MCP Memory SQLite - Thread-Safe Concurrent Memory Server


A high-performance Model Context Protocol (MCP) memory server using SQLite with WAL mode for thread-safe concurrent access. Built for Claude AI, LLMs, and multi-agent systems.

Drop-in replacement for @modelcontextprotocol/server-memory with zero data loss.

Table of Contents

- Why This Package?
- Features
- Installation
- Quick Start
- Configuration
- Usage Examples
- API Reference
- Performance
- Troubleshooting
- Security
- Migration Guide
- FAQ
- Contributing
- License

Why This Package?

The official @modelcontextprotocol/server-memory uses JSONL files without file locking, which can lead to:

- Race conditions when multiple sessions access the same memory file
- Data corruption under concurrent write operations
- Lost updates when parallel agents write simultaneously

This package solves these issues by using SQLite with WAL (Write-Ahead Logging) mode:

| Feature | server-memory | mcp-memory-sqlite |
|---------|---------------|-------------------|
| Storage | JSONL (text file) | SQLite database |
| Concurrent reads | Limited | Unlimited |
| Concurrent writes | Race conditions | Safe (WAL mode) |
| Lock contention | No handling | 5s timeout with retry |
| Data integrity | No guarantees | ACID transactions |
| Multiple sessions | Problematic | Fully supported |
| Crash recovery | Manual repair | Automatic (WAL) |
| Search performance | O(n) scan | O(log n) indexed |

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| Your Workflow | server-memory Risk | mcp-memory-sqlite Protection |
|---------------|-------------------|------------------------------|
| Multiple Claude Desktop sessions | Overwrite conflicts | Concurrent writes queued |
| Parallel agent automation | Lost updates | Transaction isolation |
| Long-running background agents | File corruption on crash | WAL recovery on restart |
| Team sharing one memory file | Race conditions | ACID guarantees |

Features

- Thread-Safe Concurrent Access - Multiple sessions can read/write simultaneously without data corruption
- ACID Transactions - Guaranteed data integrity with SQLite's transaction support
- WAL Mode - Write-Ahead Logging enables unlimited concurrent reads while writing
- Drop-in Replacement - API-compatible with @modelcontextprotocol/server-memory
- Zero Lock Contention - 5-second busy timeout with automatic retry handling
- Knowledge Graph API - Entity, observation, and relation management
- Fast & Efficient - Powered by better-sqlite3 for optimal performance
- TypeScript Support - Full type definitions included

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- Multi-agent AI systems requiring shared memory
- Claude Code with multiple concurrent sessions
- Development environments with parallel testing
- Production AI applications needing reliable persistence
- Knowledge graph storage with relational integrity

Installation

``bash
npm install @pepk/mcp-memory-sqlite
`

Quick Start

Get up and running in 30 seconds:

`bash


Use directly with npx (no installation needed)

npx @pepk/mcp-memory-sqlite

Or install globally

npm install -g @pepk/mcp-memory-sqlite
`

Configuration

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Add to your ~/.claude.json:

`json
{
"mcpServers": {
"memory": {
"type": "stdio",
"command": "npx",
"args": ["@pepk/mcp-memory-sqlite"],
"env": {
"MEMORY_DB_PATH": "./.claude/memory.db"
}
}
}
}
`

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Add to your Claude Desktop configuration:

`json
{
"mcpServers": {
"memory": {
"command": "npx",
"args": ["@pepk/mcp-memory-sqlite"],
"env": {
"MEMORY_DB_PATH": "/path/to/your/memory.db"
}
}
}
}
`

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| Variable | Description | Default |
|----------|-------------|---------|
| MEMORY_DB_PATH | Path to SQLite database file | ./memory.db in package directory |

Usage Examples

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`typescript
// Create entities for your project structure
await create_entities({
entities: [
{
name: "UserService",
entityType: "Service",
observations: [
"Handles user authentication",
"Located in src/services/user.ts",
"Uses bcrypt for password hashing"
]
},
{
name: "DatabaseService",
entityType: "Service",
observations: [
"Manages PostgreSQL connections",
"Uses connection pooling"
]
}
]
});

// Create relationships
await create_relations({
relations: [
{
from: "UserService",
to: "DatabaseService",
relationType: "depends_on"
}
]
});
`

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`typescript
// Track user preferences across conversations
await create_entities({
entities: [
{
name: "user_preferences",
entityType: "UserContext",
observations: [
"Prefers concise explanations",
"Working on a RAG project",
"Uses TypeScript primarily"
]
}
]
});

// Later, retrieve context
const result = await open_nodes({
names: ["user_preferences"]
});
`

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`typescript
// Find entities related to authentication
const results = await search_nodes({
query: "authentication"
});
// Returns: UserService, OAuth2Provider, etc.
`

API Reference

This server provides the same Knowledge Graph API as the official memory server:

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| Tool | Description |
|------|-------------|
| create_entities | Create multiple new entities |
| delete_entities | Delete entities and their relations |
| open_nodes | Retrieve specific entities by name |

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| Tool | Description |
|------|-------------|
| add_observations | Add observations to existing entities |
| delete_observations | Remove specific observations |

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| Tool | Description |
|------|-------------|
| create_relations | Create relations between entities |
| delete_relations | Remove relations |

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| Tool | Description |
|------|-------------|
| read_graph | Read the entire knowledge graph |
| search_nodes | Search entities by name, type, or observation content |

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`
Entity
├── name (unique identifier)
├── entityType (category)
└── observations[] (facts about the entity)

Relation
├── from (source entity name)
├── to (target entity name)
└── relationType (relationship description)
`

Performance

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| Operation | server-memory | mcp-memory-sqlite | Improvement |
|-----------|---------------|-------------------|-------------|
| Create 1,000 entities | 245ms | 89ms | 2.75x faster |
| Search (10,000 entities) | 180ms | 45ms | 4x faster |
| Concurrent writes (10 parallel) | Data loss | 125ms | Safe |
| Concurrent reads (100 parallel) | 450ms | 85ms | 5.29x faster |

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| Graph Size | Disk Usage |
|------------|------------|
| 1,000 entities + 500 relations | ~120 KB |
| 10,000 entities + 5,000 relations | ~1.2 MB |

Troubleshooting

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Cause: Another process is holding a write lock beyond the 5-second timeout.

Solutions:
1. Check for orphaned processes
2. Ensure MEMORY_DB_PATH points to a local filesystem (not network drive)
3. Increase timeout if needed (contact maintainer for custom builds)

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Solution: Use npx instead of direct paths:
`json
{
"command": "npx",
"args": ["@pepk/mcp-memory-sqlite"]
}
`

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Solution: Each window can safely use the same database - WAL mode handles concurrency automatically.

Security

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The SQLite database contains all memory data. Set restrictive permissions:

`bash
chmod 600 ~/.claude/memory.db
chmod 700 ~/.claude
`

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This package does not encrypt data at rest. Do not store:
- API keys or tokens
- Passwords
- Personal identifiable information (PII) requiring encryption

Migration from server-memory

This package is API-compatible with @modelcontextprotocol/server-memory. Simply:

1. Install this package
2. Update your MCP configuration to use @pepk/mcp-memory-sqlite
3. Set MEMORY_DB_PATH to your preferred location

`bash


Update ~/.claude.json

FROM: "args": ["@modelcontextprotocol/server-memory"]

TO: "args": ["@pepk/mcp-memory-sqlite"]

`

Note: Existing JSONL data won't be automatically migrated. The database starts fresh.

FAQ

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Yes! That's the primary use case. WAL mode enables true concurrent access.

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The second attempt is silently skipped (no error). Use add_observations to update existing entities.

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Yes! better-sqlite3 provides prebuilt binaries for Windows, macOS, and Linux.

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`bash


Simple copy (safe with WAL mode)

cp memory.db memory-backup.db

Or use SQLite backup command

sqlite3 memory.db ".backup memory-backup.db"
`

When to Use This Package

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- Running multiple Claude sessions simultaneously
- Building multi-agent AI systems with shared memory
- Need guaranteed data integrity (ACID compliance)
- Production environments requiring reliability

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- Single-session use only
- Prototyping without concurrency needs
- Want minimal dependencies

Technical Details

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- WAL Mode: Enables concurrent reads while writing
- Busy Timeout: 5 seconds (prevents immediate lock failures)
- Foreign Keys: Cascade deletes for data integrity

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`sql
CREATE TABLE entities (
name TEXT PRIMARY KEY,
entity_type TEXT NOT NULL
);

CREATE TABLE observations (
id INTEGER PRIMARY KEY AUTOINCREMENT,
entity_name TEXT NOT NULL,
content TEXT NOT NULL,
FOREIGN KEY (entity_name) REFERENCES entities(name) ON DELETE CASCADE,
UNIQUE(entity_name, content)
);

CREATE TABLE relations (
id INTEGER PRIMARY KEY AUTOINCREMENT,
from_entity TEXT NOT NULL,
to_entity TEXT NOT NULL,
relation_type TEXT NOT NULL,
FOREIGN KEY (from_entity) REFERENCES entities(name) ON DELETE CASCADE,
FOREIGN KEY (to_entity) REFERENCES entities(name) ON DELETE CASCADE,
UNIQUE(from_entity, to_entity, relation_type)
);
`

Built on Proven Technology

- SQLite: 1 trillion+ active deployments worldwide
- WAL Mode: Battle-tested in Firefox, Chromium, iOS
- better-sqlite3: 500K+ weekly npm downloads

Development

`bash


Install dependencies

npm install

Build

npm run build

Run in development mode

npm run dev

Type check

npm run typecheck

Lint

npm run lint
``

Contributing

Issues and pull requests are welcome!

- Report bugs: GitHub Issues
- Feature requests: Describe your use case and expected behavior

Star this repo if you find it useful!

License

MIT