Contact info

Tan | ts864@cornell.edu

Overview

Currently, the way services are deployed is basically running their Docker containers on AWS EC2 instances. This means that each service occupies a unique port on the machine. Below is a list of running services and the ports they are using.

Test and production environments are deployed separately on the EC2 instances below.

Procedure

The procedure for deploying is the same for both EC2 instances. First, download the key pair file corresponding to the instance and run

chmod 400 /path/to/DIAPER-*-key.pem

Then, ssh into the EC2 instance using

ssh -i /path/to/DIAPER-*-key.pem ec2-user@<domain>

Pull your Docker image and other relevant file from GitHub. Once pulled, navigate to your project folder and run the Docker using docker-compose up with the corresponding yml file:

// For test environments.
sudo docker-compose -f docker-compose-test.yml up -d --force-recreate
 
// For production environments.
sudo docker-compose -f docker-compose-prod.yml up -d --force-recreate

// For local development on your laptop.
// These two commands are equivalents (i.e. default is docker-compose.yml)
sudo docker-compose -f docker-compose.yml up -d --force-recreate
sudo docker-compose up -d --force-recreate

We have different yml files because production and test environments use different SSL certificates. To keep your service from blocking the console, you should run your container in detached mode using the -d option. Once a container is run in detached mode, any of its runtime errors will be hidden from the user. Thus, you need to manually check that there are no runtime errors during the launching of your service by looking at its log using

sudo docker-compose logs -f

If there are no runtime errors, you will get an output similar to the one below.

Now you can log out and the service will continue running on the EC2 instance.

Some Issues

BioHPC database timeout (Obsolete)

If you are experiencing timeout when connecting to the BioHPC database, it' probably because the EC2 instance isn't connected to Cornell's VPN. Check whether the VPN is connected with

ps -A | grep openconnect

If the output is non-empty, then the VPN is connected. If not, you can connect to the VPN using

sudo openconnect -b cuvpn.cuvpn.cornell.edu --reconnect-timeout 600

and enter necessary information as prompted.