Amazon Cloud Guide

DolphinNext supports submitting jobs to the Amazon AWS cloud by using Nextflow. It allows you to practically setup, start/stop a computing cluster and run your pipeline in the AWS infrastructure.

Configuration

Once logged in, click on the profile tab in the top right of the screen. Both SSH and Amazon Keys need to be entered in each tab. Then you can proceed with creating amazon connection profile in the run environments tab. After creating profile “start/stop” button will appear in actions column of your amazon profile as shown in the figure below:

../_images/amazon_start.png

Clicking on the start/stop button will open new window called Amazon Management Console.

Amazon Management Console

Starting and stoping AWS cloud is conducted in Amazon management console. There are two ways to open console. First option is clicking following buttons: profile > run environments > Start/Stop. Altervatively, you can quickly reach Amazon console by clicking “Amazon” button at the top of the screen. The number of active profile is displayed with green tag at the top of the amazon button.

../_images/amazon_quick.png

State of your profiles will be shown as below:

../_images/amazon_console.png

Starting Cluster

In order to active AWS cluster, click on “start” button of the profile you wanted to initiate. Following options will be prompted.

  • Nodes: Enter the number of instances, you want to initiate. First node is created as master, and the remaining as workers.
  • Use Autoscale: This is Nextflow’s critical feature which allows the cluster to adapt dynamically to the workload by changing computing recources. After clicking this option and entering number of Maximum Instances, new instances will be automatically added to the cluster when tasks wait for 5 minutes in pending status. The upper limit should be entered by Maximum Instances to control the size of cluster. By default unused instances are removed when they are not utilised.
  • Auto Shutdown: Amazon instance will be automaticaly shutdown when there is no ongoing run for 10 minutes. Note that this feature will be activated after you initiate your first run.

Profile status will be updated as Waiting for reply as soon as you click the “Activate Cluster” button. If your credentials and profile are correct, profile status will change to Initializing and Running, respectively. However, in case of missing or wrong profile information, status will turn into Terminated and reason of the error will appear next to the status. All available states of the profile are listed in table below:

Status Meaning
Inactive AWS cloud has not initiated yet.
Waiting for reply Cluster request is sent.
Initializing Cluster request is accepted and nodes are initializing.
Running AWS cloud ready to submit jobs.
Waiting for termination Cluster termination request is sent and waiting for termination.
Terminated AWS cloud has terminated.

Once the cluster initialization is complete, user@hostname will appear next to the running status as shown in figure below.

../_images/amazon_running.png

You may connect to the master node by using the following SSH command:

ssh user@hostname

Submit a Job

Similar to regular job submission, follow these steps:

  1. Select your pipeline and add into a project
  2. Initiate run

On the run page, you should select your active amazon profile as a Run Environment and click “Ready to Run” button.

Stoping Cluster

When runs are complete, you can stop cluster by clicking “stop” button on Amazon Management Console. Profile status will be updated as Waiting for termination, and in few seconds it will be changed to Terminated as soon as confirmation is received.