Log in to Anunna
Log on using ssh
One can log into the 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 (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 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.
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]@nfs01.hpcagrogenomics.wur.nl </source>
PuTTY on Windows
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Log on to worker nodes
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 Portal.
<source lang='bash'> ssh [user name]@[node name] </source>
For instance:
<source lang='bash'> ssh dummy001@node049 </source>
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]@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 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]@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 man pages. <source lang='bash'> man scp </source>
winSCP
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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, and password, 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.
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