Content from Workshops using Nectar Instances

Last updated on 2025-08-18 | Edit this page

Authors: Melbourne Bioinformatics

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Overview

The workshop you will be doing will run on a Nectar Instance. An “Instance” is Nectar terminology for a virtual machine running on the Nectar Cloud OpenStack infrastructure. An “Instance” runs on a “compute node”; i.e. a physical computer populated with processor chips, memory chips and so on.

Objectives

  • Understand what a Nectar Instance is and how it relates to the Nectar Cloud infrastructure.
  • Identify the software required to access Nectar Instances on Mac and Windows systems.
  • Successfully log in to a Nectar Instance using SSH on both Mac and Windows.
  • Transfer files between a local machine and a Nectar Instance using SCP or file transfer software.
  • Test your connection by transferring a test file (test_transfer.txt) from the instance to your local computer.
  • Understand the purpose of byobu-screen and use it to maintain long-running sessions:
    • Start a named byobu-screen session.
    • Reconnect to a screen session after disconnection.
    • Detach and terminate a screen session safely.
  • Know how to apply for your own Nectar allocation to run independent tutorials in the future.

Logging on to a Nectar Instance

You will be given an individual username, IP address and password to log on to using the SSH client tool on your computer (Terminal on Mac or PuTTY on Windows).

  • Host: The IP address of the Nectar Instance
  • Username: alpha | beta | gamma | delta | epsilon | zeta
  • Port: 22
  • Password: Provided to you separately
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Attention

  • Follow the instructions for your operating system carefully.
  • Repeated failed log in attempts might result in being locked out of the account.

Mac Users

In Terminal, type: ssh username@nectar_ip-address

You will be prompted to enter your password. After you have entered your password, hit return.

You won’t receive feedback when entering your password. Rest assured it is being entered as you type it (or paste it in). Hit return after you have typed the whole password.

Windows Users:

In PuTTY, enter the IP address as the host name and 22 for the port.

After you click “Open” you’ll be prompted to type the username you have been assigned (i.e. alpha | beta | gamma | delta | epsilon | zeta). Press enter. You will then be prompted for the password that has been given to you. Press enter.

You won’t receive feedback when entering your password. Rest assured it is being entered as you type it (or paste it in). Hit enter after you have typed the whole password.

PuTTY has a different shortcut for paste compared to what you may be used to. Instead of ctrl-v, try right-clicking in the password field to paste the contents of your clipboard.

Content from Transferring files between your computer and Nectar Instance

Last updated on 2025-08-18 | Edit this page

  • Host: The IP address of the Nectar instance
  • Username: alpha | beta | gamma | delta | epsilon | zeta
  • Port: 22
  • Password: Password that has been given to you.

Mac Users

scp can be used to transfer files. Alternatively, novice Unix users may want to use FileZilla.

Windows Users

Using file transfer software such as FileZilla or WinSCP

Content from Testing your log on

Last updated on 2025-08-18 | Edit this page

  1. Log on to your Nectar Instance
  2. Get a copy of the test_transfer.txt to your local computer.
  3. Transfer test_transfer.txt to your local computer.

Content from Byobu-screen

Last updated on 2025-08-18 | Edit this page

Some of the commands can take a while to run. Should your connection drop and the SSH session on Nectar terminates, any commands that are running will terminate too. To mitigate this, once logged on to the Nectar Instance, we’ll run byobu-screen (an enhancement for the screen terminal multiplexer) which allows us to resume a session. In other words, processes running in byobu-screen will continue to run when their window is not visible, even if you get disconnected.

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Attention

We will do this step in the workshop though feel free to try out the byobu-screen commands below.

Starting a byobu-screen session.

On Nectar, to start a byobu-screen session called workshop, type

BASH 

byobu-screen -ls

Reconnecting to a byobu-screen session.

Should your SSH session on Nectar terminate, once you log back in to your Nectar instance, list running sessions/screens:

BASH 

byobu-screen -r workshop

If it says (Attached) next to the workshop session in the list, you can access workshop which is already attached by:

BASH 

byobu-screen -r -d workshop

Detaching or Terminating a byobu-screen session.

  • To detach from workshop, type ctrl-a ctrl-d while inside the workshop session. (You will need to configure Byobu’s ctrl-a behaviour if it hasn’t already been configured (text will appear on the screen telling you this). Follow the information on the screen and select 1 for Screen mode).

  • To terminate workshop, type ctrl-d while inside the workshop session.

Content from Applying for your own Nectar Allocation

Last updated on 2025-08-18 | Edit this page

Should you wish to do this tutorial at a later stage independently, it is possible to apply for your own instance directly through a Nectar allocation. There are also many helpful Nectar Research Cloud tutorials. You will need to install your required software.