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Balena is an Linux-based High Performance Computing system specifically designed for running parallel applications.
The Balena HPC cluster can only be accessed from within the campus network, it is not available from external connections.
Unix/Mac users can access Balena using their local terminal using SSH
User should start the Xming service on the Windows system before opening a session to view graphical output
Unix/Mac users can access
sftp tools to transfer data to and from Balena.
Graphical tools like FileZilla can also be used.
The Balena cluster is a shared research resource available to all researchers in the University. There may be many users logged on at the sametime accessing the filesystem, hundred of jobs my be running on the compute nodes, with a hundred jobs queued up waiting for resources. All users must Respect the shared file systems Do not run workloads on the login nodes The two login nodes are shared among all users of the service. A single user running computational workloads will negatively impact performance and responsiveness for other users. Should an administrator discover users using the login nodes in this way, they will kill these jobs without notice. Instead, submit batch jobs or request interactive sessions on the compute nodes as detailed below. Fair use of Interactive Test and Development nodes Kinldy refrain from running production workloads on the ITD nodes. This will impact other users having a fair access to the limited resources available on the ITD nodes. The purpose of the ITD nodes is serve the testing and developing needs of our community
$HOME directory, this will suffer in performance as well as possibly impacting the responsiveness of the filesystem. Run jobs in
$SCRATCH or $DATA.
Respect the shared file systems
Do not run workloads on the login nodes
The two login nodes are shared among all users of the service. A single user running computational workloads will negatively impact performance and responsiveness for other users. Should an administrator discover users using the login nodes in this way, they will kill these jobs without notice.
Instead, submit batch jobs or request interactive sessions on the compute nodes as detailed below.
Fair use of Interactive Test and Development nodes
Kinldy refrain from running production workloads on the ITD nodes. This will impact other users having a fair access to the limited resources available on the ITD nodes.
The purpose of the ITD nodes is serve the testing and developing needs of our community
To submit a job to Balena use the sbatch command along with the job-script file.
Balena offers a high-end visualisation service, which will allow users to utilise the high-end graphics cards available on Balena to visualise large and complex graphical models from their remote desktop.
For more information about how VirtualGL work see: http://www.virtualgl.org/
The default settings should be sufficient. The table below describes the various options available.
|Walltime||1 hour||Set the time of the Visualisation session. By default the visualisation service uses the free service, making the maximum session time 6 hours.|
Will allow selected users to access the VNC session
|Allowed users||none selected||Select the users you would like to share your VNC session with. You can select multiple users by holding down the Ctrl button.|
|Nodes||1||Recommend leaving this set to 1. Unless needed for MPI based visualisation workloads.|
|Cores||1||Recommend leaving this set to 1. The visualisation nodes are fully shared to allow multiple users and do not restrict the size of jobs being run on the node.|
|CUDA offload devices||0||Will reserve a dedicated GPU card. This is only required if you are running an intensive visualisation.|
|Resolution||current desktop window size||Set the size of the resolution. By default it will use your current window size.|
|Bandwidth||auto||Auto default setting should be sufficient, but if you experience responsiveness issues then try adjusting the bandwidth setting. Lowering the bandwidth will reduce the quality of the pixel rendering to increase the responsiveness of the interactions.|
|Only Java Applet||no||To only allow visualisation access via the Java Applet.|
|Extra parameters||Additional parameters to pass to sbatch, see SBATCH options. To run a visualisation job under a premium project use "--account=project-code --time=8:00:00".|
Using the Java Applet VNC session will launch a Java version of the VNCclient from the Balena servers. This is particularly useful if you do not have a VNC client on your desktop; however the performance of the visualisation will be slightly lower.
To launch the Java Applet VNC session:
This session opens up a direct connection to the VNC service on the Visualisation nodes. You will need a VNC client/viewer installed on your desktop to be able to connect. The recommended version is TurboVNC, but you can also use TigerVNC or TightVNC, which have similar 3D performance capabilities, although other VNC clients will also work. If you do not have Administrator/root access on your local machine to install the VNC client, then you can use the VNC viewers available under the download section on the userportal home page.
To launch the Local VNC Client session:
To end a visualisation session:
The below instructions use the VMD visualisation tools to load up example data, and will allow you to interact with the molecule.
module list` should show that you have the esm module loaded; this is done be default on the visualisation nodes.
module load vmd`
vglrun` is needed before any graphical command to capture the OpenGL instructions and process them on the local graphics card.
vglrun vmd /beegfs/scratch/group/training/vis/vmd-example.pdb
module load cuda/toolkit
|Application||Version(s)||Description||Supported Hardware||License||Last Modified|
|IGV||2.4.3||The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.||MIT License|
|VMD||1.9.2||Molecular visualization program||UIUC Open Source License|
Some of the settings in your ~/.java directory will need resetting or cache cleared out. To clean out the cache use `
javaws -viewer`, the cache settings can be found from the Settings button under the General tab.
Failing that, the next simplest method would be to remove the ~/.java directory.
The environment path of vglrun is setup when the esm module is loaded. If `module list` does not show esm in the list, then you will need to load it with `module load esm`. If could be that in your ~/.bashrc or ~/.bash_profile you might have purged the modules.
Start an Interactive Test and Development session
Compiling your code
Create the slurm job script
Submit job to the scheduler