with open(self.meta_path_str, "r", encoding="utf-8") as f:
+        meta_path_str = f"{index_path}.meta.json"
+        if not Path(meta_path_str).exists():
+            raise FileNotFoundError(f"Leann metadata file not found at {meta_path_str}")
+        with open(meta_path_str, "r", encoding="utf-8") as f:
             self.meta_data = json.load(f)
         backend_name = self.meta_data["backend_name"]
         self.embedding_model = self.meta_data["embedding_model"]
@@ -394,15 +382,16 @@ class LeannSearcher:
         self.embedding_mode = self.meta_data.get(
             "embedding_mode", "sentence-transformers"
         )
+        # Backward compatibility with use_mlx
+        if self.meta_data.get("use_mlx", False):
+            self.embedding_mode = "mlx"
         self.passage_manager = PassageManager(self.meta_data.get("passage_sources", []))
         backend_factory = BACKEND_REGISTRY.get(backend_name)
         if backend_factory is None:
             raise ValueError(f"Backend '{backend_name}' not found.")
         final_kwargs = {**self.meta_data.get("backend_kwargs", {}), **backend_kwargs}
         final_kwargs["enable_warmup"] = enable_warmup
-        self.backend_impl: LeannBackendSearcherInterface = backend_factory.searcher(
-            index_path, **final_kwargs
-        )
+        self.backend_impl = backend_factory.searcher(index_path, **final_kwargs)
 
     def search(
         self,
@@ -411,39 +400,26 @@ class LeannSearcher:
         complexity: int = 64,
         beam_width: int = 1,
         prune_ratio: float = 0.0,
-        recompute_embeddings: bool = True,
+        recompute_embeddings: bool = False,
         pruning_strategy: Literal["global", "local", "proportional"] = "global",
-        expected_zmq_port: int = 5557,
+        zmq_port: int = 5557,
         **kwargs,
     ) -> List[SearchResult]:
-        logger.info("🔍 LeannSearcher.search() called:")
-        logger.info(f"  Query: '{query}'")
-        logger.info(f"  Top_k: {top_k}")
-        logger.info(f"  Additional kwargs: {kwargs}")
+        print("🔍 DEBUG LeannSearcher.search() called:")
+        print(f"  Query: '{query}'")
+        print(f"  Top_k: {top_k}")
+        print(f"  Additional kwargs: {kwargs}")
 
-        zmq_port = None
-
-        start_time = time.time()
-        if recompute_embeddings:
-            zmq_port = self.backend_impl._ensure_server_running(
-                self.meta_path_str,
-                port=expected_zmq_port,
-                **kwargs,
-            )
-            del expected_zmq_port
-        zmq_time = time.time() - start_time
-        logger.info(f"  Launching server time: {zmq_time} seconds")
+        # Use backend's compute_query_embedding method
+        # This will automatically use embedding server if available and needed
+        import time
 
         start_time = time.time()
 
-        query_embedding = self.backend_impl.compute_query_embedding(
-            query,
-            use_server_if_available=recompute_embeddings,
-            zmq_port=zmq_port,
-        )
-        # logger.info(f"  Generated embedding shape: {query_embedding.shape}")
+        query_embedding = self.backend_impl.compute_query_embedding(query, zmq_port)
+        print(f"  Generated embedding shape: {query_embedding.shape}")
         embedding_time = time.time() - start_time
-        # logger.info(f"  Embedding time: {embedding_time} seconds")
+        print(f"  Embedding time: {embedding_time} seconds")
 
         start_time = time.time()
         results = self.backend_impl.search(
@@ -458,14 +434,14 @@ class LeannSearcher:
             **kwargs,
         )
         search_time = time.time() - start_time
-        # logger.info(f"  Search time: {search_time} seconds")
-        logger.info(
+        print(f"  Search time: {search_time} seconds")
+        print(
             f"  Backend returned: labels={len(results.get('labels', [[]])[0])} results"
         )
 
         enriched_results = []
         if "labels" in results and "distances" in results:
-            logger.info(f"  Processing {len(results['labels'][0])} passage IDs:")
+            print(f"  Processing {len(results['labels'][0])} passage IDs:")
             for i, (string_id, dist) in enumerate(
                 zip(results["labels"][0], results["distances"][0])
             ):
@@ -479,25 +455,15 @@ class LeannSearcher:
                             metadata=passage_data.get("metadata", {}),
                         )
                     )
-                    
-                    # Color codes for better logging
-                    GREEN = "\033[92m"
-                    BLUE = "\033[94m"
-                    YELLOW = "\033[93m"
-                    RESET = "\033[0m"
-                    
-                    # Truncate text for display (first 100 chars)
-                    display_text = passage_data['text']
-                    logger.info(
-                        f"   {GREEN}✓{RESET} {BLUE}[{i + 1:2d}]{RESET} {YELLOW}ID:{RESET} '{string_id}' {YELLOW}Score:{RESET} {dist:.4f} {YELLOW}Text:{RESET} {display_text}"
+                    print(
+                        f"    {i + 1}. passage_id='{string_id}' -> SUCCESS: {passage_data['text']}..."
                     )
                 except KeyError:
-                    RED = "\033[91m"
-                    logger.error(
-                        f"   {RED}✗{RESET} [{i + 1:2d}] ID: '{string_id}' -> {RED}ERROR: Passage not found!{RESET}"
+                    print(
+                        f"    {i + 1}. passage_id='{string_id}' -> ERROR: Passage not found in PassageManager!"
                     )
 
-        logger.info(f"  {GREEN}✓ Final enriched results: {len(enriched_results)} passages{RESET}")
+        print(f"  Final enriched results: {len(enriched_results)} passages")
         return enriched_results
 
 
@@ -519,15 +485,15 @@ class LeannChat:
         complexity: int = 64,
         beam_width: int = 1,
         prune_ratio: float = 0.0,
-        recompute_embeddings: bool = True,
+        recompute_embeddings: bool = False,
         pruning_strategy: Literal["global", "local", "proportional"] = "global",
+        zmq_port: int = 5557,
         llm_kwargs: Optional[Dict[str, Any]] = None,
-        expected_zmq_port: int = 5557,
         **search_kwargs,
     ):
         if llm_kwargs is None:
             llm_kwargs = {}
-        search_time = time.time()
+
         results = self.searcher.search(
             question,
             top_k=top_k,
@@ -536,11 +502,9 @@ class LeannChat:
             prune_ratio=prune_ratio,
             recompute_embeddings=recompute_embeddings,
             pruning_strategy=pruning_strategy,
-            expected_zmq_port=expected_zmq_port,
+            zmq_port=zmq_port,
             **search_kwargs,
         )
-        search_time = time.time() - search_time
-        # logger.info(f"  Search time: {search_time} seconds")
         context = "\n\n".join([r.text for r in results])
         prompt = (
             "Here is some retrieved context that might help answer your question:\n\n"

packages/leann-core/src/leann/chat.py

@@ -9,7 +9,6 @@ from typing import Dict, Any, Optional, List
 import logging
 import os
 import difflib
-import torch
 
 # Configure logging
 logging.basicConfig(level=logging.INFO)
@@ -29,68 +28,6 @@ def check_ollama_models() -> List[str]:
         return []
 
 
-def check_ollama_model_exists_remotely(model_name: str) -> tuple[bool, list[str]]:
-    """Check if a model exists in Ollama's remote library and return available tags
-    
-    Returns:
-        (model_exists, available_tags): bool and list of matching tags
-    """
-    try:
-        import requests
-        import re
-        
-        # Split model name and tag
-        if ':' in model_name:
-            base_model, requested_tag = model_name.split(':', 1)
-        else:
-            base_model, requested_tag = model_name, None
-        
-        # First check if base model exists in library
-        library_response = requests.get("https://ollama.com/library", timeout=8)
-        if library_response.status_code != 200:
-            return True, []  # Assume exists if can't check
-            
-        # Extract model names from library page
-        models_in_library = re.findall(r'href="/library/([^"]+)"', library_response.text)
-        
-        if base_model not in models_in_library:
-            return False, []  # Base model doesn't exist
-        
-        # If base model exists, get available tags
-        tags_response = requests.get(f"https://ollama.com/library/{base_model}/tags", timeout=8)
-        if tags_response.status_code != 200:
-            return True, []  # Base model exists but can't get tags
-            
-        # Extract tags for this model - be more specific to avoid HTML artifacts
-        tag_pattern = rf'{re.escape(base_model)}:[a-zA-Z0-9\.\-_]+'
-        raw_tags = re.findall(tag_pattern, tags_response.text)
-        
-        # Clean up tags - remove HTML artifacts and duplicates
-        available_tags = []
-        seen = set()
-        for tag in raw_tags:
-            # Skip if it looks like HTML (contains < or >)
-            if '<' in tag or '>' in tag:
-                continue
-            if tag not in seen:
-                seen.add(tag)
-                available_tags.append(tag)
-        
-        # Check if exact model exists
-        if requested_tag is None:
-            # User just requested base model, suggest tags
-            return True, available_tags[:10]  # Return up to 10 tags
-        else:
-            exact_match = model_name in available_tags
-            return exact_match, available_tags[:10]
-            
-    except Exception:
-        pass
-    
-    # If scraping fails, assume model might exist (don't block user)
-    return True, []
-
-
 def search_ollama_models_fuzzy(query: str, available_models: List[str]) -> List[str]:
     """Use intelligent fuzzy search for Ollama models"""
     if not available_models:
@@ -306,66 +243,24 @@ def validate_model_and_suggest(model_name: str, llm_type: str) -> Optional[str]:
     if llm_type == "ollama":
         available_models = check_ollama_models()
         if available_models and model_name not in available_models:
+            # Use intelligent fuzzy search based on locally installed models
+            suggestions = search_ollama_models_fuzzy(model_name, available_models)
+            
             error_msg = f"Model '{model_name}' not found in your local Ollama installation."
-            
-            # Check if the model exists remotely and get available tags
-            model_exists_remotely, available_tags = check_ollama_model_exists_remotely(model_name)
-            
-            if model_exists_remotely and model_name in available_tags:
-                # Exact model exists remotely - suggest pulling it
-                error_msg += f"\n\nTo install the requested model:\n"
-                error_msg += f"  ollama pull {model_name}\n"
-                
-                # Show local alternatives
-                suggestions = search_ollama_models_fuzzy(model_name, available_models)
-                if suggestions:
-                    error_msg += "\nOr use one of these similar installed models:\n"
-                    for i, suggestion in enumerate(suggestions, 1):
-                        error_msg += f"  {i}. {suggestion}\n"
-                        
-            elif model_exists_remotely and available_tags:
-                # Base model exists but requested tag doesn't - suggest correct tags
-                base_model = model_name.split(':')[0]
-                requested_tag = model_name.split(':', 1)[1] if ':' in model_name else None
-                
-                error_msg += f"\n\nModel '{base_model}' exists, but tag '{requested_tag}' is not available."
-                error_msg += f"\n\nAvailable {base_model} models you can install:\n"
-                for i, tag in enumerate(available_tags[:8], 1):
-                    error_msg += f"  {i}. ollama pull {tag}\n"
-                if len(available_tags) > 8:
-                    error_msg += f"  ... and {len(available_tags) - 8} more variants\n"
-                    
-                # Also show local alternatives
-                suggestions = search_ollama_models_fuzzy(model_name, available_models)
-                if suggestions:
-                    error_msg += "\nOr use one of these similar installed models:\n"
-                    for i, suggestion in enumerate(suggestions, 1):
-                        error_msg += f"  {i}. {suggestion}\n"
-                        
+            if suggestions:
+                error_msg += "\n\nDid you mean one of these installed models?\n"
+                for i, suggestion in enumerate(suggestions, 1):
+                    error_msg += f"  {i}. {suggestion}\n"
             else:
-                # Model doesn't exist remotely - show fuzzy suggestions
-                suggestions = search_ollama_models_fuzzy(model_name, available_models)
-                error_msg += f"\n\nModel '{model_name}' was not found in Ollama's library."
-                
-                if suggestions:
-                    error_msg += "\n\nDid you mean one of these installed models?\n"
-                    for i, suggestion in enumerate(suggestions, 1):
-                        error_msg += f"  {i}. {suggestion}\n"
-                else:
-                    error_msg += "\n\nYour installed models:\n"
-                    for i, model in enumerate(available_models[:8], 1):
-                        error_msg += f"  {i}. {model}\n"
-                    if len(available_models) > 8:
-                        error_msg += f"  ... and {len(available_models) - 8} more\n"
+                error_msg += "\n\nYour installed models:\n"
+                for i, model in enumerate(available_models[:8], 1):
+                    error_msg += f"  {i}. {model}\n"
+                if len(available_models) > 8:
+                    error_msg += f"  ... and {len(available_models) - 8} more\n"
             
-            error_msg += "\n\nCommands:"
-            error_msg += "\n  ollama list                    # List installed models"
-            if model_exists_remotely and available_tags:
-                if model_name in available_tags:
-                    error_msg += f"\n  ollama pull {model_name}          # Install requested model"
-                else:
-                    error_msg += f"\n  ollama pull {available_tags[0]}    # Install recommended variant"
-            error_msg += "\n  https://ollama.com/library     # Browse available models"
+            error_msg += "\nTo list all models: ollama list"
+            error_msg += "\nTo download a new model: ollama pull <model_name>"
+            error_msg += "\nBrowse models: https://ollama.com/library"
             return error_msg
             
     elif llm_type == "hf":
@@ -480,9 +375,8 @@ class OllamaChat(LLMInterface):
             "stream": False,  # Keep it simple for now
             "options": kwargs,
         }
-        logger.debug(f"Sending request to Ollama: {payload}")
+        logger.info(f"Sending request to Ollama: {payload}")
         try:
-            logger.info(f"Sending request to Ollama and waiting for response...")
             response = requests.post(full_url, data=json.dumps(payload))
             response.raise_for_status()
 
@@ -502,7 +396,7 @@ class OllamaChat(LLMInterface):
 
 
 class HFChat(LLMInterface):
-    """LLM interface for local Hugging Face Transformers models with proper chat templates."""
+    """LLM interface for local Hugging Face Transformers models."""
 
     def __init__(self, model_name: str = "deepseek-ai/deepseek-llm-7b-chat"):
         logger.info(f"Initializing HFChat with model='{model_name}'")
@@ -513,7 +407,7 @@ class HFChat(LLMInterface):
             raise ValueError(model_error)
             
         try:
-            from transformers import AutoTokenizer, AutoModelForCausalLM
+            from transformers.pipelines import pipeline
             import torch
         except ImportError:
             raise ImportError(
@@ -522,101 +416,54 @@ class HFChat(LLMInterface):
 
         # Auto-detect device
         if torch.cuda.is_available():
-            self.device = "cuda"
+            device = "cuda"
             logger.info("CUDA is available. Using GPU.")
         elif hasattr(torch.backends, "mps") and torch.backends.mps.is_available():
-            self.device = "mps"
+            device = "mps"
             logger.info("MPS is available. Using Apple Silicon GPU.")
         else:
-            self.device = "cpu"
+            device = "cpu"
             logger.info("No GPU detected. Using CPU.")
 
-        # Load tokenizer and model
-        self.tokenizer = AutoTokenizer.from_pretrained(model_name)
-        self.model = AutoModelForCausalLM.from_pretrained(
-            model_name,
-            torch_dtype=torch.float16 if self.device != "cpu" else torch.float32,
-            device_map="auto" if self.device != "cpu" else None,
-            trust_remote_code=True
-        )
-        
-        # Move model to device if not using device_map
-        if self.device != "cpu" and "device_map" not in str(self.model):
-            self.model = self.model.to(self.device)
-        
-        # Set pad token if not present
-        if self.tokenizer.pad_token is None:
-            self.tokenizer.pad_token = self.tokenizer.eos_token
+        self.pipeline = pipeline("text-generation", model=model_name, device=device)
 
     def ask(self, prompt: str, **kwargs) -> str:
-        print('kwargs in HF: ', kwargs)
-        # Check if this is a Qwen model and add /no_think by default
-        is_qwen_model = "qwen" in self.model.config._name_or_path.lower()
-        
-        # For Qwen models, automatically add /no_think to the prompt
-        if is_qwen_model and "/no_think" not in prompt and "/think" not in prompt:
-            prompt = prompt + " /no_think"
-        
-        # Prepare chat template
-        messages = [{"role": "user", "content": prompt}]
-        
-        # Apply chat template if available
-        if hasattr(self.tokenizer, "apply_chat_template"):
-            try:
-                formatted_prompt = self.tokenizer.apply_chat_template(
-                    messages, 
-                    tokenize=False, 
-                    add_generation_prompt=True
-                )
-            except Exception as e:
-                logger.warning(f"Chat template failed, using raw prompt: {e}")
-                formatted_prompt = prompt
-        else:
-            # Fallback for models without chat template
-            formatted_prompt = prompt
+        # Map OpenAI-style arguments to Hugging Face equivalents
+        if "max_tokens" in kwargs:
+            # Prefer user-provided max_new_tokens if both are present
+            kwargs.setdefault("max_new_tokens", kwargs["max_tokens"])
+            # Remove the unsupported key to avoid errors in Transformers
+            kwargs.pop("max_tokens")
 
-        # Tokenize input
-        inputs = self.tokenizer(
-            formatted_prompt, 
-            return_tensors="pt", 
-            padding=True,
-            truncation=True,
-            max_length=2048
-        )
-        
-        # Move inputs to device
-        if self.device != "cpu":
-            inputs = {k: v.to(self.device) for k, v in inputs.items()}
+        # Handle temperature=0 edge-case for greedy decoding
+        if "temperature" in kwargs and kwargs["temperature"] == 0.0:
+            # Remove unsupported zero temperature and use deterministic generation
+            kwargs.pop("temperature")
+            kwargs.setdefault("do_sample", False)
 
-        # Set generation parameters
-        generation_config = {
-            "max_new_tokens": kwargs.get("max_tokens", kwargs.get("max_new_tokens", 512)),
-            "temperature": kwargs.get("temperature", 0.7),
-            "top_p": kwargs.get("top_p", 0.9),
-            "do_sample": kwargs.get("temperature", 0.7) > 0,
-            "pad_token_id": self.tokenizer.eos_token_id,
-            "eos_token_id": self.tokenizer.eos_token_id,
-        }
-        
-        # Handle temperature=0 for greedy decoding
-        if generation_config["temperature"] == 0.0:
-            generation_config["do_sample"] = False
-            generation_config.pop("temperature")
+        # Sensible defaults for text generation
+        params = {"max_length": 500, "num_return_sequences": 1, **kwargs}
+        logger.info(f"Generating text with Hugging Face model with params: {params}")
+        results = self.pipeline(prompt, **params)
 
-        logger.info(f"Generating with HuggingFace model, config: {generation_config}")
-        
-        # Generate
-        with torch.no_grad():
-            outputs = self.model.generate(
-                **inputs,
-                **generation_config
+        # Handle different response formats from transformers
+        if isinstance(results, list) and len(results) > 0:
+            generated_text = (
+                results[0].get("generated_text", "")
+                if isinstance(results[0], dict)
+                else str(results[0])
             )
+        else:
+            generated_text = str(results)
 
-        # Decode response
-        generated_tokens = outputs[0][inputs["input_ids"].shape[1]:]
-        response = self.tokenizer.decode(generated_tokens, skip_special_tokens=True)
-        
-        return response.strip()
+        # Extract only the newly generated portion by removing the original prompt
+        if isinstance(generated_text, str) and generated_text.startswith(prompt):
+            response = generated_text[len(prompt) :].strip()
+        else:
+            # Fallback: return the full response if prompt removal fails
+            response = str(generated_text)
+
+        return response
 
 
 class OpenAIChat(LLMInterface):

packages/leann-core/src/leann/cli.py

@@ -1,6 +1,10 @@
+#!/usr/bin/env python3
 import argparse
 import asyncio
+import sys
 from pathlib import Path
+from typing import Optional
+import os
 
 from llama_index.core import SimpleDirectoryReader
 from llama_index.core.node_parser import SentenceSplitter
@@ -12,20 +16,20 @@ class LeannCLI:
     def __init__(self):
         self.indexes_dir = Path.home() / ".leann" / "indexes"
         self.indexes_dir.mkdir(parents=True, exist_ok=True)
-
+        
         self.node_parser = SentenceSplitter(
             chunk_size=256, chunk_overlap=128, separator=" ", paragraph_separator="\n\n"
         )
-
+    
     def get_index_path(self, index_name: str) -> str:
         index_dir = self.indexes_dir / index_name
         return str(index_dir / "documents.leann")
-
+    
     def index_exists(self, index_name: str) -> bool:
         index_dir = self.indexes_dir / index_name
         meta_file = index_dir / "documents.leann.meta.json"
         return meta_file.exists()
-
+    
     def create_parser(self) -> argparse.ArgumentParser:
         parser = argparse.ArgumentParser(
             prog="leann",
@@ -37,32 +41,24 @@ Examples:
   leann search my-docs "query"             # Search in my-docs index
   leann ask my-docs "question"             # Ask my-docs index
   leann list                              # List all stored indexes
-            """,
+            """
         )
-
+        
         subparsers = parser.add_subparsers(dest="command", help="Available commands")
-
+        
         # Build command
         build_parser = subparsers.add_parser("build", help="Build document index")
         build_parser.add_argument("index_name", help="Index name")
-        build_parser.add_argument(
-            "--docs", type=str, required=True, help="Documents directory"
-        )
-        build_parser.add_argument(
-            "--backend", type=str, default="hnsw", choices=["hnsw", "diskann"]
-        )
-        build_parser.add_argument(
-            "--embedding-model", type=str, default="facebook/contriever"
-        )
-        build_parser.add_argument(
-            "--force", "-f", action="store_true", help="Force rebuild"
-        )
+        build_parser.add_argument("--docs", type=str, required=True, help="Documents directory")
+        build_parser.add_argument("--backend", type=str, default="hnsw", choices=["hnsw", "diskann"])
+        build_parser.add_argument("--embedding-model", type=str, default="facebook/contriever")
+        build_parser.add_argument("--force", "-f", action="store_true", help="Force rebuild")
         build_parser.add_argument("--graph-degree", type=int, default=32)
         build_parser.add_argument("--complexity", type=int, default=64)
         build_parser.add_argument("--num-threads", type=int, default=1)
         build_parser.add_argument("--compact", action="store_true", default=True)
         build_parser.add_argument("--recompute", action="store_true", default=True)
-
+        
         # Search command
         search_parser = subparsers.add_parser("search", help="Search documents")
         search_parser.add_argument("index_name", help="Index name")
@@ -72,21 +68,12 @@ Examples:
         search_parser.add_argument("--beam-width", type=int, default=1)
         search_parser.add_argument("--prune-ratio", type=float, default=0.0)
         search_parser.add_argument("--recompute-embeddings", action="store_true")
-        search_parser.add_argument(
-            "--pruning-strategy",
-            choices=["global", "local", "proportional"],
-            default="global",
-        )
-
+        search_parser.add_argument("--pruning-strategy", choices=["global", "local", "proportional"], default="global")
+        
         # Ask command
         ask_parser = subparsers.add_parser("ask", help="Ask questions")
         ask_parser.add_argument("index_name", help="Index name")
-        ask_parser.add_argument(
-            "--llm",
-            type=str,
-            default="ollama",
-            choices=["simulated", "ollama", "hf", "openai"],
-        )
+        ask_parser.add_argument("--llm", type=str, default="ollama", choices=["simulated", "ollama", "hf", "openai"])
         ask_parser.add_argument("--model", type=str, default="qwen3:8b")
         ask_parser.add_argument("--host", type=str, default="http://localhost:11434")
         ask_parser.add_argument("--interactive", "-i", action="store_true")
@@ -95,91 +82,81 @@ Examples:
         ask_parser.add_argument("--beam-width", type=int, default=1)
         ask_parser.add_argument("--prune-ratio", type=float, default=0.0)
         ask_parser.add_argument("--recompute-embeddings", action="store_true")
-        ask_parser.add_argument(
-            "--pruning-strategy",
-            choices=["global", "local", "proportional"],
-            default="global",
-        )
-
+        ask_parser.add_argument("--pruning-strategy", choices=["global", "local", "proportional"], default="global")
+        
         # List command
         list_parser = subparsers.add_parser("list", help="List all indexes")
-
+        
         return parser
-
+    
     def list_indexes(self):
         print("Stored LEANN indexes:")
-
+        
         if not self.indexes_dir.exists():
-            print(
-                "No indexes found. Use 'leann build <name> --docs <dir>' to create one."
-            )
+            print("No indexes found. Use 'leann build <name> --docs <dir>' to create one.")
             return
-
+        
         index_dirs = [d for d in self.indexes_dir.iterdir() if d.is_dir()]
-
+        
         if not index_dirs:
-            print(
-                "No indexes found. Use 'leann build <name> --docs <dir>' to create one."
-            )
+            print("No indexes found. Use 'leann build <name> --docs <dir>' to create one.")
             return
-
+        
         print(f"Found {len(index_dirs)} indexes:")
         for i, index_dir in enumerate(index_dirs, 1):
             index_name = index_dir.name
             status = "✓" if self.index_exists(index_name) else "✗"
-
+            
             print(f"  {i}. {index_name} [{status}]")
             if self.index_exists(index_name):
                 meta_file = index_dir / "documents.leann.meta.json"
-                size_mb = sum(
-                    f.stat().st_size for f in index_dir.iterdir() if f.is_file()
-                ) / (1024 * 1024)
+                size_mb = sum(f.stat().st_size for f in index_dir.iterdir() if f.is_file()) / (1024 * 1024)
                 print(f"     Size: {size_mb:.1f} MB")
-
+        
         if index_dirs:
             example_name = index_dirs[0].name
             print(f"\nUsage:")
-            print(f'  leann search {example_name} "your query"')
+            print(f"  leann search {example_name} \"your query\"")
             print(f"  leann ask {example_name} --interactive")
-
+    
     def load_documents(self, docs_dir: str):
         print(f"Loading documents from {docs_dir}...")
-
+        
         documents = SimpleDirectoryReader(
             docs_dir,
             recursive=True,
             encoding="utf-8",
             required_exts=[".pdf", ".txt", ".md", ".docx"],
         ).load_data(show_progress=True)
-
+        
         all_texts = []
         for doc in documents:
             nodes = self.node_parser.get_nodes_from_documents([doc])
             for node in nodes:
                 all_texts.append(node.get_content())
-
+        
         print(f"Loaded {len(documents)} documents, {len(all_texts)} chunks")
         return all_texts
-
+    
     async def build_index(self, args):
         docs_dir = args.docs
         index_name = args.index_name
         index_dir = self.indexes_dir / index_name
         index_path = self.get_index_path(index_name)
-
+        
         if index_dir.exists() and not args.force:
             print(f"Index '{index_name}' already exists. Use --force to rebuild.")
             return
-
+        
         all_texts = self.load_documents(docs_dir)
         if not all_texts:
             print("No documents found")
             return
-
+        
         index_dir.mkdir(parents=True, exist_ok=True)
-
+        
         print(f"Building index '{index_name}' with {args.backend} backend...")
-
+        
         builder = LeannBuilder(
             backend_name=args.backend,
             embedding_model=args.embedding_model,
@@ -189,107 +166,103 @@ Examples:
             is_recompute=args.recompute,
             num_threads=args.num_threads,
         )
-
+        
         for chunk_text in all_texts:
             builder.add_text(chunk_text)
-
+        
         builder.build_index(index_path)
         print(f"Index built at {index_path}")
-
+    
     async def search_documents(self, args):
         index_name = args.index_name
         query = args.query
         index_path = self.get_index_path(index_name)
-
+        
         if not self.index_exists(index_name):
-            print(
-                f"Index '{index_name}' not found. Use 'leann build {index_name} --docs <dir>' to create it."
-            )
+            print(f"Index '{index_name}' not found. Use 'leann build {index_name} --docs <dir>' to create it.")
             return
-
+        
         searcher = LeannSearcher(index_path=index_path)
         results = searcher.search(
-            query,
+            query, 
             top_k=args.top_k,
             complexity=args.complexity,
             beam_width=args.beam_width,
             prune_ratio=args.prune_ratio,
             recompute_embeddings=args.recompute_embeddings,
-            pruning_strategy=args.pruning_strategy,
+            pruning_strategy=args.pruning_strategy
         )
-
+        
         print(f"Search results for '{query}' (top {len(results)}):")
         for i, result in enumerate(results, 1):
             print(f"{i}. Score: {result.score:.3f}")
             print(f"   {result.text[:200]}...")
             print()
-
+    
     async def ask_questions(self, args):
         index_name = args.index_name
         index_path = self.get_index_path(index_name)
-
+        
         if not self.index_exists(index_name):
-            print(
-                f"Index '{index_name}' not found. Use 'leann build {index_name} --docs <dir>' to create it."
-            )
+            print(f"Index '{index_name}' not found. Use 'leann build {index_name} --docs <dir>' to create it.")
             return
-
+        
         print(f"Starting chat with index '{index_name}'...")
         print(f"Using {args.model} ({args.llm})")
-
+        
         llm_config = {"type": args.llm, "model": args.model}
         if args.llm == "ollama":
             llm_config["host"] = args.host
-
+        
         chat = LeannChat(index_path=index_path, llm_config=llm_config)
-
+        
         if args.interactive:
             print("LEANN Assistant ready! Type 'quit' to exit")
             print("=" * 40)
-
+            
             while True:
                 user_input = input("\nYou: ").strip()
-                if user_input.lower() in ["quit", "exit", "q"]:
+                if user_input.lower() in ['quit', 'exit', 'q']:
                     print("Goodbye!")
                     break
-
+                
                 if not user_input:
                     continue
-
+                
                 response = chat.ask(
-                    user_input,
+                    user_input, 
                     top_k=args.top_k,
                     complexity=args.complexity,
                     beam_width=args.beam_width,
                     prune_ratio=args.prune_ratio,
                     recompute_embeddings=args.recompute_embeddings,
-                    pruning_strategy=args.pruning_strategy,
+                    pruning_strategy=args.pruning_strategy
                 )
                 print(f"LEANN: {response}")
         else:
             query = input("Enter your question: ").strip()
             if query:
                 response = chat.ask(
-                    query,
+                    query, 
                     top_k=args.top_k,
                     complexity=args.complexity,
                     beam_width=args.beam_width,
                     prune_ratio=args.prune_ratio,
                     recompute_embeddings=args.recompute_embeddings,
-                    pruning_strategy=args.pruning_strategy,
+                    pruning_strategy=args.pruning_strategy
                 )
                 print(f"LEANN: {response}")
-
+    
     async def run(self, args=None):
         parser = self.create_parser()
-
+        
         if args is None:
             args = parser.parse_args()
-
+        
         if not args.command:
             parser.print_help()
             return
-
+        
         if args.command == "list":
             self.list_indexes()
         elif args.command == "build":
@@ -304,12 +277,11 @@ Examples:
 
 def main():
     import dotenv
-
     dotenv.load_dotenv()
-
+    
     cli = LeannCLI()
     asyncio.run(cli.run())
 
 
 if __name__ == "__main__":
-    main()
+    main()

packages/leann-core/src/leann/embedding_compute.py

@@ -6,27 +6,14 @@ Preserves all optimization parameters to ensure performance
 
 import numpy as np
 import torch
-from typing import List, Dict, Any
+from typing import List
 import logging
-import os
 
-# Set up logger with proper level
 logger = logging.getLogger(__name__)
-LOG_LEVEL = os.getenv("LEANN_LOG_LEVEL", "WARNING").upper()
-log_level = getattr(logging, LOG_LEVEL, logging.WARNING)
-logger.setLevel(log_level)
-
-# Global model cache to avoid repeated loading
-_model_cache: Dict[str, Any] = {}
 
 
 def compute_embeddings(
-    texts: List[str],
-    model_name: str,
-    mode: str = "sentence-transformers",
-    is_build: bool = False,
-    batch_size: int = 32,
-    adaptive_optimization: bool = True,
+    texts: List[str], model_name: str, mode: str = "sentence-transformers"
 ) -> np.ndarray:
     """
     Unified embedding computation entry point
@@ -35,21 +22,12 @@ def compute_embeddings(
         texts: List of texts to compute embeddings for
         model_name: Model name
         mode: Computation mode ('sentence-transformers', 'openai', 'mlx')
-        is_build: Whether this is a build operation (shows progress bar)
-        batch_size: Batch size for processing
-        adaptive_optimization: Whether to use adaptive optimization based on batch size
 
     Returns:
         Normalized embeddings array, shape: (len(texts), embedding_dim)
     """
     if mode == "sentence-transformers":
-        return compute_embeddings_sentence_transformers(
-            texts,
-            model_name,
-            is_build=is_build,
-            batch_size=batch_size,
-            adaptive_optimization=adaptive_optimization,
-        )
+        return compute_embeddings_sentence_transformers(texts, model_name)
     elif mode == "openai":
         return compute_embeddings_openai(texts, model_name)
     elif mode == "mlx":
@@ -64,28 +42,27 @@ def compute_embeddings_sentence_transformers(
     use_fp16: bool = True,
     device: str = "auto",
     batch_size: int = 32,
-    is_build: bool = False,
-    adaptive_optimization: bool = True,
 ) -> np.ndarray:
     """
-    Compute embeddings using SentenceTransformer with model caching and adaptive optimization
+    Compute embeddings using SentenceTransformer
+    Preserves all optimization parameters to ensure consistency with original embedding_server
 
     Args:
         texts: List of texts to compute embeddings for
-        model_name: Model name
+        model_name: SentenceTransformer model name
         use_fp16: Whether to use FP16 precision
-        device: Device to use ('auto', 'cuda', 'mps', 'cpu')
+        device: Device selection ('auto', 'cuda', 'mps', 'cpu')
         batch_size: Batch size for processing
-        is_build: Whether this is a build operation (shows progress bar)
-        adaptive_optimization: Whether to use adaptive optimization based on batch size
+
+    Returns:
+        Normalized embeddings array, shape: (len(texts), embedding_dim)
     """
-    # Handle empty input
-    if not texts:
-        raise ValueError("Cannot compute embeddings for empty text list")
-    logger.info(
-        f"Computing embeddings for {len(texts)} texts using SentenceTransformer, model: '{model_name}'"
+    print(
+        f"INFO: Computing embeddings for {len(texts)} texts using SentenceTransformer, model: '{model_name}'"
     )
 
+    from sentence_transformers import SentenceTransformer
+
     # Auto-detect device
     if device == "auto":
         if torch.cuda.is_available():
@@ -95,139 +72,75 @@ def compute_embeddings_sentence_transformers(
         else:
             device = "cpu"
 
-    # Apply optimizations based on benchmark results
-    if adaptive_optimization:
-        # Use optimal batch_size constants for different devices based on benchmark results
-        if device == "mps":
-            batch_size = 128  # MPS optimal batch size from benchmark
-            if model_name == "Qwen/Qwen3-Embedding-0.6B":
-                batch_size = 32
-        elif device == "cuda":
-            batch_size = 256  # CUDA optimal batch size
-        # Keep original batch_size for CPU
+    print(f"INFO: Using device: {device}")
 
-    # Create cache key
-    cache_key = f"sentence_transformers_{model_name}_{device}_{use_fp16}_optimized"
+    # Prepare model and tokenizer optimization parameters (consistent with original embedding_server)
+    model_kwargs = {
+        "torch_dtype": torch.float16 if use_fp16 else torch.float32,
+        "low_cpu_mem_usage": True,
+        "_fast_init": True,  # Skip weight initialization checks for faster loading
+    }
 
-    # Check if model is already cached
-    if cache_key in _model_cache:
-        logger.info(f"Using cached optimized model: {model_name}")
-        model = _model_cache[cache_key]
-    else:
-        logger.info(
-            f"Loading and caching optimized SentenceTransformer model: {model_name}"
-        )
-        from sentence_transformers import SentenceTransformer
+    tokenizer_kwargs = {
+        "use_fast": True,  # Use fast tokenizer for better runtime performance
+    }
 
-        logger.info(f"Using device: {device}")
+    # Load SentenceTransformer (try local first, then network)
+    print(f"INFO: Loading SentenceTransformer model: {model_name}")
 
-        # Apply hardware optimizations
-        if device == "cuda":
-            # TODO: Haven't tested this yet
-            torch.backends.cuda.matmul.allow_tf32 = True
-            torch.backends.cudnn.allow_tf32 = True
-            torch.backends.cudnn.benchmark = True
-            torch.backends.cudnn.deterministic = False
-            torch.cuda.set_per_process_memory_fraction(0.9)
-        elif device == "mps":
-            try:
-                if hasattr(torch.mps, "set_per_process_memory_fraction"):
-                    torch.mps.set_per_process_memory_fraction(0.9)
-            except AttributeError:
-                logger.warning(
-                    "Some MPS optimizations not available in this PyTorch version"
-                )
-        elif device == "cpu":
-            # TODO: Haven't tested this yet
-            torch.set_num_threads(min(8, os.cpu_count() or 4))
-            try:
-                torch.backends.mkldnn.enabled = True
-            except AttributeError:
-                pass
+    try:
+        # Try local loading (avoid network delays)
+        model_kwargs["local_files_only"] = True
+        tokenizer_kwargs["local_files_only"] = True
 
-        # Prepare optimized model and tokenizer parameters
-        model_kwargs = {
-            "torch_dtype": torch.float16 if use_fp16 else torch.float32,
-            "low_cpu_mem_usage": True,
-            "_fast_init": True,
-            "attn_implementation": "eager",  # Use eager attention for speed
-        }
-
-        tokenizer_kwargs = {
-            "use_fast": True,
-            "padding": True,
-            "truncation": True,
-        }
-
-        try:
-            # Try local loading first
-            model_kwargs["local_files_only"] = True
-            tokenizer_kwargs["local_files_only"] = True
-
-            model = SentenceTransformer(
-                model_name,
-                device=device,
-                model_kwargs=model_kwargs,
-                tokenizer_kwargs=tokenizer_kwargs,
-                local_files_only=True,
-            )
-            logger.info("Model loaded successfully! (local + optimized)")
-        except Exception as e:
-            logger.warning(f"Local loading failed ({e}), trying network download...")
-            # Fallback to network loading
-            model_kwargs["local_files_only"] = False
-            tokenizer_kwargs["local_files_only"] = False
-
-            model = SentenceTransformer(
-                model_name,
-                device=device,
-                model_kwargs=model_kwargs,
-                tokenizer_kwargs=tokenizer_kwargs,
-                local_files_only=False,
-            )
-            logger.info("Model loaded successfully! (network + optimized)")
-
-        # Apply additional optimizations based on mode
-        if use_fp16 and device in ["cuda", "mps"]:
-            try:
-                model = model.half()
-                logger.info(f"Applied FP16 precision: {model_name}")
-            except Exception as e:
-                logger.warning(f"FP16 optimization failed: {e}")
-
-        # Apply torch.compile optimization
-        if device in ["cuda", "mps"]:
-            try:
-                model = torch.compile(model, mode="reduce-overhead", dynamic=True)
-                logger.info(f"Applied torch.compile optimization: {model_name}")
-            except Exception as e:
-                logger.warning(f"torch.compile optimization failed: {e}")
-
-        # Set model to eval mode and disable gradients for inference
-        model.eval()
-        for param in model.parameters():
-            param.requires_grad_(False)
-
-        # Cache the model
-        _model_cache[cache_key] = model
-        logger.info(f"Model cached: {cache_key}")
-
-    # Compute embeddings with optimized inference mode
-    logger.info(f"Starting embedding computation... (batch_size: {batch_size})")
-
-    # Use torch.inference_mode for optimal performance
-    with torch.inference_mode():
-        embeddings = model.encode(
-            texts,
-            batch_size=batch_size,
-            show_progress_bar=is_build,  # Don't show progress bar in server environment
-            convert_to_numpy=True,
-            normalize_embeddings=False,
+        model = SentenceTransformer(
+            model_name,
             device=device,
+            model_kwargs=model_kwargs,
+            tokenizer_kwargs=tokenizer_kwargs,
+            local_files_only=True,
         )
+        print("✅ Model loaded successfully! (local + optimized)")
+    except Exception as e:
+        print(f"Local loading failed ({e}), trying network download...")
+        # Fallback to network loading
+        model_kwargs["local_files_only"] = False
+        tokenizer_kwargs["local_files_only"] = False
 
-    logger.info(
-        f"Generated {len(embeddings)} embeddings, dimension: {embeddings.shape[1]}"
+        model = SentenceTransformer(
+            model_name,
+            device=device,
+            model_kwargs=model_kwargs,
+            tokenizer_kwargs=tokenizer_kwargs,
+            local_files_only=False,
+        )
+        print("✅ Model loaded successfully! (network + optimized)")
+
+    # Apply additional optimizations (if supported)
+    if use_fp16 and device in ["cuda", "mps"]:
+        try:
+            model = model.half()
+            model = torch.compile(model)
+            print(f"✅ Using FP16 precision and compile optimization: {model_name}")
+        except Exception as e:
+            print(
+                f"FP16 or compile optimization failed, continuing with default settings: {e}"
+            )
+
+    # Compute embeddings (using SentenceTransformer's optimized implementation)
+    print("INFO: Starting embedding computation...")
+
+    embeddings = model.encode(
+        texts,
+        batch_size=batch_size,
+        show_progress_bar=False,  # Don't show progress bar in server environment
+        convert_to_numpy=True,
+        normalize_embeddings=False,  # Keep consistent with original API behavior
+        device=device,
+    )
+
+    print(
+        f"INFO: Generated {len(embeddings)} embeddings, dimension: {embeddings.shape[1]}"
     )
 
     # Validate results
@@ -240,7 +153,6 @@ def compute_embeddings_sentence_transformers(
 
 
 def compute_embeddings_openai(texts: List[str], model_name: str) -> np.ndarray:
-    # TODO: @yichuan-w add progress bar only in build mode
     """Compute embeddings using OpenAI API"""
     try:
         import openai
@@ -252,17 +164,10 @@ def compute_embeddings_openai(texts: List[str], model_name: str) -> np.ndarray:
     if not api_key:
         raise RuntimeError("OPENAI_API_KEY environment variable not set")
 
-    # Cache OpenAI client
-    cache_key = "openai_client"
-    if cache_key in _model_cache:
-        client = _model_cache[cache_key]
-    else:
-        client = openai.OpenAI(api_key=api_key)
-        _model_cache[cache_key] = client
-        logger.info("OpenAI client cached")
+    client = openai.OpenAI(api_key=api_key)
 
-    logger.info(
-        f"Computing embeddings for {len(texts)} texts using OpenAI API, model: '{model_name}'"
+    print(
+        f"INFO: Computing embeddings for {len(texts)} texts using OpenAI API, model: '{model_name}'"
     )
 
     # OpenAI has limits on batch size and input length
@@ -289,12 +194,12 @@ def compute_embeddings_openai(texts: List[str], model_name: str) -> np.ndarray:
             batch_embeddings = [embedding.embedding for embedding in response.data]
             all_embeddings.extend(batch_embeddings)
         except Exception as e:
-            logger.error(f"Batch {i} failed: {e}")
+            print(f"ERROR: Batch {i} failed: {e}")
             raise
 
     embeddings = np.array(all_embeddings, dtype=np.float32)
-    logger.info(
-        f"Generated {len(embeddings)} embeddings, dimension: {embeddings.shape[1]}"
+    print(
+        f"INFO: Generated {len(embeddings)} embeddings, dimension: {embeddings.shape[1]}"
     )
     return embeddings
 
@@ -302,30 +207,22 @@ def compute_embeddings_openai(texts: List[str], model_name: str) -> np.ndarray:
 def compute_embeddings_mlx(
     chunks: List[str], model_name: str, batch_size: int = 16
 ) -> np.ndarray:
-    # TODO: @yichuan-w add progress bar only in build mode
     """Computes embeddings using an MLX model."""
     try:
         import mlx.core as mx
         from mlx_lm.utils import load
+        from tqdm import tqdm
     except ImportError as e:
         raise RuntimeError(
             "MLX or related libraries not available. Install with: uv pip install mlx mlx-lm"
         ) from e
 
-    logger.info(
-        f"Computing embeddings for {len(chunks)} chunks using MLX model '{model_name}' with batch_size={batch_size}..."
+    print(
+        f"INFO: Computing embeddings for {len(chunks)} chunks using MLX model '{model_name}' with batch_size={batch_size}..."
     )
 
-    # Cache MLX model and tokenizer
-    cache_key = f"mlx_{model_name}"
-    if cache_key in _model_cache:
-        logger.info(f"Using cached MLX model: {model_name}")
-        model, tokenizer = _model_cache[cache_key]
-    else:
-        logger.info(f"Loading and caching MLX model: {model_name}")
-        model, tokenizer = load(model_name)
-        _model_cache[cache_key] = (model, tokenizer)
-        logger.info(f"MLX model cached: {cache_key}")
+    # Load model and tokenizer
+    model, tokenizer = load(model_name)
 
     # Process chunks in batches with progress bar
     all_embeddings = []

packages/leann-core/src/leann/embedding_server_manager.py

@@ -1,22 +1,14 @@
+import threading
 import time
 import atexit
 import socket
 import subprocess
 import sys
-import os
-import logging
 from pathlib import Path
 from typing import Optional
+import select
 import psutil
 
-# Set up logging based on environment variable
-LOG_LEVEL = os.getenv("LEANN_LOG_LEVEL", "WARNING").upper()
-logging.basicConfig(
-    level=getattr(logging, LOG_LEVEL, logging.INFO),
-    format="%(levelname)s - %(name)s - %(message)s",
-)
-logger = logging.getLogger(__name__)
-
 
 def _check_port(port: int) -> bool:
     """Check if a port is in use"""
@@ -44,11 +36,11 @@ def _check_process_matches_config(
                 cmdline, port, expected_model, expected_passages_file
             )
 
-        logger.debug(f"No process found listening on port {port}")
+        print(f"DEBUG: No process found listening on port {port}")
         return False
 
     except Exception as e:
-        logger.warning(f"Could not check process on port {port}: {e}")
+        print(f"WARNING: Could not check process on port {port}: {e}")
         return False
 
 
@@ -69,7 +61,7 @@ def _check_cmdline_matches_config(
 ) -> bool:
     """Check if command line matches our expected configuration."""
     cmdline_str = " ".join(cmdline)
-    logger.debug(f"Found process on port {port}: {cmdline_str}")
+    print(f"DEBUG: Found process on port {port}: {cmdline_str}")
 
     # Check if it's our embedding server
     is_embedding_server = any(
@@ -82,7 +74,7 @@ def _check_cmdline_matches_config(
     )
 
     if not is_embedding_server:
-        logger.debug(f"Process on port {port} is not our embedding server")
+        print(f"DEBUG: Process on port {port} is not our embedding server")
         return False
 
     # Check model name
@@ -92,8 +84,8 @@ def _check_cmdline_matches_config(
     passages_matches = _check_passages_in_cmdline(cmdline, expected_passages_file)
 
     result = model_matches and passages_matches
-    logger.debug(
-        f"model_matches: {model_matches}, passages_matches: {passages_matches}, overall: {result}"
+    print(
+        f"DEBUG: model_matches: {model_matches}, passages_matches: {passages_matches}, overall: {result}"
     )
     return result
 
@@ -140,10 +132,10 @@ def _find_compatible_port_or_next_available(
 
         # Port is in use, check if it's compatible
         if _check_process_matches_config(port, model_name, passages_file):
-            logger.info(f"Found compatible server on port {port}")
+            print(f"✅ Found compatible server on port {port}")
             return port, True
         else:
-            logger.info(f"Port {port} has incompatible server, trying next port...")
+            print(f"⚠️  Port {port} has incompatible server, trying next port...")
 
     raise RuntimeError(
         f"Could not find compatible or available port in range {start_port}-{start_port + max_attempts}"
@@ -202,17 +194,17 @@ class EmbeddingServerManager:
                 port, model_name, passages_file
             )
         except RuntimeError as e:
-            logger.error(str(e))
+            print(f"❌ {e}")
             return False, port
 
         if is_compatible:
-            logger.info(f"Using existing compatible server on port {actual_port}")
+            print(f"✅ Using existing compatible server on port {actual_port}")
             self.server_port = actual_port
             self.server_process = None  # We don't own this process
             return True, actual_port
 
         if actual_port != port:
-            logger.info(f"Using port {actual_port} instead of {port}")
+            print(f"⚠️  Using port {actual_port} instead of {port}")
 
         # Start new server
         return self._start_new_server(actual_port, model_name, embedding_mode, **kwargs)
@@ -229,21 +221,19 @@ class EmbeddingServerManager:
             return False
 
         if _check_process_matches_config(self.server_port, model_name, passages_file):
-            logger.info(
-                f"Existing server process (PID {self.server_process.pid}) is compatible"
+            print(
+                f"✅ Existing server process (PID {self.server_process.pid}) is compatible"
             )
             return True
 
-        logger.info(
-            "Existing server process is incompatible. Should start a new server."
-        )
+        print("⚠️  Existing server process is incompatible. Should start a new server.")
         return False
 
     def _start_new_server(
         self, port: int, model_name: str, embedding_mode: str, **kwargs
     ) -> tuple[bool, int]:
         """Start a new embedding server on the given port."""
-        logger.info(f"Starting embedding server on port {port}...")
+        print(f"INFO: Starting embedding server on port {port}...")
 
         command = self._build_server_command(port, model_name, embedding_mode, **kwargs)
 
@@ -251,7 +241,7 @@ class EmbeddingServerManager:
             self._launch_server_process(command, port)
             return self._wait_for_server_ready(port)
         except Exception as e:
-            logger.error(f"Failed to start embedding server: {e}")
+            print(f"❌ ERROR: Failed to start embedding server: {e}")
             return False, port
 
     def _build_server_command(
@@ -269,9 +259,7 @@ class EmbeddingServerManager:
         ]
 
         if kwargs.get("passages_file"):
-            # Convert to absolute path to ensure subprocess can find the file
-            passages_file = Path(kwargs["passages_file"]).resolve()
-            command.extend(["--passages-file", str(passages_file)])
+            command.extend(["--passages-file", str(kwargs["passages_file"])])
         if embedding_mode != "sentence-transformers":
             command.extend(["--embedding-mode", embedding_mode])
 
@@ -280,18 +268,20 @@ class EmbeddingServerManager:
     def _launch_server_process(self, command: list, port: int) -> None:
         """Launch the server process."""
         project_root = Path(__file__).parent.parent.parent.parent.parent
-        logger.info(f"Command: {' '.join(command)}")
+        print(f"INFO: Command: {' '.join(command)}")
 
-        # Let server output go directly to console
-        # The server will respect LEANN_LOG_LEVEL environment variable
         self.server_process = subprocess.Popen(
             command,
             cwd=project_root,
-            stdout=None,  # Direct to console
-            stderr=None,  # Direct to console
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
+            text=True,
+            encoding="utf-8",
+            bufsize=1,
+            universal_newlines=True,
         )
         self.server_port = port
-        logger.info(f"Server process started with PID: {self.server_process.pid}")
+        print(f"INFO: Server process started with PID: {self.server_process.pid}")
 
         # Register atexit callback only when we actually start a process
         if not self._atexit_registered:
@@ -304,19 +294,49 @@ class EmbeddingServerManager:
         max_wait, wait_interval = 120, 0.5
         for _ in range(int(max_wait / wait_interval)):
             if _check_port(port):
-                logger.info("Embedding server is ready!")
+                print("✅ Embedding server is ready!")
+                threading.Thread(target=self._log_monitor, daemon=True).start()
                 return True, port
 
-            if self.server_process and self.server_process.poll() is not None:
-                logger.error("Server terminated during startup.")
+            if self.server_process.poll() is not None:
+                print("❌ ERROR: Server terminated during startup.")
+                self._print_recent_output()
                 return False, port
 
             time.sleep(wait_interval)
 
-        logger.error(f"Server failed to start within {max_wait} seconds.")
+        print(f"❌ ERROR: Server failed to start within {max_wait} seconds.")
         self.stop_server()
         return False, port
 
+    def _print_recent_output(self):
+        """Print any recent output from the server process."""
+        if not self.server_process or not self.server_process.stdout:
+            return
+        try:
+            if select.select([self.server_process.stdout], [], [], 0)[0]:
+                output = self.server_process.stdout.read()
+                if output:
+                    print(f"[{self.backend_module_name} OUTPUT]: {output}")
+        except Exception as e:
+            print(f"Error reading server output: {e}")
+
+    def _log_monitor(self):
+        """Monitors and prints the server's stdout and stderr."""
+        if not self.server_process:
+            return
+        try:
+            if self.server_process.stdout:
+                while True:
+                    line = self.server_process.stdout.readline()
+                    if not line:
+                        break
+                    print(
+                        f"[{self.backend_module_name} LOG]: {line.strip()}", flush=True
+                    )
+        except Exception as e:
+            print(f"Log monitor error: {e}")
+
     def stop_server(self):
         """Stops the embedding server process if it's running."""
         if not self.server_process:
@@ -327,24 +347,18 @@ class EmbeddingServerManager:
             self.server_process = None
             return
 
-        logger.info(
-            f"Terminating server process (PID: {self.server_process.pid}) for backend {self.backend_module_name}..."
+        print(
+            f"INFO: Terminating server process (PID: {self.server_process.pid}) for backend {self.backend_module_name}..."
         )
         self.server_process.terminate()
 
         try:
             self.server_process.wait(timeout=5)
-            logger.info(f"Server process {self.server_process.pid} terminated.")
+            print(f"INFO: Server process {self.server_process.pid} terminated.")
         except subprocess.TimeoutExpired:
-            logger.warning(
-                f"Server process {self.server_process.pid} did not terminate gracefully, killing it."
+            print(
+                f"WARNING: Server process {self.server_process.pid} did not terminate gracefully, killing it."
             )
             self.server_process.kill()
 
-        # Clean up process resources to prevent resource tracker warnings
-        try:
-            self.server_process.wait()  # Ensure process is fully cleaned up
-        except Exception:
-            pass
-
         self.server_process = None

packages/leann-core/src/leann/interface.py

@@ -1,6 +1,6 @@
 from abc import ABC, abstractmethod
 import numpy as np
-from typing import Dict, Any, List, Literal, Optional
+from typing import Dict, Any, List, Literal
 
 
 class LeannBackendBuilderInterface(ABC):
@@ -34,13 +34,6 @@ class LeannBackendSearcherInterface(ABC):
         """
         pass
 
-    @abstractmethod
-    def _ensure_server_running(
-        self, passages_source_file: str, port: Optional[int], **kwargs
-    ) -> int:
-        """Ensure server is running"""
-        pass
-
     @abstractmethod
     def search(
         self,
@@ -51,7 +44,7 @@ class LeannBackendSearcherInterface(ABC):
         prune_ratio: float = 0.0,
         recompute_embeddings: bool = False,
         pruning_strategy: Literal["global", "local", "proportional"] = "global",
-        zmq_port: Optional[int] = None,
+        zmq_port: int = 5557,
         **kwargs,
     ) -> Dict[str, Any]:
         """Search for nearest neighbors
@@ -64,7 +57,7 @@ class LeannBackendSearcherInterface(ABC):
             prune_ratio: Ratio of neighbors to prune via approximate distance (0.0-1.0)
             recompute_embeddings: Whether to fetch fresh embeddings from server vs use stored PQ codes
             pruning_strategy: PQ candidate selection strategy - "global" (default), "local", or "proportional"
-            zmq_port: ZMQ port for embedding server communication. Must be provided if recompute_embeddings is True.
+            zmq_port: ZMQ port for embedding server communication
             **kwargs: Backend-specific parameters
 
         Returns:
@@ -74,10 +67,7 @@ class LeannBackendSearcherInterface(ABC):
 
     @abstractmethod
     def compute_query_embedding(
-        self,
-        query: str,
-        use_server_if_available: bool = True,
-        zmq_port: Optional[int] = None,
+        self, query: str, zmq_port: int = 5557, use_server_if_available: bool = True
     ) -> np.ndarray:
         """Compute embedding for a query string
 

packages/leann-core/src/leann/searcher_base.py

@@ -1,7 +1,8 @@
 import json
+import pickle
 from abc import ABC, abstractmethod
 from pathlib import Path
-from typing import Dict, Any, Literal, Optional
+from typing import Dict, Any, Literal
 
 import numpy as np
 
@@ -42,10 +43,8 @@ class BaseSearcher(LeannBackendSearcherInterface, ABC):
                 "WARNING: embedding_model not found in meta.json. Recompute will fail."
             )
 
-        self.embedding_mode = self.meta.get("embedding_mode", "sentence-transformers")
-
         self.embedding_server_manager = EmbeddingServerManager(
-            backend_module_name=backend_module_name,
+            backend_module_name=backend_module_name
         )
 
     def _load_meta(self) -> Dict[str, Any]:
@@ -69,12 +68,14 @@ class BaseSearcher(LeannBackendSearcherInterface, ABC):
                 "Cannot use recompute mode without 'embedding_model' in meta.json."
             )
 
+        embedding_mode = self.meta.get("embedding_mode", "sentence-transformers")
+
         server_started, actual_port = self.embedding_server_manager.start_server(
             port=port,
             model_name=self.embedding_model,
-            embedding_mode=self.embedding_mode,
             passages_file=passages_source_file,
             distance_metric=kwargs.get("distance_metric"),
+            embedding_mode=embedding_mode,
             enable_warmup=kwargs.get("enable_warmup", False),
         )
         if not server_started:
@@ -85,10 +86,7 @@ class BaseSearcher(LeannBackendSearcherInterface, ABC):
         return actual_port
 
     def compute_query_embedding(
-        self,
-        query: str,
-        use_server_if_available: bool = True,
-        zmq_port: int = 5557,
+        self, query: str, zmq_port: int = 5557, use_server_if_available: bool = True
     ) -> np.ndarray:
         """
         Compute embedding for a query string.
@@ -104,17 +102,12 @@ class BaseSearcher(LeannBackendSearcherInterface, ABC):
         # Try to use embedding server if available and requested
         if use_server_if_available:
             try:
-                # TODO: Maybe we can directly use this port here?
-                # For this internal method, it's ok to assume that the server is running
-                # on that port?
-
                 # Ensure we have a server with passages_file for compatibility
                 passages_source_file = (
                     self.index_dir / f"{self.index_path.name}.meta.json"
                 )
-                # Convert to absolute path to ensure server can find it
                 zmq_port = self._ensure_server_running(
-                    str(passages_source_file.resolve()), zmq_port
+                    str(passages_source_file), zmq_port
                 )
 
                 return self._compute_embedding_via_server([query], zmq_port)[
@@ -125,7 +118,7 @@ class BaseSearcher(LeannBackendSearcherInterface, ABC):
                 print("⏭️ Falling back to direct model loading...")
 
         # Fallback to direct computation
-        from .embedding_compute import compute_embeddings
+        from .api import compute_embeddings
 
         embedding_mode = self.meta.get("embedding_mode", "sentence-transformers")
         return compute_embeddings([query], self.embedding_model, embedding_mode)
@@ -172,7 +165,7 @@ class BaseSearcher(LeannBackendSearcherInterface, ABC):
         prune_ratio: float = 0.0,
         recompute_embeddings: bool = False,
         pruning_strategy: Literal["global", "local", "proportional"] = "global",
-        zmq_port: Optional[int] = None,
+        zmq_port: int = 5557,
         **kwargs,
     ) -> Dict[str, Any]:
         """
@@ -186,7 +179,7 @@ class BaseSearcher(LeannBackendSearcherInterface, ABC):
             prune_ratio: Ratio of neighbors to prune via approximate distance (0.0-1.0)
             recompute_embeddings: Whether to fetch fresh embeddings from server vs use stored PQ codes
             pruning_strategy: PQ candidate selection strategy - "global" (default), "local", or "proportional"
-            zmq_port: ZMQ port for embedding server communication. Must be provided if recompute_embeddings is True.
+            zmq_port: ZMQ port for embedding server communication
             **kwargs: Backend-specific parameters (e.g., batch_size, dedup_node_dis, etc.)
 
         Returns:

packages/leann/README.md

@@ -1,40 +0,0 @@
-# LEANN - The smallest vector index in the world
-
-LEANN is a revolutionary vector database that democratizes personal AI. Transform your laptop into a powerful RAG system that can index and search through millions of documents while using **97% less storage** than traditional solutions **without accuracy loss**.
-
-## Installation
-
-```bash
-# Default installation (HNSW backend, recommended)
-uv pip install leann
-
-# With DiskANN backend (for large-scale deployments)
-uv pip install leann[diskann]
-```
-
-## Quick Start
-
-```python
-from leann import LeannBuilder, LeannSearcher, LeannChat
-
-# Build an index
-builder = LeannBuilder(backend_name="hnsw")
-builder.add_text("LEANN saves 97% storage compared to traditional vector databases.")
-builder.build_index("my_index.leann")
-
-# Search
-searcher = LeannSearcher("my_index.leann")
-results = searcher.search("storage savings", top_k=3)
-
-# Chat with your data
-chat = LeannChat("my_index.leann", llm_config={"type": "ollama", "model": "llama3.2:1b"})
-response = chat.ask("How much storage does LEANN save?")
-```
-
-## Documentation
-
-For full documentation, visit [https://leann.readthedocs.io](https://leann.readthedocs.io)
-
-## License
-
-MIT License 

packages/leann/__init__.py

@@ -1,12 +0,0 @@
-"""
-LEANN - Low-storage Embedding Approximation for Neural Networks
-
-A revolutionary vector database that democratizes personal AI.
-"""
-
-__version__ = "0.1.0"
-
-# Re-export main API from leann-core
-from leann_core import LeannBuilder, LeannSearcher, LeannChat
-
-__all__ = ["LeannBuilder", "LeannSearcher", "LeannChat"]

packages/leann/pyproject.toml

@@ -1,42 +0,0 @@
-[build-system]
-requires = ["setuptools>=61.0"]
-build-backend = "setuptools.build_meta"
-
-[project]
-name = "leann"
-version = "0.1.9"
-description = "LEANN - The smallest vector index in the world. RAG Everything with LEANN!"
-readme = "README.md"
-requires-python = ">=3.9"
-license = { text = "MIT" }
-authors = [
-    { name = "LEANN Team" }
-]
-keywords = ["vector-database", "rag", "embeddings", "search", "ai"]
-classifiers = [
-    "Development Status :: 4 - Beta",
-    "Intended Audience :: Developers",
-    "License :: OSI Approved :: MIT License",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-]
-
-# Default installation: core + hnsw
-dependencies = [
-    "leann-core>=0.1.0",
-    "leann-backend-hnsw>=0.1.0",
-]
-
-[project.optional-dependencies]
-diskann = [
-    "leann-backend-diskann>=0.1.0",
-]
-
-[project.urls]
-Homepage = "https://github.com/yourusername/leann"
-Documentation = "https://leann.readthedocs.io"
-Repository = "https://github.com/yourusername/leann"
-Issues = "https://github.com/yourusername/leann/issues" 

pyproject.toml

@@ -33,8 +33,8 @@ dependencies = [
     "msgpack>=1.1.1",
     "llama-index-vector-stores-faiss>=0.4.0",
     "llama-index-embeddings-huggingface>=0.5.5",
-    "mlx>=0.26.3; sys_platform == 'darwin'",
-    "mlx-lm>=0.26.0; sys_platform == 'darwin'",
+    "mlx>=0.26.3",
+    "mlx-lm>=0.26.0",
     "psutil>=5.8.0",
 ]
 

research/micro/analyze_HNSW.py

@@ -0,0 +1,12 @@
+import faiss
+hnsw_index = faiss.read_index("/opt/dlami/nvme/scaling_out/indices/rpj_wiki/facebook/contriever-msmarco/hnsw/hnsw_IP_M30_efC128.index", faiss.IO_FLAG_ONDISK_SAME_DIR)
+
+# print total number of nodes
+print(hnsw_index.ntotal)
+
+# print  stats of the graph
+print(hnsw_index.hnsw.print_neighbor_stats(0))
+
+
+# save_degree_distribution
+hnsw_index.hnsw.save_degree_distribution(0, "degree_distribution_HNSW_M30.txt")

research/micro/analyze_NSG.py

@@ -0,0 +1,11 @@
+import faiss
+nsg_index = faiss.read_index("/opt/dlami/nvme/scaling_out/indices/rpj_wiki/facebook/contriever-msmarco/nsg_R16.index", faiss.IO_FLAG_ONDISK_SAME_DIR)
+
+# print total number of nodes
+print(nsg_index.ntotal)
+
+# print stats of the graph
+print(nsg_index.nsg.print_neighbor_stats(0))
+
+# save degree distribution
+nsg_index.nsg.save_degree_distribution("degree_distribution_NSG_R60.txt")

research/micro/bnbtest.py

@@ -0,0 +1,63 @@
+import torch
+import torch.nn as nn
+import time
+
+# import bitsandbytes as bnb
+from bitsandbytes.nn import Linear8bitLt
+
+# set default to half
+import torch
+torch.set_default_dtype(torch.float16)
+
+M = 2048
+N = 2048
+
+bsz =  2048
+import torch_int
+from torch_int.nn.linear import W8A8BFP32OFP32Linear, W8A8B8O8Linear, W8A8B8O8LinearReLU
+
+fp16_model = nn.Sequential(
+    nn.Linear(M, N),
+    # nn.Linear(2048, 2048)
+)
+
+int8_model = nn.Sequential(
+    Linear8bitLt(M, N, has_fp16_weights=False),
+    # Linear8bitLt(2048, 2048, has_fp16_weights=False)
+)
+
+int8_model.load_state_dict(fp16_model.state_dict())
+int8_model = int8_model.to(0) # Quantization happens here
+fp16_model = fp16_model.to(0) # Move fp16 model to GPU as well
+
+# Create random input tensor
+input_tensor = torch.randn(bsz, M, device=0)  # Batch of 1000 vectors
+
+# Speed test function
+def speed_test(model, input_tensor, name, num_iterations=100):
+    # Warmup
+    for _ in range(10):
+        _ = model(input_tensor)
+    
+    # Actual timing
+    torch.cuda.synchronize()
+    start_time = time.time()
+    
+    for _ in range(num_iterations):
+        _ = model(input_tensor)
+    
+    torch.cuda.synchronize()
+    end_time = time.time()
+    
+    avg_time = (end_time - start_time) / num_iterations
+    print(f"{name} model: {avg_time:.6f} seconds per iteration")
+    return avg_time
+
+# Run speed tests
+with torch.no_grad():  # Disable gradient calculation for inference
+    fp16_time = speed_test(fp16_model, input_tensor, "FP16")
+    int8_time = speed_test(int8_model, input_tensor, "INT8")
+    
+    # Calculate speedup
+    speedup = fp16_time / int8_time
+    print(f"INT8 is {speedup:.2f}x faster than FP16")

research/micro/data/transformer-batching-microbenchmarks.csv

@@ -0,0 +1,89 @@
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research/micro/embedd_micro.py

@@ -0,0 +1,594 @@
+# python embedd_micro.py --use_int8 Fastest
+
+import argparse
+import time
+from dataclasses import dataclass
+from typing import Dict, List, Optional, Tuple
+
+import numpy as np
+import torch
+from torch import nn
+from torchao import quantize_
+from transformers import AutoModel, BitsAndBytesConfig
+from tqdm import tqdm
+from contextlib import contextmanager
+
+@dataclass
+class BenchmarkConfig:
+    model_path: str
+    batch_sizes: List[int]
+    seq_length: int
+    num_runs: int
+    use_fp16: bool = True
+    use_int4: bool = False
+    use_int8: bool = False  # Add this parameter
+    use_cuda_graphs: bool = False
+    use_flash_attention: bool = False
+    use_linear8bitlt: bool = False
+
+
+class CUDAGraphContainer:
+    """Container for managing CUDA graphs for different batch sizes."""
+    
+    def __init__(self, model: nn.Module, seq_length: int):
+        self.model = model
+        self.seq_length = seq_length
+        self.graphs: Dict[int, CUDAGraphWrapper] = {}
+    
+    def get_or_create(self, batch_size: int) -> 'CUDAGraphWrapper':
+        if batch_size not in self.graphs:
+            self.graphs[batch_size] = CUDAGraphWrapper(
+                self.model, batch_size, self.seq_length
+            )
+        return self.graphs[batch_size]
+
+
+class CUDAGraphWrapper:
+    """Wrapper for CUDA graph capture and replay."""
+    
+    def __init__(self, model: nn.Module, batch_size: int, seq_length: int):
+        self.model = model
+        self.static_input = self._create_random_batch(batch_size, seq_length)
+        self.static_attention_mask = torch.ones_like(self.static_input)
+        
+        # Warm up
+        self._warmup()
+        
+        # Capture graph
+        self.graph = torch.cuda.CUDAGraph()
+        with torch.cuda.graph(self.graph):
+            self.static_output = self.model(
+                input_ids=self.static_input,
+                attention_mask=self.static_attention_mask
+            )
+    
+    def _create_random_batch(self, batch_size: int, seq_length: int) -> torch.Tensor:
+        return torch.randint(
+            0, 1000, (batch_size, seq_length), 
+            device="cuda", 
+            dtype=torch.long
+        )
+    
+    def _warmup(self, num_warmup: int = 3):
+        with torch.no_grad():
+            for _ in range(num_warmup):
+                self.model(
+                    input_ids=self.static_input,
+                    attention_mask=self.static_attention_mask
+                )
+    
+    def __call__(self, input_ids: torch.Tensor, attention_mask: torch.Tensor) -> torch.Tensor:
+        self.static_input.copy_(input_ids)
+        self.static_attention_mask.copy_(attention_mask)
+        self.graph.replay()
+        return self.static_output
+
+
+class ModelOptimizer:
+    """Applies various optimizations to the model."""
+    
+    @staticmethod
+    def optimize(model: nn.Module, config: BenchmarkConfig) -> nn.Module:
+        print("\nApplying model optimizations:")
+        
+        if model is None:
+            raise ValueError("Cannot optimize None model")
+        
+        # Move to GPU
+        model = model.cuda()
+        print("- Model moved to GPU")
+        
+        # FP16
+        if config.use_fp16 and not config.use_int4:
+            model = model.half()
+            # use torch compile
+            model = torch.compile(model)
+            print("- Using FP16 precision")
+        
+        # Check if using SDPA
+        if torch.version.cuda and float(torch.version.cuda[:3]) >= 11.6:
+            if hasattr(torch.nn.functional, 'scaled_dot_product_attention'):
+                print("- Using PyTorch SDPA (scaled_dot_product_attention)")
+            else:
+                print("- PyTorch SDPA not available")
+        
+        # Flash Attention
+        if config.use_flash_attention:
+            try:
+                from flash_attn.flash_attention import FlashAttention
+                print("- Flash Attention 2 available")
+                if hasattr(model.config, "attention_mode"):
+                    model.config.attention_mode = "flash_attention_2"
+                    print("  - Enabled Flash Attention 2 mode")
+            except ImportError:
+                print("- Flash Attention not available")
+        
+        # Memory efficient attention
+        try:
+            from xformers.ops import memory_efficient_attention
+            if hasattr(model, 'enable_xformers_memory_efficient_attention'):
+                model.enable_xformers_memory_efficient_attention()
+                print("- Enabled xformers memory efficient attention")
+            else:
+                print("- Model doesn't support xformers")
+        except (ImportError, AttributeError):
+            print("- Xformers not available")
+        
+        model.eval()
+        print("- Model set to eval mode")
+        
+        return model
+
+
+class Timer:
+    """Handles accurate GPU timing using CUDA events."""
+    
+    def __init__(self):
+        self.start_event = torch.cuda.Event(enable_timing=True)
+        self.end_event = torch.cuda.Event(enable_timing=True)
+    
+    @contextmanager
+    def timing(self):
+        self.start_event.record()
+        yield
+        self.end_event.record()
+        self.end_event.synchronize()
+    
+    def elapsed_time(self) -> float:
+        return self.start_event.elapsed_time(self.end_event) / 1000  # ms to seconds
+
+
+class Benchmark:
+    """Main benchmark runner."""
+    
+    def __init__(self, config: BenchmarkConfig):
+        self.config = config
+        try:
+            self.model = self._load_model()
+            if self.model is None:
+                raise ValueError("Model initialization failed - model is None")
+            
+            self.cuda_graphs = (
+                CUDAGraphContainer(self.model, config.seq_length)
+                if config.use_cuda_graphs
+                else None
+            )
+            self.timer = Timer()
+        except Exception as e:
+            print(f"ERROR in benchmark initialization: {str(e)}")
+            raise
+    
+    def _load_model(self) -> nn.Module:
+        print(f"Loading model from {self.config.model_path}...")
+        
+        try:
+            # Int4 quantization using HuggingFace integration
+            if self.config.use_int4:
+                import bitsandbytes as bnb
+                print(f"- bitsandbytes version: {bnb.__version__}")
+                
+                # 检查是否使用自定义的8bit量化
+                if hasattr(self.config, 'use_linear8bitlt') and self.config.use_linear8bitlt:
+                    print("- Using custom Linear8bitLt replacement for all linear layers")
+                    
+                    # 加载原始模型（不使用量化配置）
+                    import bitsandbytes as bnb
+                    import torch
+                    # set default to half
+                    torch.set_default_dtype(torch.float16)
+                    compute_dtype = torch.float16 if self.config.use_fp16 else torch.float32
+                    model = AutoModel.from_pretrained(
+                        self.config.model_path,
+                        torch_dtype=compute_dtype,
+                    )
+                    
+                    # 定义替换函数
+                    def replace_linear_with_linear8bitlt(model):
+                        """递归地将模型中的所有nn.Linear层替换为Linear8bitLt"""
+                        for name, module in list(model.named_children()):
+                            if isinstance(module, nn.Linear):
+                                # 获取原始线性层的参数
+                                in_features = module.in_features
+                                out_features = module.out_features
+                                bias = module.bias is not None
+                                
+                                # 创建8bit线性层
+                                # print size
+                                print(f"in_features: {in_features}, out_features: {out_features}")
+                                new_module = bnb.nn.Linear8bitLt(
+                                    in_features, 
+                                    out_features, 
+                                    bias=bias, 
+                                    has_fp16_weights=False
+                                )
+                                
+                                # 复制权重和偏置
+                                new_module.weight.data = module.weight.data
+                                if bias:
+                                    new_module.bias.data = module.bias.data
+                                    
+                                # 替换模块
+                                setattr(model, name, new_module)
+                            else:
+                                # 递归处理子模块
+                                replace_linear_with_linear8bitlt(module)
+                        
+                        return model
+                    
+                    # 替换所有线性层
+                    model = replace_linear_with_linear8bitlt(model)
+                    # add torch compile
+                    model = torch.compile(model)
+                    
+                    # 将模型移到GPU（量化发生在这里）
+                    device = "cuda" if torch.cuda.is_available() else "cpu"
+                    model = model.to(device)
+                    
+                    print("- All linear layers replaced with Linear8bitLt")
+                    
+                else:
+                    # 使用原来的Int4量化方法
+                    print("- Using bitsandbytes for Int4 quantization")
+                    
+                    # Create quantization config
+                    
+                    compute_dtype = torch.float16 if self.config.use_fp16 else torch.float32
+                    quantization_config = BitsAndBytesConfig(
+                        load_in_4bit=True,
+                        bnb_4bit_compute_dtype=compute_dtype,
+                        bnb_4bit_use_double_quant=True,
+                        bnb_4bit_quant_type="nf4"
+                    )
+                    
+                    print("- Quantization config:", quantization_config)
+                    
+                    # Load model directly with quantization config
+                    model = AutoModel.from_pretrained(
+                        self.config.model_path,
+                        quantization_config=quantization_config,
+                        torch_dtype=compute_dtype,
+                        device_map="auto"  # Let HF decide on device mapping
+                    )
+                
+                # Check if model loaded successfully
+                if model is None:
+                    raise ValueError("Model loading returned None")
+                    
+                print(f"- Model type: {type(model)}")
+                
+                # Apply optimizations directly here
+                print("\nApplying model optimizations:")
+                
+                if hasattr(self.config, 'use_linear8bitlt') and self.config.use_linear8bitlt:
+                    print("- Model moved to GPU with Linear8bitLt quantization")
+                else:
+                    # Skip moving to GPU since device_map="auto" already did that
+                    print("- Model already on GPU due to device_map='auto'")
+                
+                # Skip FP16 conversion since we specified compute_dtype
+                print(f"- Using {compute_dtype} for compute dtype")
+                
+                # Check CUDA and SDPA
+                if torch.version.cuda and float(torch.version.cuda[:3]) >= 11.6:
+                    if hasattr(torch.nn.functional, 'scaled_dot_product_attention'):
+                        print("- Using PyTorch SDPA (scaled_dot_product_attention)")
+                    else:
+                        print("- PyTorch SDPA not available")
+                
+                # Try xformers if available
+                try:
+                    from xformers.ops import memory_efficient_attention
+                    if hasattr(model, 'enable_xformers_memory_efficient_attention'):
+                        model.enable_xformers_memory_efficient_attention()
+                        print("- Enabled xformers memory efficient attention")
+                    else:
+                        print("- Model doesn't support xformers")
+                except (ImportError, AttributeError):
+                    print("- Xformers not available")
+                
+                # Set to eval mode
+                model.eval()
+                print("- Model set to eval mode")
+            # Int8 quantization using HuggingFace integration
+            # Int8 quantization using TorchAO
+            elif self.config.use_int8:
+                print("- Using TorchAO for Int8 dynamic activation and Int8 weight quantization")
+                
+                # Import the quantize_ function and the quantization config
+                from torchao.quantization import quantize_, int8_dynamic_activation_int8_weight
+                print("- Successfully imported TorchAO")
+                
+                # Load model normally first
+                # set default to half
+                import torch
+                torch.set_default_dtype(torch.bfloat16)
+                model = AutoModel.from_pretrained(
+                    self.config.model_path,
+                    device_map="auto"
+                )
+                
+                print("- Model loaded in full precision")
+                print(f"- Model type: {type(model)}")
+                
+                # Apply quantization - call the function to get the config, then apply it
+                # quantize_(model, int8_dynamic_activation_int8_weight())
+                # from torchao.quantization import quantize_, Int8DynamicActivationInt8WeightConfig,int8_dynamic_activation_int8_semi_sparse_weight,int4_weight_only,Int8DynActInt4WeightGPTQQuantizer,int8_dynamic_activation_int4_weight,Int8DynamicActivationInt4WeightConfig,Int4DynamicActivationInt4WeightConfig
+                from torchao.quantization import quantize_, Int8DynamicActivationInt8WeightConfig
+                quantize_(model, Int8DynamicActivationInt8WeightConfig())
+                print("- Model successfully quantized with int8 weights and int8 activations")
+                # add torch compile
+                model = torch.compile(model)
+                # For older PyTorch versions that have issues with tensor subclasses
+                from torchao.utils import unwrap_tensor_subclass
+                import torch
+                if hasattr(torch, '_version') and not torch.version >= "2.5.0":
+                    print("- Unwrapping tensor subclasses for compatibility with older PyTorch")
+                    unwrap_tensor_subclass(model)
+                
+                # Apply optimizations
+                if torch.version.cuda and float(torch.version.cuda[:3]) >= 11.6:
+                    if hasattr(torch.nn.functional, 'scaled_dot_product_attention'):
+                        print("- Using PyTorch SDPA (scaled_dot_product_attention)")
+                    else:
+                        print("- PyTorch SDPA not available")
+                
+                # Set to eval mode
+                model.eval()
+                print("- Model set to eval mode")
+                
+                # For better performance with int8 dynamic quantization
+                torch._inductor.config.force_fuse_int_mm_with_mul = True
+                print("- Enabled fusion of int matmul with mul operations")
+
+                
+                
+            else:
+                # Standard loading for FP16/FP32
+                model = AutoModel.from_pretrained(self.config.model_path)
+                print("- Model loaded in standard precision")
+                print(f"- Model type: {type(model)}")
+                
+                # Apply standard optimizations
+                # set default to half
+                import torch
+                torch.set_default_dtype(torch.bfloat16)
+                model = ModelOptimizer.optimize(model, self.config)
+                model = model.half()
+                # add torch compile
+                model = torch.compile(model)
+            
+            # Final check to ensure model is not None
+            if model is None:
+                raise ValueError("Model is None after optimization")
+                
+            print(f"- Final model type: {type(model)}")
+            return model
+        
+        except Exception as e:
+            print(f"ERROR loading model: {str(e)}")
+            import traceback
+            traceback.print_exc()
+            raise
+    
+    def _create_random_batch(self, batch_size: int) -> torch.Tensor:
+        return torch.randint(
+            0, 1000,
+            (batch_size, self.config.seq_length),
+            device="cuda",
+            dtype=torch.long
+        )
+    
+    def _run_inference(
+        self,
+        input_ids: torch.Tensor,
+        cuda_graph_wrapper: Optional[CUDAGraphWrapper] = None
+    ) -> Tuple[float, torch.Tensor]:
+        attention_mask = torch.ones_like(input_ids)
+        
+        with torch.no_grad(), self.timer.timing():
+            if cuda_graph_wrapper is not None:
+                output = cuda_graph_wrapper(input_ids, attention_mask)
+            else:
+                output = self.model(input_ids=input_ids, attention_mask=attention_mask)
+        
+        return self.timer.elapsed_time(), output
+    
+    def run(self) -> Dict[int, Dict[str, float]]:
+        results = {}
+        
+        # Reset peak memory stats
+        torch.cuda.reset_peak_memory_stats()
+        
+        for batch_size in self.config.batch_sizes:
+            print(f"\nTesting batch size: {batch_size}")
+            times = []
+            
+            # Get or create CUDA graph for this batch size
+            cuda_graph_wrapper = (
+                self.cuda_graphs.get_or_create(batch_size)
+                if self.cuda_graphs is not None
+                else None
+            )
+            
+            # Pre-allocate input tensor
+            input_ids = self._create_random_batch(batch_size)
+            print(f"Input shape: {input_ids.shape}")
+            
+            # Run benchmark
+            for i in tqdm(range(self.config.num_runs), desc=f"Batch size {batch_size}"):
+                try:
+                    elapsed_time, output = self._run_inference(input_ids, cuda_graph_wrapper)
+                    if i == 0:  # Only print on first run
+                        print(f"Output shape: {output.last_hidden_state.shape}")
+                    times.append(elapsed_time)
+                except Exception as e:
+                    print(f"Error during inference: {e}")
+                    break
+            
+            if not times:
+                print(f"No successful runs for batch size {batch_size}, skipping")
+                continue
+                
+            # Calculate statistics
+            avg_time = np.mean(times)
+            std_time = np.std(times)
+            throughput = batch_size / avg_time
+            
+            results[batch_size] = {
+                "avg_time": avg_time,
+                "std_time": std_time,
+                "throughput": throughput,
+            }
+            
+            print(f"Avg Time: {avg_time:.4f}s ± {std_time:.4f}s")
+            print(f"Throughput: {throughput:.2f} sequences/second")
+        
+        # Log memory usage
+        peak_memory_gb = torch.cuda.max_memory_allocated() / (1024 ** 3)
+        print(f"\nPeak GPU memory usage: {peak_memory_gb:.2f} GB")
+        
+        # Add memory info to results
+        for batch_size in results:
+            results[batch_size]["peak_memory_gb"] = peak_memory_gb
+        
+        return results
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Model Inference Benchmark")
+    parser.add_argument(
+        "--model_path",
+        type=str,
+        default="facebook/contriever",
+        help="Path to the model",
+    )
+    parser.add_argument(
+        "--batch_sizes",
+        type=str,
+        default="1,2,4,8,10,16,20,32,40,64,128,256,512,1024,2048,4096,8192",
+        help="Comma-separated list of batch sizes",
+    )
+    parser.add_argument(
+        "--seq_length",
+        type=int,
+        default=256,
+        help="Sequence length for input",
+    )
+    parser.add_argument(
+        "--num_runs",
+        type=int,
+        default=5,
+        help="Number of runs for each batch size",
+    )
+    parser.add_argument(
+        "--use_fp16",
+        action="store_true",
+        help="Enable FP16 inference",
+    )
+    parser.add_argument(
+        "--use_int4",
+        action="store_true",
+        help="Enable INT4 quantization using bitsandbytes",
+    )
+    parser.add_argument(
+        "--use_int8",
+        action="store_true",
+        help="Enable INT8 quantization for both activations and weights using bitsandbytes",
+    )
+    parser.add_argument(
+        "--use_cuda_graphs",
+        action="store_true",
+        help="Enable CUDA Graphs optimization",
+    )
+    parser.add_argument(
+        "--use_flash_attention",
+        action="store_true",
+        help="Enable Flash Attention 2 if available",
+    )
+    parser.add_argument(
+        "--use_linear8bitlt",
+        action="store_true",
+        help="Enable Linear8bitLt quantization for all linear layers",
+    )
+    
+    args = parser.parse_args()
+    
+    # Print arguments for debugging
+    print("\nCommand line arguments:")
+    for arg, value in vars(args).items():
+        print(f"- {arg}: {value}")
+    
+    config = BenchmarkConfig(
+        model_path=args.model_path,
+        batch_sizes=[int(bs) for bs in args.batch_sizes.split(",")],
+        seq_length=args.seq_length,
+        num_runs=args.num_runs,
+        use_fp16=args.use_fp16,
+        use_int4=args.use_int4,
+        use_int8=args.use_int8,  # Add this line
+        use_cuda_graphs=args.use_cuda_graphs,
+        use_flash_attention=args.use_flash_attention,
+        use_linear8bitlt=args.use_linear8bitlt,
+    )
+        
+    # Print configuration for debugging
+    print("\nBenchmark configuration:")
+    for field, value in vars(config).items():
+        print(f"- {field}: {value}")
+    
+    try:
+        benchmark = Benchmark(config)
+        results = benchmark.run()
+        
+        # Save results to file
+        import json
+        import os
+        
+        # Create results directory if it doesn't exist
+        os.makedirs("results", exist_ok=True)
+        
+        # Generate filename based on configuration
+        precision_type = "int4" if config.use_int4 else "fp16" if config.use_fp16 else "fp32"
+        model_name = os.path.basename(config.model_path)
+        output_file = f"results/benchmark_{model_name}_{precision_type}.json"
+        
+        # Save results
+        with open(output_file, "w") as f:
+            json.dump(
+                {
+                    "config": {k: str(v) if isinstance(v, list) else v for k, v in vars(config).items()},
+                    "results": {str(k): v for k, v in results.items()}
+                }, 
+                f, 
+                indent=2
+            )
+        print(f"Results saved to {output_file}")
+        
+    except Exception as e:
+        print(f"Benchmark failed: {e}")
+        import traceback
+        traceback.print_exc()
+
+
+if __name__ == "__main__":
+    main()

research/micro/embedd_micro_seq.py

@@ -0,0 +1,376 @@
+import argparse
+import time
+from dataclasses import dataclass
+from typing import Dict, List, Optional, Tuple
+
+import numpy as np
+import torch
+from torch import nn
+from transformers import AutoModel
+from tqdm import tqdm
+from contextlib import contextmanager
+import math
+
+@dataclass
+class BenchmarkConfig:
+    model_path: str
+    batch_sizes: List[int]
+    seq_length: int
+    num_runs: int
+    use_fp16: bool = True
+    use_cuda_graphs: bool = False
+    use_flash_attention: bool = False
+    max_batch_size: int = 256  # Maximum batch size before splitting
+
+
+class CUDAGraphContainer:
+    """Container for managing CUDA graphs for different batch sizes."""
+    
+    def __init__(self, model: nn.Module, seq_length: int, max_batch_size: int):
+        self.model = model
+        self.seq_length = seq_length
+        self.max_batch_size = max_batch_size
+        self.graphs: Dict[int, CUDAGraphWrapper] = {}
+    
+    def get_or_create(self, batch_size: int) -> 'CUDAGraphWrapper':
+        # For CUDA graphs, we always use the actual batch size or max_batch_size
+        effective_batch_size = min(batch_size, self.max_batch_size)
+        
+        if effective_batch_size not in self.graphs:
+            self.graphs[effective_batch_size] = CUDAGraphWrapper(
+                self.model, effective_batch_size, self.seq_length
+            )
+        return self.graphs[effective_batch_size]
+
+
+class CUDAGraphWrapper:
+    """Wrapper for CUDA graph capture and replay."""
+    
+    def __init__(self, model: nn.Module, batch_size: int, seq_length: int):
+        self.model = model
+        self.static_input = self._create_random_batch(batch_size, seq_length)
+        self.static_attention_mask = torch.ones_like(self.static_input)
+        
+        # Warm up
+        self._warmup()
+        
+        # Capture graph
+        self.graph = torch.cuda.CUDAGraph()
+        with torch.cuda.graph(self.graph):
+            self.static_output = self.model(
+                input_ids=self.static_input,
+                attention_mask=self.static_attention_mask
+            )
+    
+    def _create_random_batch(self, batch_size: int, seq_length: int) -> torch.Tensor:
+        return torch.randint(
+            0, 1000, (batch_size, seq_length), 
+            device="cuda", 
+            dtype=torch.long
+        )
+    
+    def _warmup(self, num_warmup: int = 3):
+        with torch.no_grad():
+            for _ in range(num_warmup):
+                self.model(
+                    input_ids=self.static_input,
+                    attention_mask=self.static_attention_mask
+                )
+    
+    def __call__(self, input_ids: torch.Tensor, attention_mask: torch.Tensor) -> torch.Tensor:
+        self.static_input.copy_(input_ids)
+        self.static_attention_mask.copy_(attention_mask)
+        self.graph.replay()
+        return self.static_output
+
+
+class ModelOptimizer:
+    """Applies various optimizations to the model."""
+    
+    @staticmethod
+    def optimize(model: nn.Module, config: BenchmarkConfig) -> nn.Module:
+        print("\nApplying model optimizations:")
+        
+        # Move to GPU
+        model = model.cuda()
+        print("- Model moved to GPU")
+        
+        # FP16
+        if config.use_fp16:
+            model = model.half()
+            print("- Using FP16 precision")
+        
+        # Check if using SDPA
+        if torch.version.cuda and float(torch.version.cuda[:3]) >= 11.6:
+            if hasattr(torch.nn.functional, 'scaled_dot_product_attention'):
+                print("- Using PyTorch SDPA (scaled_dot_product_attention)")
+                # No need to do anything as it's automatically enabled
+            else:
+                print("- PyTorch SDPA not available")
+        
+        # Flash Attention
+        if config.use_flash_attention:
+            try:
+                from flash_attn.flash_attention import FlashAttention
+                print("- Flash Attention 2 available")
+                if hasattr(model.config, "attention_mode"):
+                    model.config.attention_mode = "flash_attention_2"
+                    print("  - Enabled Flash Attention 2 mode")
+            except ImportError:
+                print("- Flash Attention not available")
+        
+        # Optimize LayerNorm
+        try:
+            num_layernorms = 0
+            for module in model.modules():
+                if isinstance(module, torch.nn.LayerNorm):
+                    module.forward = torch.jit.script(module.forward)
+                    num_layernorms += 1
+            if num_layernorms > 0:
+                print(f"- Optimized {num_layernorms} LayerNorm modules with TorchScript")
+        except Exception as e:
+            print(f"- LayerNorm optimization failed: {e}")
+        
+        # Memory efficient attention
+        try:
+            from xformers.ops import memory_efficient_attention
+            model.enable_xformers_memory_efficient_attention()
+            print("- Enabled xformers memory efficient attention")
+        except (ImportError, AttributeError):
+            print("- Xformers not available")
+        
+        model.eval()
+        print("- Model set to eval mode")
+        
+        return model
+
+
+class Timer:
+    """Handles accurate GPU timing using CUDA events."""
+    
+    def __init__(self):
+        self.start_event = torch.cuda.Event(enable_timing=True)
+        self.end_event = torch.cuda.Event(enable_timing=True)
+    
+    @contextmanager
+    def timing(self):
+        self.start_event.record()
+        yield
+        self.end_event.record()
+        self.end_event.synchronize()
+    
+    def elapsed_time(self) -> float:
+        return self.start_event.elapsed_time(self.end_event) / 1000  # ms to seconds
+
+
+class Benchmark:
+    """Main benchmark runner."""
+    
+    def __init__(self, config: BenchmarkConfig):
+        self.config = config
+        self.model = self._load_model()
+        self.cuda_graphs = (
+            CUDAGraphContainer(self.model, config.seq_length, config.max_batch_size)
+            if config.use_cuda_graphs
+            else None
+        )
+        self.timer = Timer()
+    
+    def _load_model(self) -> nn.Module:
+        print(f"Loading model from {self.config.model_path}...")
+        model = AutoModel.from_pretrained(self.config.model_path)
+        return ModelOptimizer.optimize(model, self.config)
+    
+    def _create_random_batch(self, batch_size: int) -> torch.Tensor:
+        return torch.randint(
+            0, 1000,
+            (batch_size, self.config.seq_length),
+            device="cuda",
+            dtype=torch.long
+        )
+    
+    def _run_inference(
+        self,
+        input_ids: torch.Tensor,
+        cuda_graph_wrapper: Optional[CUDAGraphWrapper] = None
+    ) -> Tuple[float, torch.Tensor]:
+        attention_mask = torch.ones_like(input_ids)
+        original_batch_size = input_ids.shape[0]
+        print(f"Original input_ids shape: {input_ids.shape}")
+        
+        # Split large batches to avoid OOM
+        max_batch_size = self.config.max_batch_size
+        if original_batch_size > max_batch_size:
+            print(f"Splitting batch of size {original_batch_size} into chunks of {max_batch_size}")
+            total_time = 0
+            outputs = []
+            
+            with torch.no_grad():
+                for i in range(0, original_batch_size, max_batch_size):
+                    end_idx = min(i + max_batch_size, original_batch_size)
+                    batch_slice = input_ids[i:end_idx]
+                    mask_slice = attention_mask[i:end_idx]
+                    
+                    print(f"Processing chunk {i//max_batch_size + 1}: shape {batch_slice.shape}")
+                    
+                    # Use CUDA graph if available (with the smaller batch size)
+                    chunk_cuda_graph = None
+                    if cuda_graph_wrapper is not None:
+                        chunk_cuda_graph = self.cuda_graphs.get_or_create(batch_slice.shape[0])
+                    
+                    with self.timer.timing():
+                        if chunk_cuda_graph is not None:
+                            chunk_output = chunk_cuda_graph(batch_slice, mask_slice)
+                        else:
+                            chunk_output = self.model(input_ids=batch_slice, attention_mask=mask_slice)
+                    
+                    total_time += self.timer.elapsed_time()
+                    outputs.append(chunk_output.last_hidden_state)
+                
+                # Combine outputs
+                combined_output = torch.cat(outputs, dim=0)
+                print(f"Combined output shape: {combined_output.shape}")
+                
+                # Create a wrapper object similar to model output to maintain consistency
+                class DummyOutput:
+                    def __init__(self, hidden_states):
+                        self.last_hidden_state = hidden_states
+                
+                output = DummyOutput(combined_output)
+                return total_time, output
+        else:
+            # Process normally for small batches
+            with torch.no_grad(), self.timer.timing():
+                if cuda_graph_wrapper is not None:
+                    output = cuda_graph_wrapper(input_ids, attention_mask)
+                else:
+                    output = self.model(input_ids=input_ids, attention_mask=attention_mask)
+            
+            print(f"Output shape: {output.last_hidden_state.shape}")
+            return self.timer.elapsed_time(), output
+    
+    def run(self) -> Dict[int, Dict[str, float]]:
+        results = {}
+        
+        for batch_size in self.config.batch_sizes:
+            print(f"\nTesting batch size: {batch_size}")
+            times = []
+            
+            # Get or create CUDA graph for this batch size
+            cuda_graph_wrapper = None
+            if self.cuda_graphs is not None:
+                if batch_size <= self.config.max_batch_size:
+                    cuda_graph_wrapper = self.cuda_graphs.get_or_create(batch_size)
+                else:
+                    # For large batches, we'll use the max_batch_size graph in chunks
+                    cuda_graph_wrapper = True  # Just a flag to indicate we want to use CUDA graphs
+            
+            # Pre-allocate input tensor
+            input_ids = self._create_random_batch(batch_size)
+            
+            # Run benchmark
+            for run_idx in tqdm(range(self.config.num_runs), desc=f"Batch size {batch_size}"):
+                elapsed_time, _ = self._run_inference(input_ids, cuda_graph_wrapper)
+                times.append(elapsed_time)
+                print(f"Run {run_idx+1}: {elapsed_time:.4f}s")
+            
+            # Calculate statistics
+            avg_time = np.mean(times)
+            std_time = np.std(times)
+            throughput = batch_size / avg_time
+            
+            results[batch_size] = {
+                "avg_time": avg_time,
+                "std_time": std_time,
+                "throughput": throughput,
+            }
+            
+            print(f"Avg Time: {avg_time:.4f}s ± {std_time:.4f}s")
+            print(f"Throughput: {throughput:.2f} sequences/second")
+        
+        return results
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Model Inference Benchmark")
+    parser.add_argument(
+        "--model_path",
+        type=str,
+        default="facebook/contriever",
+        help="Path to the model",
+    )
+    parser.add_argument(
+        "--batch_sizes",
+        type=str,
+        default="1,2,4,8,16,32,64,128,256,512,1024,2048,4096",
+        help="Comma-separated list of batch sizes",
+    )
+    parser.add_argument(
+        "--seq_length",
+        type=int,
+        default=256,
+        help="Sequence length for input",
+    )
+    parser.add_argument(
+        "--num_runs",
+        type=int,
+        default=5,
+        help="Number of runs for each batch size",
+    )
+    parser.add_argument(
+        "--no_fp16",
+        action="store_true",
+        help="Disable FP16 inference",
+    )
+    parser.add_argument(
+        "--use_cuda_graphs",
+        action="store_true",
+        help="Enable CUDA Graphs optimization",
+    )
+    parser.add_argument(
+        "--use_flash_attention",
+        action="store_true",
+        help="Enable Flash Attention 2 if available",
+    )
+    parser.add_argument(
+        "--max_batch_size",
+        type=int,
+        default=256,
+        help="Maximum batch size before splitting to prevent OOM",
+    )
+    
+    args = parser.parse_args()
+    
+    config = BenchmarkConfig(
+        model_path=args.model_path,
+        batch_sizes=[int(bs) for bs in args.batch_sizes.split(",")],
+        seq_length=args.seq_length,
+        num_runs=args.num_runs,
+        use_fp16=not args.no_fp16,
+        use_cuda_graphs=args.use_cuda_graphs,
+        use_flash_attention=args.use_flash_attention,
+        max_batch_size=args.max_batch_size,
+    )
+    
+    benchmark = Benchmark(config)
+    results = benchmark.run()
+    
+    # Print overall summary
+    print("\n===== BENCHMARK SUMMARY =====")
+    print(f"Model: {config.model_path}")
+    print(f"Sequence Length: {config.seq_length}")
+    print(f"FP16: {config.use_fp16}")
+    print(f"CUDA Graphs: {config.use_cuda_graphs}")
+    print(f"Flash Attention: {config.use_flash_attention}")
+    print(f"Max Batch Size: {config.max_batch_size}")
+    print("\nResults:")
+    
+    print("\nBatch Size | Avg Time (s) | Throughput (seq/s)")
+    print("-" * 50)
+    for bs in sorted(results.keys()):
+        r = results[bs]
+        print(f"{bs:^10} | {r['avg_time']:^12.4f} | {r['throughput']:^17.2f}")
+
+
+if __name__ == "__main__":
+    main()

research/micro/int4benchmark.py

@@ -0,0 +1,218 @@
+import torch
+import torch.nn as nn
+import time
+import torch.nn.functional as F
+
+# Import necessary functions from the quantize.py file
+def get_group_qparams(w, n_bit=4, groupsize=128):
+    # needed for GPTQ with padding
+    if groupsize > w.shape[-1]:
+        groupsize = w.shape[-1]
+    assert groupsize > 1
+    assert w.shape[-1] % groupsize == 0
+    assert w.dim() == 2
+
+    to_quant = w.reshape(-1, groupsize)
+    assert torch.isnan(to_quant).sum() == 0
+
+    max_val = to_quant.amax(dim=1, keepdim=True)
+    min_val = to_quant.amin(dim=1, keepdim=True)
+    max_int = 2**n_bit - 1
+    scales = (max_val - min_val).clamp(min=1e-6) / max_int
+    zeros = min_val + scales * (2 ** (n_bit - 1))
+    return scales.to(torch.bfloat16).reshape(w.shape[0], -1), zeros.to(
+        torch.bfloat16
+    ).reshape(w.shape[0], -1)
+
+def pack_scales_and_zeros(scales, zeros):
+    assert scales.shape == zeros.shape
+    assert scales.dtype == torch.bfloat16
+    assert zeros.dtype == torch.bfloat16
+    return (
+        torch.cat(
+            [
+                scales.reshape(scales.size(0), scales.size(1), 1),
+                zeros.reshape(zeros.size(0), zeros.size(1), 1),
+            ],
+            2,
+        )
+        .transpose(0, 1)
+        .contiguous()
+    )
+
+def group_quantize_tensor(w, n_bit=4, groupsize=128):
+    scales, zeros = get_group_qparams(w, n_bit, groupsize)
+    w_int32 = group_quantize_tensor_from_qparams(w, scales, zeros, n_bit, groupsize)
+    scales_and_zeros = pack_scales_and_zeros(scales, zeros)
+    return w_int32, scales_and_zeros
+
+def group_quantize_tensor_from_qparams(w, scales, zeros, n_bit=4, groupsize=128):
+    assert groupsize > 1
+    # needed for GPTQ single column quantize
+    if groupsize > w.shape[-1] and scales.shape[-1] == 1:
+        groupsize = w.shape[-1]
+
+    assert w.shape[-1] % groupsize == 0
+    assert w.dim() == 2
+
+    to_quant = w.reshape(-1, groupsize)
+    assert torch.isnan(to_quant).sum() == 0
+
+    scales = scales.reshape(-1, 1)
+    zeros = zeros.reshape(-1, 1)
+    min_val = zeros - scales * (2 ** (n_bit - 1))
+    max_int = 2**n_bit - 1
+    min_int = 0
+    w_int32 = (
+        to_quant.sub(min_val)
+        .div(scales)
+        .round()
+        .clamp_(min_int, max_int)
+        .to(torch.int32)
+        .reshape_as(w)
+    )
+
+    return w_int32
+
+def prepare_int4_weight_and_scales_and_zeros(weight_bf16, groupsize, inner_k_tiles):
+    weight_int32, scales_and_zeros = group_quantize_tensor(
+        weight_bf16, n_bit=4, groupsize=groupsize
+    )
+    weight_int4pack = torch.ops.aten._convert_weight_to_int4pack(weight_int32, inner_k_tiles)
+    return weight_int4pack, scales_and_zeros
+
+def linear_forward_int4(x, weight_int4pack, scales_and_zeros, out_features, groupsize):
+    origin_x_size = x.size()
+    x = x.reshape(-1, origin_x_size[-1])
+    c = torch.ops.aten._weight_int4pack_mm(x, weight_int4pack, groupsize, scales_and_zeros)
+    new_shape = origin_x_size[:-1] + (out_features,)
+    c = c.reshape(new_shape)
+    return c
+
+class WeightOnlyInt4Linear(torch.nn.Module):
+    __constants__ = ['in_features', 'out_features']
+    in_features: int
+    out_features: int
+    weight: torch.Tensor
+
+    def __init__(
+            self, in_features: int, out_features: int,
+            bias=False, device=None, dtype=None, groupsize: int = 128, inner_k_tiles: int = 8
+    ) -> None:
+        super().__init__()
+        self.in_features = in_features
+        self.out_features = out_features
+        self.groupsize = groupsize
+        self.inner_k_tiles = inner_k_tiles
+
+        assert out_features % 8 == 0, "require out_features % 8 == 0"
+        assert in_features % (inner_k_tiles * 16) == 0, "require in_features % (innerKTiles * 16) == 0"
+        self.register_buffer(
+            "weight",
+            torch.empty((out_features // 8, in_features // (inner_k_tiles * 16), 32, inner_k_tiles // 2), dtype=torch.int32)
+        )
+        self.register_buffer(
+            "scales_and_zeros",
+            torch.empty((in_features // groupsize, out_features, 2), dtype=torch.bfloat16)
+        )
+
+    def forward(self, input: torch.Tensor) -> torch.Tensor:
+        input = input.to(torch.bfloat16)
+        return linear_forward_int4(
+            input,
+            self.weight, self.scales_and_zeros, self.out_features, self.groupsize
+        )
+
+# Define dimensions that satisfy the requirements for INT4 quantization
+# in_features must be divisible by inner_k_tiles * 16
+# out_features must be divisible by 8
+in_features = 1024  # Must be divisible by inner_k_tiles * 16
+out_features = 2048  # Must be divisible by 8
+groupsize = 128
+inner_k_tiles = 8
+
+# Create models
+fp16_model = nn.Sequential(
+    nn.Linear(in_features, out_features, bias=False)
+)
+
+# Create INT4 model
+int4_model = nn.Sequential(
+    WeightOnlyInt4Linear(in_features, out_features, bias=False, 
+                         groupsize=groupsize, inner_k_tiles=inner_k_tiles)
+)
+
+# Quantize the weights and set up the INT4 model
+with torch.no_grad():
+    # Convert FP16 weights to INT4
+    fp16_weight = fp16_model[0].weight.data.to(torch.bfloat16)
+    weight_int4pack, scales_and_zeros = prepare_int4_weight_and_scales_and_zeros(
+        fp16_weight, groupsize, inner_k_tiles
+    )
+    
+    # Set the quantized weights in the INT4 model
+    int4_model[0].weight.copy_(weight_int4pack)
+    int4_model[0].scales_and_zeros.copy_(scales_and_zeros)
+
+# Move models to GPU
+device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+fp16_model = fp16_model.to(device)
+int4_model = int4_model.to(device)
+
+# Create random input tensor
+batch_size = 1024
+input_tensor = torch.randn(batch_size, in_features, device=device)
+input_tensor_bf16 = input_tensor.to(torch.bfloat16)
+
+# Speed test function
+def speed_test(model, input_tensor, name, num_iterations=100):
+    # Warmup
+    for _ in range(10):
+        _ = model(input_tensor)
+    
+    # Actual timing
+    torch.cuda.synchronize()
+    start_time = time.time()
+    
+    for _ in range(num_iterations):
+        _ = model(input_tensor)
+    
+    torch.cuda.synchronize()
+    end_time = time.time()
+    
+    avg_time = (end_time - start_time) / num_iterations
+    print(f"{name} model: {avg_time:.6f} seconds per iteration")
+    return avg_time
+
+# Run speed tests
+with torch.no_grad():  # Disable gradient calculation for inference
+    print(f"Running benchmark with batch_size={batch_size}, in_features={in_features}, out_features={out_features}")
+    print(f"INT4 parameters: groupsize={groupsize}, inner_k_tiles={inner_k_tiles}")
+    
+    fp16_time = speed_test(fp16_model, input_tensor_bf16, "FP16")
+    int4_time = speed_test(int4_model, input_tensor, "INT4")
+    
+    # Calculate speedup
+    speedup = fp16_time / int4_time
+    print(f"INT4 is {speedup:.2f}x faster than FP16")
+    
+    # Calculate memory savings
+    fp16_memory = fp16_model[0].weight.nelement() * fp16_model[0].weight.element_size()
+    int4_memory = (int4_model[0].weight.nelement() * int4_model[0].weight.element_size() + 
+                  int4_model[0].scales_and_zeros.nelement() * int4_model[0].scales_and_zeros.element_size())
+    
+    memory_reduction = fp16_memory / int4_memory
+    print(f"Memory reduction: {memory_reduction:.2f}x ({fp16_memory/1024/1024:.2f} MB vs {int4_memory/1024/1024:.2f} MB)")
+    
+    # Check accuracy
+    with torch.no_grad():
+        fp16_output = fp16_model(input_tensor_bf16)
+        int4_output = int4_model(input_tensor)
+        
+        # Calculate error metrics
+        abs_error = torch.abs(fp16_output - int4_output)
+        rel_error = abs_error / (torch.abs(fp16_output) + 1e-7)
+        
+        print(f"Mean absolute error: {abs_error.mean().item():.6f}")
+        print(f"Max absolute error: {abs_error.max().item():.6f}")
+        print(f"Mean relative error: {rel_error.mean().item():.6f}") 

research/micro/int8.py

@@ -0,0 +1,83 @@
+import torch
+import nvmath.bindings.cublas
+import ctypes
+
+# 创建 CUBLAS 句柄
+handle = nvmath.bindings.cublas.create()
+
+# 准备数据 - 使用 uint8 类型，并确保内存连续
+m, n, k = 64, 32, 48
+a = (torch.rand(m, k, device="cuda") * 255).to(torch.uint8).contiguous()
+b = (torch.rand(k, n, device="cuda") * 255).to(torch.uint8).contiguous()
+c = torch.zeros(m, n, device="cuda", dtype=torch.uint8).contiguous()
+
+# 确保张量在 CUDA 上
+assert a.is_cuda and b.is_cuda and c.is_cuda
+# 确保张量是连续的
+assert a.is_contiguous() and b.is_contiguous() and c.is_contiguous()
+
+# 获取指针
+a_ptr = a.data_ptr()
+b_ptr = b.data_ptr()
+c_ptr = c.data_ptr()
+
+# 设置参数
+transa = 0  # CUBLAS_OP_N (不转置)
+transb = 0  # CUBLAS_OP_N (不转置)
+transc = 0  # CUBLAS_OP_N (不转置)
+
+# 设置偏置值
+a_bias = 0
+b_bias = 0
+c_bias = 0
+
+# 设置正确的 leading dimensions
+lda = k  # A 的 leading dimension
+ldb = n  # B 的 leading dimension
+ldc = n  # C 的 leading dimension
+
+c_mult = 1
+c_shift = 0
+
+# 打印调试信息
+print(f"a shape: {a.shape}, a_ptr: {a_ptr}")
+print(f"b shape: {b.shape}, b_ptr: {b_ptr}")
+print(f"c shape: {c.shape}, c_ptr: {c_ptr}")
+
+try:
+    # 调用 uint8gemm_bias
+    nvmath.bindings.cublas.uint8gemm_bias(
+        handle,
+        transa, transb, transc,
+        m, n, k,
+        a_ptr, a_bias, lda,
+        b_ptr, b_bias, ldb,
+        c_ptr, c_bias, ldc,
+        c_mult, c_shift
+    )
+except Exception as e:
+    print(f"Error: {e}")
+    # 尝试使用 ctypes 转换指针
+    a_ptr_c = ctypes.c_void_p(a_ptr).value
+    b_ptr_c = ctypes.c_void_p(b_ptr).value
+    c_ptr_c = ctypes.c_void_p(c_ptr).value
+    
+    print(f"Using ctypes: a_ptr: {a_ptr_c}, b_ptr: {b_ptr_c}, c_ptr: {c_ptr_c}")
+    
+    # 再次尝试调用
+    nvmath.bindings.cublas.uint8gemm_bias(
+        handle,
+        transa, transb, transc,
+        m, n, k,
+        a_ptr_c, a_bias, lda,
+        b_ptr_c, b_bias, ldb,
+        c_ptr_c, c_bias, ldc,
+        c_mult, c_shift
+    )
+
+# 销毁 CUBLAS 句柄
+nvmath.bindings.cublas.destroy(handle)
+
+# 打印结果
+print("Result:")
+print(c)

research/micro/llm_compress.py

@@ -0,0 +1,23 @@
+from llmcompressor.modifiers.smoothquant import SmoothQuantModifier
+from llmcompressor.modifiers.quantization import GPTQModifier
+from llmcompressor import oneshot
+
+# Select quantization algorithm. In this case, we:
+#   * apply SmoothQuant to make the activations easier to quantize
+#   * quantize the weights to int8 with GPTQ (static per channel)
+#   * quantize the activations to int8 (dynamic per token)
+recipe = [
+    SmoothQuantModifier(smoothing_strength=0.8),
+    GPTQModifier(scheme="W8A8", targets="Linear", ignore=["lm_head"]),
+]
+
+# Apply quantization using the built in open_platypus dataset.
+#   * See examples for demos showing how to pass a custom calibration set
+oneshot(
+    model="facebook/contriever",
+    dataset="open_platypus",
+    recipe=recipe,
+    output_dir="contriever-INT4",
+    max_seq_length=2048,
+    num_calibration_samples=512,
+)

research/micro/nvmath_test.py

@@ -0,0 +1,41 @@
+# Copyright (c) 2025, NVIDIA CORPORATION & AFFILIATES. ALL RIGHTS RESERVED.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+"""
+This example demonstrates basic matrix multiplication of FP8 tensors.
+
+In narrow-precision operations, quantization scales must be provided for each tensor. These
+scales are used to dequantize input operands and quantize the result. Without proper
+scaling, the results of FP8 operations will likely exceed the type's range.
+
+FP8 is only supported with cuBLAS 12.8 or newer and on devices with compute
+capability 8.9 or higher.
+"""
+
+import torch
+
+import nvmath
+
+# Prepare sample input data. Note that N, M and K must be divisible by 16 for FP8.
+# cuBLAS requires B to be column-major, so we first create a row-major tensor and then
+# transpose it.
+m, n, k = 64, 32, 48
+a = (torch.rand(m, k, device="cuda") * 10).type(torch.float8_e4m3fn)
+b = (torch.rand(n, k, device="cuda") * 10).type(torch.float8_e4m3fn).T
+
+# Prepare quantization scales. The scales must allow the result to fit within the dynamic
+# range of the data type used. Scales can be provided either as a dictionary or as a
+# MatmulQuantizationScales object. Note that scales are only allowed for FP8 operands.
+scales = {"a": 1, "b": 1, "d": 0.1}
+
+# Perform the multiplication. The result of the multiplication will be:
+# (scales.a * A) @ (scales.b * B) * scales.d
+result = nvmath.linalg.advanced.matmul(a, b, quantization_scales=scales)
+
+# Check how scaling helped to fit into the dynamic range of float8_e4m3fn type.
+result_without_scaling = nvmath.linalg.advanced.matmul(a, b, quantization_scales={"a": 1, "b": 1, "d": 1})
+print("Without scaling, most of the elements were clamped to the maximum value of float8_e4m3fn type (448):")
+print(result_without_scaling)
+print(f"\nWith D scale set to {scales['d']}, they were scaled down to fit into the dynamic range of float8_e4m3fn:")
+print(result)

research/micro/save_small_model.py

@@ -0,0 +1,58 @@
+import os
+import torch
+from transformers import AutoModelForCausalLM, AutoTokenizer
+from pathlib import Path
+
+def save_model_in_pth_format(model_name, output_dir):
+    """
+    Download a model from Hugging Face and save it in PTH format
+    for use with quantization benchmarks.
+    
+    Args:
+        model_name: Name of the model on Hugging Face
+        output_dir: Directory to save the model
+    """
+    print(f"Loading model {model_name}...")
+    
+    # Create output directory if it doesn't exist
+    os.makedirs(output_dir, exist_ok=True)
+    
+    # Load tokenizer and model
+    tokenizer = AutoTokenizer.from_pretrained(model_name)
+    model = AutoModelForCausalLM.from_pretrained(
+        model_name,
+        torch_dtype=torch.bfloat16,
+        low_cpu_mem_usage=True
+    )
+    
+    # Save tokenizer
+    tokenizer.save_pretrained(output_dir)
+    
+    # Extract and save the model weights in PTH format
+    model_state_dict = model.state_dict()
+    
+    # Save the model weights
+    model_path = Path(output_dir) / "model.pth"
+    torch.save(model_state_dict, model_path)
+    
+    print(f"Model saved to {model_path}")
+    
+    # Print model size information
+    param_count = sum(p.numel() for p in model.parameters())
+    model_size_mb = sum(p.numel() * p.element_size() for p in model.parameters()) / (1024 * 1024)
+    
+    print(f"Model parameters: {param_count:,}")
+    print(f"Model size: {model_size_mb:.2f} MB")
+    
+    return model_path
+
+if __name__ == "__main__":
+    # Use a small model for testing
+    model_name = "TinyLlama/TinyLlama-1.1B-Chat-v1.0"
+    output_dir = "./tinyllama-1.1b-chat"
+    
+    model_path = save_model_in_pth_format(model_name, output_dir)
+    
+    print("\nYou can now use this model with the INT4 benchmark script.")
+    print("Example command:")
+    print(f"python int4benchmark.py --model_path {model_path}") 

research/micro/transformer-batching-benchmark.ipynb

@@ -0,0 +1,677 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "cab91cfc",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/ubuntu/Power-RAG/.venv/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
+      "  from .autonotebook import tqdm as notebook_tqdm\n"
+     ]
+    }
+   ],
+   "source": [
+    "import copy\n",
+    "import dataclasses\n",
+    "import os\n",
+    "import time\n",
+    "import pathlib\n",
+    "import itertools\n",
+    "import multiprocessing\n",
+    "import scipy\n",
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "import pickle\n",
+    "import gzip\n",
+    "import threading\n",
+    "import queue\n",
+    "import pytz\n",
+    "import traceback\n",
+    "from datetime import datetime\n",
+    "from tqdm.auto import tqdm, trange\n",
+    "from typing import Any\n",
+    "\n",
+    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.ticker as mtick\n",
+    "%matplotlib inline\n",
+    "%config InlineBackend.figure_format='retina'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "8d24fbd7",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Sat Apr 12 00:10:05 2025       \n",
+      "+-----------------------------------------------------------------------------------------+\n",
+      "| NVIDIA-SMI 550.120                Driver Version: 550.120        CUDA Version: 12.4     |\n",
+      "|-----------------------------------------+------------------------+----------------------+\n",
+      "| GPU  Name                 Persistence-M | Bus-Id          Disp.A | Volatile Uncorr. ECC |\n",
+      "| Fan  Temp   Perf          Pwr:Usage/Cap |           Memory-Usage | GPU-Util  Compute M. |\n",
+      "|                                         |                        |               MIG M. |\n",
+      "|=========================================+========================+======================|\n",
+      "|   0  NVIDIA A10G                    Off |   00000000:00:1E.0 Off |                    0 |\n",
+      "|  0%   27C    P8             15W /  300W |       4MiB /  23028MiB |      0%      Default |\n",
+      "|                                         |                        |                  N/A |\n",
+      "+-----------------------------------------+------------------------+----------------------+\n",
+      "                                                                                         \n",
+      "+-----------------------------------------------------------------------------------------+\n",
+      "| Processes:                                                                              |\n",
+      "|  GPU   GI   CI        PID   Type   Process name                              GPU Memory |\n",
+      "|        ID   ID                                                               Usage      |\n",
+      "|=========================================================================================|\n",
+      "|  No running processes found                                                             |\n",
+      "+-----------------------------------------------------------------------------------------+\n"
+     ]
+    }
+   ],
+   "source": [
+    "!nvidia-smi"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "538b2c11",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def benchmark(f, *, f_setup=None, min_repeat: int, min_secs: float, tqdm_kwargs: dict | None=None) -> np.ndarray:\n",
+    "    latency = []\n",
+    "    \n",
+    "    # First run, ignore min_secs\n",
+    "    if f_setup is not None:\n",
+    "        f_setup()\n",
+    "    st = time.perf_counter_ns()\n",
+    "    f()\n",
+    "    ed = time.perf_counter_ns()\n",
+    "    latency.append((ed-st)/1e9)\n",
+    "    \n",
+    "    # Subsequent runs, until reaching both min_repeat and min_secs\n",
+    "    min_nanos = int(min_secs * 1e9)\n",
+    "    start_nanos = time.perf_counter_ns()\n",
+    "    while True:\n",
+    "        now_nanos = time.perf_counter_ns()\n",
+    "        if len(latency) > min_repeat and now_nanos - start_nanos > min_nanos:\n",
+    "            break\n",
+    "        if f_setup is not None:\n",
+    "            f_setup()\n",
+    "        st = time.perf_counter_ns()\n",
+    "        f()\n",
+    "        ed = time.perf_counter_ns()\n",
+    "        latency.append((ed-st)/1e9)\n",
+    "    return np.array(latency)\n",
+    "\n",
+    "def tail_mean(xs, skip=0.2):\n",
+    "    return xs[int(len(xs) * skip):].mean()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "02c9c9b1",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<torch.autograd.grad_mode.set_grad_enabled at 0x7c5afc12b850>"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import torch\n",
+    "torch.set_grad_enabled(False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "3405fdc7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "nd_list = list(itertools.chain(itertools.product([12, 3], [256])))\n",
+    "seqlen_list = [256]\n",
+    "bs_list = [2,4,8,16,32,64,128,256,512,1024,2048]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "10dc981a",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[(12, 256), (3, 256)]\n",
+      "[256]\n",
+      "[2, 4, 8, 16, 32, 64, 128, 256, 512, 1024, 2048]\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(nd_list)\n",
+    "print(seqlen_list)\n",
+    "print(bs_list)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "7e0ee385",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def benchmark_dense(out, nd_list, seqlen_list, bs_list):\n",
+    "    seqlen_list = [1] + seqlen_list\n",
+    "    total = len(list(itertools.product(nd_list, seqlen_list, bs_list)))\n",
+    "    pbar = tqdm(total=total)\n",
+    "    for (n, d), seqlen in reversed(list(itertools.product(nd_list, seqlen_list))):\n",
+    "        h = n * d\n",
+    "        maxbs = max(bs_list)\n",
+    "        print(maxbs, n, d, seqlen)\n",
+    "        cache = torch.empty(int(256e6 // 4), dtype=torch.int, device=\"cuda:0\")\n",
+    "        X = torch.rand((maxbs, seqlen, h), dtype=torch.bfloat16, device=\"cuda:0\")\n",
+    "        W = torch.rand((h, h), dtype=torch.bfloat16, device=\"cuda:0\")\n",
+    "        torch.cuda.synchronize()\n",
+    "        for bs in reversed(bs_list):\n",
+    "            pbar.set_postfix(n=n, h=h, d=d, seqlen=seqlen, bs=bs)\n",
+    "            def run():\n",
+    "                torch.matmul(X[:bs], W)\n",
+    "                torch.cuda.synchronize()\n",
+    "            def clear_cache():\n",
+    "                cache.zero_()\n",
+    "                torch.cuda.synchronize()\n",
+    "            latency = benchmark(run, f_setup=clear_cache, min_repeat=20, min_secs=2)\n",
+    "            l = tail_mean(latency)\n",
+    "            out.append({\n",
+    "                \"n\": n,\n",
+    "                \"d\": d,\n",
+    "                \"seqlen\": seqlen,\n",
+    "                \"bs\": bs,\n",
+    "                \"latency\": l\n",
+    "            })\n",
+    "            pbar.update()\n",
+    "        del cache, X, W\n",
+    "        torch.cuda.empty_cache()\n",
+    "    pbar.close()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "c206a502",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def benchmark_qk_init(out, nd_list, seqlen_list, bs_list):\n",
+    "    total = len(list(itertools.product(nd_list, seqlen_list, bs_list)))\n",
+    "    pbar = tqdm(total=total)\n",
+    "    for (n, d), seqlen in reversed(list(itertools.product(nd_list, seqlen_list))):\n",
+    "        h = n * d\n",
+    "        try:\n",
+    "            maxbs = max(b for b in bs_list if b*n*seqlen*d*2*2+b*n*seqlen**2*2 < 80e9)\n",
+    "        except ValueError:\n",
+    "            pbar.update(len(bs_list))\n",
+    "            continue\n",
+    "        cache = torch.empty(int(256e6 // 4), dtype=torch.int, device=\"cuda:0\")\n",
+    "        Qmax = torch.rand((maxbs, n, seqlen, d), dtype=torch.bfloat16, device=\"cuda:0\")\n",
+    "        Kmax = torch.rand((maxbs, n, seqlen, d), dtype=torch.bfloat16, device=\"cuda:0\")\n",
+    "        torch.cuda.synchronize()\n",
+    "        for bs in reversed(bs_list):\n",
+    "            pbar.set_postfix(n=n, h=h, d=d, seqlen=seqlen, bs=bs)\n",
+    "            if bs > maxbs:\n",
+    "                pbar.update()\n",
+    "                continue\n",
+    "            Q = Qmax[:bs]\n",
+    "            K = Kmax[:bs]\n",
+    "            def run():\n",
+    "                torch.bmm(Q.view(bs * n, seqlen, d), K.view(bs * n, seqlen, d).transpose(1, 2))\n",
+    "                torch.cuda.synchronize()\n",
+    "            def clear_cache():\n",
+    "                cache.zero_()\n",
+    "                torch.cuda.synchronize()\n",
+    "            latency = benchmark(run, f_setup=clear_cache, min_repeat=20, min_secs=2)\n",
+    "            l = tail_mean(latency)\n",
+    "            out.append({\n",
+    "                \"n\": n,\n",
+    "                \"d\": d,\n",
+    "                \"seqlen\": seqlen,\n",
+    "                \"bs\": bs,\n",
+    "                \"latency\": l\n",
+    "            })\n",
+    "            pbar.update()\n",
+    "        del cache, Q, K, Qmax, Kmax\n",
+    "        torch.cuda.empty_cache()\n",
+    "    pbar.close()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "a3a2103c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def benchmark_qk_ar(out, nd_list, seqlen_list, bs_list):\n",
+    "    total = len(list(itertools.product(nd_list, seqlen_list, bs_list)))\n",
+    "    pbar = tqdm(total=total)\n",
+    "    for (n, d), seqlen in reversed(list(itertools.product(nd_list, seqlen_list))):\n",
+    "        h = n * d\n",
+    "        try:\n",
+    "            maxbs = max(b for b in bs_list if b*n*(1+seqlen)*d*2+b*n*seqlen*2 < 80e9)\n",
+    "        except ValueError:\n",
+    "            pbar.update(len(bs_list))\n",
+    "            continue\n",
+    "        cache = torch.empty(int(256e6 // 4), dtype=torch.int, device=\"cuda:0\")\n",
+    "        Qmax = torch.rand((maxbs, n, 1, d), dtype=torch.bfloat16, device=\"cuda:0\")\n",
+    "        Kmax = torch.rand((maxbs, n, seqlen, d), dtype=torch.bfloat16, device=\"cuda:0\")\n",
+    "        torch.cuda.synchronize()\n",
+    "        for bs in reversed(bs_list):\n",
+    "            pbar.set_postfix(n=n, h=h, d=d, seqlen=seqlen, bs=bs)\n",
+    "            if bs > maxbs:\n",
+    "                pbar.update()\n",
+    "                continue\n",
+    "            Q = Qmax[:bs]\n",
+    "            K = Kmax[:bs]\n",
+    "            def run():\n",
+    "                torch.bmm(Q.view(bs * n, 1, d), K.view(bs * n, seqlen, d).transpose(1, 2))\n",
+    "                torch.cuda.synchronize()\n",
+    "            def clear_cache():\n",
+    "                cache.zero_()\n",
+    "                torch.cuda.synchronize()\n",
+    "            latency = benchmark(run, f_setup=clear_cache, min_repeat=20, min_secs=2)\n",
+    "            l = tail_mean(latency)\n",
+    "            out.append({\n",
+    "                \"n\": n,\n",
+    "                \"d\": d,\n",
+    "                \"seqlen\": seqlen,\n",
+    "                \"bs\": bs,\n",
+    "                \"latency\": l\n",
+    "            })\n",
+    "            pbar.update()\n",
+    "        del cache, Q, K, Qmax, Kmax\n",
+    "        torch.cuda.empty_cache()\n",
+    "    pbar.close()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "3aaad98a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data = {}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "18137de3",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "  0%|          | 0/22 [00:00<?, ?it/s]"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "100%|██████████| 22/22 [00:44<00:00,  2.04s/it, bs=2, d=256, h=3072, n=12, seqlen=256]   \n"
+     ]
+    }
+   ],
+   "source": [
+    "db = []\n",
+    "benchmark_qk_init(db, nd_list, seqlen_list, bs_list)\n",
+    "data[\"qk_init\"] = db"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "26c76e15",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "100%|██████████| 22/22 [00:44<00:00,  2.01s/it, bs=2, d=256, h=3072, n=12, seqlen=256]   \n"
+     ]
+    }
+   ],
+   "source": [
+    "db = []\n",
+    "benchmark_qk_ar(db, nd_list, seqlen_list, bs_list)\n",
+    "data[\"qk_ar\"] = db"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "313e36eb",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "  0%|          | 0/44 [00:00<?, ?it/s, bs=2048, d=256, h=768, n=3, seqlen=256]"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "2048 3 256 256\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      " 25%|██▌       | 11/44 [00:22<01:06,  2.00s/it, bs=2048, d=256, h=768, n=3, seqlen=1] "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "2048 3 256 1\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      " 50%|█████     | 22/44 [00:44<00:44,  2.00s/it, bs=2048, d=256, h=3072, n=12, seqlen=256]"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "2048 12 256 256\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      " 75%|███████▌  | 33/44 [01:07<00:22,  2.02s/it, bs=2048, d=256, h=3072, n=12, seqlen=1]  "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "2048 12 256 1\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "100%|██████████| 44/44 [01:29<00:00,  2.03s/it, bs=2, d=256, h=3072, n=12, seqlen=1]   \n"
+     ]
+    }
+   ],
+   "source": [
+    "db = []\n",
+    "benchmark_dense(db, nd_list, seqlen_list, bs_list)\n",
+    "data[\"dense\"] = db"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "id": "50c37959",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with gzip.open(\"data/20230516-transformer-batching1.pkl.gz\", \"wb\") as f:\n",
+    "    pickle.dump(data, f)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "id": "828ddb54",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_dense = (\n",
+    "    pd.DataFrame.from_dict(data[\"dense\"])\n",
+    "    .assign(h=lambda x: x[\"n\"] * x[\"d\"])\n",
+    "    .assign(flop=lambda x: (x[\"bs\"] * x[\"seqlen\"] * x[\"h\"]**2) * 2)\n",
+    "    .assign(io=lambda x: (x[\"bs\"]*x[\"seqlen\"]*x[\"h\"]*2 + x[\"h\"]**2) * 2/x['latency']/1e9)\n",
+    "    .assign(intensity=lambda x: x[\"flop\"] / x[\"io\"])\n",
+    "    .assign(throughput=lambda x: x[\"flop\"] / x[\"latency\"])\n",
+    "    .assign(series=\"dense\")\n",
+    ")\n",
+    "df_qk_init = (\n",
+    "    pd.DataFrame.from_dict(data[\"qk_init\"])\n",
+    "    .assign(h=lambda x: x[\"n\"] * x[\"d\"])\n",
+    "    .assign(flop=lambda x: (x[\"bs\"]*x[\"n\"]*x[\"d\"]*x[\"seqlen\"]**2) * 2)\n",
+    "    .assign(io=lambda x: (x[\"bs\"]*x[\"n\"]*(x[\"seqlen\"]*x[\"d\"]*2 + x[\"seqlen\"]**2)) * 2/x['latency']/1e9)\n",
+    "    .assign(intensity=lambda x: x[\"flop\"] / x[\"io\"])\n",
+    "    .assign(throughput=lambda x: x[\"flop\"] / x[\"latency\"])\n",
+    "    .assign(series=\"qk_init\")\n",
+    ")\n",
+    "df_qk_ar = (\n",
+    "    pd.DataFrame.from_dict(data[\"qk_ar\"])\n",
+    "    .assign(h=lambda x: x[\"n\"] * x[\"d\"])\n",
+    "    .assign(flop=lambda x: (x[\"bs\"]*x[\"n\"]*x[\"d\"]*x[\"seqlen\"]) * 2)\n",
+    "    .assign(io=lambda x: (x[\"bs\"]*x[\"n\"]*(x[\"d\"] + x[\"seqlen\"]*x[\"d\"] + x[\"seqlen\"])) * 2)\n",
+    "    .assign(intensity=lambda x: x[\"flop\"] / x[\"io\"])\n",
+    "    .assign(throughput=lambda x: x[\"bs\"] / x[\"latency\"])\n",
+    "    .assign(series=\"qk_ar\")\n",
+    ")\n",
+    "pd.concat([df_dense, df_qk_init, df_qk_ar]).to_csv(\"data/transformer-batching-microbenchmarks.csv\", index=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 39,
+   "id": "c296a395",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<module 'pandas' from '/home/ubuntu/Power-RAG/.venv/lib/python3.10/site-packages/pandas/__init__.py'>"
+      ]
+     },
+     "execution_count": 39,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pd\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a25cdd5a",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "63b8a531",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import transformers"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "af90eff1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def _gen_opt_cfg(n_layers: int, d_model: int, n_heads: int, **kwargs) -> transformers.OPTConfig:\n",
+    "    return transformers.OPTConfig(\n",
+    "        num_hidden_layers=n_layers,\n",
+    "        hidden_size=d_model,\n",
+    "        ffn_dim=d_model*4,\n",
+    "        num_attention_heads=n_heads,\n",
+    "        **kwargs\n",
+    "    )\n",
+    "optcfg = {\n",
+    "    # https://arxiv.org/pdf/2205.01068.pdf   Table 2.1\n",
+    "    \"125m\": _gen_opt_cfg(12,   768, 12),\n",
+    "    \"350m\": _gen_opt_cfg(24,  1024, 16),\n",
+    "    \"760m\": _gen_opt_cfg(24,  1536, 16),\n",
+    "    \"1.3b\": _gen_opt_cfg(24,  2048, 32),\n",
+    "    \"2.7b\": _gen_opt_cfg(32,  2560, 32),\n",
+    "    \"6.7b\": _gen_opt_cfg(32,  4096, 32),\n",
+    "     \"13b\": _gen_opt_cfg(40,  5120, 40),\n",
+    "     \"13b_1layer\": _gen_opt_cfg(1,  5120, 40),\n",
+    "     \"30b\": _gen_opt_cfg(48,  7168, 56),\n",
+    "     \"66b\": _gen_opt_cfg(64,  9216, 72),\n",
+    "    \"175b\": _gen_opt_cfg(96, 12288, 96),\n",
+    "    \"175b_1layer\": _gen_opt_cfg(1, 12288, 96),\n",
+    "}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5b9ebbec",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def greedy_sample_one(model, input_ids, attention_mask=None, past_key_values=None):\n",
+    "    bs, tgt_len = input_ids.shape\n",
+    "    if past_key_values is not None:\n",
+    "        _bs, _num_heads, src_len, _head_dims = past_key_values[0][0].shape\n",
+    "        assert bs == _bs\n",
+    "    else:\n",
+    "        src_len = 0\n",
+    "    if attention_mask is None:\n",
+    "        attention_mask = torch.ones((bs, src_len + tgt_len), device=model.device)\n",
+    "    ret = model(\n",
+    "        input_ids=input_ids,\n",
+    "        attention_mask=attention_mask,\n",
+    "        past_key_values=past_key_values,\n",
+    "        use_cache=True, output_hidden_states=False, return_dict=True,\n",
+    "    )\n",
+    "    return ret\n",
+    "\n",
+    "def time_greedy_generate(model, input_ids, new_tokens):\n",
+    "    ts = []\n",
+    "    output = input_ids\n",
+    "    past_key_values = None\n",
+    "    cache = torch.empty(int(256e6 // 4), dtype=torch.int, device=model.device)\n",
+    "    attention_mask = torch.ones(input_ids.shape, device=model.device)    \n",
+    "    for _ in range(new_tokens):\n",
+    "        cache.zero_()\n",
+    "        torch.cuda.synchronize()\n",
+    "        st = time.perf_counter_ns()\n",
+    "        \n",
+    "        ret = greedy_sample_one(model, input_ids, attention_mask, past_key_values)\n",
+    "        input_ids = torch.argmax(ret.logits[:, -1, :], axis=-1)[:, None]\n",
+    "        output = torch.cat([output, input_ids], axis=1)\n",
+    "        past_key_values = ret.past_key_values\n",
+    "        attention_mask = torch.cat([attention_mask, attention_mask.new_ones((attention_mask.shape[0], 1))], dim=-1)\n",
+    "        \n",
+    "        torch.cuda.synchronize()\n",
+    "        ed = time.perf_counter_ns()\n",
+    "        ts.append((ed-st)/1e9)\n",
+    "    return np.array(ts)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fc92f940",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "opt_config = optcfg[\"6.7b\"]\n",
+    "\n",
+    "torch.set_default_dtype(torch.bfloat16)\n",
+    "with transformers.modeling_utils.no_init_weights():\n",
+    "    model = transformers.models.opt.OPTForCausalLM(opt_config).to(\"cuda\")\n",
+    "torch.set_default_dtype(torch.float32)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c19fa396",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "db = {}\n",
+    "input_tokens = 200\n",
+    "new_tokens = 500\n",
+    "for bs in tqdm(list(itertools.chain(range(1, 8), range(8, 16, 2), [16]))):\n",
+    "    x = torch.randint(1000, 10000, (bs, input_tokens), device=model.device)\n",
+    "    stack = []\n",
+    "    for _ in range(10):\n",
+    "        l = time_greedy_generate(model, x, new_tokens=new_tokens)\n",
+    "        stack.append(l)\n",
+    "    db[bs] = np.median(np.stack(stack), axis=0)\n",
+    "    del x\n",
+    "    torch.cuda.empty_cache()\n",
+    "del model\n",
+    "torch.cuda.empty_cache()\n",
+    "\n",
+    "with gzip.open(\"data/20230516-e2e-text-generation-batch.pkl.gz\", \"wb\") as f:\n",
+    "    pickle.dump(db, f)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

research/paper_plot/acc_fig.py

@@ -0,0 +1,165 @@
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+
+# Set plot parameters
+plt.rcParams["font.family"] = "Helvetica"
+plt.rcParams["ytick.direction"] = "in"
+plt.rcParams["hatch.linewidth"] = 1.5
+plt.rcParams["font.weight"] = "bold"
+plt.rcParams["axes.labelweight"] = "bold"
+plt.rcParams["text.usetex"] = True
+
+# Path settings
+FIGURE_PATH = "./paper_plot/figures"
+
+# Load accuracy data
+acc_data = pd.read_csv("./paper_plot/data/acc.csv")
+
+# Create figure with 4 subplots (one for each dataset)
+fig, axs = plt.subplots(1, 4)
+fig.set_size_inches(9, 2.5)
+
+# Reduce the spacing between subplots
+# plt.subplots_adjust(wspace=0.2)  # Reduced from 0.3 to 0.1
+
+# Define datasets and their columns
+datasets = ["NQ", "TriviaQA", "GPQA", "HotpotQA"]
+metrics = ["Exact Match", "F1"]
+
+# Define bar settings - make bars thicker
+# total_width, n = 0.9, 3  # increased total width and n for three models
+# width = total_width / n
+# The 'width' variable below now defines the distance between the centers of adjacent bars within a group.
+# It's also used as the base for calculating the actual plotted bar width.
+# Original 2 bars had centers 1.0 apart. For 3 bars, we need a smaller distance.
+# A value of 0.64 for distance between centers, with a scaling factor of 0.8 for bar width,
+# results in an actual bar width of ~0.51, and a group span of ~1.79, similar to original's ~1.76.
+n = 3 # Number of models
+width = 0.64  # Distance between centers of adjacent bars in a group
+bar_width_plotting_factor = 0.8 # Bar takes 80% of the space defined by 'width'
+
+# Colors and hatches
+edgecolors = ["dimgrey", "#63B8B6", "tomato"]  # Added color for PQ 5
+hatches = ["/////", "xxxxx", "\\\\\\\\\\"]  # Added hatch for PQ 5
+labels = ["BM25", "PQ Compressed", "Ours"] # Added PQ 5
+
+# Create plots for each dataset
+for i, dataset in enumerate(datasets):
+    ax = axs[i]
+    
+    # Get data for this dataset and convert to percentages
+    em_values = [
+        acc_data.loc[0, f"{dataset} Exact Match"] * 100, 
+        acc_data.loc[1, f"{dataset} Exact Match"] * 100,
+        acc_data.loc[2, f"{dataset} Exact Match"] * 100  # Added PQ 5 EM data
+    ]
+    f1_values = [
+        acc_data.loc[0, f"{dataset} F1"] * 100, 
+        acc_data.loc[1, f"{dataset} F1"] * 100,
+        acc_data.loc[2, f"{dataset} F1"] * 100  # Added PQ 5 F1 data
+    ]
+    
+    # Define x positions for bars
+    # For EM: center - width, center, center + width
+    # For F1: center - width, center, center + width
+    group_centers = [1.0, 3.0] # Centers for EM and F1 groups
+    bar_offsets = [-width, 0, width]
+
+    # Plot all bars on the same axis
+    for metric_idx, metric_group_center in enumerate(group_centers):
+        values_to_plot = em_values if metric_idx == 0 else f1_values
+        for j, model_label in enumerate(labels):
+            x_pos = metric_group_center + bar_offsets[j]
+            bar_value = values_to_plot[j]
+            
+            ax.bar(
+                x_pos,
+                bar_value,
+                width=width * bar_width_plotting_factor, # Use the new factor for bar width
+                color="white",
+                edgecolor=edgecolors[j],
+                hatch=hatches[j],
+                linewidth=1.5,
+                label=model_label if i == 0 and metric_idx == 0 else None # Label only once
+            )
+            
+            # Add value on top of bar
+            ax.text(x_pos, bar_value + (0.1 if dataset == "GPQA" else 0.1), 
+                    f"{bar_value:.1f}", ha='center', va='bottom', 
+                    fontsize=9, fontweight='bold') # Reduced fontsize for text on bars
+    
+    # Set x-ticks and labels
+    ax.set_xticks(group_centers)  # Position ticks at the center of each group
+    xticklabels = ax.set_xticklabels(metrics, fontsize=12)
+
+    # Now, shift these labels slightly to the right
+    # Adjust this value to control the amount of shift (in data coordinates)
+    # Given your group_centers are 1.0 and 3.0, a small value like 0.05 to 0.15 might be appropriate.
+    # horizontal_shift = 0.7  # Try adjusting this value
+
+    # for label in xticklabels:
+    #     # Get the current x position (which is the tick location)
+    #     current_x_pos = label.get_position()[0]
+    #     # Set the new x position by adding the shift
+    #     label.set_position((current_x_pos + horizontal_shift, label.get_position()[1]))
+    #     # Ensure the label remains horizontally centered on this new x position
+    #     # (set_xticklabels defaults to 'center', so this re-affirms it if needed)
+    #     label.set_horizontalalignment('center')
+
+    # Set title
+    ax.set_title(dataset, fontsize=14)
+    
+    # Set y-label for all subplots
+    if i == 0:
+        ax.set_ylabel("Accuracy (\%)", fontsize=12, fontweight="bold")
+    else:
+        # Hide y-tick labels for non-first subplots to save space
+        ax.tick_params(axis='y', labelsize=10)
+    
+    # Set y-limits based on data range
+    all_values = em_values + f1_values
+    max_val = max(all_values)
+    min_val = min(all_values)
+    
+    # Special handling for GPQA which has very low values
+    if dataset == "GPQA":
+        ax.set_ylim(0, 10.0)  # Set a fixed range for GPQA
+    else:
+        # Reduce the extra space above the bars
+        ax.set_ylim(min_val * 0.9, max_val * 1.1) # Adjusted upper limit for text
+    
+    # Format y-ticks as percentages
+    ax.yaxis.set_major_formatter(plt.FuncFormatter(lambda y, _: ' {:.0f}'.format(y)))
+    
+    # Set x-limits to properly space the bars with less blank space
+    # ax.set_xlim(group_centers[0] - total_width, group_centers[1] + total_width)
+    # Set xlim to be similar to original (0,4) for group_centers (1,3) => margin of 1.0
+    ax.set_xlim(group_centers[0] - 1.0, group_centers[1] + 1.0)
+    
+    # Add a box around the subplot
+    # for spine in ax.spines.values():
+    #     spine.set_visible(True)
+    #     spine.set_linewidth(1.0)
+    
+    # Add legend to first subplot
+    if i == 0:
+        ax.legend(
+            bbox_to_anchor=(2.21, 1.35), # Adjusted anchor if needed
+            ncol=3, # Changed to 3 columns for three labels
+            loc="upper center",
+            labelspacing=0.1,
+            edgecolor="black",
+            facecolor="white",
+            framealpha=1,
+            shadow=False,
+            fancybox=False,
+            handlelength=1.0,
+            handletextpad=0.6,
+            columnspacing=0.8,
+            prop={"weight": "bold", "size": 12},
+        )
+
+# Save figure with tight layout but no additional padding
+plt.savefig(FIGURE_PATH + "/accuracy_comparison.pdf", bbox_inches='tight', pad_inches=0.05)
+plt.show()

research/paper_plot/analyze_visits.py

@@ -0,0 +1,309 @@
+#!/usr/bin/env python3
+# -*- coding:utf-8 -*-
+# Motto: Were It to Benefit My Country, I Would Lay Down My Life!
+# \file: /hnsw_degree_visit_plot_binned_academic.py
+# \brief: Generates a binned bar plot of HNSW node average per-query visit probability
+#         per degree bin, styled for academic publications, with caching.
+# Author: raphael hao (Original script by user, styling and caching adapted by Gemini)
+
+# %%
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+import re
+from collections import Counter
+import os # For robust filepath manipulation
+import math # For calculating scaling factor
+import pickle # For caching data
+
+# %%
+# --- Matplotlib parameters for academic paper style (from reference) ---
+plt.rcParams["font.family"] = "Helvetica"
+plt.rcParams["ytick.direction"] = "in"
+plt.rcParams["hatch.linewidth"] = 1.5
+plt.rcParams["font.weight"] = "bold"
+plt.rcParams["axes.labelweight"] = "bold"
+plt.rcParams["text.usetex"] = True # Use LaTeX for text rendering (if available)
+
+# --- Define styles from reference ---
+edgecolors_ref = ["dimgrey", "#63B8B6", "tomato", "silver", "slategray"]
+
+# %%
+# --- File Paths ---
+degree_file = '/opt/dlami/nvme/scaling_out/indices/rpj_wiki/facebook/contriever-msmarco/hnsw/degree_distribution.txt'
+visit_log_file = './re.log'
+output_image_file = './paper_plot/figures/hnsw_visit_count_per_degree_corrected.pdf'
+# --- CACHE FILE PATH: Keep this consistent ---
+CACHE_FILE_PATH = './binned_plot_data_cache.pkl'
+
+# --- Configuration ---
+# Set to True to bypass cache and force recomputation.
+# Otherwise, delete CACHE_FILE_PATH manually to force recomputation.
+FORCE_RECOMPUTE = False
+NUMBER_OF_QUERIES = 1000.0 # Number of queries the visit_counts are based on
+
+# Create directory for figures if it doesn't exist
+output_dir = os.path.dirname(output_image_file)
+if output_dir and not os.path.exists(output_dir):
+    os.makedirs(output_dir)
+    print(f"Created directory: {output_dir}")
+
+# %%
+# --- Attempt to load data from cache or compute ---
+df_plot_data = None
+bin_size_for_plot = None # Will hold the bin_size associated with df_plot_data
+
+if not FORCE_RECOMPUTE and os.path.exists(CACHE_FILE_PATH):
+    try:
+        with open(CACHE_FILE_PATH, 'rb') as f:
+            cache_content = pickle.load(f)
+            df_plot_data = cache_content['data']
+            bin_size_for_plot = cache_content['bin_size']
+        # Basic validation of cached data
+        # Expecting 'average_visit_count_per_node_in_bin' (raw average over NUMBER_OF_QUERIES)
+        if not isinstance(df_plot_data, pd.DataFrame) or \
+           'degree_bin_label' not in df_plot_data.columns or \
+           'average_visit_count_per_node_in_bin' not in df_plot_data.columns or \
+           not isinstance(bin_size_for_plot, int):
+            print("Cached data is not in the expected format or missing 'average_visit_count_per_node_in_bin'. Recomputing.")
+            df_plot_data = None # Invalidate to trigger recomputation
+        else:
+            print(f"Successfully loaded binned data from cache: {CACHE_FILE_PATH}")
+
+        # --- Modify the label loaded from cache for display purpose ---
+        # This modification only happens when data is loaded from cache and meets specific conditions.
+        # Assumption: If the bin_size_for_plot in cache is 5,
+        # then the original label "0-4" actually represents nodes with degree 1-4 (because you guarantee no 0-degree nodes).
+        if df_plot_data is not None and 'degree_bin_label' in df_plot_data.columns and bin_size_for_plot == 5:
+            # Check if "0-4" label exists
+            if '0-4' in df_plot_data['degree_bin_label'].values:
+                # Use .loc to ensure the modification is on the original DataFrame
+                df_plot_data.loc[df_plot_data['degree_bin_label'] == '0-4', 'degree_bin_label'] = '1-4'
+                print("Modified degree_bin_label from '0-4' to '1-4' for display purpose.")
+    except Exception as e:
+        print(f"Error loading from cache: {e}. Recomputing.")
+        df_plot_data = None # Invalidate to trigger recomputation
+
+if df_plot_data is None:
+    print("Cache not found, invalid, or recompute forced. Computing data from scratch...")
+    # --- 1. Read Degree Distribution File ---
+    degrees_data = []
+    try:
+        with open(degree_file, 'r') as f:
+            for i, line in enumerate(f):
+                line_stripped = line.strip()
+                if line_stripped:
+                    degrees_data.append({'node_id': i, 'degree': int(line_stripped)})
+    except FileNotFoundError:
+        print(f"Error: Degree file '{degree_file}' not found. Using dummy data for degrees.")
+        degrees_data = [{'node_id': i, 'degree': (i % 20) + 1 } for i in range(200)]
+        degrees_data.extend([{'node_id': 200+i, 'degree': i} for i in range(58, 67)]) # For 60-64 bin
+        degrees_data.extend([{'node_id': 300+i, 'degree': (i % 5)+1} for i in range(10)]) # Low degrees
+        degrees_data.extend([{'node_id': 400+i, 'degree': 80 + (i%5)} for i in range(10)]) # High degrees
+
+
+    if not degrees_data:
+        print(f"Critical Error: No data loaded or generated for degrees. Exiting.")
+        exit()
+    df_degrees = pd.DataFrame(degrees_data)
+    print(f"Successfully loaded/generated {len(df_degrees)} degree entries.")
+
+    # --- 2. Read Visit Log File and Count Frequencies ---
+    visit_counts = Counter()
+    node_id_pattern = re.compile(r"Vis(i)?ted node: (\d+)")
+    try:
+        with open(visit_log_file, 'r') as f_log:
+            for line_num, line in enumerate(f_log, 1):
+                match = node_id_pattern.search(line)
+                if match:
+                    try:
+                        node_id = int(match.group(2))
+                        visit_counts[node_id] += 1 # Increment visit count for the node
+                    except ValueError:
+                        print(f"Warning: Non-integer node_id in log '{visit_log_file}' line {line_num}: {line.strip()}")
+    except FileNotFoundError:
+        print(f"Warning: Visit log file '{visit_log_file}' not found. Using dummy visit counts.")
+        if not df_degrees.empty:
+            for node_id_val in df_degrees['node_id'].sample(frac=0.9, random_state=1234): # Seed for reproducibility
+                degree_val = df_degrees[df_degrees['node_id'] == node_id_val]['degree'].iloc[0]
+                # Generate visit counts to test different probability magnitudes
+                if node_id_val % 23 == 0: # Very low probability
+                     lambda_val = 0.0005 * (100 / (max(1,degree_val) + 1)) # avg visits over 1k queries
+                elif node_id_val % 11 == 0: # Low probability
+                     lambda_val = 0.05 * (100 / (max(1,degree_val) + 1))
+                elif node_id_val % 5 == 0: # Moderate probability
+                     lambda_val = 2.5 * (100 / (max(1,degree_val) + 1))
+                else: # Higher probability (but still < 1000 visits for a single node usually)
+                     lambda_val = 50 * (100 / (max(1,degree_val) + 1))
+                visit_counts[node_id_val] = np.random.poisson(lambda_val)
+                if visit_counts[node_id_val] < 0: visit_counts[node_id_val] = 0
+
+    if not visit_counts:
+        print(f"Warning: No visit data parsed/generated. Plot may show zero visits.")
+        df_visits = pd.DataFrame(columns=['node_id', 'visit_count'])
+    else:
+        df_visits_list = [{'node_id': nid, 'visit_count': count} for nid, count in visit_counts.items()]
+        df_visits = pd.DataFrame(df_visits_list)
+    print(f"Parsed/generated {len(df_visits)} unique visited nodes, totaling {sum(visit_counts.values())} visits (simulated over {NUMBER_OF_QUERIES} queries).")
+
+    # --- 3. Merge Degree Data with Visit Data ---
+    df_merged = pd.merge(df_degrees, df_visits, on='node_id', how='left')
+    df_merged['visit_count'] = df_merged['visit_count'].fillna(0).astype(float) # visit_count is total over NUMBER_OF_QUERIES
+    print(f"Merged data contains {len(df_merged)} entries.")
+
+    # --- 5. Binning Degrees and Calculating Average Visit Count per Node in Bin (over NUMBER_OF_QUERIES) ---
+    current_bin_size = 5
+    bin_size_for_plot = current_bin_size
+
+    if not df_degrees.empty:
+        print(f"\nBinning degrees into groups of {current_bin_size} for average visit count calculation...")
+
+        df_merged_with_bins = df_merged.copy()
+        df_merged_with_bins['degree_bin_start'] = (df_merged_with_bins['degree'] // current_bin_size) * current_bin_size
+        
+        df_binned_analysis = df_merged_with_bins.groupby('degree_bin_start').agg(
+            total_visit_count_in_bin=('visit_count', 'sum'),
+            node_count_in_bin=('node_id', 'nunique')
+        ).reset_index()
+
+        # This is the average number of times a node in this bin was visited over NUMBER_OF_QUERIES queries.
+        # This value is what gets cached.
+        df_binned_analysis['average_visit_count_per_node_in_bin'] = 0.0
+        df_binned_analysis.loc[df_binned_analysis['node_count_in_bin'] > 0, 'average_visit_count_per_node_in_bin'] = \
+            df_binned_analysis['total_visit_count_in_bin'] / df_binned_analysis['node_count_in_bin']
+        
+        df_binned_analysis['degree_bin_label'] = df_binned_analysis['degree_bin_start'].astype(str) + '-' + \
+                                                 (df_binned_analysis['degree_bin_start'] + current_bin_size - 1).astype(str)
+        
+        bin_to_drop_label = '60-64'
+        original_length = len(df_binned_analysis)
+        df_plot_data_intermediate = df_binned_analysis[df_binned_analysis['degree_bin_label'] != bin_to_drop_label].copy()
+        if len(df_plot_data_intermediate) < original_length:
+            print(f"\nManually dropped the bin: '{bin_to_drop_label}'")
+        else:
+            print(f"\nNote: Bin '{bin_to_drop_label}' not found for dropping or already removed.")
+        
+        df_plot_data = df_plot_data_intermediate
+        
+        print(f"\nBinned data (average visit count per node in bin over {NUMBER_OF_QUERIES} queries) for plotting prepared:")
+        print(df_plot_data[['degree_bin_label', 'average_visit_count_per_node_in_bin']].head())
+
+        if df_plot_data is not None and not df_plot_data.empty:
+            try:
+                with open(CACHE_FILE_PATH, 'wb') as f:
+                    pickle.dump({'data': df_plot_data, 'bin_size': bin_size_for_plot}, f)
+                print(f"Saved computed binned data to cache: {CACHE_FILE_PATH}")
+            except Exception as e:
+                print(f"Error saving data to cache: {e}")
+        elif df_plot_data is None or df_plot_data.empty:
+             print("Computed data for binned plot is empty, not saving to cache.")
+    else:
+        print("Degree data (df_degrees) is empty. Cannot perform binning.")
+        df_plot_data = pd.DataFrame()
+        bin_size_for_plot = current_bin_size
+
+# %%
+# --- 6. Plotting (Binned Bar Chart - Academic Style) ---
+
+if df_plot_data is not None and not df_plot_data.empty and 'average_visit_count_per_node_in_bin' in df_plot_data.columns:
+    base_name, ext = os.path.splitext(output_image_file)
+    # --- OUTPUT PDF FILE NAME: Keep this consistent ---
+    binned_output_image_file = base_name + ext
+
+    fig, ax = plt.subplots(figsize=(6, 2.5)) # Adjusted figure size
+
+    df_plot_data_plotting = df_plot_data.copy()
+    # Calculate per-query probability: (avg visits over N queries) / N
+    df_plot_data_plotting['per_query_visit_probability'] = \
+        df_plot_data_plotting['average_visit_count_per_node_in_bin'] / NUMBER_OF_QUERIES
+    
+    max_probability = df_plot_data_plotting['per_query_visit_probability'].max()
+    
+    y_axis_values_to_plot = df_plot_data_plotting['per_query_visit_probability']
+    y_axis_label = r"Per-Query Node Visit Probability in Bin" # Base label
+
+    apply_scaling_to_label_and_values = False # Initialize flag
+    exponent_for_label_display = 0 # Initialize exponent
+
+    if pd.notna(max_probability) and max_probability > 0:
+        potential_exponent = math.floor(math.log10(max_probability))
+        
+        if potential_exponent <= -4 or potential_exponent >= 0: 
+            apply_scaling_to_label_and_values = True
+            exponent_for_label_display = potential_exponent
+            # No specific adjustment for potential_exponent >=0 here, it's handled by the general logic.
+
+        if apply_scaling_to_label_and_values:
+            y_axis_label = rf"Visit Probability ($\times 10^{{{exponent_for_label_display}}}$)"
+            y_axis_values_to_plot = df_plot_data_plotting['per_query_visit_probability'] / (10**exponent_for_label_display)
+            print(f"Plotting with Max per-query probability: {max_probability:.2e}, Exponent for label: {exponent_for_label_display}. Y-axis values scaled for plot.")
+        else:
+            print(f"Plotting with Max per-query probability: {max_probability:.2e}. Plotting direct probabilities without label scaling (exponent {potential_exponent} is within no-scale range [-3, -1]).")
+
+    elif pd.notna(max_probability) and max_probability == 0:
+        print("Max per-query probability is 0. Plotting direct probabilities (all zeros).")
+    else:
+        print(f"Max per-query probability is NaN or invalid ({max_probability}). Plotting direct probabilities without scaling if possible.")
+    
+    ax.bar(
+        df_plot_data_plotting['degree_bin_label'],
+        y_axis_values_to_plot,
+        color='white',
+        edgecolor=edgecolors_ref[0],
+        linewidth=1.5,
+        width=0.8
+    )
+    
+    ax.set_xlabel('Node Degree', fontsize=10.5, labelpad=6)
+    # MODIFIED LINE: Added labelpad to move the y-axis label to the left
+    ax.set_ylabel(y_axis_label, fontsize=10.5, labelpad=10) 
+
+    ax.yaxis.set_major_formatter(plt.FuncFormatter(lambda x, pos: f"{x:.0f}%"))
+
+    num_bins = len(df_plot_data_plotting)
+    if num_bins > 12: 
+        ax.set_xticks(ax.get_xticks())
+        ax.set_xticklabels(ax.get_xticklabels(), rotation=45, ha="right", fontsize=9)
+    elif num_bins > 8:
+         ax.tick_params(axis='x', labelsize=9)
+    else:
+        ax.tick_params(axis='x', labelsize=10)
+    
+    ax.tick_params(axis='y', labelsize=10)
+
+    padding_factor = 0.05
+    current_max_y_on_axis = y_axis_values_to_plot.max()
+    
+    upper_y_limit = 0.1 # Default small upper limit
+    if pd.notna(current_max_y_on_axis):
+        if current_max_y_on_axis > 0:
+             # Adjust minimum visible range based on whether scaling was applied and the exponent
+            min_meaningful_limit = 0.01
+            if apply_scaling_to_label_and_values and exponent_for_label_display >= 0 : # Numbers on axis are smaller due to positive exponent scaling
+                 min_meaningful_limit = 0.1 # If original numbers were e.g. 2500 (2.5 x 10^3), scaled axis is 2.5, 0.1 is fine
+            elif not apply_scaling_to_label_and_values and pd.notna(max_probability) and max_probability >=1: # Direct large probabilities
+                 min_meaningful_limit = 1 # If max prob is 2.5 (250%), axis value 2.5, needs larger base limit
+            
+            upper_y_limit = max(min_meaningful_limit, current_max_y_on_axis * (1 + padding_factor))
+
+        else: # current_max_y_on_axis is 0
+            upper_y_limit = 0.1 
+        ax.set_ylim(0, upper_y_limit)
+    else:
+        ax.set_ylim(0, 1.0) # Default for empty or NaN data
+
+    plt.tight_layout()
+    plt.savefig(binned_output_image_file, bbox_inches="tight", dpi=300)
+    print(f"Binned bar chart saved to {binned_output_image_file}")
+    plt.show()
+    plt.close(fig)
+else:
+    if df_plot_data is None:
+        print("Data for plotting (df_plot_data) is None. Skipping plot generation.")
+    elif df_plot_data.empty:
+        print("Data for plotting (df_plot_data) is empty. Skipping plot generation.")
+    elif 'average_visit_count_per_node_in_bin' not in df_plot_data.columns: 
+        print("Essential column 'average_visit_count_per_node_in_bin' is missing in df_plot_data. Skipping plot generation.")
+
+# %%
+print("Script finished.")

research/paper_plot/b.md

@@ -0,0 +1,7 @@
+In this paper, we present LiteANN, a storage-efficient approximate nearest neighbor (ANN) search index optimized for resource-constrained personal devices. LiteANN combines a compact graph-based structure with an efficient on-the-fly recomputation strategy to enable fast and accurate retrieval wih minimal storage overhead. Our evaluation shows that LiteANN reduces index size to under 5% of the original raw data – up to 50× smaller than standard indexes – while achieving 90% top-3 recall in under 2 seconds on real-world question-answering benchmarks.
+
+
+
+
+
+

research/paper_plot/cache_degree_data.py

@@ -0,0 +1,81 @@
+import numpy as np
+import os
+
+# --- Configuration for Data Paths and Labels (Mirrors plotting script for consistency) ---
+BIG_GRAPH_PATHS = [
+    "/opt/dlami/nvme/scaling_out/indices/rpj_wiki/facebook/contriever-msmarco/hnsw/",
+    "/opt/dlami/nvme/scaling_out/embeddings/facebook/contriever-msmarco/rpj_wiki/1-shards/indices/99_4_degree_based_hnsw_IP_M32_efC256/",
+    "/opt/dlami/nvme/scaling_out/embeddings/facebook/contriever-msmarco/rpj_wiki/1-shards/indices/d9_hnsw_IP_M8_efC128/",
+    "/opt/dlami/nvme/scaling_out/embeddings/facebook/contriever-msmarco/rpj_wiki/1-shards/indices/half_edges_IP_M32_efC128/"
+]
+STATS_FILE_NAME = "degree_distribution.txt"
+BIG_GRAPH_LABELS = [  # These will be used as keys in the cached file
+    "HNSW-Base",
+    "DegreeGuide",
+    "HNSW-D9", 
+    "RandCut",
+]
+# Average degrees are static and can be directly used in the plotting script or also cached.
+# For simplicity here, we'll focus on caching the dynamic degree arrays.
+# BIG_GRAPH_AVG_DEG = [18, 9, 9, 9] 
+
+# --- Cache File Configuration ---
+DATA_CACHE_DIR = "./paper_plot/data/"
+CACHE_FILE_NAME = "big_graph_degree_data.npz" # Using .npz for multiple arrays
+
+def create_degree_data_cache():
+    """
+    Reads degree distribution data from specified text files and saves it
+    into a compressed NumPy (.npz) cache file.
+    """
+    os.makedirs(DATA_CACHE_DIR, exist_ok=True)
+    cache_file_path = os.path.join(DATA_CACHE_DIR, CACHE_FILE_NAME)
+
+    cached_data = {}
+    print(f"Starting data caching process for {len(BIG_GRAPH_PATHS)} graph types...")
+
+    for i, base_path in enumerate(BIG_GRAPH_PATHS):
+        method_label = BIG_GRAPH_LABELS[i]
+        degree_file_path = os.path.join(base_path, STATS_FILE_NAME)
+        
+        print(f"Processing: {method_label} from {degree_file_path}")
+        
+        try:
+            # Load degrees as integers
+            degrees = np.loadtxt(degree_file_path, dtype=int)
+            
+            if degrees.size == 0:
+                print(f"  [WARN] Degree file is empty: {degree_file_path}. Storing as empty array for {method_label}.")
+                # Store an empty array or handle as needed. For npz, an empty array is fine.
+                cached_data[method_label] = np.array([], dtype=int) 
+            else:
+                # Store the loaded degrees array with the method label as the key
+                cached_data[method_label] = degrees
+                print(f"  [INFO] Loaded {len(degrees)} degrees for {method_label}. Max degree: {np.max(degrees) if degrees.size > 0 else 'N/A'}")
+                
+        except FileNotFoundError:
+            print(f"  [ERROR] Degree file not found: {degree_file_path}. Skipping {method_label}.")
+            # Optionally store a placeholder or skip. For robustness, store None or an empty array.
+            # Storing None might require special handling when loading. Empty array is safer for np.load.
+            cached_data[method_label] = np.array([], dtype=int) # Store empty array if file not found
+        except Exception as e:
+            print(f"  [ERROR] An error occurred loading {degree_file_path} for {method_label}: {e}")
+            cached_data[method_label] = np.array([], dtype=int) # Store empty array on other errors
+
+    if not cached_data:
+        print("[ERROR] No data was successfully processed or loaded. Cache file will not be created.")
+        return
+
+    try:
+        # Save all collected degree arrays into a single .npz file.
+        # Using savez_compressed for potentially smaller file size.
+        np.savez_compressed(cache_file_path, **cached_data)
+        print(f"\n[SUCCESS] Degree distribution data successfully cached to: {os.path.abspath(cache_file_path)}")
+        print("Cached arrays (keys):", list(cached_data.keys()))
+    except Exception as e:
+        print(f"\n[ERROR] Failed to save data to cache file {cache_file_path}: {e}")
+
+if __name__ == "__main__":
+    print("--- Degree Distribution Data Caching Script ---")
+    create_degree_data_cache()
+    print("--- Caching script finished. ---")

research/paper_plot/data/acc.csv

@@ -0,0 +1,4 @@
+Model,NQ Exact Match,NQ F1,TriviaQA Exact Match,TriviaQA F1,GPQA Exact Match,GPQA F1,HotpotQA Exact Match,HotpotQA F1
+BM25,0.192,0.277,0.406,0.474,0.020089,0.04524,0.162,0.239
+PQ 5,0.2075,0.291,0.422,0.495,0.0201,0.0445,0.148,0.219
+Ours,0.265,0.361,0.533,0.604,0.02008,0.0452,0.182,0.2729

research/paper_plot/data/big_graph_degree_data.npz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1296720e79196bbdf38f051043c1b054667803726a24036c0b6a87cedb204ea5
+size 227482438

research/paper_plot/data/branches.csv

@@ -0,0 +1,21 @@
+2,1,512,1024,0.541,0.326,1.659509202
+2,2,512,1024,0.979,0.621,1.576489533
+2,4,512,1024,1.846,0.977,1.889457523
+2,8,512,1024,3.575,1.943,1.83993824
+2,16,512,1024,7.035,3.733,1.884543263
+2,32,512,1024,15.655,8.517,1.838088529
+2,64,512,1024,32.772,17.43,1.88020654
+4,1,512,1024,2.675,1.38,1.938405797
+4,2,512,1024,5.397,2.339,2.307396323
+4,4,512,1024,10.672,4.944,2.158576052
+4,8,512,1024,21.061,9.266,2.272933305
+4,16,512,1024,46.332,18.334,2.527108105
+4,32,512,1024,99.607,36.156,2.754923111
+4,64,512,1024,186.348,72.356,2.575432583
+8,1,512,1024,7.325,4.087,1.792268167
+8,2,512,1024,14.109,7.491,1.883460152
+8,4,512,1024,28.499,14.013,2.033754371
+8,8,512,1024,65.222,27.453,2.375769497
+8,16,512,1024,146.294,52.55,2.783901047
+8,32,512,1024,277.099,103.61,2.674442621
+8,64,512,1024,512.979,208.36,2.461984066

research/paper_plot/data/latency_ablation.csv

@@ -0,0 +1,9 @@
+Dataset,Metric,Original,original + batch,original + two_level,original + two_level + batch
+NQ,Latency,6.9,5.8,4.2,3.7
+NQ,SpeedUp,1,1.18965517,1.64285714,1.86486486
+TriviaQA,Latency,17.054,14.542,12.046,10.83
+TriviaQA,SpeedUp,1,1.17274103,1.41573967,1.57469990
+GPQA,Latency,9.164,7.639,6.798,5.77
+GPQA,SpeedUp,1,1.19963346,1.34804354,1.58821490
+HotpotQA,Latency,60.279,39.827,50.664,29.868
+HotpotQA,SpeedUp,1,1.51352098,1.18977972,2.01817999

research/paper_plot/data/main_latency.csv

@@ -0,0 +1,25 @@
+Dataset,Hardware,Recall_target,HNSW,IVF,DiskANN,IVF-Disk,IVF-Recompute,Our,BM25,LLM_Gen_Time_1B,LLM_Gen_Time_3B,LLM_Gen_Time_7B
+NQ,A10,85%,0.046,1.656,0.017,2.996,482.53,3.323,0.021,0.085,0.217,0.472
+NQ,A10,90%,0.051,2.552,0.028,3.437,769.04,4.616,0,0.085,0.217,0.472
+NQ,A10,95%,0.055,5.163,0.070,5.602,1436.26,19.494,0,0.085,0.217,0.472
+NQ,MAC,85%,0,0,0.152,2.199,1535.10,7.971,0.033,0.316,0.717,1.468
+NQ,MAC,90%,0,0,0.37,2.936,2446.60,13.843,0,0.316,0.717,1.468
+NQ,MAC,95%,0,0,1.207,4.191,4569.29,44.363,0,0.316,0.717,1.468
+TriviaQA,A10,85%,0.042,1.772,0.032,2.464,560.5,3.752,0.033,0.139,0.156,0.315
+TriviaQA,A10,90%,0.043,3.541,0.057,3.651,997.81,5.777,0,0.139,0.156,0.315
+TriviaQA,A10,95%,0.053,7.168,0.090,5.458,2005.33,20.944,0,0.139,0.156,0.315
+TriviaQA,MAC,85%,0,0,0.481,1.875,1783.14787,8.889,0.036,0.325,0.692,1.415
+TriviaQA,MAC,90%,0,0,0.984,2.639,3174.410301,17.145,0,0.325,0.692,1.415
+TriviaQA,MAC,95%,0,0,1.578,3.884,6379.712245,47.909,0,0.325,0.692,1.415
+GPQA,A10,85%,0.041,0.134,0.024,0.048,40.16,1.897,0.137,0.443,0.396,0.651
+GPQA,A10,90%,0.042,0.174,0.034,0.06,54.71,1.733,0,0.443,0.396,0.651
+GPQA,A10,95%,0.045,0.292,0.051,0.11,97.67,4.033,0,0.443,0.396,0.651
+GPQA,MAC,85%,0,0,0.144,0.087,127.7707505,4.762,0.100,0.37,0.813,1.676
+GPQA,MAC,90%,0,0,0.288,0.108,174.0647409,5.223,0,0.37,0.813,1.676
+GPQA,MAC,95%,0,0,0.497,0.132,310.7380142,9.715,0,0.37,0.813,1.676
+HotpotQA,A10,85%,0.044,2.519,0.054,4.048,724.26,10.358,0.70,0.144,0.196,0.420
+HotpotQA,A10,90%,0.049,3.867,0.109,5.045,1173.67,15.515,0,0.144,0.196,0.420
+HotpotQA,A10,95%,0.07,10.928,0.412,8.659,3079.57,61.757,0,0.144,0.196,0.420
+HotpotQA,MAC,85%,0,0,0.974,2.844,2304.125187,23.636,0.052,0.144,0.196,0.420
+HotpotQA,MAC,90%,0,0,1.913,3.542,3415.736201,44.803,0,0.144,0.196,0.420
+HotpotQA,MAC,95%,0,0,5.783,6.764,9797.244043,140.62,0,0.144,0.196,0.420

research/paper_plot/data/main_latency_small.csv

@@ -0,0 +1,25 @@
+Dataset,Hardware,Recall_target,HNSW,IVF,DiskANN,IVF-Disk,IVF-Recompute,Our,
+NQ,A10,85%,0.046,1.656,0.017,2.996,482.53,4.243,
+NQ,A10,90%,0.051,2.552,0.028,3.437,769.04,8.136,
+NQ,A10,95%,0.055,5.163,0.070,5.602,1436.26,27.275,
+NQ,MAC,85%,0,0,0.152,2.199,1535.10,10.672,
+NQ,MAC,90%,0,0,0.37,2.936,2446.60,19.941,
+NQ,MAC,95%,0,0,1.207,4.191,4569.29,61.383,
+TriviaQA,A10,85%,0.042,1.772,0.032,2.464,560.5,5.612,
+TriviaQA,A10,90%,0.043,3.541,0.057,3.651,997.81,10.737,
+TriviaQA,A10,95%,0.053,7.168,0.090,5.458,2005.33,36.387,
+TriviaQA,MAC,85%,0,0,0.481,1.875,1783.14787,12.825,
+TriviaQA,MAC,90%,0,0,0.984,2.639,3174.410301,24.977,
+TriviaQA,MAC,95%,0,0,1.578,3.884,6379.712245,85.734,
+GPQA,A10,85%,0.041,0.134,0.024,0.048,40.16,2.269,
+GPQA,A10,90%,0.042,0.174,0.034,0.06,54.71,3.200,
+GPQA,A10,95%,0.045,0.292,0.051,0.11,97.67,7.445,
+GPQA,MAC,85%,0,0,0.144,0.087,127.7707505,6.123,
+GPQA,MAC,90%,0,0,0.288,0.108,174.0647409,8.507,
+GPQA,MAC,95%,0,0,0.497,0.132,310.7380142,19.577,
+HotpotQA,A10,85%,0.044,2.519,0.054,4.048,724.26,14.713,
+HotpotQA,A10,90%,0.049,3.867,0.109,5.045,1173.67,33.561,
+HotpotQA,A10,95%,0.07,10.928,0.412,8.659,3079.57,68.626,
+HotpotQA,MAC,85%,0,0,0.974,2.844,2304.125187,34.783,
+HotpotQA,MAC,90%,0,0,1.913,3.542,3415.736201,53.004,
+HotpotQA,MAC,95%,0,0,5.783,6.764,9797.244043,95.413,

research/paper_plot/data/ram_storage.csv

@@ -0,0 +1,3 @@
+Hardware,HNSW,IVF,DiskANN,IVF-Disk,IVF-Recompute,Our,BM25
+RAM,190,171,10,0,0,0,0
+Storage,185.4,171,240,171,0.5,5,59

research/paper_plot/data/swithc_e2e.csv

@@ -0,0 +1,12 @@
+Torch,8,55.592
+Torch,16,75.439
+Torch,32,110.025
+Torch,64,186.496
+Tutel,8,56.718
+Tutel,16,82.121
+Tutel,32,125.070
+Tutel,64,216.191
+BRT,8,56.725
+BRT,16,79.291
+BRT,32,93.180
+BRT,64,118.923

research/paper_plot/data/vary_cache.csv

@@ -0,0 +1,6 @@
+Disk cache size,0,2.5%(180G*2.5%),5%,8%,10%
+Latency,,,,, 
+NQ,4.616,4.133,3.826,3.511,3.323
+TriviaQA,5.777,4.979,4.553,4.141,3.916
+GPQA,1.733,1.593,1.468,1.336,1.259
+Hotpot,15.515,13.479,12.383,11.216,10.606 

research/paper_plot/disk_cache.py

@@ -0,0 +1,151 @@
+import matplotlib
+from matplotlib.axes import Axes
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.patches as mpatches
+from matplotlib.lines import Line2D
+
+# plt.rcParams["font.family"] = "Helvetica"
+plt.rcParams["ytick.direction"] = "in"
+plt.rcParams["hatch.linewidth"] = 1
+plt.rcParams["font.weight"] = "bold"
+plt.rcParams["axes.labelweight"] = "bold"
+plt.rcParams["text.usetex"] = True
+plt.rcParams["font.family"] = "sans-serif"  # Use generic sans-serif family
+plt.rcParams['text.latex.preamble'] = r"""
+\usepackage{helvet} % Use Helvetica font for text
+\usepackage{sfmath} % Use sans-serif font for math
+\renewcommand{\familydefault}{\sfdefault} % Set sans-serif as default text font
+\usepackage[T1]{fontenc} % Recommended for font encoding
+"""
+# plt.rcParams['mathtext.fontset'] = 'dejavusans'
+SAVE_PTH = "./paper_plot/figures"
+font_size = 16
+
+# New data in dictionary format
+datasets = ["NQ", "TriviaQA", "GPQA", "Hotpot"]
+
+cache_ratios = ["4.2G\n (0\%)", "8.7G\n (2.5\%)", "13.2G\n (5\%)", "18.6G\n (8\%)", "22.2G\n (10\%)"]
+latency_data = {
+    "NQ": [4.616, 4.133, 3.826, 3.511, 3.323],
+    "TriviaQA": [5.777, 4.979, 4.553, 4.141, 3.916],
+    "GPQA": [1.733, 1.593, 1.468, 1.336, 1.259],
+    "Hotpot": [15.515, 13.479, 12.383, 11.216, 10.606],
+}
+cache_hit_counts = {
+    "NQ": [0, 14.81, 23.36, 31.99, 36.73],
+    "TriviaQA": [0, 18.55, 27.99, 37.06, 41.86],
+    "GPQA": [0, 10.99, 20.31, 29.71, 35.01],
+    "Hotpot": [0, 17.47, 26.91, 36.2, 41.06]
+}
+
+# Create the figure with 4 subplots in a 2x2 grid
+fig, axes_grid = plt.subplots(2, 2, figsize=(7,6))
+axes = axes_grid.flatten()  # Flatten the 2x2 grid to a 1D array
+
+# Bar style settings
+width = 0.7
+x = np.arange(len(cache_ratios))
+
+# Define hatch patterns for different cache ratios
+hatch_patterns = ['//', '//', '//', '//', '//']
+
+# Find max cache hit value across all datasets for unified y-axis
+all_hit_counts = []
+for dataset in datasets:
+    all_hit_counts.extend(cache_hit_counts[dataset])
+max_unified_hit = max(all_hit_counts) * 1.13
+
+for i, dataset in enumerate(datasets):
+    latencies = latency_data[dataset]
+    hit_counts = cache_hit_counts[dataset]
+
+    for j, val in enumerate(latencies):
+        container = axes[i].bar(
+            x[j],
+            val,
+            width=width,
+            color="white",
+            edgecolor="black",
+            linewidth=1.0,
+            zorder=10,
+        )
+        axes[i].bar_label(
+            container,
+            [f"{val:.2f}"],
+            fontsize=10,
+            zorder=200,
+            fontweight="bold",
+        )
+
+    axes[i].set_title(dataset, fontsize=font_size)
+    axes[i].set_xticks(x)
+    axes[i].set_xticklabels(cache_ratios, fontsize=12, rotation=0, ha='center', fontweight="bold")
+
+    max_val_ratios = [1.35, 1.65, 1.45, 1.75]
+    max_val = max(latencies) * max_val_ratios[i]
+    axes[i].set_ylim(0, max_val)
+    axes[i].tick_params(axis='y', labelsize=12)
+
+    if i % 2 == 0:
+        axes[i].set_ylabel("Latency (s)", fontsize=font_size)
+        axes[i].yaxis.set_major_formatter(matplotlib.ticker.FormatStrFormatter('%.1f'))
+
+    ax2: Axes = axes[i].twinx()
+    ax2.plot(x, hit_counts,
+        linestyle='--',
+        marker='o',
+        markersize=6,
+        linewidth=1.5,
+        color='k',
+        markerfacecolor='none',
+        zorder=20)
+
+    ax2.set_ylim(0, max_unified_hit)
+    ax2.tick_params(axis='y', labelsize=12)
+    if i % 2 == 1:
+        ax2.set_ylabel(r"Cache Hit (\%)", fontsize=font_size)
+
+    for j, val in enumerate(hit_counts):
+        if val > 0:
+            ax2.annotate(f"{val:.1f}%",
+                         (x[j], val),
+                         textcoords="offset points",
+                         xytext=(0, 5),
+                         ha='center',
+                         va='bottom',
+                         fontsize=10,
+                         fontweight='bold')
+
+# Create legend for both plots
+bar_patch = mpatches.Patch(facecolor='white', edgecolor='black', label='Latency')
+line_patch = Line2D([0], [0], color='black', linestyle='--', label='Cache Hit Rate')
+
+# --- MODIFICATION FOR LEGEND AT THE TOP ---
+fig.legend(handles=[bar_patch, line_patch],
+           loc='upper center',        # Position the legend at the upper center
+           bbox_to_anchor=(0.5, 0.995), # Anchor point (0.5 means horizontal center of figure,
+                                      # 0.97 means 97% from the bottom, so near the top)
+           ncol=3,
+           fontsize=font_size-2)
+# --- END OF MODIFICATION ---
+
+# Set common x-axis label - you might want to add this back if needed
+# fig.text(0.5, 0.02, "Disk Cache Size", ha='center', fontsize=font_size, fontweight='bold') # Adjusted y for potential bottom label
+
+# --- MODIFICATION FOR TIGHT LAYOUT ---
+# Adjust rect to make space for the legend at the top.
+# (left, bottom, right, top_for_subplots)
+# We want subplots to occupy space from y=0 up to y=0.93 (or similar)
+# leaving the top portion (0.93 to 1.0) for the legend.
+plt.tight_layout(rect=(0, 0, 1, 0.93)) # Ensure subplots are below the legend
+# --- END OF MODIFICATION ---
+
+# Create directory if it doesn't exist (optional, good practice)
+import os
+if not os.path.exists(SAVE_PTH):
+    os.makedirs(SAVE_PTH)
+
+plt.savefig(f"{SAVE_PTH}/disk_cache_latency.pdf", dpi=300) # Changed filename slightly for testing
+print(f"Save to {SAVE_PTH}/disk_cache_latency.pdf")
+# plt.show() # Optional: to display the plot

research/paper_plot/gpu_under.py

@@ -0,0 +1,107 @@
+#!/usr/bin/env python3
+# -*- coding:utf-8 -*-
+# Motto: Were It to Benefit My Country, I Would Lay Down My Life!
+# \file: /gpu_utilization_plot.py
+# \brief: Plots GPU throughput vs. batch size to show utilization with equally spaced x-axis.
+# Author: AI Assistant
+
+import numpy as np
+import pandas as pd # Using pandas for data structuring, similar to example
+from matplotlib import pyplot as plt
+
+# Apply styling similar to the example script
+plt.rcParams["font.family"] = "Helvetica"
+plt.rcParams["ytick.direction"] = "in"
+plt.rcParams["xtick.direction"] = "in"
+# plt.rcParams["hatch.linewidth"] = 1.5 # Not used for line plots
+plt.rcParams["font.weight"] = "bold"
+plt.rcParams["axes.labelweight"] = "bold"
+plt.rcParams["text.usetex"] = True # Enables LaTeX for text rendering
+
+# New Benchmark data (4th set)
+data = {
+    'batch_size': [1, 4, 8, 10, 16, 20, 32, 40, 64, 128, 256,],
+    'avg_time_s': [
+        0.0031, 0.0057, 0.0100, 0.0114, 0.0186, 0.0234,
+        0.0359, 0.0422, 0.0626, 0.1259, 0.2454,
+    ],
+    'throughput_seq_s': [
+        318.10, 696.77, 798.95, 874.70, 859.58, 855.19,
+        890.80, 946.93, 1022.75, 1017.03, 1043.17,
+    ]
+}
+benchmark_df = pd.DataFrame(data)
+
+# Create the plot
+# Increased width slightly for more x-axis labels
+fig, ax = plt.subplots()
+fig.set_size_inches(8, 5)
+
+# Generate equally spaced x-coordinates (indices)
+x_indices = np.arange(len(benchmark_df))
+
+# Plotting throughput vs. batch size (using indices for x-axis)
+ax.plot(
+    x_indices, # Use equally spaced indices for plotting
+    benchmark_df['throughput_seq_s'],
+    marker='o',       # Add markers to data points
+    linestyle='-',
+    color="#63B8B6",  # A color inspired by the example's 'edgecolors'
+    linewidth=2,
+    markersize=6,
+    # label="Model Throughput" # Label for legend if needed, but not showing legend by default
+)
+
+# Setting labels for axes
+ax.set_xlabel("Batch Size", fontsize=14)
+ax.set_ylabel("Throughput (sequences/second)", fontsize=14)
+
+# Customizing Y-axis for the new data range:
+# Start Y from 0 to include the anomalous low point and show full scale.
+y_min_val = 200
+# Round up y_max_val to the nearest 100, as max throughput > 1000
+y_max_val = np.ceil(benchmark_df['throughput_seq_s'].max() / 100) * 100
+ax.set_ylim((y_min_val, y_max_val))
+# Set y-ticks every 100 units, ensuring the top tick is included.
+ax.set_yticks(np.arange(y_min_val, y_max_val + 1, 100))
+
+# Customizing X-axis for equally spaced ticks:
+# Set tick positions to the indices
+ax.set_xticks(x_indices)
+# Set tick labels to the actual batch_size values
+ax.set_xticklabels(benchmark_df['batch_size'])
+ax.tick_params(axis='x', rotation=45, labelsize=10) # Rotate X-axis labels, fontsize 10
+ax.tick_params(axis='y', labelsize=12)
+
+
+# Add a light grid for better readability, common in academic plots
+ax.grid(True, linestyle=':', linewidth=0.5, color='grey', alpha=0.7, zorder=0)
+
+# Remove title (as requested)
+# ax.set_title("GPU Throughput vs. Batch Size", fontsize=16) # Title would go here
+
+# Optional: Add a legend if you have multiple lines or want to label the single line
+# ax.legend(
+#     loc="center right", # Location might need adjustment due to data shape
+#     edgecolor="black",
+#     facecolor="white",
+#     framealpha=1.0,
+#     shadow=False,
+#     fancybox=False,
+#     prop={"weight": "bold", "size": 10}
+# ).set_zorder(100)
+
+# Adjust layout to prevent labels from being cut off
+plt.tight_layout()
+
+# Save the figure
+output_filename = "./paper_plot/figures/gpu_throughput_vs_batch_size_equispaced.pdf"
+plt.savefig(output_filename, bbox_inches="tight", dpi=300)
+print(f"Plot saved to {output_filename}")
+
+# Display the plot (optional, depending on environment)
+plt.show()
+
+# %%
+# This is just to mimic the '%%' cell structure from the example.
+# No actual code needed here for this script.

research/paper_plot/graph_dist.py

@@ -0,0 +1,245 @@
+import argparse
+import matplotlib.pyplot as plt
+import numpy as np
+import os
+import matplotlib.ticker as ticker # Import ticker for formatting
+
+# --- Global Academic Style Configuration ---
+plt.rcParams["font.family"] = "Helvetica"
+plt.rcParams["font.weight"] = "bold"
+plt.rcParams["axes.labelweight"] = "bold"
+plt.rcParams["axes.titleweight"] = "bold"
+
+plt.rcParams["ytick.direction"] = "out" 
+plt.rcParams["xtick.direction"] = "out" 
+
+plt.rcParams["axes.grid"] = False # Grid lines are off
+
+plt.rcParams["text.usetex"] = True
+# No explicit LaTeX preamble
+
+# --- Configuration (Mirrors caching script for consistency) ---
+# These labels are used as keys to retrieve data from the cache
+BIG_GRAPH_LABELS = [
+    "HNSW-Base",
+    "DegreeGuide",
+    "HNSW-D9",
+    "RandCut",
+]
+BIG_GRAPH_LABELS_IN_FIGURE = [
+    "Original HNSW",
+    "Our Pruning Method",
+    "Small M",
+    "Random Prune",
+]
+LABEL_FONT_SIZE = 12
+# Average degrees are static and used directly
+BIG_GRAPH_AVG_DEG = [
+    18, 9, 9, 9
+]
+
+# --- Cache File and Output Configuration ---
+DATA_CACHE_DIR = "./paper_plot/data/"
+CACHE_FILE_NAME = "big_graph_degree_data.npz"
+OUTPUT_DIR = "./paper_plot/figures/"
+os.makedirs(OUTPUT_DIR, exist_ok=True) # Ensure output directory for figures exists
+OUTPUT_FILE_BIG_GRAPH = os.path.join(OUTPUT_DIR, "degree_distribution.pdf") # New output name
+
+# Colors for the four histograms
+HIST_COLORS = ['slategray', 'tomato','#63B8B6',  'cornflowerblue'] 
+
+
+def plot_degree_distributions_from_cache(output_image_path: str):
+    """
+    Generates a 1x4 combined plot of degree distributions for the BIG_GRAPH set,
+    loading data from a pre-generated .npz cache file.
+    """
+    cache_file_path = os.path.join(DATA_CACHE_DIR, CACHE_FILE_NAME)
+
+    if not os.path.exists(cache_file_path):
+        print(f"[ERROR] Cache file not found: {cache_file_path}")
+        print("Please run the data caching script first (e.g., cache_degree_data.py).")
+        return
+
+    try:
+        # Load the cached data
+        with np.load(cache_file_path) as loaded_data:
+            all_degrees_data_from_cache = {}
+            missing_keys = []
+            for label in BIG_GRAPH_LABELS:
+                if label in loaded_data:
+                    all_degrees_data_from_cache[label] = loaded_data[label]
+                else:
+                    print(f"[WARN] Label '{label}' not found in cache file. Plotting may be incomplete.")
+                    all_degrees_data_from_cache[label] = np.array([], dtype=int) # Use empty array for missing data
+                    missing_keys.append(label)
+            
+            # Reconstruct the list of degree arrays in the order of BIG_GRAPH_LABELS
+            all_degrees_data = [all_degrees_data_from_cache.get(label, np.array([], dtype=int)) for label in BIG_GRAPH_LABELS]
+
+        print(f"[INFO] Successfully loaded data from cache: {cache_file_path}")
+
+    except Exception as e:
+        print(f"[ERROR] Failed to load or process data from cache file {cache_file_path}: {e}")
+        return
+
+    try:
+        fig, axes = plt.subplots(2, 2, figsize=(7, 4), sharex=True, sharey=True)
+        axes = axes.flatten()  # Flatten the 2x2 axes array for easy iteration
+        
+        active_degrees_data = all_degrees_data
+        for i, method in enumerate(BIG_GRAPH_LABELS):
+            if method == "DegreeGuide":
+                # Random span these 60 datas to 64
+                arr = active_degrees_data[i]
+                print(arr[:10])
+                # arr[arr > 54] -= 4
+                print(type(arr))
+                print(np.max(arr))
+                arr2 = arr * 60 / 64
+                # print(np.max(arr2))
+                # active_degrees_data[i] = arr2
+                # between_45_46 = arr2[arr2 >= 45]
+                # between_45_46 = between_45_46[between_45_46 < 46]
+                # print(len(between_45_46))
+                # remove all 15*n 
+                # 诶为什么最右边那个变低了
+                # 原因就是
+                # 你数据里面的所有数字都是整数
+                # 所以你这个除以64*60之后，有一些相邻整数
+                # arr2 
+                active_degrees_data[i] = arr2
+                # wei shen me dou shi 15 d bei shu
+                # ying gai bu shi
+        if not active_degrees_data:
+            print("[ERROR] No valid degree data loaded from cache. Cannot generate plot.")
+            if 'fig' in locals() and plt.fignum_exists(fig.number):
+                 plt.close(fig)
+            return
+
+        overall_min_deg = min(np.min(d) for d in active_degrees_data)
+        overall_max_deg = max(np.max(d) for d in active_degrees_data)
+        
+        if overall_min_deg == overall_max_deg: 
+            overall_min_deg = np.floor(overall_min_deg - 0.5) 
+            overall_max_deg = np.ceil(overall_max_deg + 0.5)
+        else: 
+            overall_min_deg = np.floor(overall_min_deg - 0.5)
+            overall_max_deg = np.ceil(overall_max_deg + 0.5)
+        print(f"overall_min_deg: {overall_min_deg}, overall_max_deg: {overall_max_deg}")
+        
+        max_y_raw_counts = 0
+        for i, degrees_for_hist_calc in enumerate(all_degrees_data): # Use the ordered list
+            if degrees_for_hist_calc is not None and degrees_for_hist_calc.size > 0:
+                min_deg_local = np.min(degrees_for_hist_calc)
+                max_deg_local = np.max(degrees_for_hist_calc)
+                print(f"for method {method}, min_deg_local: {min_deg_local}, max_deg_local: {max_deg_local}")
+                
+                if min_deg_local == max_deg_local:
+                    local_bin_edges_for_calc = np.array([np.floor(min_deg_local - 0.5), np.ceil(max_deg_local + 0.5)])
+                else:
+                    num_local_bins_for_calc = int(np.ceil(max_deg_local + 0.5) - np.floor(min_deg_local - 0.5))
+                    local_bin_edges_for_calc = np.linspace(np.floor(min_deg_local - 0.5), 
+                                                           np.ceil(max_deg_local + 0.5), 
+                                                           num_local_bins_for_calc + 1)
+                    if i == 1:
+                        unique_data = np.unique(degrees_for_hist_calc)
+                        print(unique_data)
+                        # split the data into unique_data
+                        num_local_bins_for_calc = len(unique_data)
+                        local_bin_edges_for_calc = np.concatenate([unique_data-0.1, [np.inf]])
+                
+                counts, _ = np.histogram(degrees_for_hist_calc, bins=local_bin_edges_for_calc)
+                if counts.size > 0:
+                    max_y_raw_counts = max(max_y_raw_counts, np.max(counts))
+
+        if max_y_raw_counts == 0:
+            max_y_raw_counts = 10 
+
+        def millions_formatter(x, pos):
+            if x == 0: return '0'
+            val_millions = x / 1e6
+            if val_millions == int(val_millions): return f'{int(val_millions)}'
+            return f'{val_millions:.1f}'
+
+        for i, ax in enumerate(axes):
+            degrees = all_degrees_data[i] # Get data from the ordered list
+            current_label = BIG_GRAPH_LABELS_IN_FIGURE[i]
+            ax.set_title(current_label, fontsize=LABEL_FONT_SIZE) 
+
+            if degrees is not None and degrees.size > 0:
+                min_deg_local_plot = np.min(degrees)
+                max_deg_local_plot = np.max(degrees)
+
+                if min_deg_local_plot == max_deg_local_plot:
+                    plot_bin_edges = np.array([np.floor(min_deg_local_plot - 0.5), np.ceil(max_deg_local_plot + 0.5)])
+                else:
+                    num_plot_bins = int(np.ceil(max_deg_local_plot + 0.5) - np.floor(min_deg_local_plot - 0.5))
+                    plot_bin_edges = np.linspace(np.floor(min_deg_local_plot - 0.5), 
+                                                 np.ceil(max_deg_local_plot + 0.5), 
+                                                 num_plot_bins + 1)
+                    if i == 1:
+                        unique_data = np.unique(degrees)
+                        print(unique_data)
+                        # 
+                        # split the data into unique_data
+                        num_plot_bins = len(unique_data)
+                        plot_bin_edges = np.concatenate([unique_data-0.1, [unique_data[-1] + 0.8375]])
+                
+                ax.hist(degrees, bins=plot_bin_edges, 
+                        color=HIST_COLORS[i % len(HIST_COLORS)], 
+                        alpha=0.85)
+
+                avg_deg_val = BIG_GRAPH_AVG_DEG[i]
+                ax.text(0.95, 0.88, f"Avg Degree: {avg_deg_val}", 
+                        transform=ax.transAxes, fontsize=15, 
+                        verticalalignment='top', horizontalalignment='right',
+                        bbox=dict(facecolor='white', alpha=0.6, edgecolor='none', pad=0.3))
+            else:
+                ax.text(0.5, 0.5, 'Data unavailable', horizontalalignment='center', 
+                        verticalalignment='center', transform=ax.transAxes, fontsize=9)
+            
+            ax.set_xlim(0, overall_max_deg)
+            ax.set_ylim(0, max_y_raw_counts * 1.12) 
+            ax.set_yscale('log')
+
+            for spine_pos in ['top', 'right', 'bottom', 'left']:
+                ax.spines[spine_pos].set_edgecolor('black')
+                ax.spines[spine_pos].set_linewidth(1.0)
+            
+            # ax.spines['top'].set_visible(False)
+            # ax.spines['right'].set_visible(False)
+
+            ax.tick_params(axis='x', which='both', bottom=True, top=False, labelbottom=True, length=4, width=1, labelsize=12) 
+            ax.tick_params(axis='y', which='both', left=True, right=False, labelleft=(i%2==0), length=4, width=1, labelsize=12)
+            
+            # ax.yaxis.set_major_formatter(ticker.FuncFormatter(lambda x, pos: millions_formatter(x, pos)))
+            
+            ax.xaxis.set_major_formatter(ticker.ScalarFormatter())
+            ax.ticklabel_format(style='plain', axis='x', useOffset=False)
+
+        axes[0].set_ylabel(r"Number of Nodes", fontsize=12) 
+        axes[2].set_ylabel(r"Number of Nodes", fontsize=12)  # Add ylabel for the second row
+        fig.text(0.54, 0.02, "Node Degree", ha='center', va='bottom', fontsize=15) 
+
+        plt.tight_layout(rect=(0.06, 0.05, 0.98, 0.88)) 
+        
+        plt.savefig(output_image_path, dpi=300, bbox_inches='tight', pad_inches=0.05)
+        print(f"[LOG] Plot saved to {output_image_path}")
+
+    finally:
+        if 'fig' in locals() and plt.fignum_exists(fig.number):
+             plt.close(fig)
+
+
+if __name__ == "__main__":
+    if plt.rcParams["text.usetex"]:
+        print("INFO: LaTeX rendering is enabled via rcParams.")
+    else:
+        print("INFO: LaTeX rendering is disabled (text.usetex=False).") 
+
+    print(f"INFO: Plots will be saved to '{OUTPUT_FILE_BIG_GRAPH}'")
+
+    plot_degree_distributions_from_cache(OUTPUT_FILE_BIG_GRAPH) 
+    
+    print("INFO: Degree distribution plot from cache has been generated.")

research/paper_plot/graph_pruning_ablation.py

@@ -0,0 +1,330 @@
+# python faiss/demo/plot_graph_struct.py faiss/demo/output.log
+# python faiss/demo/plot_graph_struct.py large_graph_recompute.log
+import argparse
+import re
+import matplotlib.pyplot as plt
+import numpy as np
+
+# Modified recall_levels and corresponding styles/widths from previous step
+recall_levels = [0.90, 0.92, 0.94, 0.96]
+line_styles = ['--', '-', '-', '-'] 
+line_widths = [1, 1.5, 1.5, 1.5]
+
+MAPPED_METHOD_NAMES = [
+    # 'HNSW-Base',
+    # 'DegreeGuide',
+    # 'HNSW-D9',
+    # 'RandCut',
+    "Original HNSW",
+    "Our Pruning Method",
+    "Small M",
+    "Random Prune",
+]
+
+PERFORMANCE_PLOT_PATH = './paper_plot/figures/H_hnsw_performance_comparison.pdf'
+SAVED_PATH = './paper_plot/figures/H_hnsw_recall_comparison.pdf'
+
+def extract_data_from_log(log_content):
+    """Extract method names, recall lists, and recompute lists from the log file."""
+    
+    method_pattern = r"Building HNSW index with ([^\.]+)\.\.\.|Building HNSW index with ([^\n]+)..."
+    recall_list_pattern = r"recall_list: (\[[\d\., ]+\])"
+    recompute_list_pattern = r"recompute_list: (\[[\d\., ]+\])"
+    avg_neighbors_pattern = r"neighbors per node: ([\d\.]+)"
+    
+    method_matches = re.findall(method_pattern, log_content)
+    # Temporary list for raw method identifiers from regex
+    _methods_raw_identifiers_regex = []
+    for match in method_matches:
+        method_ident = match[0] if match[0] else match[1]
+        _methods_raw_identifiers_regex.append(method_ident.strip().rstrip('.'))
+    
+    recall_lists_str = re.findall(recall_list_pattern, log_content)
+    recompute_lists_str = re.findall(recompute_list_pattern, log_content)
+    avg_neighbors_str_list = re.findall(avg_neighbors_pattern, log_content) # Keep as string list for now
+
+    # Determine if regex approach was sufficient, similar to original logic
+    # This check helps decide if we use regex-extracted names or fallback to split-parsing
+    _min_len_for_regex_path = min(
+        len(_methods_raw_identifiers_regex) if _methods_raw_identifiers_regex else 0,
+        len(recall_lists_str) if recall_lists_str else 0,
+        len(recompute_lists_str) if recompute_lists_str else 0,
+        len(avg_neighbors_str_list) if avg_neighbors_str_list else 0
+    )
+
+    methods = [] # This will hold the final display names
+
+    if _min_len_for_regex_path < 4 : # Fallback path if regex didn't get enough (e.g., for 4 methods)
+        # print("Regex approach failed or yielded insufficient data, trying direct extraction...")
+        sections = log_content.split("Building HNSW index with ")[1:]
+        methods_temp = []
+        for section in sections:
+            method_name_raw = section.split("\n")[0].strip().rstrip('.')
+            # Apply new short names in fallback
+            if method_name_raw == 'hnsw_IP_M30_efC128': mapped_name = MAPPED_METHOD_NAMES[0]
+            elif method_name_raw.startswith('99_4_degree'): mapped_name = MAPPED_METHOD_NAMES[1]
+            elif method_name_raw.startswith('d9_hnsw'): mapped_name = MAPPED_METHOD_NAMES[2]
+            elif method_name_raw.startswith('half'): mapped_name = MAPPED_METHOD_NAMES[3]
+            else: mapped_name = method_name_raw # Fallback to raw if no rule
+            methods_temp.append(mapped_name)
+        methods = methods_temp
+        # If fallback provides fewer than 4 methods, reordering later might not apply or error
+        # print(f"Direct extraction found {len(methods)} methods: {methods}")
+    else: # Regex path considered sufficient
+        methods_temp = []
+        for raw_name in _methods_raw_identifiers_regex:
+            # Apply new short names for regex path too
+            if raw_name == 'hnsw_IP_M30_efC128': mapped_name = MAPPED_METHOD_NAMES[0]
+            elif raw_name.startswith('99_4_degree'): mapped_name = MAPPED_METHOD_NAMES[1]
+            elif raw_name.startswith('d9_hnsw'): mapped_name = MAPPED_METHOD_NAMES[2]
+            elif raw_name.startswith('half'): mapped_name = MAPPED_METHOD_NAMES[3] # Assumes 'half' is a good prefix
+            else: mapped_name = raw_name # Fallback to cleaned raw name
+            methods_temp.append(mapped_name)
+        methods = methods_temp
+        # print(f"Regex extraction found {len(methods)} methods: {methods}")
+
+    # Convert string lists of numbers to actual numbers
+    avg_neighbors = [float(avg) for avg in avg_neighbors_str_list]
+
+    # Reordering (This reordering is crucial for color consistency if colors are fixed by position)
+    # It assumes methods[0] is Base, methods[1] is Our, etc., *before* this reordering step
+    # if that was the natural order from logs. The reordering swaps 3rd and 4th items.
+    if len(methods) >= 4 and \
+       len(recall_lists_str) >= 4 and \
+       len(recompute_lists_str) >= 4 and \
+       len(avg_neighbors) >= 4:
+        # This reordering means:
+        # Original order assumed: HNSW-Base, DegreeGuide, HNSW-D9, RandCut
+        # After reorder: HNSW-Base, DegreeGuide, RandCut, HNSW-D9
+        methods = [methods[0], methods[1], methods[3], methods[2]]
+        recall_lists_str = [recall_lists_str[0], recall_lists_str[1], recall_lists_str[3], recall_lists_str[2]]
+        recompute_lists_str = [recompute_lists_str[0], recompute_lists_str[1], recompute_lists_str[3], recompute_lists_str[2]]
+        avg_neighbors = [avg_neighbors[0], avg_neighbors[1], avg_neighbors[3], avg_neighbors[2]]
+    # else:
+        # print("Warning: Not enough elements to perform standard reordering. Using data as found.")
+
+
+    if len(avg_neighbors) > 0 and avg_neighbors_str_list[0] == "17.35": # Note: avg_neighbors_str_list used for string comparison
+        target_avg_neighbors = [18, 9, 9, 9] # This seems to be a specific adjustment based on a known log state
+        current_len = len(avg_neighbors)
+        # Ensure this reordering matches the one applied to `methods` if avg_neighbors were reordered with them
+        # If avg_neighbors was reordered, this hardcoding might need adjustment or be applied pre-reorder.
+        # For now, assume it applies to the (potentially reordered) avg_neighbors list.
+        avg_neighbors = target_avg_neighbors[:current_len]
+
+
+    recall_lists = [eval(recall_list) for recall_list in recall_lists_str]
+    recompute_lists = [eval(recompute_list) for recompute_list in recompute_lists_str]
+    
+    # Final truncation to ensure all lists have the same minimum length
+    min_length = min(len(methods), len(recall_lists), len(recompute_lists), len(avg_neighbors))
+    
+    methods = methods[:min_length]
+    recall_lists = recall_lists[:min_length]
+    recompute_lists = recompute_lists[:min_length]
+    avg_neighbors = avg_neighbors[:min_length]
+    
+    return methods, recall_lists, recompute_lists, avg_neighbors
+
+
+def plot_recall_comparison(methods, recall_lists, recompute_lists, avg_neighbors, current_recall_levels):
+    """Create a line chart comparing computation costs at different recall levels, with academic style."""    
+    plt.rcParams["font.family"] = "Helvetica"
+    plt.rcParams["ytick.direction"] = "in"
+    # plt.rcParams["hatch.linewidth"] = 1.5 # From example, but not used in line plot
+    plt.rcParams["font.weight"] = "bold"
+    plt.rcParams["axes.labelweight"] = "bold"
+    plt.rcParams["text.usetex"] = True # Ensure LaTeX is available or set to False
+    
+    computation_costs = []
+    for i, method_name in enumerate(methods): # methods now contains short names
+        method_costs = []
+        for level in current_recall_levels:
+            recall_idx = next((idx for idx, recall in enumerate(recall_lists[i]) if recall >= level), None)
+            if recall_idx is not None:
+                method_costs.append(recompute_lists[i][recall_idx])
+            else:
+                method_costs.append(None) 
+        computation_costs.append(method_costs)
+
+    fig, ax = plt.subplots(figsize=(5,2.5))
+    
+    # Modified academic_colors for consistency
+    # HNSW-Base (Grey), DegreeGuide (Red), RandCut (Cornflowerblue), HNSW-D9 (DarkBlue)
+    # academic_colors = ['dimgrey', 'tomato', 'cornflowerblue', '#003366', 'forestgreen', 'crimson']
+    academic_colors = [ 'slategray', 'tomato', 'cornflowerblue','#63B8B6',]
+    markers = ['o', '*', '^', 'D', 'v', 'P']
+    # Origin, Our, Random, SmallM
+
+
+    for i, method_name in enumerate(methods): # method_name is now short, e.g., 'HNSW-Base'
+        color_idx = i % len(academic_colors)
+        marker_idx = i % len(markers)
+        
+        y_values_plot = [val if val is not None else np.nan for val in computation_costs[i]]
+        y_values_plot = [val / 10000 if val is not None else np.nan for val in computation_costs[i]]
+
+        if method_name == MAPPED_METHOD_NAMES[0]: # Original HNSW-Base
+            linestyle = '--'
+        else:
+            linestyle = '-'
+        if method_name == MAPPED_METHOD_NAMES[1]: # Our Pruning Method
+            marker_size = 12
+        elif method_name == MAPPED_METHOD_NAMES[2]: # Small M
+            marker_size = 7.5
+        else:
+            marker_size = 8
+        if method_name == MAPPED_METHOD_NAMES[1]: # Our Pruning Method
+            zorder = 10
+        else:
+            zorder = 1
+        
+        # for random prune
+        if method_name == MAPPED_METHOD_NAMES[3]:
+            y_values_plot[0] += 0.12 # To prevent overlap with our method
+        elif method_name == MAPPED_METHOD_NAMES[1]:
+            y_values_plot[0] -= 0.06 # To prevent overlap with original hnsw
+
+        ax.plot(current_recall_levels, y_values_plot, 
+                 label=f"{method_name} (Avg Degree: {int(avg_neighbors[i])})", # Uses new short names
+                 color=academic_colors[color_idx], marker=markers[marker_idx], markeredgecolor='#FFFFFF80', # zhege miaobian shibushi buhaokan()
+                 markersize=marker_size, linewidth=2, linestyle=linestyle, zorder=zorder)
+
+    ax.set_xlabel('Recall Target', fontsize=9, fontweight="bold")
+    ax.set_ylabel('Nodes to Recompute', fontsize=9, fontweight="bold")
+    ax.set_xticks(current_recall_levels)
+    ax.set_xticklabels([f'{level*100:.0f}\%' for level in current_recall_levels], fontsize=10)
+    ax.tick_params(axis='y', labelsize=10)
+
+    ax.set_ylabel(r'Nodes to Recompute ($\mathbf{\times 10^4}$)', fontsize=9, fontweight="bold")
+
+    # Legend styling (already moved up from previous request)
+    ax.legend(loc='lower center', bbox_to_anchor=(0.5, 1.02), ncol=2, 
+              fontsize=6, edgecolor="black", facecolor="white", framealpha=1,
+              shadow=False, fancybox=False, prop={"weight": "normal", "size": 8})
+    
+    # No grid lines: ax.grid(True, linestyle='--', alpha=0.7)
+    
+    # Spines adjustment for academic look
+    ax.spines['top'].set_visible(False)
+    ax.spines['right'].set_visible(False)
+    ax.spines['left'].set_linewidth(1.0)
+    ax.spines['bottom'].set_linewidth(1.0)
+
+    annot_recall_level_92 = 0.92
+    if annot_recall_level_92 in current_recall_levels:
+        annot_recall_idx_92 = current_recall_levels.index(annot_recall_level_92)
+        method_base_name = "Our Pruning Method"
+        method_compare_92_name = "Small M"
+
+        if method_base_name in methods and method_compare_92_name in methods:
+            idx_base = methods.index(method_base_name)
+            idx_compare_92 = methods.index(method_compare_92_name)
+            cost_base_92 = computation_costs[idx_base][annot_recall_idx_92] / 10000
+            cost_compare_92 = computation_costs[idx_compare_92][annot_recall_idx_92] / 10000
+
+            if cost_base_92 is not None and cost_compare_92 is not None and cost_base_92 > 0:
+                ratio_92 = cost_compare_92 / cost_base_92
+                ax.annotate("", xy=(annot_recall_level_92, cost_compare_92),
+                            xytext=(annot_recall_level_92, cost_base_92),
+                            arrowprops=dict(arrowstyle="<->", color='#333333',
+                                            lw=1.5, mutation_scale=15,
+                                            shrinkA=3, shrinkB=3),
+                            zorder=10) # Arrow drawn first
+
+                text_x_pos_92 = annot_recall_level_92 # Text x is on the arrow line
+                text_y_pos_92 = (cost_base_92 + cost_compare_92) / 2
+                plot_ymin, plot_ymax = ax.get_ylim() # Boundary checks
+                if text_y_pos_92 < plot_ymin + (plot_ymax-plot_ymin)*0.05: text_y_pos_92 = plot_ymin + (plot_ymax-plot_ymin)*0.05
+                if text_y_pos_92 > plot_ymax - (plot_ymax-plot_ymin)*0.05: text_y_pos_92 = plot_ymax - (plot_ymax-plot_ymin)*0.05
+
+                ax.text(text_x_pos_92, text_y_pos_92, f"{ratio_92:.2f}x",
+                        fontsize=9, color='black',
+                        va='center', ha='center', # Centered horizontally and vertically
+                        bbox=dict(boxstyle='square,pad=0.25', # Creates space around text
+                                  fc='white',    # Face color matches plot background
+                                  ec='white',    # Edge color matches plot background
+                                  alpha=1.0),              # Fully opaque
+                        zorder=11) # Text on top of arrow
+
+    # --- Annotation for performance gap at 96% recall (0.96) ---
+    annot_recall_level_96 = 0.96
+    if annot_recall_level_96 in current_recall_levels:
+        annot_recall_idx_96 = current_recall_levels.index(annot_recall_level_96)
+        method_base_name = "Our Pruning Method"
+        method_compare_96_name = "Random Prune"
+
+        if method_base_name in methods and method_compare_96_name in methods:
+            idx_base = methods.index(method_base_name)
+            idx_compare_96 = methods.index(method_compare_96_name)
+            cost_base_96 = computation_costs[idx_base][annot_recall_idx_96] / 10000
+            cost_compare_96 = computation_costs[idx_compare_96][annot_recall_idx_96] / 10000
+
+            if cost_base_96 is not None and cost_compare_96 is not None and cost_base_96 > 0:
+                ratio_96 = cost_compare_96 / cost_base_96
+                ax.annotate("", xy=(annot_recall_level_96, cost_compare_96),
+                            xytext=(annot_recall_level_96, cost_base_96),
+                            arrowprops=dict(arrowstyle="<->", color='#333333',
+                                            lw=1.5, mutation_scale=15,
+                                            shrinkA=3, shrinkB=3),
+                            zorder=10) # Arrow drawn first
+
+                text_x_pos_96 = annot_recall_level_96 # Text x is on the arrow line
+                text_y_pos_96 = (cost_base_96 + cost_compare_96) / 2
+                plot_ymin, plot_ymax = ax.get_ylim() # Boundary checks
+                if text_y_pos_96 < plot_ymin + (plot_ymax-plot_ymin)*0.05: text_y_pos_96 = plot_ymin + (plot_ymax-plot_ymin)*0.05
+                if text_y_pos_96 > plot_ymax - (plot_ymax-plot_ymin)*0.05: text_y_pos_96 = plot_ymax - (plot_ymax-plot_ymin)*0.05
+
+                ax.text(text_x_pos_96, text_y_pos_96, f"{ratio_96:.2f}x",
+                        fontsize=9, color='black',
+                        va='center', ha='center', # Centered horizontally and vertically
+                        bbox=dict(boxstyle='square,pad=0.25', # Creates space around text
+                                  fc='white',    # Face color matches plot background
+                                  ec='white',    # Edge color matches plot background
+                                  alpha=1.0),              # Fully opaque
+                        zorder=11) # Text on top of arrow
+
+
+    plt.tight_layout(pad=0.5)
+    plt.savefig(SAVED_PATH, bbox_inches="tight", dpi=300)
+    plt.show()
+
+# --- Main script execution ---
+parser = argparse.ArgumentParser()
+parser.add_argument("log_file", type=str, default="./demo/output.log")
+args = parser.parse_args()
+
+try:
+    with open(args.log_file, 'r') as f:
+        log_content = f.read()
+except FileNotFoundError:
+    print(f"Error: Log file '{args.log_file}' not found.")
+    exit()
+
+methods, recall_lists, recompute_lists, avg_neighbors = extract_data_from_log(log_content)
+
+if methods: 
+    # plot_performance(methods, recall_lists, recompute_lists, avg_neighbors)
+    # print(f"Performance plot saved to {PERFORMANCE_PLOT_PATH}")
+    
+    plot_recall_comparison(methods, recall_lists, recompute_lists, avg_neighbors, recall_levels)
+    print(f"Recall comparison plot saved to {SAVED_PATH}")
+
+    print("\nMethod Summary:")
+    for i, method in enumerate(methods):
+        print(f"{method}:")
+        if i < len(avg_neighbors): # Check index bounds
+             print(f"  - Average neighbors per node: {avg_neighbors[i]:.2f}")
+        
+        for level in recall_levels:
+            if i < len(recall_lists) and i < len(recompute_lists): # Check index bounds
+                recall_idx = next((idx for idx, recall_val in enumerate(recall_lists[i]) if recall_val >= level), None)
+                if recall_idx is not None:
+                    print(f"  - Computations needed for {level*100:.0f}% recall: {recompute_lists[i][recall_idx]:.0f}")
+                else:
+                    print(f"  - Does not reach {level*100:.0f}% recall in the test")
+            else:
+                print(f"  - Data missing for recall/recompute lists for method {method}")
+        print()
+else:
+    print("No data extracted from the log file. Cannot generate plots or summary.")

research/paper_plot/main_exp.py

@@ -0,0 +1,441 @@
+import matplotlib.pyplot as plt
+import seaborn as sns
+import matplotlib.lines as mlines
+import pandas as pd
+import numpy as np
+from matplotlib.patches import FancyArrowPatch
+
+sns.set_theme(style="ticks", font_scale=1.2)
+plt.rcParams['axes.grid'] = True          
+plt.rcParams['axes.grid.which'] = 'major'  
+plt.rcParams['grid.linestyle'] = '--'
+plt.rcParams['grid.color'] = 'gray'
+plt.rcParams['grid.alpha'] = 0.3
+plt.rcParams['xtick.minor.visible'] = False
+plt.rcParams['ytick.minor.visible'] = False
+plt.rcParams["font.family"] = "Helvetica"
+plt.rcParams["text.usetex"] = True
+plt.rcParams["font.weight"] = "bold"
+plt.rcParams["axes.labelweight"] = "bold"
+# Generation(LLama 1B)	Generation(LLama 3B)	Generation(LLama 7B)
+# 0.085s	0.217s	0.472s
+# llm_inference_time=[0.085, 0.217, 0.472, 0] # Will be replaced by CSV data
+# llm_inference_time_for_mac = [0.316, 0.717, 1.468, 0] # Will be replaced by CSV data
+
+def parse_latency_data(csv_path):
+    df = pd.read_csv(csv_path)
+    latency_data = {}
+    llm_gen_times = {}  # To store LLM generation times: (dataset, hardware) -> time
+    
+    for _, row in df.iterrows():
+        dataset = row['Dataset']
+        hardware = row['Hardware']
+        recall_target_str = row['Recall_target'].replace('%', '')
+        try:
+            recall_target = float(recall_target_str)
+        except ValueError:
+            print(f"Warning: Could not parse recall_target '{row['Recall_target']}'. Skipping row.")
+            continue
+
+        if (dataset, hardware) not in llm_gen_times: # Read once per (dataset, hardware)
+            llm_time_val = pd.to_numeric(row.get('LLM_Gen_Time_1B'), errors='coerce')
+            if not pd.isna(llm_time_val):
+                llm_gen_times[(dataset, hardware)] = llm_time_val
+            else:
+                llm_gen_times[(dataset, hardware)] = np.nan # Store NaN if unparsable/missing
+
+        cols_to_skip = ['Dataset', 'Hardware', 'Recall_target',
+                        'LLM_Gen_Time_1B', 'LLM_Gen_Time_3B', 'LLM_Gen_Time_7B']
+
+        for col in df.columns:
+            if col not in cols_to_skip:
+                method_name = col
+                key = (dataset, hardware, method_name)
+                if key not in latency_data:
+                    latency_data[key] = []
+                try:
+                    latency_value = float(row[method_name])
+                    latency_data[key].append((recall_target, latency_value))
+                except ValueError:
+                    # Handle cases where latency might be non-numeric (e.g., 'N/A' or empty)
+                    print(f"Warning: Could not parse latency for {method_name} at {dataset}/{hardware}/Recall {recall_target} ('{row[method_name]}'). Skipping this point.")
+                    latency_data[key].append((recall_target, np.nan)) # Or skip appending
+
+    # Sort by recall for consistent plotting
+    for key in latency_data:
+        latency_data[key].sort(key=lambda x: x[0])
+    return latency_data, llm_gen_times
+
+def parse_storage_data(csv_path):
+    df = pd.read_csv(csv_path)
+    storage_data = {}
+    # Assuming the first column is 'MetricType' (RAM/Storage) and subsequent columns are methods
+    # And the header row is like: MetricType, Method1, Method2, ...
+    # Transpose to make methods as rows for easier lookup might be an option,
+    # but let's try direct parsing.
+    
+    # Find the row for RAM and Storage
+    ram_row = df[df.iloc[:, 0] == 'RAM'].iloc[0]
+    storage_row = df[df.iloc[:, 0] == 'Storage'].iloc[0]
+    
+    methods = df.columns[1:] # First column is the metric type label
+    for method in methods:
+        storage_data[method] = {
+            'RAM': pd.to_numeric(ram_row[method], errors='coerce'),
+            'Storage': pd.to_numeric(storage_row[method], errors='coerce')
+        }
+    return storage_data
+
+# Load data
+latency_csv_path = 'paper_plot/data/main_latency.csv'
+storage_csv_path = 'paper_plot/data/ram_storage.csv'
+latency_data, llm_generation_times = parse_latency_data(latency_csv_path)
+storage_info = parse_storage_data(storage_csv_path)
+
+# --- Determine unique Datasets and Hardware combinations to plot for ---
+unique_dataset_hardware_configs = sorted(list(set((d, h) for d, h, m in latency_data.keys())))
+
+if not unique_dataset_hardware_configs:
+    print("Error: No (Dataset, Hardware) combinations found in latency data. Check CSV paths and content.")
+    exit()
+
+# --- Define constants for plotting ---
+all_method_names = sorted(list(set(m for d,h,m in latency_data.keys())))
+if not all_method_names:
+    # Fallback if latency_data is empty but storage_info might have method names
+    all_method_names = sorted(list(storage_info.keys()))
+
+if not all_method_names:
+    print("Error: No method names found in data. Cannot proceed with plotting.")
+    exit()
+    
+method_markers = {
+    'HNSW': 'o', 
+    'IVF': 'X', 
+    'DiskANN': 's', 
+    'IVF-Disk': 'P', 
+    'IVF-Recompute': '^', 
+    'Our': '*',
+    'BM25': "v"
+    # Add more if necessary, or make it dynamic
+}
+method_display_names = {
+    'IVF-Recompute': 'IVF-Recompute (EdgeRAG)',
+    # 其他方法保持原名
+}
+
+# Ensure all methods have a marker
+default_markers = ['^', 'v', '<', '>', 'H', 'h', '+', 'x', '|', '_']
+next_default_marker = 0
+for mn in all_method_names:
+    if mn not in method_markers:
+        print(f"mn: {mn}")
+        method_markers[mn] = default_markers[next_default_marker % len(default_markers)]
+        next_default_marker +=1
+
+recall_levels_present = sorted(list(set(r for key in latency_data for r, l in latency_data[key])))
+# Define colors for up to a few common recall levels, add more if needed
+base_recall_colors = {
+    85.0: "#1f77b4", # Blue
+    90.0: "#ff7f0e", # Orange
+    95.0: "#2ca02c", # Green
+    # Add more if other recall % values exist
+}
+recall_colors = {}
+color_palette = sns.color_palette("viridis", n_colors=len(recall_levels_present))
+
+for idx, r_level in enumerate(recall_levels_present):
+    recall_colors[r_level] = base_recall_colors.get(r_level, color_palette[idx % len(color_palette)])
+
+
+# --- Determine global x (latency) and y (storage) limits for consistent axes ---
+all_latency_values = []
+all_storage_values = []
+raw_data_size = 76  # Raw data size in GB
+
+for ds_hw_key in unique_dataset_hardware_configs:
+    current_ds, current_hw = ds_hw_key
+    for method_name in all_method_names:
+        # Get storage for this method
+        disk_storage = storage_info.get(method_name, {}).get('Storage', np.nan)
+        if not np.isnan(disk_storage):
+            all_storage_values.append(disk_storage)
+        
+        # Get latencies for this method under current_ds, current_hw
+        latency_key = (current_ds, current_hw, method_name)
+        if latency_key in latency_data:
+            for recall, latency in latency_data[latency_key]:
+                if not np.isnan(latency):
+                    all_latency_values.append(latency)
+
+# Add padding to limits
+min_lat = min(all_latency_values) if all_latency_values else 0.001
+max_lat = max(all_latency_values) if all_latency_values else 1
+min_store = min(all_storage_values) if all_storage_values else 0
+max_store = max(all_storage_values) if all_storage_values else 1
+
+# Convert storage values to proportion of raw data
+min_store_proportion = min_store / raw_data_size if all_storage_values else 0
+max_store_proportion = max_store / raw_data_size if all_storage_values else 0.1
+
+# Padding for log scale latency - adjust minimum to be more reasonable
+lat_log_min = -1  # Changed from -2 to -1 to set minimum to 10^-1 (0.1s)
+lat_log_max = np.log10(max_lat) if max_lat > 0 else 3   # default to 1000 s
+lat_padding = (lat_log_max - lat_log_min) * 0.05
+global_xlim = [10**(lat_log_min - lat_padding), 10**(lat_log_max + lat_padding)]
+if global_xlim[0] <= 0: global_xlim[0] = 0.1  # Changed from 0.01 to 0.1
+
+# Padding for linear scale storage proportion
+store_padding = (max_store_proportion - min_store_proportion) * 0.05
+global_ylim = [max(0, min_store_proportion - store_padding), max_store_proportion + store_padding]
+if global_ylim[0] >= global_ylim[1]: # Avoid inverted or zero range
+    global_ylim[1] = global_ylim[0] + 0.1
+
+# After loading the data and before plotting, add this code to reorder the datasets
+# Find where you define all_datasets (around line 95)
+
+# Original code:
+all_datasets = sorted(list(set(ds for ds, _ in unique_dataset_hardware_configs)))
+
+# Replace with this to specify the exact order:
+all_datasets_unsorted = list(set(ds for ds, _ in unique_dataset_hardware_configs))
+desired_order = ['NQ', 'TriviaQA',  'GPQA','HotpotQA']
+all_datasets = [ds for ds in desired_order if ds in all_datasets_unsorted]
+# Add any datasets that might be in the data but not in our desired_order list
+all_datasets.extend([ds for ds in all_datasets_unsorted if ds not in desired_order])
+
+# Then the rest of your code remains the same:
+a10_configs = [(ds, 'A10') for ds in all_datasets if (ds, 'A10') in unique_dataset_hardware_configs]
+mac_configs = [(ds, 'MAC') for ds in all_datasets if (ds, 'MAC') in unique_dataset_hardware_configs]
+
+# Create two figures - one for A10 and one for MAC
+hardware_configs = [a10_configs, mac_configs]
+hardware_names = ['A10', 'MAC']
+
+for fig_idx, configs_for_this_figure in enumerate(hardware_configs):
+    if not configs_for_this_figure:
+        continue
+
+    num_cols_this_figure = len(configs_for_this_figure)
+    # 1 row, num_cols_this_figure columns
+    fig, axs = plt.subplots(1, num_cols_this_figure, figsize=(7 * num_cols_this_figure, 6), sharex=True, sharey=True, squeeze=False)
+    
+    # fig.suptitle(f"Latency vs. Storage ({hardware_names[fig_idx]})", fontsize=18, y=0.98)
+
+    for subplot_idx, (current_ds, current_hw) in enumerate(configs_for_this_figure):
+        ax = axs[0, subplot_idx] # Accessing column in the first row
+        ax.set_title(f"{current_ds}", fontsize=25) # No need to show hardware in title since it's in suptitle
+
+        for method_name in all_method_names:
+            marker = method_markers.get(method_name, '+') 
+            disk_storage = storage_info.get(method_name, {}).get('Storage', np.nan)
+
+            latency_points_key = (current_ds, current_hw, method_name)
+            if latency_points_key in latency_data:
+                points_for_method = latency_data[latency_points_key]
+                print(f"points_for_method: {points_for_method}")
+                for recall, latency in points_for_method:
+                    # Only skip if latency is invalid (since we need log scale for x-axis)
+                    # But allow zero storage since y-axis is now linear
+                    if np.isnan(latency) or np.isnan(disk_storage) or latency <= 0:
+                        continue
+                    
+                    # Add LLM generation time from CSV
+                    current_llm_add_time = llm_generation_times.get((current_ds, current_hw))
+                    if current_llm_add_time is not None and not np.isnan(current_llm_add_time):
+                        latency = latency + current_llm_add_time
+                    else:
+                        raise ValueError(f"No LLM generation time found for {current_ds} on {current_hw}")
+
+                    # Special handling for BM25
+                    if method_name == 'BM25':
+                        # BM25 is only valid for 85% recall points (other points are 0)
+                        if recall != 85.0:
+                            continue
+                        color = 'grey'
+                    else:
+                        # Use the color for target recall
+                        color = recall_colors.get(recall, 'grey')
+                    
+                    # Convert storage to proportion
+                    disk_storage_proportion = disk_storage / raw_data_size
+                    size = 80
+                    
+                    x_offset = -50
+                    if current_ds == 'GPQA':
+                        x_offset = -32
+
+                    # Apply a small vertical offset to IVF-Recompute points to make them more visible
+                    if method_name == 'IVF-Recompute':
+                        # Add a small vertical offset (adjust the 0.05 value as needed)
+                        disk_storage_proportion += 0.07
+                        size = 80
+                    if method_name == 'DiskANN':
+                        size = 50
+                    if method_name == 'Our':
+                        size = 140
+                        disk_storage_proportion += 0.05
+                        # Add "Pareto Frontier" label to Our method points
+                        
+                        if recall == 95:
+                            ax.annotate('Ours', 
+                                    (latency, disk_storage_proportion),
+                                    xytext=(x_offset, 25),  # Increased leftward offset from -65 to -120
+                                    textcoords='offset points',
+                                    fontsize=20,
+                                    color='red',
+                                   weight='bold',
+                                   bbox=dict(boxstyle="round,pad=0.3", fc="white", ec="red", alpha=0.7))
+                    # Increase size for BM25 points
+                    if method_name == 'BM25':
+                        size = 70
+                    size*=5
+                    
+                    ax.scatter(latency, disk_storage_proportion, marker=marker, color=color, 
+                               s=size, alpha=0.85, edgecolors='black', linewidths=0.7)
+                    
+            
+
+        
+        ax.set_xscale("log")
+        ax.set_yscale("linear") # CHANGED from log scale to linear scale for Y-axis
+        
+        # Generate appropriate powers of 10 based on your data range
+        min_power = -1
+        max_power = 4
+        log_ticks = [10**i for i in range(min_power, max_power+1)]
+
+        # Set custom tick positions
+        ax.set_xticks(log_ticks)
+
+        # Create custom bold LaTeX labels with 10^n format
+        log_tick_labels = [fr'$\mathbf{{10^{{{i}}}}}$' for i in range(min_power, max_power+1)]
+        ax.set_xticklabels(log_tick_labels, fontsize=24)
+
+        # Apply global limits
+        if subplot_idx == 0:
+            ax.set_xlim(global_xlim)
+            ax.set_ylim(global_ylim)
+
+        ax.grid(True, which="major", linestyle="--", linewidth=0.6, alpha=0.7)
+        # Remove minor grid lines completely
+        ax.grid(False, which="minor")
+        
+        # Remove ticks
+        # First set the shared parameters for both axes
+        ax.tick_params(axis='both', which='both', length=0, labelsize=24)
+
+        # Then set the padding only for the x-axis
+        ax.tick_params(axis='x', which='both', pad=10)
+        
+        if subplot_idx == 0: # Y-label only for the leftmost subplot
+            ax.set_ylabel("Proportional Size", fontsize=24)
+        
+        # X-label for all subplots in a 1xN layout can be okay, or just the middle/last one.
+        # Let's put it on all for now.
+        ax.set_xlabel("Latency (s)", fontsize=25)
+
+        # Display 100%, 200%, 300% for yaxis
+        ax.set_yticks([1, 2, 3])
+        ax.set_yticklabels(['100\%', '200\\%', '300\\%'])
+
+        # Create a custom arrow with "Better" text inside
+        # Create the arrow patch with a wider shaft
+        arrow = FancyArrowPatch(
+            (0.8, 0.8),  # Start point (top-right)
+            (0.65, 0.6),  # End point (toward bottom-left)
+            transform=ax.transAxes,
+            arrowstyle='simple,head_width=40,head_length=35,tail_width=20',  # Increased arrow dimensions
+            facecolor='white',
+            edgecolor='black',
+            linewidth=3,  # Thicker outline
+            zorder=5
+        )
+        
+        # Add the arrow to the plot
+        ax.add_patch(arrow)
+        
+        # Calculate the midpoint of the arrow for text placement
+        mid_x = (0.8 + 0.65) / 2 + 0.002 + 0.01
+        mid_y = (0.8 + 0.6) / 2 + 0.01
+        
+        # Add the "Better" text at the midpoint of the arrow
+        ax.text(mid_x, mid_y, 'Better', 
+                transform=ax.transAxes,
+                ha='center', 
+                va='center',
+                fontsize=16,  # Increased font size from 12 to 16
+                fontweight='bold',
+                rotation=40,  # Rotate to match arrow direction
+                zorder=6)  # Ensure text is on top of arrow
+
+    # Create legends (once per figure)
+    method_legend_handles = []
+    for method, marker_style in method_markers.items():
+        if method in all_method_names: 
+            print(f"method: {method}")
+            # Use black color for BM25 in the legend
+            if method == 'BM25':
+                method_legend_handles.append(mlines.Line2D([], [], color='black', marker=marker_style, linestyle='None',
+                                markersize=10, label=method))
+            else:
+                if method in method_display_names:
+                    method = method_display_names[method]
+                method_legend_handles.append(mlines.Line2D([], [], color='black', marker=marker_style, linestyle='None',
+                                markersize=10, label=method))
+    
+    recall_legend_handles = []
+    sorted_recall_levels = sorted(recall_colors.keys())
+    for r_level in sorted_recall_levels:
+        recall_legend_handles.append(mlines.Line2D([], [], color=recall_colors[r_level], marker='o', linestyle='None',
+                                   markersize=20, label=f"Target Recall={r_level:.0f}\%"))
+
+    # 将图例分成两行：第一行是方法，第二行是召回率
+    if fig_idx == 0:
+        # 从方法列表中先排除'Our'
+        other_methods = [m for m in all_method_names if m != 'Our']
+        # 按照需要的顺序创建方法列表（将'Our'放在最后）
+        ordered_methods = other_methods + (['Our'] if 'Our' in all_method_names else [])
+        
+        # 按照新顺序创建方法图例句柄
+        method_legend_handles = []
+        for method in ordered_methods:
+            if method in method_markers:
+                marker_style = method_markers[method]
+                # 使用显示名称映射
+                display_name = method_display_names.get(method, method)
+                color = 'black'
+                marker_size = 22
+                if method == 'Our':
+                    marker_size = 27
+                elif 'IVF-Recompute' in method or 'EdgeRAG' in method:
+                    marker_size = 17
+                elif 'DiskANN' in method:
+                    marker_size = 19
+                elif 'BM25' in method:
+                    marker_size = 20
+                method_legend_handles.append(mlines.Line2D([], [], color=color, marker=marker_style, 
+                                        linestyle='None', markersize=marker_size, label=display_name))
+    
+        # 创建召回率图例（第二行）- 注意位置调整，放在方法图例下方
+        recall_legend = fig.legend(handles=recall_legend_handles, 
+                    loc='upper center', bbox_to_anchor=(0.5, 1.05),  # y坐标降低，放在第一行下方
+                    ncol=len(recall_legend_handles), fontsize=28)
+
+
+        # 创建方法图例（第一行）
+        method_legend = fig.legend(handles=method_legend_handles, 
+                    loc='upper center', bbox_to_anchor=(0.5, 0.91),
+                    ncol=len(method_legend_handles), fontsize=28)
+        
+        # 添加图例到渲染器
+        fig.add_artist(method_legend)
+        fig.add_artist(recall_legend)
+
+    # 调整布局，为顶部的两行图例留出更多空间
+    plt.tight_layout(rect=(0, 0, 1.0, 0.74))  # 顶部空间从0.9调整到0.85，给两行图例留出更多空间
+    
+    save_path = f'./paper_plot/figures/main_exp_fig_{fig_idx+1}.pdf'
+    plt.savefig(save_path, dpi=300, bbox_inches='tight') 
+    print(f"Saved figure {fig_idx+1} to {save_path}")
+    plt.show()

research/paper_plot/main_latency.py

@@ -0,0 +1,163 @@
+import csv
+
+import numpy as np
+import matplotlib.pyplot as plt
+import csv
+
+plt.rcParams["font.family"] = "Helvetica"
+plt.rcParams["ytick.direction"] = "in"
+plt.rcParams["hatch.linewidth"] = 1
+plt.rcParams["font.weight"] = "bold"
+plt.rcParams["axes.labelweight"] = "bold"
+plt.rcParams["text.usetex"] = True
+SAVE_PTH = "./paper_plot/figures"
+font_size = 16
+
+# Generation(LLama 1B)	Generation(LLama 3B)	Generation(LLama 7B)
+# 0.085s	0.217s	0.472s
+llm_inference_time=[0.085, 0.217, 0.472, 0]
+
+USE_LLM_INDEX = 3 # +0
+
+file_path = "./paper_plot/data/main_latency.csv"
+
+with open(file_path, mode="r", newline="") as file:
+    reader = csv.reader(file)
+    data = list(reader)
+
+# 打印原始数据
+for row in data:
+    print(",".join(row))
+
+
+
+
+models = ["A10", "MAC"]
+datasets = ["NQ", "TriviaQA", "GPQA", "HotpotQA"]
+data = [[float(cell) if cell.isdigit() else cell for cell in row] for row in data[1:]]
+for k, model in enumerate(models):
+
+    fig, axes = plt.subplots(1, 4)
+    fig.set_size_inches(20, 3)
+    plt.subplots_adjust(wspace=0, hspace=0)
+
+    total_width, n = 6, 6
+    group = 1
+    width = total_width * 0.9 / n
+    x = np.arange(group) * n
+    exit_idx_x = x + (total_width - width) / n
+    edgecolors = ["dimgrey", "#63B8B6", "tomato", "slategray", "mediumpurple", "green", "red", "blue", "yellow", "silver"]
+    # hatches = ["", "\\\\", "//", "||", "x", "--", "..", "", "\\\\", "//", "||", "x", "--", ".."]
+    hatches =["\\\\\\","\\\\"]
+
+    labels = [
+        "HNSW",
+        "IVF",
+        "DiskANN",
+        "IVF-Disk",
+        "IVF-Recompute",
+        "Our",
+        # "DGL-OnDisk",
+    ]
+    if k == 0:
+        x_labels = "GraphSAGE"
+    else:
+        x_labels = "GAT"
+
+    yticks = [0.01, 0.1, 1, 10, 100, 1000,10000]  # Log scale ticks
+    val_limit = 15000  # Upper limit for the plot
+
+    for i in range(4):
+        axes[i].set_yscale('log')  # Set y-axis to logarithmic scale
+        axes[i].set_yticks(yticks)
+        axes[i].set_ylim(0.01, val_limit)  # Lower limit should be > 0 for log scale
+
+        axes[i].tick_params(axis="y", labelsize=10)
+
+        axes[i].set_xticks([])
+        # axes[i].set_xticklabels()
+        axes[i].set_xlabel(datasets[i], fontsize=font_size)
+        axes[i].grid(axis="y", linestyle="--")
+        axes[i].set_xlim(exit_idx_x[0] - 0.15 * width - 0.2, exit_idx_x[0] + (n-0.25)* width + 0.2)
+        for j in range(n):
+            ##TODO add label
+
+            # num = float(data[i * 2 + k][j + 3])
+            # plot_label = [num]
+            # if j == 6 and i == 3:
+            #     plot_label = ["N/A"]
+            #     num = 0
+            local_hatches=["////","\\\\","xxxx"]
+            # here add 3 bars rather than one bar TODO 
+            print('exit_idx_x',exit_idx_x)
+            
+            # Check if all three models for this algorithm are OOM (data = 0)
+            is_oom = True
+            for m in range(3):
+                if float(data[i * 6 + k*3 + m][j + 3]) != 0:
+                    is_oom = False
+                    break
+                    
+            if is_oom:
+                # Draw a cross for OOM instead of bars
+                pos = exit_idx_x + j * width + width * 0.3  # Center position for cross
+                marker_size = width * 150  # Size of the cross
+                axes[i].scatter(pos, 0.02, marker='x', color=edgecolors[j], s=marker_size, 
+                               linewidth=4, label=labels[j] if j < len(labels) else "", zorder=20)
+            else:
+                # Create three separate bar calls instead of trying to plot multiple bars at once
+                for m in range(3):
+                    num = float(data[i * 6 + k*3 +m][j + 3]) +llm_inference_time[USE_LLM_INDEX]
+                    plot_label = [num]
+                    pos = exit_idx_x + j * width + width * 0.3 * m
+                    print(f"j: {j}, m: {m}, pos: {pos}")
+                    # For log scale, we need to ensure values are positive
+                    plot_value = max(0.01, num) if num < val_limit else val_limit
+                    container = axes[i].bar(
+                        pos,
+                        plot_value,
+                        width=width * 0.3,
+                        color="white",
+                        edgecolor=edgecolors[j],
+                        # edgecolor="k",
+                        hatch=local_hatches[m],  # Use different hatches for each of the 3 bars
+                        linewidth=1.0,
+                        label=labels[j] if m == 0 else "",  # Only add label for the first bar
+                        zorder=10,
+                    )
+            # axes[i].bar_label(
+            #     container,
+            #     plot_label,
+            #     fontsize=font_size - 2,
+            #     zorder=200,
+            #     fontweight="bold",
+            # )
+
+    if k == 0:
+        axes[0].legend(
+            bbox_to_anchor=(3.25, 1.02),
+            ncol=7,
+            loc="lower right",
+            # fontsize=font_size,
+            # markerscale=3,
+            labelspacing=0.2,
+            edgecolor="black",
+            facecolor="white",
+            framealpha=1,
+            shadow=False,
+            # fancybox=False,
+            handlelength=2,
+            handletextpad=0.5,
+            columnspacing=0.5,
+            prop={"weight": "bold", "size": font_size},
+        ).set_zorder(100)
+
+    axes[0].set_ylabel("Runtime (log scale)", fontsize=font_size, fontweight="bold")
+    axes[0].set_yticklabels([r"$10^{-2}$", r"$10^{-1}$", r"$10^{0}$", r"$10^{1}$", r"$10^{2}$", r"$10^{3}$",r"$10^{4}$"], fontsize=font_size)
+    axes[1].set_yticklabels([])
+    axes[2].set_yticklabels([])
+    axes[3].set_yticklabels([])
+
+    plt.savefig(f"{SAVE_PTH }/speed_{model}_revised.pdf", bbox_inches="tight", dpi=300)
+    ## print save
+    print(f"{SAVE_PTH }/speed_{model}_revised.pdf")

research/paper_plot/main_memory_storage.py

@@ -0,0 +1,85 @@
+from matplotlib import pyplot as plt
+from matplotlib.gridspec import GridSpec
+
+# Comment Test
+ 
+# om script.settings import DATA_PATH, FIGURE_PATH
+# DATA_PATH ="/home/ubuntu/Power-RAG/paper_plot/data"
+# FIGURE_PATH = "/home/ubuntu/Power-RAG/paper_plot/figures"
+plt.rcParams["font.family"] = "Helvetica"
+plt.rcParams["ytick.direction"] = "in"
+plt.rcParams["hatch.linewidth"] = 2
+plt.rcParams["font.weight"] = "bold"
+plt.rcParams["axes.labelweight"] = "bold"
+plt.rcParams["text.usetex"] = True
+
+import numpy as np
+import pandas as pd
+
+# Load the RAM and Storage data directly from CSV
+data = pd.read_csv("./paper_plot/data/ram_storage.csv")
+
+# Explicitly reorder columns to ensure "Our" is at the end
+cols = list(data.columns)
+if "Our" in cols and cols[-1] != "Our":
+    cols.remove("Our")
+    cols.append("Our")
+    data = data[cols]
+
+# Set up the figure with two columns
+fig = plt.figure(figsize=(12, 3))
+gs = GridSpec(1, 2, figure=fig)
+ax1 = fig.add_subplot(gs[0, 0])  # Left panel for RAM
+ax2 = fig.add_subplot(gs[0, 1])  # Right panel for Storage
+
+# Define the visual style elements
+edgecolors = ["dimgrey", "#63B8B6", "tomato", "slategray", "silver", "navy"]
+hatches = ["/////", "\\\\\\\\\\"]
+
+# Calculate positions for the bars
+methods = data.columns[1:]  # Skip the 'Hardware' column
+num_methods = len(methods)
+# Reverse the order of methods for display (to have "Our" at the bottom)
+methods = list(methods)[::-1]
+y_positions = np.arange(num_methods)
+bar_width = 0.6
+
+# Plot RAM data in left panel
+ram_bars = ax1.barh(
+    y_positions,
+    data.iloc[0, 1:].values[::-1],  # Reverse the data to match reversed methods
+    height=bar_width,
+    color="white",
+    edgecolor=edgecolors[0],
+    hatch=hatches[0],
+    linewidth=1.0,
+    label="RAM",
+    zorder=10,
+)
+ax1.set_title("RAM Usage", fontsize=14, fontweight='bold')
+ax1.set_yticks(y_positions)
+ax1.set_yticklabels(methods, fontsize=14)
+ax1.set_xlabel("Size (\\textit{GB})", fontsize=14)
+ax1.xaxis.set_tick_params(labelsize=14)
+
+# Plot Storage data in right panel
+storage_bars = ax2.barh(
+    y_positions, 
+    data.iloc[1, 1:].values[::-1],  # Reverse the data to match reversed methods
+    height=bar_width,
+    color="white",
+    edgecolor=edgecolors[1],
+    hatch=hatches[1],
+    linewidth=1.0,
+    label="Storage",
+    zorder=10,
+)
+ax2.set_title("Storage Usage", fontsize=14, fontweight='bold')
+ax2.set_yticks(y_positions)
+ax2.set_yticklabels(methods, fontsize=14)
+ax2.set_xlabel("Size (\\textit{GB})", fontsize=14)
+ax2.xaxis.set_tick_params(labelsize=14)
+
+plt.tight_layout()
+plt.savefig("./paper_plot/figures/ram_storage_double_column.pdf", bbox_inches="tight", dpi=300)
+print("Saving the figure to ./paper_plot/figures/ram_storage_double_column.pdf")

research/paper_plot/recompute_bottle.py

@@ -0,0 +1,141 @@
+#!/usr/bin/env python3
+# -*- coding:utf-8 -*-
+# Motto: Were It to Benefit My Country, I Would Lay Down My Life!
+# \file: /bottleneck_breakdown.py
+# \brief: Illustrates the query time bottleneck on consumer devices (Final Version - Font & Legend Adjust).
+# Author: Gemini Assistant (adapted from user's style and feedback)
+
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.ticker import FuncFormatter # Not strictly needed for just font, but imported if user wants to try
+
+# Set matplotlib styles similar to the example
+plt.rcParams["font.family"] = "Helvetica" # Primary font family
+plt.rcParams["ytick.direction"] = "in"
+plt.rcParams["xtick.direction"] = "in"
+plt.rcParams["hatch.linewidth"] = 1.0
+plt.rcParams["font.weight"] = "bold"
+plt.rcParams["axes.labelweight"] = "bold"
+
+plt.rcParams["text.usetex"] = True
+# Attempt to make LaTeX use Helvetica as the main font
+plt.rcParams['text.latex.preamble'] = r"""
+\usepackage{helvet}       % helvetica font
+\usepackage{sansmath}     % helvetica for math
+\sansmath                % activate sansmath
+\renewcommand{\familydefault}{\sfdefault} % make sans-serif the default family
+"""
+
+
+# Final Data for the breakdown (3 Segments)
+labels_raw = [ # Raw labels before potential LaTeX escaping
+    'IO: Text + PQ Lookup',
+    'CPU: Tokenize + Distance Compute',
+    'GPU: Embedding Recompute',
+]
+# Times in ms, ordered for stacking
+times_ms = np.array([
+    8.009,   # Quantization
+    16.197,  # Search
+    76.512,  # Embedding Recomputation
+])
+
+total_time_ms = times_ms.sum()
+percentages = (times_ms / total_time_ms) * 100
+
+# Prepare labels for legend, escaping for LaTeX if active
+labels_legend = []
+# st1 = r'&' # Not needed as current labels_raw don't have '&'
+for label, time, perc in zip(labels_raw, times_ms, percentages):
+    # Construct the percentage string carefully for LaTeX
+    perc_str = f"{perc:.1f}" + r"\%" # Correct way to form 'NN.N\%'
+    # label_tex = label.replace('&', st1) # Use if '&' is in labels_raw
+    label_tex = label # Current labels_raw are clean for LaTeX
+    labels_legend.append(
+        f"{label_tex}\n({time:.1f}ms, {perc_str})"
+    )
+
+# Styling based on user's script
+# Using first 3 from the provided lists
+edgecolors_list = ["dimgrey", "#63B8B6", "tomato", "silver", "slategray"]
+hatches_list = ["/////", "xxxxx", "\\\\\\\\\\"]
+
+edgecolors = edgecolors_list[:3]
+hatches = hatches_list[:3]
+fill_color = "white"
+
+# Create the figure and axes
+# Adjusted figure size to potentially accommodate legend on the right
+fig, ax = plt.subplots()
+fig.set_size_inches(7, 1.5) # Width increased slightly, height adjusted
+# Adjusted right margin for external legend, bottom for x-label
+plt.subplots_adjust(left=0.12, right=0.72, top=0.95, bottom=0.25)
+
+# Create the horizontal stacked bar
+bar_height = 0.2
+y_pos = 0
+
+left_offset = 0
+for i in range(len(times_ms)):
+    ax.barh(
+        y_pos,
+        times_ms[i],
+        height=bar_height,
+        left=left_offset,
+        color=fill_color,
+        edgecolor=edgecolors[i],
+        hatch=hatches[i],
+        linewidth=1.5,
+        label=labels_legend[i],
+        zorder=10
+    )
+    text_x_pos = left_offset + times_ms[i] / 2
+    if times_ms[i] > total_time_ms * 0.03: # Threshold for displaying text
+        ax.text(
+            text_x_pos,
+            y_pos,
+            f"{times_ms[i]:.1f}ms",
+            ha='center',
+            va='center',
+            fontsize=8,
+            fontweight='bold',
+            color='black',
+            zorder=20,
+            bbox=dict(facecolor='white', edgecolor='none', pad=0.5, alpha=0.8)
+        )
+    left_offset += times_ms[i]
+
+# Set plot limits and labels
+ax.set_xlim([0, total_time_ms * 1.02])
+ax.set_xlabel("Time (ms)", fontsize=14, fontweight='bold', x=0.75, )
+
+# Y-axis: Remove y-ticks and labels
+ax.set_yticks([])
+ax.set_yticklabels([])
+
+# Legend: Placed to the right of the plot
+ax.legend(
+    # (x, y) for anchor, (0,0) is bottom left, (1,1) is top right of AXES
+    # To place outside on the right, x should be > 1
+    bbox_to_anchor=(1.03, 0.5), # x > 1 means outside to the right, y=0.5 for vertical center
+    ncol=1, # Single column for a taller, narrower legend
+    loc="center left", # Anchor the legend's left-center to bbox_to_anchor point
+    labelspacing=0.5, # Adjust spacing
+    edgecolor="black",
+    facecolor="white",
+    framealpha=1,
+    shadow=False,
+    fancybox=False,
+    handlelength=1.5,
+    handletextpad=0.6,
+    columnspacing=1.5,
+    prop={"weight": "bold", "size": 9},
+).set_zorder(100)
+
+# Save the figure (using the original generic name as requested)
+output_filename = "./bottleneck_breakdown.pdf"
+# plt.tight_layout() # tight_layout might conflict with external legend; adjust subplots_adjust instead
+plt.savefig(output_filename, bbox_inches="tight", dpi=300)
+print(f"Saved plot to {output_filename}")
+
+# plt.show() # Uncomment to display plot interactively