NeuroDebian Virtual Machine¶
We find the approach taken by NeuroDebian and the progress it made so far very pleasant and promising. [...] The NeuroDebian team helped us to improve the quality of our software and of some of our processes by review, constructive suggestions and even software patches. The availability of the NeuroDebian Virtual Machine was instrumental for fast porting of the Psychtoolbox to a 64 bit Linux environment.
—– [2011-06-21] Dipl. Inf., Psychtoolbox lead developer, Department for Cognitive and Computational Psychophysics, Max Planck Institute for Biological Cybernetics, Tuebingen, Germany
For those who are not yet running a Debian-based operation system we offer a virtual machine that can be used with VirtualBox, allowing users to benefit from a Debian-based research environment on other operating systems. This virtual machine initially comes as a compact Debian installation that can, once installed, be equipped with a large variety of neuroscience software with just a few mouse clicks (e.g. AFNI, Caret, FSL, PyMVPA).
Downloads¶
NeuroDebian 6.0.5 image (32bit) [~559MB]
This image should work on virtually all systems that are supported by VirtualBox and can be used whenever the, otherwise preferable, 64bit image is not compatible with a host machine.
NeuroDebian 6.0.5 image (64bit) [~575MB]
This image only works on 64bit host machines with active hardware virtualization support. The should include all recent Apple hardware and most 64bit Windows systems.
Virtual appliances above carry guest additions for 4.x series of the VirtualBox. If you still have VirtualBox 3.x, use previous 6.0.2 virtual appliances:
- NeuroDebian 6.0.2 image (32bit) [~545MB]
- NeuroDebian 6.0.2 image (64bit) [~560MB]
Note
This older virtual appliances are distributed as a zip file. Please extract all files from the .zip file, using appropriate software for your operating system.
Note
You can verify that you have downloaded archives correctly using md5sums -c MD5SUMS . You can also verify the authenticity of the MD5SUMS itself using gpg –verify MD5SUMS.gpg signed with NeuroDebian archive key.
VirtualBox download page (Windows, Linux, Mac, Solaris)
This webpage offers installers of the VirtualBox application, as well as the documentation.
Changes¶
6.0.5 – 10 Nov 2011
- Updated core system to Debian squeeze 6.0.3
- Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10
- ~/host is now symlinked to correct path /media/sf_host
- brain user is added to vboxsf group so mounted host directories should become readily available
- Root partition size and swap space got doubled in size (40GB and 2GB correspondingly). Space is allocated dynamically so the actual size of the virtual drive should not grow unless you use it
6.0.4 – 13 Jun 2011
- Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
6.0.3 – 12 Jun 2011 [Superseded in the archive by 6.0.4]
- Updated to Squeeze 6.0.1
- Updated VirtualBox guest additions to 4.0.4 from backports.debian.org
- Appliance is available as a single file (.ova) ready for the import
6.0.2 – 08 Feb 2011
6.0.1 – 01 Dec 2010
Documentation¶
The virtual machine contains an installation of Debian 6.0 (squeeze) with a GNOME desktop environment. All installed software comes from standard Debian packages, or prospective Debian packages from NeuroDebian. This means that all contained software is readily available for any system running a Debian operating system (or a recent Ubuntu release). The virtual machine can be seen as a showcase of what Debian for neuroscience research feels like. Moreover, once downloaded this virtual machine can be kept up to date, just as any other Debian installation. Using convenient graphical package management tools users will benefit from security bug fixes provided by the Debian project for the whole operating system, as well as from software updates for neuroscience-related packages.
Installation¶
The following video shows how to get the NeuroDebian virtual machine running on your machine. The installation is shown for Mac OS X. It should, however, be very similar on a Windows box. If you cannot watch the video, please take a look at the written instructions below.
First download and install a recent version of VirtualBox. VirtualBox is a virtualization software that is freely available for Windows, MacOS X, Solaris, and Linux. VirtualBox comes with a comprehensive manual that should answer potential questions regarding installation and maintenance.
Next, download the most recent version of the NeuroDebian virtual machine from the Downloads section. Start VirtualBox and select “Import Appliance” from the file menu.
The next dialog will ask you to choose a virtual machine. Please navigate to the extracted NeuroDebian download and select the .ova (or extracted .ovf for older appliances shipped as .zip) file.
You can finish importing of NeuroDebian by clicking on next a couple of times. There is no need to change anything, as we will get through the settings in a second. Importing of the virtual machine will take a short while, as it is distributed in a compressed format that now gets extracted (total extracted size about 2 GB). Once imported, the NeuroDebian virtual machine will appear in the list of available machines. Do not start it yet, but select NeuroDebian and hit the Settings button. In the following dialog you’ll have a chance to configure the machine. You can assign the amount of RAM that should be made available to it (for serious fMRI data processing, please allow at least 2 GB). If you have a recent computer with multiple CPU cores, you can also decide how many cores should be used by the virtual machine.
However, most important is the Shared Folders setup. Shared folders allow the virtual machine to access the local harddrive of the host computer. This is an easy way to access data on the computer without duplicating it or using the network to access it. The virtual machine is preconfigured to access a shared folder named labeled “host”. Click on the add button to select a folder that shall be accessible by the machine (e.g. your home directory) and put “host” as the folder name and mark it to be auto-mounted. Note, the folder name is simply a label. Your directory will not be renamed.
If you have a large screen you should increase the display memory to 32 MB in the Display settings. Also you might like to enable the support for 3D Acceleration
Finally, close the settings dialog. You have now completed the setup, and you can start the virtual machine by hitting the Start button. A new window will appear showing the boot process. After a short while the NeuroDebian desktop will appear, and a setup wizard will guide your through the final steps of the configuration. You can now explore the system. The virtual machine is connected with your host computer, and shares its Internet connection. Via this connection you can update the contained software packages at any time.
The virtual machine logs yourself in automatically. The name of the virtual machine user is brain and the password is neurodebian. The root password is also neurodebian. In most cases, however, you should not be forced to type the password, since sudo is configured to work without it.
Note
For increased security you might want to change the default password. You can do so by opening a terminal window and running the passwd command.
Working with the virtual machine¶
The next video is a demonstration of some basic desktop integration features. It shows how to use the virtual machine in full-screen and seamless mode, shared folder access, software installation, as well as suspending and resuming the virtual machine.
Troubleshooting¶
Updating the VM or installing new packages doesn’t work.
The VM uses as service that tries to figure out the best/closest package repository for you. In some network environments this service might not work well, or not at all. To check if this is a problem, you can modify the respective configuration by hand. Edit /etc/apt/sources.list (you need to use sudo for that) and replace the package repository URL with a mirror close to you. A comprehensive list of mirrors is available at: http://www.debian.org/mirror/list
Pick one and replace all geomirror.debian.net URLs with the new mirror URL. For example, in Canada you might want to change:
deb http://i386-geomirror.debian.net/debian squeeze main non-free contribto:
deb http://ftp.ca.debian.org/debian/ squeeze main non-free contribOnly modify lines that refer to geomirror (all of them), but do not modify entries for security.debian.org.
I cannot hear sounds played in the virtual machine.
By default the sound is muted. To enable playback launch the mixer applet by clicking on the mixer icon in the task bar. Unmute the master volume control. Now click on the “Volume control” to load the channel mixer dialog. Unmute the “Master” and “PCM” channels and raise the volume as desired. You should now be able to hear sounds played within the virtual machines through your host computer’s speakers.
I have upgraded VirtualBox from 3.x series to 4.x, and my VM lost mounted host directories.
NeuroDebian VMs prior 6.0.3 were shipped with guest additions from 3.x series of VirtualBox and some initial versions of VirtualBox in 4.x series have failed to mount host directories properly. VirtualBox 4.0.8 seems to work fine with guest additions from 3.x series. If you nevertheless want to upgrade guest additions within NeuroDebian VM, please rebuild the version available from the backports:
sudo apt-get install -y linux-headers-2.6-amd64 # or -686 for 32bit sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-dkms \ virtualbox-ose-guest-utils virtualbox-ose-guest-x11and reboot VM.
