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The HPC is changing

We will soon be switching to a new High Performance Cluster, called Double Helix. This will mean that some of the commands you use to connect to the HPC and call modules will change. We will inform you by email when you are switching over, allowing you to make the necessary changes to your scripts. Please check our HPC changeover notes for more details on what will change.

Accessing the HPC

The HPC is accessed via ssh from the terminal.

Basic login

The following is an example of a Research Network user, Jane Doe, connecting via ssh.

1
ssh jdoe@corp.gel.ac@phpgridzlogn001.int.corp.gel.ac

You will then be prompted for your password, and once entered, will be connected to the HPC.

The specific address will change depending on what group you belong to. The general format is username@corp.gel.ac@phpgridzlogn00N.int.corp.gel.ac, where username will be your Genomics England username and N will depend on your group. See the table below for more information.

Login nodes access address

Name Who
phpgridzlogn001.int.corp.gel.ac Research Network and Clinical Researchers
phpgridzlogn002.int.corp.gel.ac Research Network and Clinical Researchers
phpgridzlogn004.int.corp.gel.ac Commercial (Discovery Forum)
phpgridzlogn003.int.corp.gel.ac Internal users

How to make your login automatic

Using SSH Keys

If you do not want to enter a password each time you connect, you can create a ssh key and ssh config file that will make logging in easier.

Create a ssh key in your .ssh folder, which is located in /home/<username>/.ssh. This is not on the HPC, so if you've logged in, please open a new terminal.

cd.ssh
ssh-keygen

Follow the prompts to name your ssh key (I suggest cluster as a good name) and leave the password blank.

Creating SSH keys

Next, create a ssh config file called config in the .ssh folder,

nano config

the above will open the file. Add the following information and format:

Host cluster
    Hostname phpgridzlogn00N.int.corp.gel.ac
    User <your username>@corp.gel.ac
    IdentityFile ~/.ssh/cluster

Sending your key to the remote

Copy your new ssh public key to the HPC

ssh-copy-id -i cluster.pub cluster

This will ask for your password, then copy the ssh key to the HPC.

Now, instead of having to type

ssh jdoe@corp.gel.ac@phpgridzlogn001.int.corp.gel.ac

You can connect by typing

ssh cluster