How to connect to Pawsey’s Nimbus Instance

Background

Bioinformatics research inevitably requires a powerful computing facility. This is because Bioinformatics analysis involves a large sequence dataset. Pawsey Supercomputer Centre, Perth, offers a great solution to it. The centre provides with a custom-tailored computing infrastructure to all Australian researchers. It also has a strong support team comprised of professional Bioinformaticians to help researchers along with their computing journey.

Pawsey Supercomputer Centre has two types of computing facilities- high performance computing (HPC) and cloud based virtual machine called ‘Nimbus Instance’.

Here, I outline the steps to get connected to Pawsey's ‘Nimbus Instance’.

Method

Step 1: Make an application to have access to ‘Nimbus Instance’ (https://apply.pawsey.org.au/)

Step 2: Log in into https://nimbus.pawsey.org.au and build an instance

As a part of this step, you will generate ‘a key pair’ that will be required for ssh connection via any ‘secure shell (ssh)’ client (software) (https://pawsey.atlassian.net/wiki/spaces/US/pages/51915082/Create+a+Nimbus+Instance)

Step 3: Attach a storage volume to your Instance

Instructions are here:

https://pawsey.atlassian.net/wiki/spaces/US/pages/51923113/Manage+a+Data+Volume#ManageaDataVolume-AttachaDataVolume

Step 4: Access your Instance through a ssh client

To access the Pawsey’s Nimbus Instance, see the instructions in the following link:

https://support.pawsey.org.au/documentation/display/US/Access+and+Use+Your+Nimbus+Instance#AccessandUseYourNimbusInstance-LoginviaWindowswithPuTTY

Note:

• In your Instance, you have two IP addresses: one Instance-specific and one external. You need the external IP address in this step

• You need to add an inbound and outbound rule for Port 22 to your local computer’s firewall

• Pay attention to the remote host name. It is not just the IP address but ubuntu@IP_address

Here is an example of connecting to Pawsey’s Ubuntu Instance using MobaXterm:

• See the MobaXterm screenshot below (Fig. 1)

• Enter remote host as

ssh ubuntu@Public_external_IP_for_your_instance

• Tick the ‘Specify username’ box. It is the username that you use to log in into your Nimbus Instance website (dashboard)

• Tick the ‘Use private key’ box. Browse to your key. It is a file with ‘.pem’ extension. Select it and press OK.

Now, ssh connection established and you can use your Instance

Figure 1. ssh connection to Nimbus Instance via MobaXterm

Step 5: Transfer your data to your Instance that you want to analyse

Data can be transferred back and forth between your ‘local computer’ and ‘Instance’ using one of the following options:

• command line in your shell

• MobaXterm’s drag and drop function, or

• a software, for example, WinSCP, FileZila etc.

How to use FileZilla for transferring data?

You need to download it and log in into it with the following details:

Host: same as Step 4, Username and Password: same as your Pawsey account, Port: 22, Passphrase: the one that you have generated with Putty at Step 4

The End