1. Deployment Issues

1.1. Deployment Fails with 'Cannot Start Instance'

Issue: Upon running fly deploy, the deployment fails with a vague error message like cannot start instance or machine failed to start.

Root Causes:
  • Missing or invalid CMD or ENTRYPOINT in the Dockerfile.
  • Incorrect [processes] configuration in fly.toml.
  • Health checks failing at boot time due to uninitialized services.
Solution:
  • Ensure your Dockerfile defines either a CMD or ENTRYPOINT. If using buildpacks, verify that a proper Procfile or fly.toml process is specified.
  • Check health checks in fly.toml and confirm they don’t execute before the app is ready. Add a grace_period or disable for debugging:
[[services.ports]]  handlers = ["http"]  port = 8080[checks]  [checks.http]    grace_period = "10s"

1.2. 'No Space Left on Device' Errors

Issue: Your app crashes or fails to deploy due to ephemeral disk exhaustion on Fly.io instances.

Root Causes:
  • Excessive logging or temporary file generation inside the container.
  • Fly.io default VM sizes include only 256MB–1GB of storage.
Solution:
  • Use the fly scale vm command to increase memory and disk size:
fly scale vm shared-cpu-1x --memory 1024 --vm-size shared-cpu-1x
  • Mount a persistent volume for large files or database usage:
fly volumes create data --region ord --size 5fly deploy --volume data:/data

2. Networking and DNS Problems

2.1. Application Fails with '502 Bad Gateway'

Issue: Accessing your application via its public Fly.io hostname returns a 502 error.

Root Causes:
  • The internal app port may not be correctly exposed.
  • The container may be listening on the wrong interface (e.g., localhost only).
Solution:
  • Ensure your app listens on 0.0.0.0 and the correct port (typically 8080):
app.listen(process.env.PORT || 8080, '0.0.0.0')
  • Verify the correct port is exposed in fly.toml:
[services]  internal_port = 8080

2.2. Custom Domains Not Resolving

Issue: A custom domain is added in the Fly.io dashboard but fails to resolve or validate.

Root Causes:
  • Incorrect CNAME or A/AAAA DNS records.
  • Domain DNS propagation delays or misconfiguration.
Solution:
  • Run fly certs check yourdomain.com to verify DNS setup.
  • For apex domains, use A/AAAA records pointing to Fly.io’s IPs. For subdomains, CNAMEs should point to your app’s .fly.dev hostname.

3. Logging and Observability

3.1. Logs Appear Incomplete or Missing

Issue: Log output is missing from fly logs even though the app is running.

Root Causes:
  • Fly.io relies on stdout/stderr for logs. Apps using logging frameworks that buffer output may delay log visibility.
  • Logging to a file instead of stdout.
Solution:
  • Use unbuffered stdout. In Python:
python -u app.py
  • Ensure your logger is configured for stdout. For example, in Node.js:
console.log("Server started")

3.2. Cannot View Logs of Crashed Instances

Issue: When an instance crashes early, you don’t see its output in fly logs.

Root Causes:
  • Logs are ephemeral and crash logs may not be captured in time.
Solution:
  • Use fly status to check recent failures and fly ssh console to examine instance state before it’s cleaned up.
  • Temporarily disable auto-restarts for debugging:
fly deploy --auto-restart=false

4. Scaling and Availability Problems

4.1. App Not Running in Desired Region

Issue: Traffic is routed to unintended regions or latency is high.

Root Causes:
  • Fly.io uses Anycast, and traffic may route to the closest available instance.
  • No instance is deployed in the closest region to users.
Solution:
  • Deploy apps across multiple regions:
fly scale count 1 --region ordfly scale count 1 --region sin
  • Use fly regions list and fly status to confirm instance distribution.

5. CI/CD Integration Pitfalls

5.1. GitHub Actions Failing on 'flyctl auth'

Issue: CI deployments via GitHub Actions fail during authentication.

Root Causes:
  • Missing or misconfigured Fly.io access tokens.
Solution:
  • Create a personal access token with fly auth token and store it in GitHub Secrets as FLY_API_TOKEN.
  • Reference it in your workflow:
- name: Fly Deploy  run: flyctl deploy --remote-only  env:    FLY_API_TOKEN: ${{ secrets.FLY_API_TOKEN }}

Conclusion

Fly.io is a powerful platform that provides significant advantages in latency and scale by deploying applications at the edge. However, mastering Fly requires understanding the nuances of its deployment model, DNS configuration, logging mechanisms, and performance tuning. Troubleshooting in Fly is a mix of infrastructure-level insight and app-level configuration. With best practices in place—like ensuring correct port exposure, setting up regional scaling, and proactively monitoring logs—teams can leverage Fly.io for resilient and performant app delivery.

FAQs

1. How can I debug failing health checks?

Use fly ssh console to log into a live instance and manually hit health check endpoints using curl or check logs for errors during app startup.

2. Can I use persistent volumes with multiple regions?

Volumes are tied to a specific region. You cannot attach a volume to instances in multiple regions simultaneously. Consider external storage solutions for distributed state.

3. How can I handle zero-downtime deployments?

Use fly deploy with careful service configuration and a proper health check to ensure new instances pass health checks before terminating old ones.

4. Why is my app listening on localhost only?

Containers must bind to 0.0.0.0, not 127.0.0.1. Modify your code to listen on all interfaces to allow Fly.io routing to work properly.

5. How do I monitor Fly.io metrics?

Use fly dashboard for basic stats or integrate Prometheus/Grafana via exported metrics endpoints from your app or custom agents.