Getting started
Basic Linux requirements
Please note that all of our HPC systems are running under Linux, so a basic knowledge of the Linux command line is essential. There are numerous excellent tutorials around the web for a first introduction to Linux and its shell and we think one of them can be found in the
UNIX/Linux tutorial for Beginners
of the University of Surrey.
Remote access, VPN
For security reasons, our cluster systems are behind a firewall and are accessible only from inside the University's domain IPs. If you want to access the systems from outside, you need to set up a VPN connection. See the zid instructions for setting up a VPN client for various operating systems.
By default, the VPN client will route all traffic through the University network, making your client effectively part of the UIBK network. All your IP connections will appear to originate from within UIBK in this case. This also means that while your VPN client is connected, you will have no access to your local network, and you may have performance degradation when using external data services.
If you prefer not to lose local connectivity, use the Split Tunnel VPN setup by appending the string _split or _splithpc to your user ID, i.e. connect to the VPN using the user ID cXXXyyyy_split or cXXXyyyy_splithpc. The _split suffix will allow access to all services behind the UIBK firewall; _splithpc additionally enables connections to MACH2 and VSC. Connections to all other destinations will be directly from your device (i.e. will not be tunneled).
Please note: The option_splithpc is of interest only for a relatively small audience (users of HPC systems operated by external partners) and is not mentioned in the general VPN documentation.
Login procedure
Connect to the desired cluster using the respective host name of the cluster's login node:
| Cluster | Login node hostname |
| LCC3 | lcc3.uibk.ac.at |
| LEO3e | leo3e.uibk.ac.at |
| LEO4 | leo4.uibk.ac.at |
| LEO5 | leo5.uibk.ac.at |
Linux workstation
How to connect
Access to the login nodes is via SSH. In Linux, login to the head node of your choice by executing the following command in your local shell:
ssh -l username cluster-name
To enable X11 forwarding, necessary for programs with graphical user interfaces such as graphical editors or the graphical interfaces of Matlab, the TotalView debugger, etc. simply add the -X option (uppercase X) to the command line above:
ssh -X -l username login-node
Some useful settings
On your Linux client workstation, upon first using ssh, a directory $HOME/.ssh will be created automatically. Here you may create a configuration file $HOME/.ssh/config with various defaults. We consider the following to be particularly useful:
| Setting | What it does |
|---|---|
| ForwardX11 yes | Automatically enables X11 forwarding, so no need to use the -X command line option |
| TCPKeepAlive yes ServerAliveInterval 100 |
Long distance connections have a tendency to break. These two options appear to mitigate this problem. |
Windows workstation
To access a Linux server from a Windows workstation, you need a terminal emulator that supports the SSH protocol and an X-Windows server. We recommend the following:
PuTTY as SSH client and terminal emulator
Install the PuTTY client to establish a remote connection to our HPC systems and to provide you with a terminal (command line interface) to the login node on your Windows system. When opening PuTTY, simply enter the fully qualified domain name of the desired login node into the "Host Name"-field and klick the "Open" button. You are then asked to enter username and password and are subsequently provided with the Linux command line. If you do not get PuTTY's login session dialog box automatically, select the 'Session' panel from its left-hand selection menu.
If you are connecting for the first time, you are presented with an RSA fingerprint and asked for its authenticity. To play it safe, compare the given fingerprint with the table above before continuing.
Further usage instructions can be found at this zid page. PuTTY is also available via the University's free software download area.
Installing a local X server
In order to open X Windows applications, such as graphical editors or the graphical interfaces of Matlab, the TotalView debugger, etc. remotely on your local Windows PC, you need to have a local X server installed. We remommand to install the XMing X Server, which can be obtained in its newest version from the University's software download area by all University employees. An outdated Public Domain release of Xming can be found at sourceforge.net. Since this version is defective (e.g. dysfunctional clipboard integration), we definitely recommend to use the new Xming version available in the zid software download area.
In any case, for good display quality, you also need the Xming fonts, which can be downloaded from the same location.
When you create a shortcut for starting the Xming server, the following command line options have turned out to be usefu in the "Properties / Shortcut / Target" setting:
"C:\Program Files\Xming\Xming.exe" :0 -resize -clipboard -multiwindow -nolisten inet6 -dpi 150
- -resize
- X will respond to Windows display resolution changes
- -clipboard
- Enable integration between X11 clipboard and Windows clipboard. Necessary for Copy/Paste between Windows programs and X11 clients.
- -multiwindow
- Run in multiwindow mode. Uses Windows as X11 window manager.
- -nolisten inet6
- Disable IPV6
- -dpi nnn
- DPI setting. Affects scaling of fonts. Start with your monitor's resolution and adjust if necessary until satisfied.
Enabling X11 forwarding with PuTTY
X Windows applications called from whichever terminal emulator you use, will only work on your Windows PC if X11 forwarding via ssh was enabled, and of course, only if the X server of your choice is up and running. In case of Exceed, a corresponding active program button in the Windows taskbar will indicate a running X server.
Proceed with the following simple steps to configure X11 forwarding in PuTTY:
- Select the 'Connection->SSH->X11' panel from the left -hand selection menu.
- Enter 127.0.0.1:0 into the 'X display location' dialog box. (Usually the Windows X display server will install itself as display number 0 on your local machine; if necessary consult your specific X server's manual.)
- Check the 'enable X11 forwarding' check box.
Now open your desired SSH session and enter e.g. xclock on the command line to test your X11 enabled connection.
OS X Workstation
The OpenSSH client should be preinstalled. Install the XQuartz X Server, then follow the instructions for Linux workstations.
Please note: when XQuartz is not running, it should normally be started automatically at the first connection with ssh -X. Users have reported that this autostart capability may be disabled after an OS upgrade. In this case, either start the X Server manually or reinstall XQuartz.
Change your password
Passwords on the LEO/LCC clusters are managed independently of the central zid passwords (e.g. your mail password). All LEO/LCC clusters have a shared password, so changing your password on one cluster will immediately affect all other clusters. When the first cluster account is created for a login name, its password will be the initial password as printed on your "Benutzerbewilligung" form.
Change your password by issuing
passwd
on the command line. After typing your current password you have to input your new password twice (no visual feedback).
Note: Your password should at least be 8 characters long, contain upper and lower case letters, as well as numbers or symbols, to be considered reasonably secure.
File transfer
To transfer your files from and to our systems, we recommend the following methods:
Linux workstation
Use the command line scp program to transfer your files. To upload a file to a destination on a HPC system, use a command similar to the following:
scp SourceFile username@login-node:directory/TargetFile
You can omit the specification of TargetFile if you want to leave the file's name unchanged. Conversely, to transfer a file from a HPC system to your local current directory, issue
scp username@login-node:directory/TargetFile SourceFile
Notes:
- Use scp -r ... to copy entire directories recursively, but be very careful, as scp resolves symbolic links to their destination and blindly copies every file it finds this way across the network!
- To avoid the above problem with symbolic links, or if speed is an issue, use rsync instead of scp, especially when you need to update small differences in large datasets, which exist on both ends.
Windows workstation
Use the open source free SFTP client WinSCP for file transfer from and to a Windows system and see the zid's howto for a quick introduction to WinSCP usage.
WinSCP is also available via the University's free software download area.
Important Usage Note: If a file upload results in a quota overflow, the WinSCP client will give you a misleading error message "Received SSH2_MSG_CHANNEL_DATA for nonexistent channel 0". One likely reason for exceeding quota is that you you are trying to upload large amounts of data to $HOME instead of $SCRATCH
Further topics
Proceed with the following topics (preferably in the given order) to get acquainted with the usage of our HPC systems: