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IA migration §2: polish — trim Windows/PuTTY walkthrough, move worker-node section to Compute Nodes, fix links (via update-page on MediaWiki MCP Server)
 
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== Log on using ssh ==
This page explains how to connect to Anunna over SSH. Once you are logged in, see [[Login Nodes]] for what the login nodes are for, and [[Policies and Terms of Use]] for the rules that apply.
One can log into the [[B4F_cluster | B4F Cluster]] (more specifically the nfs server) using ssh. The address of the nfs server is:
  nfs01.hpcagrogenomics.wur.nl


To log on one has to use an ssh ([http://en.wikipedia.org/wiki/Secure_Shell secure shell]) client. Such client systems are always available from Linux or MacOS systems. For Window an ssh-client may need to be installed. The most popular ssh-client for Windows is [http://www.chiark.greenend.org.uk/~sgtatham/putty/ Putty].
== Connecting ==


=== CLI from a Linux/MacOSX terminal ===
You log in to Anunna using the Secure Shell protocol (SSH) on the default port (TCP 22). The address of the login server is:
A Command Line Interface ([http://en.wikipedia.org/wiki/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'>
login.anunna.wur.nl
ssh [user name]@nfs01.hpcagrogenomics.wur.nl
</source>


=== PuTTY on Windows ===
You are automatically redirected to a currently valid login server. An SSH client is built in on Linux and macOS; on Windows you usually install one, such as [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY] or MobaXTerm.
<need a volunteer to write some text here>


== Log on to worker nodes ==
Note that access may be restricted to certain IP ranges, and SSH may be blocked where port 22 is closed by a firewall. (For example, WUR FB-IT does not allow port 22 over WiFi to certain systems.)


Once logged into the nfs server, it is then possible to log on to any of the worker nodes. Logging on to the worker nodes does not require password authentication, you should therefore not be prompted to provide a password. Before logging onto a node it should be checked whether that node is busy. Status of nodes can be ascertained through the [[ BCM_on_B4F_cluster|BCM Portal]].
'''The login server is an access point only — it is not for CPU- or memory-intensive work.''' Anything beyond light, interactive use belongs in a job; see [[Login Nodes]] and [[Scheduler Overview (Slurm)]].


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


For instance:
An SSH client is available from any Linux or macOS terminal:


<source lang='bash'>
<syntaxhighlight lang="bash">
ssh dummy001@node049
ssh <username>@login.anunna.wur.nl
</source>
</syntaxhighlight>


== File transfer using ssh-based file transfer protocols ==
If the connection is refused, check your firewall settings — SSH needs port 22 open.
=== 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 ([http://en.wikipedia.org/wiki/Secure_copy secure copy]). For instance, copying a folder containing several files from scomp1090/lx6 can be achieved like this:
=== Windows ===


Syntax of the scp command requires from-to order:
On Windows you connect with an SSH client such as '''MobaXTerm''' or '''PuTTY'''. In either case, set the remote host to <code>login.anunna.wur.nl</code> and enter your username (not your email address) and WUR password. No characters appear while you type your password — this is normal.


<source lang='bash'>
For key-based login, generate an SSH key pair with the client's key generator (MobaKeygen in MobaXTerm, or PuTTYgen for PuTTY), protect it with a passphrase, and add the public key to <code>~/.ssh/authorized_keys</code> on Anunna. PuTTY users can hold the key in Pageant so they do not have to type the passphrase each time. See the [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY homepage] for full instructions.
scp FROM_SOURCE TO_DESTINATION
</source>


<source lang='bash'>
== Logging in without a password ==
scp -pr /home/WUR/[username]/folder_to_transfer [username]@nfs01.hpcagrogenomics.wur.nl:/lustre/scratch/WUR/ABGC/
</source>


This example assumes a user that is part of the ABGC user group. See the [[Lustre_PFS_layout | 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 [http://en.wikipedia.org/wiki/Man_page man pages].
You can configure SSH to log in without typing your password each time; see [[ssh_without_password|SSH without password]].


<source lang='bash'>
== Connecting to a compute node ==
man scp
</source>


=== rsync ===
To open a shell or a direct connection on a compute node where your job is running, see [[Compute Nodes]].
The [http://en.wikipedia.org/wiki/Rsync 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 FROM_SOURCE TO_DESTINATION
</source>
e.g.:
<source lang='bash'>
rsync -av /home/WUR/[username]/folder_to_transfer [username]@nfs01.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 [http://en.wikipedia.org/wiki/Man_page man pages].
<source lang='bash'>
man scp
</source>
 
=== winSCP ===
<need a windows user as a volunteer to write some text....>
 
=== FileZilla ===
 
=== Samba/CIFS based protocols ===
The Common Interface File System ([http://en.wikipedia.org/wiki/Cifs CIFS]) is commonly used in and between Windows systems for file sharing.
<is this going to be enabled on the Cluster?.


== See also ==
== See also ==
* [[B4F_cluster | B4F Cluster]]
* [[Login Nodes]]
* [[Compute Nodes]]
* [[Data Transfer Methods]]
* [[ssh_without_password|SSH without password]]
* [[Scheduler Overview (Slurm)]]


== External links ==
== External links ==
* [http://en.wikipedia.org/wiki/Secure_Shell Secure Shell on Wikipedia]
* [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY homepage]
* [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY homepage]
* [http://winscp.net/eng/index.php WinSCP homepage]
* [https://filezilla-project.org FileZilla homepage]

Latest revision as of 12:20, 18 June 2026

This page explains how to connect to Anunna over SSH. Once you are logged in, see Login Nodes for what the login nodes are for, and Policies and Terms of Use for the rules that apply.

Connecting

You log in to Anunna using the Secure Shell protocol (SSH) on the default port (TCP 22). The address of the login server is: 

login.anunna.wur.nl

You are automatically redirected to a currently valid login server. An SSH client is built in on Linux and macOS; on Windows you usually install one, such as PuTTY or MobaXTerm.

Note that access may be restricted to certain IP ranges, and SSH may be blocked where port 22 is closed by a firewall. (For example, WUR FB-IT does not allow port 22 over WiFi to certain systems.)

The login server is an access point only — it is not for CPU- or memory-intensive work. Anything beyond light, interactive use belongs in a job; see Login Nodes and Scheduler Overview (Slurm).

Linux and macOS

An SSH client is available from any Linux or macOS terminal: 

ssh <username>@login.anunna.wur.nl

If the connection is refused, check your firewall settings — SSH needs port 22 open.

Windows

On Windows you connect with an SSH client such as MobaXTerm or PuTTY. In either case, set the remote host to login.anunna.wur.nl and enter your username (not your email address) and WUR password. No characters appear while you type your password — this is normal.

For key-based login, generate an SSH key pair with the client's key generator (MobaKeygen in MobaXTerm, or PuTTYgen for PuTTY), protect it with a passphrase, and add the public key to ~/.ssh/authorized_keys on Anunna. PuTTY users can hold the key in Pageant so they do not have to type the passphrase each time. See the PuTTY homepage for full instructions.

Logging in without a password

You can configure SSH to log in without typing your password each time; see SSH without password.

Connecting to a compute node

To open a shell or a direct connection on a compute node where your job is running, see Compute Nodes.

See also

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