Log in to Anunna

Log on using ssh

One can log into the B4F Cluster (more specifically the nfs server) using ssh (default port tcp 22). The address of the login server is:

 login.hpcagrogenomics.wur.nl

To log on one has to use an ssh (secure shell) client. Such client systems are always available from Linux or MacOS systems. For Windows an ssh-client may need to be installed. The most popular ssh-client for Windows is PuTTY.

Note that current access may be restricted to certain IP-ranges. Furthermore, ssh-protocols may be prohibited on systems where port 22 is unavailable due to firewall.

The ssh-connection can also be configured to work without password, which means that no password needs to be provided at each log-in or secure copy attempt.

 IMPORTANT: the Login server can only act as access point and is not to be used for any serious CPU or RAM intensive work. 
 Anything requiring even moderate resources should be scheduled using SLURM!

CLI from a Linux/MacOSX terminal

A Command Line Interface (CLI) ssh client is available from any Linux or MacOSX terminal. Secure shell (ssh) protocols require port 22 to be open. Should a connection be refused, the firewall settings of the system should be checked. Alternatively, local ICT regulations may prohibit the use of port 22. Wageningen UR FB-ICT for instance does not allow traffic through port 22 over WiFi to certain systems.

<source lang='bash'> ssh [user name]@login.hpcagrogenomics.wur.nl </source>

PuTTY on Windows

Putty is a free, powerful, and widely used SSH client that runs on Windows. It is extremely useful for those people who have a computer running Windows on their desk but must remotely connect to a computer running UNIX/Linux. Putty is one of a set of utilities that all work together to provide convenient connectivity between Windows and UNIX/Linux environments. Some of these utilities include:

• Putty -- the SSH client
• Pageant -- the authentication agent used with Putty
• Puttygen -- the RSA key generation utility
• Pscp -- the SCP secure file copy utility

Depending on your tasks, the above utilities are probably your minimum set of tools to make convenient connections and file transfers between a computer running Windows and a computer running UNIX/Linux.

Putty Configuration

Putty is able to store the configuration or connection profiles for a number of remote UNIX/Linix clients. Each of profile can be created and later edited by Right-clicking on a putty window header and choosing "New Session...". The minimum set of items that need to be configured for a given connection are:

• Session
  • Host Name [login.hpcagrogenomics.wur.nl]
  • Saved Session name [your name for this connection]
• Terminal
  • Keyboard
    • Backspace key -> Control-H
• Connection
  • Data
    • Auto-login username [your remote username]
  • SSH
    • Auth
      • Private key file for authentication [pathname to your .ppk file]

Obviously, there are many other useful things that can be configured and customized in Putty but the above list should be considered a minimum. Please note that after making any change to a putty session you must explicitly save your changes.

Creating an SSH Key Pair

Puttygen is the utility used for creating both a .ppk file (private key) and the public authorized key information. Briefly, here are the steps needed to create a key pair:

• Run (double-click) the Puttygen application
• Click on "Generate"
• Replace the comment with something meaningful -- maybe your name
• Type in your passphrase (password) twice
• Save the .ppk file in a secure location on your Windows computer
• Use your mouse to copy the public key string then paste it into the ~/.ssh/authorized_keys file on the remote computer

Note: The full pathname of this .ppk file is used in the last step of Putty configuration as described above.

Using Pageant as an Interface for Putty

Pageant is a Putty helper program that is used for two main purposes:

• Pageant is used to hold the passphrase to your key pair
• Pageant is used as a convenience application to run a Putty session from any of your saved profiles

There is no configuration needed in Pageant. You simply need to run this program at login. Any easy way to do this is to create a shortcut in your startup folder that points to the Pageant executable. Once this has been done, every time you log in you will see a little icon of a computer with a hat in your taskbar. The first step in using this is to right-click on it and select "Add Key". Navigate to your .ppk file and select "Open". It will prompt you for your passphrase. At this point your passphrase has been conveniently stored for you so that when you use Putty to connect to your various remote computers, you won't have to type in your passphrase over and over again. The next step is to right-click on the Pageant icon again and select one of your saved sessions. If you have done everything correctly you will be logged right in so that you no longer have to type your passphrase.

Log on to worker nodes

In a complete emergency, it is then possible to log on to any of the worker nodes via the login node. Logging on to the worker nodes does not require password authentication, you should therefore not be prompted to provide a password. This is not normally allowed - be aware that running tasks outside of SLURM is prohibited, but so far there has not been any serious abuse of this. This is provided to allow you to get a little more insight in what your job is doing.

<source lang='bash'> ssh [user name]@[node name] </source>

For instance:

<source lang='bash'> ssh dummy001@node049 </source>

Again, it is not permitted to run jobs outside the scheduling software (slurm). So logging on to a worker node is for analyses of running jobs only.

File transfer using ssh-based file transfer protocols

Copying files to/from the cluster: scp

From any Posix-compliant system (Linux/MacOSX) terminal files and folder can be transferred to and from the cluster using an ssh-based file copying protocol called scp (secure copy). For instance, copying a folder containing several files from scomp1090/lx6 can be achieved like this:

Syntax of the scp command requires from-to order:

<source lang='bash'> scp <source> <destination> </source>

<source lang='bash'> scp -pr /home/WUR/[username]/folder_to_transfer [username]@login.hpcagrogenomics.wur.nl:/lustre/scratch/WUR/ABGC/ </source>

This example assumes a user that is part of the ABGC user group. See the Lustre Parallel File System layout page for further details. The -p flag will preserve the file metadata such as timestamps. The -r flag allows for recursive copying. Further options can be found in the man pages.

<source lang='bash'> man scp </source>

rsync

The rsync protocol, like the scp protocol, allow CLI-based copying of files. The rsync protocol, however, will only transfer those files between systems that have changed, i.e. it synchronises the files, hence the name. The rsync protocol is very well suited for making regular backups and file syncs between file systems. Like the scp command, syntax is in the from-to order. <source lang='bash'> rsync <source> <destination> </source> e.g.: <source lang='bash'> rsync -av /home/WUR/[username]/folder_to_transfer [username]@login.hpcagrogenomics.wur.nl:/lustre/scratch/WUR/ABGC/ </source> The -a flag will preserve file metadata and allows for recursive copying, amongst others. The -v flag provides verbose output. Further options can be found in the man pages. <source lang='bash'> man scp </source>

WinSCP

WinSCP is a free and open source (S)FTP client for Microsoft Windows. By providing the hostname (login.hpcagrogenomics.wur.nl), your username, and password, using SFTP protocol and port 22, you can login. After login files can be transferred between a local system (PC) and the cluster.

FileZilla

FileZilla is a free and open source graphical (S)FTP client. It is available for Linux, MacOSX, and Windows. By providing the address, username, password and server type (Unix, see Site Manager;Advanced), files can be transferred between a local system and the cluster. Furthermore, the graphical interface allows for easy browsing of files on the Cluster. Detailed instruction can be found on the FileZilla Wiki.

Samba/CIFS based protocols

The Common Interface File System (CIFS) is commonly used in and between Windows systems for file sharing. It is only available to clients within WURnet. If you enter the following UNC path \\nfs01.hpcagrogenomics.wur.nl\[username] in your Windows client, it will list the available (authenticated) shares (your home directory).

See also

• B4F Cluster
• Monitor cluster status with BCM
• Submit jobs with Slurm
• ssh without password

External links

• secure shell on Wikipedia
• PuTTY homepage
• WinSCP homepage
• FileZilla homepage
• The Common Interface File System (CIFS) on Wikipedia