SuperClaude/docs/Reference/mcp-server-guide.md

MCP Server Troubleshooting Guide

MCP Server Focus: Model Context Protocol (MCP) servers provide enhanced capabilities like documentation lookup (Context7), UI generation (Magic), and advanced reasoning (Sequential). This guide covers installation, configuration, and operational troubleshooting for all MCP servers.

Server-Specific Solutions: Each MCP server has unique requirements and common failure patterns. This guide provides targeted solutions for each server type and general MCP troubleshooting strategies.

MCP Server Overview

Available MCP Servers

Core MCP Servers:

• Context7: Official documentation lookup and framework patterns
• Sequential: Multi-step reasoning and complex analysis
• Magic: Modern UI component generation from 21st.dev patterns
• Playwright: Browser automation and E2E testing
• Morphllm: Pattern-based code editing with token optimization
• Serena: Semantic code understanding and project memory

Server Requirements:

• Node.js 16.0.0 or higher
• npm or yarn package manager
• Stable network connection for some servers
• Sufficient system memory (2GB+ recommended)

Installation and Configuration Issues

Node.js and npm Problems

Issue: Node.js Version Incompatibility

Error Message: ERROR: MCP servers require Node.js 16+ but found Node.js 14.x

Diagnosis:

node --version
npm --version

Solution 1: Update Node.js (Linux/Ubuntu)

curl -fsSL https://deb.nodesource.com/setup_lts.x | sudo -E bash -
sudo apt-get install -y nodejs

Solution 2: Use Node Version Manager (nvm)

curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.0/install.sh | bash
source ~/.bashrc
nvm install node
nvm use node

Solution 3: Manual Node.js installation

• Download from https://nodejs.org/
• Follow platform-specific installation instructions

Verification:

node --version  # Should be 16.0.0+
npm --version   # Should be 8.0.0+

Issue: npm Permission Problems

# Error message
ERROR: EACCES: permission denied, access '/usr/local/lib/node_modules'

# Solution 1: Configure npm for user directory
mkdir ~/.npm-global
npm config set prefix '~/.npm-global'
echo 'export PATH=~/.npm-global/bin:$PATH' >> ~/.profile
source ~/.profile

# Solution 2: Fix npm permissions
sudo chown -R $(whoami) $(npm config get prefix)/{lib/node_modules,bin,share}

# Solution 3: Use npx for package execution
npx @context7/mcp-server --version

# Verification
npm list -g --depth=0
npm config get prefix

MCP Server Installation Failures

Issue: Context7 MCP Server Installation Failed

# Error message
ERROR: Failed to install @context7/mcp-server

# Diagnosis
npm list -g @context7/mcp-server
node --version

# Solution 1: Clean npm cache and reinstall
npm cache clean --force
npm install -g @context7/mcp-server

# Solution 2: Use alternative registry
npm install -g @context7/mcp-server --registry https://registry.npmjs.org/

# Solution 3: Manual installation verification
npm info @context7/mcp-server
npm install -g @context7/mcp-server@latest

# Verification
npm list -g @context7/mcp-server
node -e "console.log('Context7 installation test')"

Issue: Sequential MCP Server Dependencies Missing

# Error message
ERROR: Sequential MCP server missing required dependencies

# Diagnosis
npm list -g @sequential/mcp-server
npm list -g | grep -E "typescript|@types"

# Solution 1: Install dependencies explicitly
npm install -g typescript @types/node
npm install -g @sequential/mcp-server

# Solution 2: Force reinstall with dependencies
npm uninstall -g @sequential/mcp-server
npm install -g @sequential/mcp-server --save-dev

# Solution 3: Check package integrity
npm audit --global
npm update -g

# Verification
npm list -g @sequential/mcp-server

Issue: Magic UI Generator Installation Problems

# Error message
ERROR: @magic/ui-generator installation failed - build dependencies missing

# Diagnosis
npm list -g @magic/ui-generator
which gcc make  # Check build tools

# Solution 1: Install build dependencies (Linux)
sudo apt install build-essential python3-dev

# Solution 2: Install build dependencies (macOS)
xcode-select --install

# Solution 3: Use pre-built binaries
npm install -g @magic/ui-generator --ignore-scripts

# Verification
npm list -g @magic/ui-generator

Connection and Communication Issues

MCP Server Connection Failures

Issue: Context7 Server Not Connecting

# Error message
ERROR: MCP server 'context7' failed to connect

# Diagnosis
# Check Node.js installation
node --version  # Should be 16.0.0 or higher
npm list -g @context7/mcp-server

# Check server configuration
cat ~/.claude/CLAUDE.md | grep -i context7

# Solution 1: Restart Claude Code session
# MCP servers restart with Claude Code session restart

# Solution 2: Reconfigure MCP servers
python3 -m SuperClaude install --components mcp --force

# Solution 3: Manual server testing
node -e "console.log('Node.js working')"
npm test @context7/mcp-server

# Solution 4: Check network connectivity
ping context7-server.example.com  # If server requires network
curl -I https://context7-api.example.com/health  # Health check

# Verification
# Try Context7 functionality in Claude Code
# Should respond to documentation requests

Issue: MCP Server Communication Timeout

# Error message
ERROR: MCP server request timeout after 30 seconds

# Diagnosis
# Check network connectivity and server health
ping 8.8.8.8  # Basic connectivity
curl -I https://api.example.com/health  # API health

# Check system resources
top
free -h

# Solution 1: Reduce operation complexity
# Break complex tasks into smaller parts

# Solution 2: Restart Claude Code session
# MCP servers restart with Claude Code session restart

# Solution 3: Disable problematic server temporarily
# Use --no-mcp flag for operations

# Solution 4: Increase timeout (if configurable)
# Check MCP server configuration files

# Verification
# Test with simple operations first
# Gradually increase complexity

Issue: Multiple MCP Servers Conflicting

# Error message
ERROR: MCP server port conflicts detected

# Diagnosis
netstat -tlnp | grep :8000  # Check port usage
ps aux | grep -E "context7|sequential|magic"

# Solution 1: Sequential server restart
# Restart Claude Code to reset all MCP servers

# Solution 2: Configure different ports
# Edit MCP server configuration files
# Usually in ~/.claude/ or server-specific directories

# Solution 3: Use selective server activation
# Use specific server flags instead of --all-mcp

# Verification
netstat -tlnp | grep -E "8000|8001|8002"  # Check port assignments

Server-Specific Troubleshooting

Context7 Documentation Server

Issue: Context7 Not Finding Documentation

# Symptoms: Context7 activated but returns no documentation

# Diagnosis
# Test Context7 connection
node -e "const c7 = require('@context7/mcp-server'); console.log('Context7 loaded');"

# Solution 1: Update Context7 server
npm update -g @context7/mcp-server

# Solution 2: Clear Context7 cache
rm -rf ~/.context7/cache/  # If cache directory exists

# Solution 3: Use explicit library keywords
# Use specific framework names in requests

# Solution 4: Verify internet connection
curl -I https://docs.react.dev/  # Example API test

# Verification
# Try specific documentation requests
# Should return relevant framework information

Issue: Context7 Returning Outdated Information

# Symptoms: Context7 returns old documentation versions

# Solution 1: Update Context7 server
npm uninstall -g @context7/mcp-server
npm install -g @context7/mcp-server@latest

# Solution 2: Clear documentation cache
rm -rf ~/.context7/  # Clear cache if exists

# Solution 3: Force documentation refresh
# Restart Claude Code session completely

# Verification
# Check documentation dates in responses
# Should return current framework versions

Sequential Reasoning Server

Issue: Sequential Server Internal Errors

# Error message
ERROR: Sequential reasoning server encountered internal error

# Diagnosis
# Check Sequential server logs
tail -f ~/.claude/logs/sequential-mcp.log  # If logs exist

# Check server installation
npm list -g @sequential/mcp-server

# Solution 1: Restart Claude Code session
# This restarts all MCP servers including Sequential

# Solution 2: Use alternative reasoning approach
# Use native Claude reasoning without MCP servers

# Solution 3: Reinstall Sequential MCP
npm uninstall -g @sequential/mcp-server
npm install -g @sequential/mcp-server@latest

# Solution 4: Check memory availability
free -h  # Ensure sufficient memory for complex reasoning

# Verification
# Test with simple analysis tasks first
# Should provide structured reasoning output

Issue: Sequential Server Memory Overload

# Symptoms: Sequential server crashes or becomes unresponsive

# Diagnosis
top | grep -E "sequential|node"
free -h

# Solution 1: Reduce analysis complexity
# Break complex problems into smaller parts

# Solution 2: Increase system memory or swap
sudo swapon --show  # Check swap status

# Solution 3: Use scope limiting
# Focus analysis on specific components

# Verification
ps aux | grep sequential  # Check process status

Magic UI Generator

Issue: Magic Not Generating UI Components

# Symptoms: UI component requests not producing expected output

# Diagnosis
# Check Magic server installation
npm list -g @magic/ui-generator
cat ~/.claude/CLAUDE.md | grep -i magic

# Solution 1: Verify Magic server installation
npm list -g @magic/ui-generator
npm install -g @magic/ui-generator@latest

# Solution 2: Use explicit Magic activation
# Include "component", "UI", or "interface" keywords

# Solution 3: Check component request format
# Use descriptive requests for better Magic activation

# Solution 4: Test Magic server directly
node -e "const magic = require('@magic/ui-generator'); console.log('Magic loaded');"

# Verification
# Should produce complete UI components with modern patterns

Issue: Magic Components Not Framework-Compliant

# Symptoms: Generated components don't match framework patterns

# Solution 1: Use framework-specific keywords
# Include "React", "Vue", "Angular" in requests

# Solution 2: Combine with Context7
# Use both Magic and Context7 for framework-compliant components

# Solution 3: Update Magic server
npm update -g @magic/ui-generator

# Verification
# Generated components should follow framework conventions

Playwright Browser Automation

Issue: Playwright Browser Installation Failures

# Error message
ERROR: Playwright browser automation failed - browser not installed

# Diagnosis
npm list -g playwright
npx playwright --version

# Solution 1: Install Playwright browsers
npx playwright install
npx playwright install-deps

# Solution 2: Install specific browsers
npx playwright install chromium
npx playwright install firefox
npx playwright install webkit

# Solution 3: Fix browser dependencies (Linux)
sudo apt-get install libnss3 libatk-bridge2.0-0 libdrm2 libgtk-3-0

# Verification
npx playwright --version
ls ~/.cache/ms-playwright/  # Check browser installations

Issue: Playwright Browser Launch Failures

# Error message
ERROR: Browser launch failed - display not available

# Diagnosis
echo $DISPLAY  # Check X11 display
ps aux | grep Xvfb  # Check virtual display

# Solution 1: Use headless mode
# Set headless: true in Playwright configuration

# Solution 2: Install virtual display (Linux)
sudo apt-get install xvfb
export DISPLAY=:99
Xvfb :99 -screen 0 1024x768x24 &

# Solution 3: Use Docker for browser testing
docker run -it --rm playwright:latest

# Verification
# Should successfully launch browsers in headless mode

Morphllm Pattern Editor

Issue: Morphllm Pattern Application Failures

# Symptoms: Pattern-based edits not applying correctly

# Diagnosis
npm list -g @morphllm/mcp-server

# Solution 1: Update Morphllm server
npm update -g @morphllm/mcp-server

# Solution 2: Use more specific patterns
# Provide explicit pattern descriptions

# Solution 3: Check file permissions
ls -la target-files/  # Ensure write permissions

# Verification
# Pattern edits should be applied consistently across files

Serena Project Memory

Issue: Serena Session Persistence Failures

# Symptoms: Project context not persisting between sessions

# Diagnosis
ls ~/.claude/sessions/  # Check session storage
ls ~/.serena/  # Check Serena-specific storage

# Solution 1: Verify session save operations
# Ensure proper session saving before closing

# Solution 2: Check storage permissions
ls -la ~/.claude/sessions/
chmod 755 ~/.claude/sessions/

# Solution 3: Reinstall Serena server
# Remove existing Serena registration
claude mcp remove serena
# Reinstall using uvx
uvx --from git+https://github.com/oraios/serena serena --help
# Re-register with Claude
claude mcp add serena -- uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context ide-assistant

# Verification
# Session context should persist across Claude Code restarts

Performance and Optimization

MCP Server Performance Issues

Issue: Slow MCP Server Response Times

# Symptoms: MCP server operations causing delays

# Diagnosis
# Check MCP server installation and health
npm list -g | grep -E "context7|sequential|magic|playwright"
top | grep node

# Solution 1: Selective MCP server usage
# Use only needed servers for specific tasks

# Solution 2: Restart Claude Code session
# This restarts all MCP servers fresh

# Solution 3: Local fallback mode
# Use --no-mcp flag for pure native operations

# Solution 4: Update all MCP servers
npm update -g

# Verification
time node -e "console.log('Node.js speed test')"
# Should complete successfully

Issue: MCP Server Memory Leaks

# Symptoms: Increasing memory usage over time

# Diagnosis
top | grep node  # Monitor Node.js processes
ps aux --sort=-%mem | head -10

# Solution 1: Regular Claude Code session restarts
# Restart sessions periodically during heavy usage

# Solution 2: Monitor specific servers
htop  # Monitor individual MCP server processes

# Solution 3: Use memory-efficient patterns
# Avoid keeping large data sets in MCP server memory

# Verification
free -h  # Monitor memory usage trends

Resource Management

Issue: Multiple MCP Servers Competing for Resources

# Symptoms: System slowdown when multiple servers active

# Diagnosis
top | grep -E "node|mcp"
iostat 1 3  # Check I/O usage

# Solution 1: Use targeted server activation
# Activate only needed servers per task

# Solution 2: Increase system resources
# Add more RAM or CPU cores if possible

# Solution 3: Queue MCP operations
# Avoid simultaneous heavy operations

# Solution 4: Use MCP server priorities
# Configure resource allocation in MCP settings

# Verification
top  # Monitor resource usage during operations

Advanced MCP Configuration

Custom MCP Server Configuration

Issue: Default MCP Configuration Not Optimal

# Symptoms: MCP servers not performing optimally for specific use cases

# Solution 1: Locate configuration files
find ~/.claude/ -name "*mcp*" -type f
find ~/.config/ -name "*mcp*" -type f

# Solution 2: Customize server settings
# Edit server-specific configuration files
# Common locations: ~/.claude/mcp-config.json

# Solution 3: Environment variable configuration
export MCP_CONTEXT7_TIMEOUT=60
export MCP_SEQUENTIAL_MEMORY_LIMIT=2048

# Verification
# Test with custom configuration
# Should show improved performance for specific use cases

Issue: MCP Server Load Balancing

# Symptoms: Uneven load distribution across MCP servers

# Solution 1: Configure server priorities
# Edit MCP configuration to balance loads

# Solution 2: Use round-robin server selection
# Implement rotation logic in server calls

# Solution 3: Monitor server performance
# Track response times and adjust accordingly

# Verification
# Observe balanced resource usage across servers

Debugging and Diagnostics

MCP Server Health Monitoring

Comprehensive MCP Health Check:

# MCP Server System Diagnostics
echo "=== MCP Server Health Check ==="

# Node.js environment
echo "Node.js version: $(node --version)"
echo "npm version: $(npm --version)"

# Server installations
echo "=== Installed MCP Servers ==="
npm list -g | grep -E "context7|sequential|magic|playwright|morphllm|serena"

# Process monitoring
echo "=== Running MCP Processes ==="
ps aux | grep -E "node.*mcp|mcp.*server" | head -5

# Resource usage
echo "=== Resource Usage ==="
echo "Memory: $(free -h | grep Mem | awk '{print $3 "/" $2}')"
echo "CPU Load: $(uptime | awk -F'load average:' '{print $2}')"

# Network connectivity (if required)
echo "=== Network Status ==="
ping -c 1 8.8.8.8 > /dev/null && echo "✅ Network OK" || echo "❌ Network Issue"

MCP Server Functionality Test:

# Test each MCP server individually
echo "=== MCP Server Functionality Test ==="

# Context7 test
if npm list -g @context7/mcp-server > /dev/null 2>&1; then
    echo "✅ Context7 installed"
else
    echo "❌ Context7 missing"
fi

# Sequential test
if npm list -g @sequential/mcp-server > /dev/null 2>&1; then
    echo "✅ Sequential installed"
else
    echo "❌ Sequential missing"
fi

# Magic test
if npm list -g @magic/ui-generator > /dev/null 2>&1; then
    echo "✅ Magic installed"
else
    echo "❌ Magic missing"
fi

# Playwright test
if npx playwright --version > /dev/null 2>&1; then
    echo "✅ Playwright installed"
else
    echo "❌ Playwright missing"
fi

MCP Server Log Analysis

Log Collection and Analysis:

# Collect MCP server logs
echo "=== MCP Server Logs ==="

# Check common log locations
find ~/.claude/ -name "*.log" -type f 2>/dev/null
find /tmp/ -name "*mcp*.log" -type f 2>/dev/null
find /var/log/ -name "*mcp*.log" -type f 2>/dev/null

# Check npm logs
npm config get logs-max
ls ~/.npm/_logs/ 2>/dev/null | tail -5

# System logs for Node.js processes
journalctl -u node* --since "1 hour ago" 2>/dev/null | tail -10

Emergency Recovery

Complete MCP Reset

Full MCP Server Reset Procedure:

# Emergency MCP Reset
echo "=== Emergency MCP Server Reset ==="

# Step 1: Stop all Claude Code sessions
echo "Stop all Claude Code sessions and wait 30 seconds"

# Step 2: Backup current state
cp -r ~/.claude ~/.claude.mcp.backup.$(date +%Y%m%d)

# Step 3: Remove all MCP servers
npm list -g | grep -E "context7|sequential|magic|playwright|morphllm|serena" | awk '{print $2}' | xargs npm uninstall -g

# Step 4: Clear npm cache
npm cache clean --force

# Step 5: Reinstall MCP servers
python3 -m SuperClaude install --components mcp --force

# Step 6: Verification
npm list -g | grep -E "context7|sequential|magic|playwright|morphllm|serena"

# Step 7: Test functionality
echo "Test MCP servers in Claude Code after restart"

Related Resources

MCP-Specific Documentation

• Core SuperClaude Guide: ../User-Guide/mcp-servers.md - MCP server overview and usage
• Common Issues: common-issues.md - General troubleshooting procedures
• Diagnostic Reference: diagnostic-reference.md - Advanced diagnostic procedures

External Resources

• Node.js Official: https://nodejs.org/ - Node.js installation and documentation
• npm Documentation: https://docs.npmjs.com/ - Package manager documentation
• Playwright Guide: https://playwright.dev/ - Browser automation documentation

Support Channels

• GitHub Issues: MCP-specific problems
• GitHub Discussions: MCP server community support

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MCP Server Priority: When troubleshooting, address servers in order of dependency: Node.js → npm → individual servers → Claude Code integration. Most MCP issues resolve with proper Node.js setup and server reinstallation.

Verification Pattern: After MCP solutions, always verify with:

• ✅ node --version - Should be 16.0.0+
• ✅ npm list -g | grep mcp - Should show installed servers
• ✅ Test server functionality in Claude Code - Should respond without errors