Last updated Jul 24th 2015, RB.
Two models of client are available. The thin-client is a small desktop device, while the workstation is a larger tower PC. The workstation has a more powerful CPU than the thin-client. The workstation is recommended for users who need to run local analysis regularly, or those who are developing GPU code.
Workstation - Lenovo P510
Xeon E5-1650 v4 (6 Cores)
Nvidia Quadro P2000
Thin Client - Lenovo P320 Tiny
i5-7500T (4 Cores)
Nvidia Quadro P600
Both systems run Redhat 6. This is the same environment running on the cluster. All software available on the BioHPC cluster can be used on the clients, which are ideal for developing and testing code and analysis workflows.
They have direct access to the cluster's file system over the campus 10GB network. You can access your home, project and other shared directories within the GUI interface. This makes transfering files to other BioHPC users fast and easy.
BioHPC users have roaming profiles. This means your documents and settings will are available on all BioHPC systems.
Workstations and thin clients come with Bash and preconfigured to test scripts before submitting them to the cluster.
Access to Windows applications is possible via a Virtual Machine which can easily installed easily.
The following are basic settings that you'll want to make to your profile.
Create directory bookmarks to quickly access the project and work folders.
You can change shortcuts under
System > Preferences > Keyboard Shortcuts
Modules are used to deploy multiple versions of different software tools.
See what modules are available
View loaded modules
Load a module
Remove a module
Workstations and thin clients come with Bash and SBGrid preconfigured to test scripts before submitting them to the cluster. The example script below compares two data sets and outputs an image to display the results.
Run a script with Bash
Check the Output Folder
You can submit jobs to the cluster using sbatch instead of bash. The following is the same example script as used above.
Submit a job to with the sbatch command
Check the queue with the squeue command
Check the output folder
If you need to visually interact with your data you can run a Graphical User Interface (GUI) or Graphical Processing Unit (GPU) session on the cluster. For example, you could open a remote GUI session to work with large images that require more memory than is available on your workstation. A remote GPU session executes on a node with an Nvidia GPU card. These nodes offer hardware rendering as opposed to the software rendering on non-GPU nodes.
To begin one of these sessions use the remoteGUI or remoteGPU command. Then, use cat remoteGUI.txt to display the port number for your session.
To connect to the session, open TurboVNC (Applications>Accessories>TurboVNCViewer), and enter nucleus.biohpc.swmed.edu:port# and you password.
The BioHPC VirtualBox Image Manager allows you to copy a preconfigured Windows 8.1 VM to your local machine. This can be used to access Microsoft Office and other Windows applications. Please let us know if you need to use other versions of Windows or Linux.
To open the program click on Applications>BioHPC>BioHPC Virtual Machine Manager.
When the application opens click on an available VM and click add to copy it to your computer's ~/shared directory. This could take up to 15 minutes depending on your network connection. The size of the ~/shared directory is limited to 364GB on Workstations and 50GB on thin clients.
Once you have copied the VM, you can control it with the Virtual Box Manager.
Applications>System Tools>Virtual Box Manager
The Windows virtual drive is 40GB, but you can increase the size with the following command.
For example, to increae the 40GB virtual drive to 45GB you would use the following command.
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