Connecting to the RHPC cluster

Contents

• Connecting to the RHPC cluster

  • Get access and login to the servers

  • To connect to the servers with ssh (highly recommended)

    • Ubuntu/WSL: Connect to rhpc

    • Ubuntu/WSL/MacOS: To jump between rhpc servers

    • Connect to rhpc with Windows Powershell (necessary for PyCharm Remote Deployment):

    • Windows Powershell: To jump between rhpc servers

    • Not recommended: Option to manually add ssh keys to the rhpc server:

Get access and login to the servers

You can get access to the system by sending an e-mail to the RHPC admins (rhpc-admin@nki.nl) after asking permission to Jonas Teuwen (send with Jonas in CC). They will then create an account for you on the server, set up a password and help you set up an authenticator app. You will need these to login to the server without an ssh connection.

Here are the commands to login to the server:

https://wiki.rhpc.nki.nl/wiki/index.php/Login_to_RHPC

If you do this, you will be prompted to provide several passwords. First, it’s the two factors for rhpc.nki.nl as described above. Then, the password is the concatenation of your set password and the 2FA code. So if your password is F00!b4r? and your 2fa code is 123 123, the password here would be F00!b4r?123123.

To connect to the servers with ssh (highly recommended)

If you are a windows user, install windows subsystem for linux (wsl) or ubuntu. If you are planning to use Pycharm remote deployment (very likely), then also set up the connection through Windows Powershell as explained below. Do not use the MobaXterm option, as this is more difficult to set up and offers less benefits like the direct ssh connection or connecting to the servers through Pycharm.

For this you need to create a shh key pair.

Ubuntu/WSL: Connect to rhpc

1. Open shell

2. Generate ssh key pair with: ssh-keygen -t rsa -b 4096 -C "USERNAME@rhpc.nki.nl"

   1. First prompt: Press enter to accept the default file location in which the public (id_rsa.pub) and private (id_rsa) key pair should be saved.

   2. Second prompt: Enter a passphrase to encrypt your private key!

3. Type ssh-add

4. Go to the .ssh folder cd ~/.ssh

5. Type cat id_rsa.pub → Prints the public key to the shell, so you can easily copy it Ctrl+C

6. Send the public key to the rhpc-admins so they can add it: rhpc-admin@nki.nl

You should now be able to connect to the rhpc server via ssh without a password after the rhpc admins add your ssh key to the cluster. Test this with command: ssh rhpc

Ubuntu/WSL/MacOS: To jump between rhpc servers

1. Create an ssh config file in ~/.ssh/config, with the following information:

ControlMaster auto
ControlPath <your home folder on local machine>/.ssh/tmp/%h_%p_%r

Host rhpc
  User <enter your RHPC username>
  HostName rhpc.nki.nl
  ServerAliveInterval 60
  ForwardAgent yes
  Compression yes
  ForwardX11 yes

Host rhpc-gaia
  Hostname gaia
  User <enter your RHPC username>
  ProxyJump rhpc

Host rhpc-euctemon
  Hostname euctemon
  User <enter your RHPC username>
  ProxyJump rhpc

Host rhpc-galileo
  Hostname galileo
  User <enter your RHPC username>
  ProxyJump rhpc

Host rhpc-herakles
  Hostname herakles
  User <enter your RHPC username>
  ProxyJump rhpc

Host rhpc-plato
  Hostname plato
  User <enter your RHPC username>
  ProxyJump rhpc

Host rhpc-schrodinger
  Hostname schrodinger
  User <enter your RHPC username>
  ProxyJump rhpc

Host rhpc-ptolemaeus
  Hostname ptolemaeus
  User <enter your RHPC username>
  ProxyJump rhpc

Host rhpc-aristarchus
  Hostname aristarchus
  User <enter your RHPC username>
  ProxyJump rhpc

Host rhpc-eudoxus
  Hostname eudoxus
  User <enter your RHPC username>
  ProxyJump rhpc

Host rhpc-alanturing
  Hostname alanturing
  User <enter your RHPC username>
  ProxyJump rhpc

Host rhpc-roentgen
  Hostname roentgen
  User <enter your RHPC username>
  ProxyJump rhpc

Host rhpc-hamilton
  Hostname hamilton
  User <enter your RHPC username>
  ProxyJump rhpc

2. chmod 600 config

3. Create a ~/.ssh/tmp folder and give proper permissions (chmod 700).

4. Also give proper permissions to your RSA key with chmod 600 ~/.ssh/id_rsa and chmod 600 ~/.ssh/id_rsa.pub.

You will then be able to directly jump over the rhpc.nki.nl host by logging in for instance with ssh rhpc-ptolemaeus. Also PyCharm remote deployment should work.

Connect to rhpc with Windows Powershell (necessary for PyCharm Remote Deployment):

1. Make sure OpenSSH Client is in Apps & Features. If not, install it.

2. Run as administrator the Windows command prompt or Windows Powershell. Do not use Ubuntu or WSL. Windows cmd and WSL need to make separate ssh connections to the server. Pycharm remote deployment on Windows is only possible through the ssh connection made by the Windows cmd to the remote server.

3. Ideally, make sure that the folder C:Users\ *username*/.ssh/ is empty to avoid any conflicts. (rm * )

4. Type ssh-keygen or ssh-keygen -t rsa -b 4096 -C "USERNAME@rhpc.nki.nl"

5. Press enter to save your ssh private and public ssh keys in folder C:Users\ *username*/.ssh/.

6. You’ll be asked to enter a passphrase. Hit Enter to skip this step.

7. The system will generate the key pair, and display the  key fingerprint and a randomart image.

8. On your local windows machine, open WSL and navigate to /mnt/c/Users/username/.ssh (Not !! ~/.ssh as this is a different directory in WSL).

9. You should see two files. The identification is saved in the

   id_rsa file and the public key is labeled id_rsa.pub. This is your SSH key pair.

10. To add the private ssh-key to the ssh agent in Windows Powershell:

    1. By default the ssh-agent service is disabled. Allow it to be manually started for the next step to work.

       # Make sure you’re running as an Administrator.

       Get-Service ssh-agent | Set-Service -StartupType Manual

       # Start the service

       Start-Service ssh-agent

       # This should return a status of Running

       Get-Service ssh-agent

       # Now load your key files into ssh-agent

       ssh-add C:\Users\username\.ssh\id_rsa (private key)

11. Print your public ssh key that you generated for the connection to the server with cat id_rsa.pub. Then copy the key.

12. Send the public key to the rhpc-admins so they can add it: rhpc-admin@nki.nl

You should now be able to connect to the rhpc server via ssh without a password after the rhpc admins add your ssh key to the cluster. Test this with command: ssh rhpc

Windows Powershell: To jump between rhpc servers

1. Create a config file that contains:

   Host rhpc
     User <username>
     HostName rhpc.nki.nl
     ServerAliveInterval 60
     ForwardAgent yes
     Compression yes
     ForwardX11 yes
   
   Host rhpc-aristarchus
     User <username>
     HostName aristarchus
     ProxyCommand ssh -W %h:%p rhpc
   
   Host rhpc-ptolemaeus
     User <username>
     HostName ptolemaeus
     ProxyCommand ssh -W %h:%p rhpc
   
   Host rhpc-eudoxus
     Hostname eudoxus
     User <enter your RHPC username>
     ProxyCommand ssh -W %h:%p rhpc
   
   Host rhpc-euctemon
     Hostname euctemon
     User <enter your RHPC username>
     ProxyCommand ssh -W %h:%p rhpc
   
   Host rhpc-galileo
     Hostname galileo
     User <enter your RHPC username>
     ProxyCommand ssh -W %h:%p rhpc
   
   Host rhpc-herakles
     Hostname herakles
     User <enter your RHPC username>
     ProxyCommand ssh -W %h:%p rhpc
   
   Host rhpc-gaia
     Hostname gaia
     User <enter your RHPC username>
     ProxyCommand ssh -W %h:%p rhpc
   
   Host rhpc-alanturing
     Hostname alanturing
     User <enter your RHPC username>
     ProxyCommand ssh -W %h:%p rhpc
   
   Host rhpc-roentgen
     Hostname roentgen
     User <enter your RHPC username>
     ProxyCommand ssh -W %h:%p rhpc
   
   Host rhpc-schrodinger
     Hostname schrodinger
     User <enter your RHPC username>
     ProxyCommand ssh -W %h:%p rhpc
   
   Host rhpc-hamilton
     Hostname hamilton
     User <enter your RHPC username>
     ProxyCommand ssh -W %h:%p rhpc
   
   Host rhpc-plato
     Hostname plato
     User <enter your RHPC username>
     ProxyCommand ssh -W %h:%p rhpc
   

   Save as config (no extention) in the C:/Users/your_username/.ssh directory.

2. You will now be able to directly jump over the rhpc.nki.nl host by logging in for instance with ssh rhpc-ptolemaeus.Also PyCharm remote deployment should work.

Not recommended: Option to manually add ssh keys to the rhpc server:

This option does not allow jumping between servers without a password.

1. Connect to the rhpc server (not one of the machines like aristarchus) with: ssh rhpc (if your wsl ssh connection is already set up) or alternatively with ssh username@rhpc.nki.nl and use your password and authenticator to login

2. Go to ~/.ssh/ on rhpc server

3. Create file authorized_keys with no extension (for example with nano authorized_keys ).

4. Paste the public ssh key in the file. It appears as one line. Save the file.

5. Important! Change permissions for authorised keys: chmod 700 authorized_keys