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neurondb/README.md

NeuronDB — PostgreSQL AI ecosystem

PostgreSQL 16/17/18 CI: NeuronDB CI: NeuronMCP CI: Integration Security scan Docker GPU Backends

Version Status License: Proprietary Docs GitHub Stars

Vector search, embeddings, and ML primitives in PostgreSQL, with optional services for agents, MCP, and a desktop UI.

Tip

New here? Start with Docs/getting-started/simple-start.md or jump to QUICKSTART.md.

Developer Tools: Try the quickstart data pack, SQL recipe library, and CLI helpers for faster development!

Hello NeuronDB (60 seconds)

Get vector search working in under a minute:

📋 Quick Start Checklist
  • Docker and Docker Compose installed
  • Ports 5433, 8080, 8081, 3000 available
  • 4 GB+ RAM available
  • Ready to run commands

Step-by-Step Guide

Step 1: Start PostgreSQL with NeuronDB

# Start NeuronDB (CPU profile, default)
docker compose up -d neurondb

# Wait for service to be healthy (about 30-60 seconds)
docker compose ps

Step 2: Create Extension

# Connect and create extension
psql "postgresql://neurondb:neurondb@localhost:5433/neurondb" \
  -c "CREATE EXTENSION IF NOT EXISTS neurondb;"

Step 3: Create Table, Insert Vectors, and Search

# Create table, insert vectors, create index, and search
psql "postgresql://neurondb:neurondb@localhost:5433/neurondb" <<EOF
CREATE TABLE documents (
  id SERIAL PRIMARY KEY,
  content TEXT,
  embedding vector(3)
);

INSERT INTO documents (content, embedding) VALUES
  ('Machine learning algorithms', '[0.1,0.2,0.3]'::vector),
  ('Neural networks and deep learning', '[0.2,0.3,0.4]'::vector),
  ('Natural language processing', '[0.3,0.4,0.5]'::vector);

CREATE INDEX ON documents USING hnsw (embedding vector_cosine_ops);

SELECT id, content, embedding <=> '[0.15,0.25,0.35]'::vector AS distance
FROM documents
ORDER BY embedding <=> '[0.15,0.25,0.35]'::vector
LIMIT 3;
EOF

Expected output:

 id |              content               |     distance      
----+------------------------------------+-------------------
  1 | Machine learning algorithms        | 0.141421356237309
  2 | Neural networks and deep learning  | 0.173205080756888
  3 | Natural language processing       | 0.244948974278318
(3 rows)

[!SUCCESS] Congratulations! You've successfully set up vector search. The results show documents ordered by similarity to your query vector, with the closest match first.

[!SECURITY] The default password (neurondb) is for development only. Always change it in production by setting POSTGRES_PASSWORD in your .env file. See Service URLs & ports for connection details.

📑 Table of Contents

Expand full table of contents

🎯 What You Can Build

NeuronDB enables you to build powerful AI applications directly in PostgreSQL:

🔍 Semantic & Hybrid Search

Combine vector similarity with SQL filters and full-text search:

-- Find similar documents with metadata filters
SELECT content, embedding <=> query_vector AS similarity
FROM documents
WHERE category = 'technology'
  AND created_at > '2024-01-01'
ORDER BY embedding <=> query_vector
LIMIT 10;

Use cases:

  • Document search with filters
  • Product recommendations
  • Content discovery
  • Similarity matching
📄 RAG Pipelines

Build retrieval-augmented generation systems with Postgres-native primitives:

-- Generate embedding for query
WITH query AS (SELECT embed_text('your question') AS q_vec)
-- Retrieve relevant context
SELECT content, embedding <=> q.q_vec AS distance
FROM documents, query q
ORDER BY embedding <=> q.q_vec
LIMIT 5;

Use cases:

  • Question answering systems
  • Document Q&A
  • Knowledge bases
  • Chatbots with context
🤖 Agent Backends

Create AI agents with durable memory and tool execution:

  • ✅ Persistent memory with vector search
  • ✅ Tool execution (SQL, HTTP, Code, Shell)
  • ✅ Multi-agent collaboration
  • ✅ Workflow orchestration
  • ✅ Budget and cost management

Use cases:

  • Autonomous agents
  • Workflow automation
  • Data analysis agents
  • Customer service bots
🔌 MCP Integrations

Connect MCP clients (Claude Desktop, etc.) to NeuronDB:

  • ✅ 600+ tools available via MCP
  • ✅ Vector operations
  • ✅ ML pipeline tools
  • ✅ PostgreSQL administration
  • ✅ Dataset loading

Use cases:

  • Claude Desktop integration
  • LLM tool access
  • Database management via LLMs
  • Automated workflows

⭐ What Makes NeuronDB Different

📊 Feature Comparison
Feature NeuronDB Typical Alternatives
Index types HNSW, IVF, PQ, hybrid, multi-vector Limited (usually just HNSW)
GPU acceleration CUDA, ROCm, Metal (3 backends) Single backend or CPU-only
Benchmark coverage RAGAS, MTEB, BEIR integrated Manual setup required
Agent runtime ✅ NeuronAgent included ❌ External services needed
MCP server ✅ NeuronMCP included (600+ tools) ❌ Separate integration required
Desktop UI ✅ NeuronDesktop included ❌ Build your own
ML algorithms 52+ algorithms Extension only (limited)
SQL functions 665+ functions Typically <100
🎯 Key Advantages

🚀 Performance

  • 10x faster HNSW index building than pgvector
  • SIMD-optimized distance calculations
  • GPU acceleration for embeddings and ML
  • Efficient memory management

🔧 Developer Experience

  • Complete ecosystem - Database + Agent + MCP + UI
  • SQL-first - Everything accessible via SQL
  • Rich tooling - CLI helpers, examples, recipes
  • Comprehensive docs - 60+ documentation files

🏢 Enterprise Ready

  • Production features - Monitoring, backups, HA
  • Security - RBAC, encryption, audit logging
  • Scalability - Horizontal and vertical scaling
  • Observability - Prometheus metrics, structured logging

Installation

Pick one component

Choose what you need:

Component Setup Command What you get
NeuronDB only (extension) docker compose up -d neurondb Vector search, ML algorithms, embeddings in PostgreSQL
NeuronDB + NeuronMCP docker compose up -d neurondb neuronmcp Above + MCP server for Claude Desktop, etc.
NeuronDB + NeuronAgent docker compose up -d neurondb neuronagent Above + Agent runtime with REST API
Full stack docker compose up -d All components including NeuronDesktop UI

Note

All components run independently. The root docker-compose.yml starts everything together for convenience, but you can run individual services as needed. You can also run each component independently (see component READMEs).

Quick start (Docker)

Option 1: Use published images (recommended)

Pull pre-built images from GitHub Container Registry:

# Pull latest images
docker compose pull

# Start services
docker compose up -d

# Wait for services to be healthy (30-60 seconds)
docker compose ps

# Verify all services are running
./scripts/neurondb-healthcheck.sh quick

What you'll see:

  • 5 services starting: neurondb, neuronagent, neuronmcp, neurondesk-api, neurondesk-frontend
  • All services should show "healthy" status after initialization

Tip

For specific versions, see Container Images documentation. Published images are available starting with v1.0.0.

Option 2: Build from source

# Build and start all services
docker compose up -d --build

# Monitor build progress (first time takes 5-10 minutes)
docker compose logs -f

# Once built, wait for services to be healthy
docker compose ps

# Verify all services are running
./scripts/neurondb-healthcheck.sh quick

Build time: First build takes 5-10 minutes depending on your system. Subsequent starts are 30-60 seconds.

Prerequisites checklist
  • Docker 20.10+ installed
  • Docker Compose 2.0+ installed
  • 4 GB+ RAM available
  • Ports 5433, 8080, 8081, 3000 available

Important

Prefer a step-by-step guide? See QUICKSTART.md.

New Developer Tools: After setup, try the quickstart data pack for sample data, SQL recipe library for ready-to-run queries, and CLI helpers for index management!

[!SECURITY] Default credentials are for development only. In production, set strong passwords via environment variables or .env file.

Native install

Install components directly on your system without Docker.

NeuronDB Extension

Install the NeuronDB extension directly into your existing PostgreSQL installation.

Build and install steps

Prerequisites:

  • PostgreSQL 16, 17, or 18 development headers
  • C compiler (gcc or clang)
  • Make

Build:

cd NeuronDB
make
sudo make install

Enable extension:

CREATE EXTENSION neurondb;

Configure (if needed):

Some features require preloading. Add to postgresql.conf:

shared_preload_libraries = 'neurondb'

Then restart PostgreSQL:

sudo systemctl restart postgresql

Configuration parameters (GUCs):

# Vector index settings
neurondb.hnsw_ef_search = 40          # HNSW search quality
neurondb.enable_seqscan = on          # Allow sequential scans

# Memory settings
neurondb.maintenance_work_mem = 256MB # Index build memory

Upgrade path:

-- Check current extension version
SELECT extversion FROM pg_extension WHERE extname = 'neurondb';

-- Expected output: 2.0

-- Upgrade to latest (if newer version available)
ALTER EXTENSION neurondb UPDATE;

-- Verify upgrade (returns JSONB with detailed version info)
SELECT neurondb.version();

[!NOTE] SELECT extversion FROM pg_extension WHERE extname = 'neurondb'; returns the extension version as text (e.g., 2.0).
SELECT neurondb.version(); returns a JSONB object with version, PostgreSQL version, and capabilities information.

For detailed installation instructions, see NeuronDB/install.md.

Ecosystem Components (NeuronMCP, NeuronAgent, NeuronDesktop)

Install NeuronMCP, NeuronAgent, and NeuronDesktop from source with automated scripts.

Quick Installation:

# Install all components
sudo ./scripts/install-components.sh

# Install specific components
sudo ./scripts/install-components.sh neuronmcp neuronagent

# Install with system services enabled
sudo ./scripts/install-components.sh --enable-service

Prerequisites:

  • Go 1.23+ (for building)
  • PostgreSQL 16+ with NeuronDB extension
  • Node.js 18+ (for NeuronDesktop)

Manual Installation:

See Native Installation Guide for detailed instructions.

Service Management:

# Start services
./scripts/manage-services.sh start

# Check status
./scripts/manage-services.sh status

# View logs
./scripts/manage-services.sh logs neuronagent

For service management details, see Service Management Guide.

Minimal mode (extension only)

Use NeuronDB as a PostgreSQL extension only, without the Agent, MCP, or Desktop services.

Benefits:

  • ✅ No extra services or ports
  • ✅ Minimal resource footprint
  • ✅ Full vector search, ML algorithms, and embeddings
  • ✅ Works with any PostgreSQL client

Installation:

Follow the Native install steps above. That's it! You now have vector search and ML capabilities in PostgreSQL.

Usage:

-- Create a table with vectors
CREATE TABLE documents (
  id SERIAL PRIMARY KEY,
  content TEXT,
  embedding VECTOR(1536)
);

-- Create HNSW index
CREATE INDEX ON documents USING hnsw (embedding vector_cosine_ops);

-- Vector similarity search
SELECT id, content
FROM documents
ORDER BY embedding <=> '[0.1, 0.2, ...]'::vector
LIMIT 10;

No additional services, ports, or configuration required!

Service URLs & ports

Service How to reach it Default credentials Notes
NeuronDB (PostgreSQL) postgresql://neurondb:neurondb@localhost:5433/neurondb User: neurondb, Password: neurondb ⚠️ Dev only Container: neurondb-cpu, Service: neurondb
NeuronAgent http://localhost:8080/health Health: no auth. API: API key required Container: neuronagent, Service: neuronagent
NeuronDesktop UI http://localhost:3000 No auth (development mode) Container: neurondesk-frontend, Service: neurondesk-frontend
NeuronDesktop API http://localhost:8081/health Health: no auth. API: varies by config Container: neurondesk-api, Service: neurondesk-api
NeuronMCP stdio (JSON-RPC 2.0) N/A (MCP protocol) Container: neurondb-mcp, Service: neuronmcp. No HTTP port.

Warning

Production Security: The default credentials shown above are for development only. Always use strong, unique passwords in production. Set POSTGRES_PASSWORD and other secrets via environment variables or a .env file (see env.example).

Documentation

Module-wise Documentation

NeuronDB documentation
NeuronAgent documentation
NeuronMCP documentation
NeuronDesktop documentation

Repo layout

Component Path What it is
NeuronDB NeuronDB/ PostgreSQL extension with vector search, ML algorithms, GPU acceleration (CUDA/ROCm/Metal), embeddings, RAG pipeline, hybrid search, and background workers
NeuronAgent NeuronAgent/ Agent runtime + REST/WebSocket API (Go) with multi-agent collaboration, DAG-based workflow engine with human-in-the-loop (HITL), hierarchical memory management, planning & reflection, evaluation framework, budget & cost management, 18+ tools (SQL, HTTP, Code, Shell, Browser, Visualization, Filesystem, Memory, Collaboration, NeuronDB tools, Multimodal, Web Search, Retrieval, Analytics), Prometheus metrics, RBAC, audit logging, and background workers
NeuronMCP NeuronMCP/ MCP server for MCP-compatible clients (Go) with 600+ tools (100+ vector operations, complete ML pipeline, RAG operations, 100+ PostgreSQL admin tools, dataset loading, debugging, composition, workflow, plugins), middleware system (validation, logging, timeout, error handling, auth, rate limiting), enterprise features (Prometheus metrics, webhooks, circuit breaker, caching, connection pooling), batch operations, progress tracking, authentication (JWT, API keys, OAuth2), and full MCP protocol support (prompts, sampling/completions, resources)
NeuronDesktop NeuronDesktop/ Web UI + API for the ecosystem providing a unified interface

Component READMEs

Examples

Benchmarks

NeuronDB includes a benchmark suite to evaluate vector search, hybrid search, and RAG performance.

Quick start

Run all benchmarks:

cd NeuronDB/benchmark
./run_bm.sh

This validates connectivity and runs the vector/hybrid/RAG benchmark groups.

Benchmark suite

Benchmark Purpose Datasets Metrics
Vector Vector similarity search performance SIFT-128, GIST-960, GloVe-100 QPS, Recall, Latency (avg, p50, p95, p99)
Hybrid Combined vector + full-text search BEIR (nfcorpus, msmarco, etc.) NDCG, MAP, Recall, Precision
RAG End-to-end RAG pipeline quality MTEB, BEIR, RAGAS Faithfulness, Relevancy, Context Precision

Vector Performance Benchmark

NeuronDB HNSW index building performance compared to pgvector:

Test Environment:

  • PostgreSQL: 18.0
  • CPU: Apple Silicon (aarch64-apple-darwin)
  • RAM: 256MB maintenance_work_mem
  • Index Parameters: m = 16, ef_construction = 200
  • Distance Metric: L2 (Euclidean)

Performance Formula:

The speedup factor is calculated as:

$$Speedup = \frac{Time_{pgvector}}{Time_{NeuronDB}}$$

For throughput (vectors per second):

$$Throughput = \frac{Vector\ Count}{Build\ Time\ (seconds)}$$

Results:

Test Case NeuronDB Optimized pgvector Speedup Throughput (NeuronDB)
50K vectors (128-dim L2) 606ms (0.606s) ✅ 6,108ms (6.108s) 10.1× 82,508 vec/s
50K vectors (128-dim Cosine) 583ms (0.583s) ✅ 5,113ms (5.113s) 8.8× 85,763 vec/s
10K vectors (768-dim L2) 146ms (0.146s) ✅ 3,960ms (3.960s) 27.1× 68,493 vec/s
100K vectors (128-dim L2) 1,208ms (1.208s) ✅ 15,696ms (15.696s) 13.0× 82,781 vec/s

Optimizations Applied:

  • ✅ In-memory graph building using maintenance_work_mem
  • ✅ Efficient neighbor finding during insert (not after flush)
  • ✅ SIMD-optimized distance calculations (AVX2/NEON)
  • ✅ Squared distance optimization (avoiding sqrt() overhead)
  • ✅ Optimized flush with pre-computed neighbors

Benchmark Scripts:

How to Run:

# Create separate databases for fair comparison
psql -d postgres -c "CREATE DATABASE neurondb_bench;"
psql -d postgres -c "CREATE DATABASE pgvector_bench;"

# Run NeuronDB benchmark
psql -d neurondb_bench -f NeuronDB/benchmark/vector/neurondb_vector.sql

# Run pgvector benchmark
psql -d pgvector_bench -f NeuronDB/benchmark/vector/pgvector.sql

Note

Both benchmarks use identical test parameters (same vector generation pattern, same index parameters) to ensure fair comparison. See NeuronDB/benchmark/vector/README.md for detailed benchmark documentation.

Reproducible benchmarks

To reproduce benchmark results:

# Use exact Docker image tags (see releases)
docker pull ghcr.io/neurondb/neurondb-postgres:v1.0.0-pg17-cpu

# Run with documented hardware profile
cd NeuronDB/benchmark
./run_bm.sh --hardware-profile "cpu-8core-16gb"

# Individual benchmark with exact parameters
cd NeuronDB/benchmark/vector
./run_bm.py --prepare --load --run \
  --datasets sift-128-euclidean \
  --max-queries 1000 \
  --index hnsw \
  --ef-search 40
Benchmark Results & Hardware Specs

Test Environment:

  • CPU: 13th Gen Intel(R) Core(TM) i5-13400F (16 cores)
  • RAM: 31.1 GB
  • GPU: NVIDIA GeForce RTX 5060, 8151 MiB
  • PostgreSQL: 18.1

Vector Search Benchmarks:

Metric Value
Dataset sift-128-euclidean
Dimensions 128
Training Vectors 1,000,000
Test Queries 10,000
Index Type HNSW
Recall@10 1.000
QPS 1.90
Avg Latency 525.62 ms
p50 Latency 524.68 ms
p95 Latency 546.62 ms
p99 Latency 555.52 ms

Hybrid Search Benchmarks:

Status: Not run (see NeuronDB/benchmark/README.md for details)

RAG Pipeline Benchmarks:

Status: Completed (verification passed)

[!NOTE] For detailed benchmark results, reproducible configurations, and additional datasets, see NeuronDB/benchmark/README.md.

Run individual benchmarks
# Vector benchmark
cd NeuronDB/benchmark/vector
./run_bm.py --prepare --load --run --datasets sift-128-euclidean --max-queries 100

# Hybrid benchmark
cd NeuronDB/benchmark/hybrid
./run_bm.py --prepare --load --run --datasets nfcorpus --model all-MiniLM-L6-v2

# RAG benchmark
cd NeuronDB/benchmark/rag
./run_bm.py --prepare --verify --run --benchmarks mteb

GPU profiles (CUDA / ROCm / Metal)

The root docker-compose.yml supports multiple GPU backends via Docker Compose profiles:

Available profiles:

  • CPU (default): docker compose up -d or docker compose --profile cpu up -d
  • CUDA (NVIDIA): docker compose --profile cuda up -d
  • ROCm (AMD): docker compose --profile rocm up -d
  • Metal (Apple Silicon): docker compose --profile metal up -d

Ports differ per profile (see env.example):

  • CPU: POSTGRES_PORT=5433 (default)
  • CUDA: POSTGRES_CUDA_PORT=5434
  • ROCm: POSTGRES_ROCM_PORT=5435
  • Metal: POSTGRES_METAL_PORT=5436

Example: Start with CUDA support

# Stop CPU services first
docker compose down

# Start CUDA profile
docker compose --profile cuda up -d

# Verify CUDA services are running
docker compose ps

# Connect to CUDA-enabled PostgreSQL
psql "postgresql://neurondb:neurondb@localhost:5434/neurondb" -c "SELECT neurondb.version();"

GPU Requirements:

  • CUDA: NVIDIA GPU with CUDA 12.2+ and nvidia-container-toolkit
  • ROCm: AMD GPU with ROCm 5.7+ and proper device access
  • Metal: Apple Silicon (M1/M2/M3) Mac with macOS 13+
Common Docker commands
# Stop everything (keep data volumes)
docker compose down

# Stop everything (delete data volumes - WARNING: deletes all data!)
docker compose down -v

# See status of all services
docker compose ps

# Tail logs for all services
docker compose logs -f

# Tail logs for specific services
docker compose logs -f neurondb neuronagent neuronmcp neurondesk-api neurondesk-frontend

# View last 100 lines of logs
docker compose logs --tail=100

# View logs for specific service
docker compose logs neurondb

Operations

Key operational considerations for production:

Contributing / security / license

Project statistics

Stats snapshot (may change)
  • 665+ SQL functions in NeuronDB extension
  • 52+ ML algorithms supported
  • 600+ MCP tools available
  • 4 integrated components working together
  • 3 PostgreSQL versions supported (16, 17, 18)
  • 4 GPU platforms supported (CPU, CUDA, ROCm, Metal)
Platform & version coverage
Category Supported Versions
PostgreSQL 16, 17, 18
Go 1.21, 1.22, 1.23, 1.24
Node.js 18 LTS, 20 LTS, 22 LTS
Operating Systems Ubuntu 20.04, Ubuntu 22.04, macOS 13 (Ventura), macOS 14 (Sonoma)
Architectures linux/amd64, linux/arm64

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