Virtual Machines

From CNI Wiki

Jump to: navigation, search

The CNI has received funding from BIO-X Neuroventures for a high-powered compute server which will be used to provide computational resources to CNI users.

NOTE: CNI is switching to LXC - Please visit the LXC page to learn more about getting started with LXC.

VM accounts

VM accounts are created based upon scanning group membership. If you would like an account or a VM setup for your group, please contact us.

Data access

Users can access their data from NIMS using NIMSfs. All your NIMS data are available in /nimsfs. This means you don't need to download anything. Once you log in to your VM there should be a link to /nimsfs on your desktop.

Note that NIMSfs is a read-only filesystem, so you can't save anything there.

All analysis should be done and results saved to the scratch folder located at /scratch (a link can be found on each user's desktop.)


Each VM has the following software pre-installed (from NeuroDebian wherever possible):

  • Freesurfer (v5.3.0)
  • fsl mrtix afni octave ants itksnap ipython1x python-numpy python-scipy python-nipype python-nibabel python-dipy python-nitime python-nipy mricron mriconvert gifti-bin dicomnifti nifti2dicom qnifti2dicom

If specific software is required please contact us.


The machine which hosts the Virtual Machines boasts 768 GB of RAM and 4X Intel(R) Xeon(R) CPU E5-4650 processors. Each VM will be configured to match specific needs for processing.

X-Window sessions

We have configured the CNIVMs to use FreeNX. FreeNX is a system that allows a user to access the desktop of their CNIVM from another machine over the Internet. You can use this to login graphically to your CNIVM desktop from a remote location. Users that want access to a desktop session on their CNIVM should follow directions below to install and configure the OpenNX client, which works hand-in-hand with FreeNX.

OpenNX Client

Software dependencies

Before installing the opennx client you will need to install an X Window System for your specific operating system.

  • Most linux clients will have an X Window System installed by default.

Client installation

To install the OpenNX client on Windows, OSX, or Linux:

  1. Download the client from
  2. Follow typical installation procedures

Client configuration

Before you can use the OpenNX client you must configure the connection to the CNIVM - which will refer to in the following directions as 'CNIVM' - please check your VM name before you follow these instructions.

  1. Run the OpenNX Connection Wizard > Click 'Next'
  2. Enter a session name and host name NOTE: The session name is arbitrary and meant to help you remember a given session, however, the Host is important and must be the hostname that was provided to you by the CNI when your VM was configured.
  3. Select the appropriate internet connection type for your configuration (usually WAN or LAN).
  4. Hit Next
  5. Choose 'Custom' for the X Desktop >> then click on "Settings"
  6. In the Session Settings window > Choose 'Run the following command' and enter 'startlubuntu' as the command > Under Options, choose 'New Virtual Desktop'
  7. Back in the Wizard Choose 'Available Area' for size of desktop and click 'Next'
  8. Make sure 'Enable SSL encryption of all traffic' is selected > Click 'Next'
  9. Choose to create a shortcut on your desktop for this connection > Click 'Finish'
  • OSX users might experience a crash of the Wizard when you click finish - this will not affect the creation of the session. Simply click 'Ignore'

Session Initialization

To initialize a previously configured session

  1. Start the OpenNX client
  2. Choose your session from the session dropdown list
  3. Enter your login credentials > Username and Password
  4. Click > 'Login'
  5. You will likely see messages about accepting and saving host information. Choose 'yes' for each window that appears and 'don't show again' as appropriate.
  • If all goes well, you should now see your desktop
  • OSX users will get a warning message about /usr/sbin/cupsd and execution permissions. If you'd like to avoid this warning you can make the executable "more" executable by running the following line in Terminal: sudo chmod ga+x /usr/sbin/cupsd

Session Management

Depending on your workflow you might want to return to a session if some work is still ongoing. OpenNX allows you to resume your session if you disconnect from it, or if it was unexpectedly terminated. Of course, you can also end your session once you are done working on a project.

Ending a session
There are a couple of ways to end a session
  1. Clicking Close: Click the close button for the x-window > You will then be prompted with the window in figure 1 below. From here you can select to either "Disconnect" or "End" your session. Clicking "End" will close the session and stop all your running jobs and close all your windows. The next time you login you will have a "fresh" working state.
  2. Shutdown": From within the lubuntu desktop Choose > Shutdown and click yes when prompted to shutdown the computer >> This will not actually shutdown the computer, just your session.
Disconnecting and resuming a session
If you would like to continue working on your session at a later time, then you want to simply disconnect from it and reconnect later. Follow the steps below.
  1. Click the close button for the x-window OR close your X Window (xming or Xquartx)
  2. You will then be prompted with the window in figure 1 below. From here you can select to either "Disconnect" or "End" your session. Clicking "Disconnect" will allow you to reattach to your session at a later time. This allows you to save your state and not have jobs or windows close when you stop your session.
  3. Reattaching: Open an OpenNX session as described in the previous section - choose the session you wish to resume and click "Resume"
Personal tools