Docker Issues

Troubleshooting

Common issues and solutions for mcpbr.

Docker Issues

Docker Not Running

Symptom: Error connecting to Docker daemon

Solution:

=== "macOS" bash open -a Docker # Wait for Docker to start, then verify docker info

=== "Linux" bash sudo systemctl start docker docker info

=== "Windows" Start Docker Desktop from the Start menu, then verify: bash docker info

Pre-built Image Not Found

Symptom: Warning about falling back to building from scratch

Solution: This is normal for some tasks. You can manually pull:

docker pull ghcr.io/epoch-research/swe-bench.eval.x86_64.astropy__astropy-12907

Or disable pre-built images to always build from scratch:

mcpbr run -c config.yaml --no-prebuilt

Orphaned Docker Resources

Symptom: Old mcpbr containers, volumes, or networks consuming resources or causing "already exists" errors

Solution:

# Preview what would be removed (resources older than 24 hours)
mcpbr cleanup --dry-run

# Remove orphaned resources with confirmation
mcpbr cleanup

# Force remove all resources immediately
mcpbr cleanup -f

# Remove only specific resource types
mcpbr cleanup --containers-only
mcpbr cleanup --volumes-only
mcpbr cleanup --networks-only

# Customize retention period (e.g., 48 hours)
mcpbr cleanup --retention-hours 48

When to use: After crashes, interruptions, or when switching evaluation configurations

Safety features:

• Default 24-hour retention policy prevents removing active evaluations
• Confirmation prompt before removal (use -f to skip)
• Dry-run mode to preview changes
• Detailed reporting of removed resources

Performance Issues

Slow on Apple Silicon

Symptom: Tasks take much longer than expected on M1/M2/M3 Macs

Explanation: mcpbr uses x86_64 Docker images that run via emulation on ARM64.

Solutions:

1. Install Rosetta 2 for better emulation:

   softwareupdate --install-rosetta
   

2. Reduce concurrency to avoid resource contention:

   max_concurrent: 2
   

3. Increase timeouts:

   timeout_seconds: 600
   

Task Timeouts

Symptom: Tasks fail with "Timeout" error

Solutions:

1. Increase timeout in config:

   timeout_seconds: 600  # 10 minutes
   

2. Reduce max iterations if agent is looping:

   max_iterations: 20
   

3. Use a faster model for testing:

   model: "haiku"
   

API Issues

API Key Not Set

Symptom: "ANTHROPIC_API_KEY environment variable not set"

Solution:

export ANTHROPIC_API_KEY="sk-ant-..."

Add to your shell profile (.bashrc, .zshrc) for persistence.

API Key Invalid

Symptom: Authentication errors from Anthropic API

Solutions:

1. Verify the key format (should start with sk-ant-):

   echo $ANTHROPIC_API_KEY
   

2. Check key permissions in Anthropic Console

3. Ensure no extra whitespace:

   export ANTHROPIC_API_KEY="sk-ant-..." # No spaces
   

Rate Limiting

Symptom: API rate limit errors

Solutions:

1. Reduce concurrency:

   max_concurrent: 2
   

2. Add delays between tasks (requires code modification)

3. Check your API tier limits in Anthropic Console

CLI Issues

Claude CLI Not Found

Symptom: "Claude Code CLI (claude) not found in PATH"

Solution:

# Install Claude CLI
npm install -g @anthropic-ai/claude-code

# Verify installation
which claude

If installed but not found, check your PATH includes npm global binaries:

export PATH="$PATH:$(npm config get prefix)/bin"

Command Not Found: mcpbr

Symptom: "mcpbr: command not found"

Solutions:

1. Ensure mcpbr is installed:

   pip install mcpbr
   

2. Check it's in your PATH:

   pip show mcpbr | grep Location
   

3. Use the full path or module:

   python -m mcpbr --help
   

MCP Server Issues

Server Not Starting

Symptom: "Warning: MCP server add failed"

Solutions:

1. Test the server independently:

   npx -y @modelcontextprotocol/server-filesystem /tmp/test
   

2. Check environment variables:

   echo $SUPERMODEL_API_KEY  # If using Supermodel
   

3. Verify the command exists:

   which npx  # or python, node, etc.
   

Tools Not Appearing

Symptom: MCP tools not being used by the agent

Possible causes:

1. Server not registering tools correctly
2. Tool descriptions unclear
3. Built-in tools sufficient for the task

Debug steps:

1. Enable verbose logging:

   mcpbr run -c config.yaml -vv --log-dir logs/
   

2. Check per-instance logs for tool registration

3. Review tool_usage in results JSON

MCP Server Logs

New in v3.0.0: mcpbr now captures MCP server logs automatically.

Log Location: ~/.mcpbr_state/logs/{instance_id}_mcp.log

What's captured:

• MCP server stdout and stderr
• Claude CLI's MCP-related output
• Tool call errors and timeouts

How to access:

# View logs for a specific instance
cat ~/.mcpbr_state/logs/django__django-11905_mcp.log

# View logs for all instances
ls ~/.mcpbr_state/logs/

# Follow logs in real-time during evaluation
tail -f ~/.mcpbr_state/logs/*.log

Error messages now include log paths:

Error: Task execution timed out after 1200s.
       MCP server 'supermodel' was registered successfully
       but the agent failed to complete within the timeout.
       MCP server logs saved to: ~/.mcpbr_state/logs/django__django-11905_mcp.log

MCP Tool Timeouts

Symptom: MCP tool calls timing out or failing with "Request failed"

Explanation: Some MCP servers (like Supermodel's codebase analyzer) can take several minutes to respond. Claude CLI has default timeouts that may be too short.

Solution: Configure MCP timeouts in your config file:

mcp_server:
  name: "supermodel"
  command: "npx"
  args:
    - "-y"
    - "@supermodeltools/mcp-server"
    - "{workdir}"
  startup_timeout_ms: 60000      # 60 seconds for server to start
  tool_timeout_ms: 900000        # 15 minutes for tool calls
  env:
    SUPERMODEL_API_KEY: "${SUPERMODEL_API_KEY}"

Recommended timeouts by server type:

Debug steps if timeouts persist:

1. Check MCP server logs (see above)
2. Test the tool independently:

   # For Supermodel
   npx -y @supermodeltools/mcp-server /tmp/test
   

3. Increase task timeout to allow for multiple retries:

   timeout_seconds: 1200  # 20 minutes
   

Registration Failures

Symptom: "MCP server registration failed" or "MCP server registration timed out"

New in v3.0.0: Detailed error messages showing exactly what failed.

Example errors:

MCP server registration failed (exit 1):
  npx: command not found

MCP server registration timed out after 60s.
  The MCP server may have failed to start or is hanging.

Solutions:

1. Command not found: Ensure the MCP server command is in PATH:

   which npx  # Should return a path
   

2. Slow server startup: If your server takes >60s to start, this is unusual but you can modify the registration timeout in code (default is 60s)

3. Environment variables missing: Check MCP server logs to see what's missing:

   cat ~/.mcpbr_state/logs/{instance_id}_mcp.log
   

Evaluation Issues

Patch Not Applying

Symptom: "Patch does not apply" error

Explanation: The agent's changes don't apply cleanly to the original repository state.

This can happen when:

• Agent modified files that conflict with test patches
• Agent created files instead of modifying existing ones
• Git state is inconsistent

Note: This is often an agent behavior issue, not an mcpbr bug.

Tests Failing

Symptom: Tests fail even though patch applies

Debug steps:

1. Check per-instance logs for test output:

   cat logs/instance_id_mcp_*.json | jq '.events[-5:]'
   

2. Review the fail_to_pass results in JSON output

3. The agent may have made an incorrect fix

No Patch Generated

Symptom: "No changes made by Claude Code"

Possible causes:

1. Agent didn't find a solution
2. Agent made changes then reverted them
3. Max iterations reached without completing

Solutions:

1. Increase max_iterations:

   max_iterations: 30
   

2. Review logs to understand agent behavior

Getting Help

Gathering Debug Information

When reporting issues, include:

# Version info
mcpbr --version
python --version
docker --version

# Environment
echo $ANTHROPIC_API_KEY | head -c 10  # First 10 chars only

# Run with verbose logging
mcpbr run -c config.yaml -n 1 -vv --log-dir debug-logs/

Where to Get Help

• GitHub Issues - Bug reports
• GitHub Discussions - Questions

Common Log Locations