Troubleshooting

This guide covers common issues you may encounter when deploying and managing Shipyard infrastructure, along with their solutions.

Tailscale Issues

Tailscale Not Connecting

Symptoms:

Subnet router doesn’t appear in Tailscale admin console
Device shows as offline
Cannot ping VPC private IPs

Solutions:

Check instance has internet access

Verify the Tailscale router instance is in a public subnet with internet gateway access:

# SSH to the instance (if possible)
aws ec2-instance-connect ssh --instance-id i-xxxxx

# Test internet connectivity
ping 8.8.8.8

Verify auth key is valid

Check that your auth key:

Hasn’t expired
Is properly set in environment variables
Has correct permissions and tags

Create a new key at Tailscale Admin if needed.

Check Tailscale service logs

# SSH to the instance
sudo journalctl -u tailscaled -f

# Check user-data script execution
cat /var/log/user-data.log

Restart Tailscale service

sudo systemctl restart tailscaled
sudo tailscale up --authkey=$TAILSCALE_AUTH_KEY --advertise-routes=10.0.0.0/16

Subnet Routes Not Working

Symptoms:

Can see subnet router in Tailscale admin
Cannot ping VPC private IPs
kubectl cannot connect to EKS

Solutions:

Verify routes are approved

Go to Tailscale Machines
Find your subnet router
Check that subnet routes are shown and approved
If not approved, click “Review” and approve them manually

Check ACL auto-approvers

Ensure your Tailscale ACL includes:

{
  "autoApprovers": {
    "routes": {
      "10.0.0.0/8": ["tag:aws-router"],
      "172.16.0.0/12": ["tag:aws-router"],
      "192.168.0.0/16": ["tag:aws-router"]
    }
  },
  "tagOwners": {
    "tag:aws-router": ["autogroup:admin"]
  }
}

Update at Tailscale ACLs

Verify security groups

Check that the subnet router security group allows:

Outbound: All traffic to 0.0.0.0/0
Inbound: All traffic from VPC CIDR (10.0.0.0/16)

EKS Issues

EKS API Not Accessible

Symptoms:

kubectl commands timeout
“Unable to connect to the server” errors
Connection refused errors

Solutions:

Verify Tailscale connection

tailscale status

# Test VPC connectivity
ping 10.0.1.10

Update kubeconfig

aws eks update-kubeconfig --name dev-eks-cluster --region us-east-2

Verify AWS credentials

aws sts get-caller-identity

Ensure the returned identity has EKS access.

Check cluster endpoint

aws eks describe-cluster --name dev-eks-cluster --region us-east-2 \
  --query 'cluster.endpoint' --output text

Verify this is a private endpoint within your VPC.

Verify security group rules

Check that the EKS cluster security group allows:

Port 443 from VPC CIDR
All traffic from node security group

Pods Not Starting

Symptoms:

Pods stuck in Pending state
ImagePullBackOff errors
CrashLoopBackOff errors

Solutions:

Check pod events

kubectl describe pod <pod-name> -n <namespace>

Look for errors in the Events section.

Insufficient resources

# Check node resources
kubectl top nodes

# Check pod resource requests
kubectl describe pod <pod-name> -n <namespace> | grep -A5 Requests

If nodes are at capacity, scale your node group.

Image pull issues

# Check if image exists
docker pull <image-name>

# Verify imagePullSecrets if using private registry
kubectl get secrets -n <namespace>

Application errors

# Check pod logs
kubectl logs <pod-name> -n <namespace>

# Check previous instance logs if pod is restarting
kubectl logs <pod-name> -n <namespace> --previous

Vault Issues

Vault Not Initializing

Symptoms:

Vault pods show 0/1 ready
vault status shows sealed
Initialization fails

Solutions:

Check pod status

kubectl get pods -n vault
kubectl describe pod vault-0 -n vault

Check pod logs

kubectl logs -n vault vault-0

Look for errors related to KMS or DynamoDB.

Verify KMS key permissions

Ensure the EKS node IAM role has permissions:

kms:Decrypt
kms:Encrypt
kms:DescribeKey

On the KMS key used for Vault auto-unseal.

Verify DynamoDB access

# Check if table exists
aws dynamodb describe-table --table-name vault-storage-dev

Ensure the node IAM role has DynamoDB permissions.

Manual initialization (if needed)

# Exec into Vault pod
kubectl exec -n vault vault-0 -- vault operator init

# Save the output securely!

Vault Sealed

Symptoms:

Vault status shows Sealed: true
Applications cannot access secrets

Solutions:

# Check Vault status
kubectl exec -n vault vault-0 -- vault status

# Vault should auto-unseal with KMS
# If it remains sealed, check KMS permissions

# Check Vault logs for unseal errors
kubectl logs -n vault vault-0 | grep -i unseal

# Restart Vault pod if needed
kubectl delete pod -n vault vault-0

Certificate Issues

Certificates Not Issuing

Symptoms:

Certificate shows Ready: False
Let’s Encrypt challenges fail
TLS errors when accessing services

Solutions:

Check certificate status

kubectl get certificates -A
kubectl describe certificate <cert-name> -n <namespace>

Check challenges

kubectl get challenges -A
kubectl describe challenge <challenge-name> -n <namespace>

Verify Cloudflare API token

# Test API token
curl -X GET "https://api.cloudflare.com/client/v4/user/tokens/verify" \
  -H "Authorization: Bearer $CLOUDFLARE_API_TOKEN"

Ensure the token has:

Zone:DNS:Edit
Zone:Zone:Read

Check cert-manager logs

kubectl logs -n cert-manager deployment/cert-manager

Check rate limits

Let’s Encrypt has rate limits:

50 certificates per domain per week
5 failed validations per hour

Use staging issuer for testing:

issuerRef:
  name: letsencrypt-staging
  kind: ClusterIssuer

Terraform Issues

State Lock Errors

Symptoms:

“Error acquiring the state lock”
Terraform operations hang

Solutions:

# Check lock status
aws dynamodb get-item --table-name shipyard-terraform-locks-dev \
  --key '{"LockID": {"S": "<lock-id>"}}'

# Force unlock (use with caution!)
terraform force-unlock <lock-id>

Only use force-unlock if you’re certain no other Terraform process is running.

Resource Already Exists

Symptoms:

“AlreadyExists” errors
“Resource already exists” errors

Solutions:

Import existing resource

terraform import <resource-type>.<resource-name> <resource-id>

Example:

terraform import aws_s3_bucket.state_bucket shipyard-terraform-state-dev

Remove from state

If the resource should not be managed by Terraform:

terraform state rm <resource-type>.<resource-name>

Rename in Terraform

If there’s a naming conflict, update the resource name in your Terraform code.

Provider Configuration Errors

Symptoms:

“Error configuring provider”
Authentication errors

Solutions:

# Verify AWS credentials
aws sts get-caller-identity

# Verify environment variables
env | grep TF_VAR
env | grep AWS

# Re-initialize Terraform
rm -rf .terraform
terraform init

ArgoCD Issues

Applications Out of Sync

Symptoms:

Application shows “OutOfSync” status
Deployed resources don’t match Git

Solutions:

# Check application status
kubectl get application <app-name> -n argocd -o yaml

# Sync application
argocd app sync <app-name>

# Force sync (ignores differences)
argocd app sync <app-name> --force

# Check sync errors
argocd app get <app-name>

GitHub Integration Not Working

Symptoms:

ApplicationSets not discovering repos
“Failed to list repositories” errors

Solutions:

Verify GitHub App credentials

kubectl get secret -n argocd github-app-secret -o yaml

Ensure:

App ID is correct
Installation ID is correct
Private key is valid

Check GitHub App permissions

In GitHub, verify the app has:

Repository: Contents (Read)
Repository: Metadata (Read)

Check ArgoCD application controller logs

kubectl logs -n argocd deployment/argocd-application-controller

Network Issues

DNS Not Resolving

Symptoms:

Services not accessible by domain name
“Name or service not known” errors

Solutions:

# Check external-dns pod
kubectl get pods -n external-dns

# Check external-dns logs
kubectl logs -n external-dns deployment/external-dns

# Verify Cloudflare DNS records
curl -X GET "https://api.cloudflare.com/client/v4/zones/<zone-id>/dns_records" \
  -H "Authorization: Bearer $CLOUDFLARE_API_TOKEN"

# Test DNS resolution
nslookup vault.yourdomain.com
dig vault.yourdomain.com

Load Balancer Not Created

Symptoms:

Ingress has no external IP/hostname
Service of type LoadBalancer stuck pending

Solutions:

# Check AWS Load Balancer Controller logs
kubectl logs -n kube-system deployment/aws-load-balancer-controller

# Verify ingress annotations
kubectl get ingress <ingress-name> -n <namespace> -o yaml

# Check service events
kubectl describe service <service-name> -n <namespace>

# Verify subnet tags
aws ec2 describe-subnets --filters Name=vpc-id,Values=<vpc-id> \
  --query 'Subnets[*].[SubnetId,Tags]'

Getting More Help

If you continue to experience issues:

Check logs: Most issues can be diagnosed from pod and service logs
Review AWS Console: Check CloudWatch logs, security groups, and IAM permissions
Verify prerequisites: Ensure all required tools and accounts are properly configured
Check resource quotas: AWS service quotas may limit resource creation

Destroying Resources

If you need to start over, learn how to safely tear down infrastructure

Getting Started

Deployment

Operations

Tailscale Issues

Tailscale Not Connecting

Subnet Routes Not Working

EKS Issues

EKS API Not Accessible

Pods Not Starting

Vault Issues

Vault Not Initializing

Vault Sealed

Certificate Issues

Certificates Not Issuing

Terraform Issues

State Lock Errors

Resource Already Exists

Provider Configuration Errors

ArgoCD Issues

Applications Out of Sync

GitHub Integration Not Working

Network Issues

DNS Not Resolving

Load Balancer Not Created

Getting More Help

Destroying Resources

Build docs developers (and LLMs) love

Getting Started

Deployment

Operations

Documentation Index

​Tailscale Issues

​Tailscale Not Connecting

​Subnet Routes Not Working

​EKS Issues

​EKS API Not Accessible

​Pods Not Starting

​Vault Issues

​Vault Not Initializing

​Vault Sealed

​Certificate Issues

​Certificates Not Issuing

​Terraform Issues

​State Lock Errors

​Resource Already Exists

​Provider Configuration Errors

​ArgoCD Issues

​Applications Out of Sync

​GitHub Integration Not Working

​Network Issues

​DNS Not Resolving

​Load Balancer Not Created

​Getting More Help

Destroying Resources

Build docs developers (and LLMs) love

Tailscale Issues

Tailscale Not Connecting

Subnet Routes Not Working

EKS Issues

EKS API Not Accessible

Pods Not Starting

Vault Issues

Vault Not Initializing

Vault Sealed

Certificate Issues

Certificates Not Issuing

Terraform Issues

State Lock Errors

Resource Already Exists

Provider Configuration Errors

ArgoCD Issues

Applications Out of Sync

GitHub Integration Not Working

Network Issues

DNS Not Resolving

Load Balancer Not Created

Getting More Help