3 NeuroDebian Virtual Machine
4 ===========================
10 For those who are not yet running a Debian-based operation system we offer a
11 `virtual machine`_ that can be used with `VirtualBox`_, allowing users to benefit
12 from a Debian-based research environment on other operating systems.
13 This virtual machine initially comes as a compact Debian installation that can,
14 once installed, be equipped with a large variety of neuroscience software with
15 just a few mouse clicks (e.g. AFNI_, Caret_, FSL_, PyMVPA_).
17 .. _virtual machine: http://en.wikipedia.org/wiki/Virtual_machine
18 .. _AFNI: http://afni.nimh.nih.gov/afni/
19 .. _Caret: http://brainvis.wustl.edu/wiki/index.php/Caret:About
20 .. _FSL: http://www.fmrib.ox.ac.uk/fsl/
21 .. _PyMVPA: http://www.pymvpa.org
27 * `NeuroDebian 6.0.5 image (32bit)
28 <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.5_i386.ova>`_ [~559MB]
30 *This image should work on virtually all systems that are supported by*
31 VirtualBox_ *and can be used whenever the, otherwise preferable, 64bit image
32 is not compatible with a host machine.*
34 * `NeuroDebian 6.0.5 image (64bit)
35 <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.5_amd64.ova>`_ [~575MB]
37 *This image only works on 64bit host machines with active hardware
38 virtualization support. The should include all recent Apple hardware and most
39 64bit Windows systems.*
41 Virtual appliances above carry guest additions for 4.x series of the
42 VirtualBox. If you still have VirtualBox 3.x, use previous 6.0.2
45 * `NeuroDebian 6.0.2 image (32bit)
46 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
48 * `NeuroDebian 6.0.2 image (64bit)
49 <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
53 This older virtual appliances are distributed as a `zip` file. Please
54 extract all files from the `.zip` file, using appropriate software
55 for your operating system.
59 You can verify that you have downloaded archives correctly using
61 <http://neuro.debian.net/debian/vm/MD5SUMS>`_ . You can also verify
62 the authenticity of the `MD5SUMS
63 <http://neuro.debian.net/debian/vm/MD5SUMS>`_ itself using `gpg
65 <http://neuro.debian.net/debian/vm/MD5SUMS.gpg>`_ signed with
66 NeuroDebian archive key.
68 * `VirtualBox download page <http://www.virtualbox.org/wiki/Downloads>`_ (Windows, Linux, Mac,
71 *This webpage offers installers of the VirtualBox application, as well as the
79 * Updated core system to Debian squeeze 6.0.3
80 * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10
82 - ``~/host`` is now symlinked to correct path ``/media/sf_host``
83 - ``brain`` user is added to ``vboxsf`` group so mounted host
84 directories should become readily available
86 * Root partition size and swap space got doubled in size (40GB
87 and 2GB correspondingly). Space is allocated dynamically so
88 the actual size of the virtual drive should not grow unless
93 * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
95 6.0.3 -- 12 Jun 2011 [Superseded in the archive by 6.0.4]
97 * Updated to Squeeze 6.0.1
98 * Updated VirtualBox guest additions to 4.0.4 from backports.debian.org
99 * Appliance is available as a single file (.ova) ready for the import
108 The virtual machine contains an installation of `Debian 6.0 (squeeze)`_ with a
109 GNOME_ desktop environment. All installed software comes from standard Debian
110 packages, or prospective Debian packages from NeuroDebian. This means that all
111 contained software is readily available for any system running a Debian
112 operating system (or a recent Ubuntu release). The virtual machine can be seen
113 as a showcase of what Debian for neuroscience research feels like. Moreover,
114 once downloaded this virtual machine can be kept up to date, just as any other
115 Debian installation. Using convenient graphical package management tools users
116 will benefit from security bug fixes provided by the Debian project for the
117 whole operating system, as well as from software updates for
118 neuroscience-related packages.
120 .. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze
121 .. _GNOME: http://www.gnome.org/
127 The following video shows how to get the NeuroDebian virtual machine running
128 on your machine. The installation is shown for Mac OS X. It should, however, be
129 very similar on a Windows box. If you cannot watch the video, please take a
130 look at the written instructions below.
134 <iframe title="YouTube video player"
135 class="youtube-player"
139 src="http://www.youtube.com/embed/eqfjKV5XaTE?hd=1"
140 frameborder="0"></iframe>
142 First download and install a recent version of VirtualBox_. VirtualBox is a
143 virtualization software that is freely available for Windows, MacOS X, Solaris,
144 and Linux. VirtualBox comes with a comprehensive manual that should answer
145 potential questions regarding installation and maintenance.
147 .. _VirtualBox: http://www.virtualbox.org
149 Next, download the most recent version of the NeuroDebian virtual machine from
150 the Downloads_ section. Start VirtualBox and select "Import Appliance" from the file
153 .. image:: pics/vm_import_app.jpg
155 The next dialog will ask you to choose a virtual machine. Please navigate to the
156 extracted NeuroDebian download and select the `.ova` (or extracted
157 `.ovf` for older appliances shipped as `.zip`) file.
159 .. image:: pics/vm_import_wizard.jpg
161 You can finish importing of NeuroDebian by clicking on *next* a couple of
162 times. There is no need to change anything, as we will get through the
163 settings in a second. Importing of the virtual machine will take a short
164 while, as it is distributed in a compressed format that now gets extracted
165 (total extracted size about 2 GB). Once imported, the NeuroDebian virtual
166 machine will appear in the list of available machines. Do **not** start it yet,
167 but select NeuroDebian and hit the *Settings* button. In the following dialog
168 you'll have a chance to configure the machine. You can assign the amount of RAM
169 that should be made available to it (for serious fMRI data processing, please
170 allow at least 2 GB). If you have a recent computer with multiple CPU cores,
171 you can also decide how many cores should be used by the virtual machine.
173 .. image:: pics/vm_add_host_folder.jpg
175 However, most important is the *Shared Folders* setup. Shared folders allow the
176 virtual machine to access the local harddrive of the host computer. This is an
177 easy way to access data on the computer without duplicating it or using the
178 network to access it. The virtual machine is preconfigured to access a shared
179 folder named labeled "host". Click on the *add* button to select a folder that
180 shall be accessible by the machine (e.g. your home directory) and put "host" as
181 the folder name and mark it to be auto-mounted. Note, the folder name is simply a label. Your directory will
184 .. image:: pics/vm_host_folder.jpg
186 If you have a large screen you should increase the display memory to
187 32 MB in the *Display* settings. Also you might like to enable the
188 support for 3D Acceleration
190 .. image:: pics/vm_settings_display.jpg
192 Finally, close the settings dialog. You have now completed the setup, and you
193 can start the virtual machine by hitting the *Start* button. A new window will
194 appear showing the boot process. After a short while the NeuroDebian desktop
195 will appear, and a setup wizard will guide your through the final steps of the
196 configuration. You can now explore the system. The virtual machine is connected
197 with your host computer, and shares its Internet connection. Via this
198 connection you can update the contained software packages at any time.
200 .. image:: pics/vm_settings.jpg
202 The virtual machine logs yourself in automatically. The name of the virtual
203 machine user is `brain` and the password is `neurodebian`. The *root* password
204 is also `neurodebian`. In most cases, however, you should not be forced to type
205 the password, since `sudo` is configured to work without it.
209 For increased security you might want to change the default password. You can
210 do so by opening a terminal window and running the ``passwd`` command.
213 Working with the virtual machine
214 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
216 The next video is a demonstration of some basic desktop integration features.
217 It shows how to use the virtual machine in full-screen and seamless mode, shared
218 folder access, software installation, as well as suspending and resuming the
223 <iframe title="YouTube video player"
224 class="youtube-player"
228 src="http://www.youtube.com/embed/OV7fYSEoOeQ?hd=1"
229 frameborder="0"></iframe>
232 .. _chap_vm_troubleshooting:
237 Updating the VM or installing new packages doesn't work.
239 The VM uses as service that tries to figure out the best/closest package
240 repository for you. In some network environments this service might not work
241 well, or not at all. To check if this is a problem, you can modify the
242 respective configuration by hand. Edit ``/etc/apt/sources.list`` (you need to
243 use ``sudo`` for that) and replace the package repository URL with a mirror
244 close to you. A comprehensive list of mirrors is available at:
245 http://www.debian.org/mirror/list
247 Pick one and replace all ``geomirror.debian.net`` URLs with the new mirror
248 URL. For example, in Canada you might want to change::
250 deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib
254 deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib
256 Only modify lines that refer to ``geomirror`` (all of them), but do **not**
257 modify entries for ``security.debian.org``.
259 I cannot hear sounds played in the virtual machine.
261 By default the sound is muted. To enable playback launch the mixer applet by
262 clicking on the mixer icon in the task bar. Unmute the master volume control.
263 Now click on the "Volume control" to load the channel mixer dialog. Unmute
264 the "Master" and "PCM" channels and raise the volume as desired. You should
265 now be able to hear sounds played within the virtual machines through your
266 host computer's speakers.
268 I have upgraded VirtualBox from 3.x series to 4.x, and my VM lost
269 mounted host directories.
271 NeuroDebian VMs prior 6.0.3 were shipped with guest additions from
272 3.x series of VirtualBox and some initial versions of VirtualBox in
273 4.x series have failed to mount host directories properly.
274 VirtualBox 4.0.8 seems to work fine with guest additions from 3.x
275 series. If you nevertheless want to upgrade guest additions within
276 NeuroDebian VM, please rebuild the version available from the
279 sudo apt-get install -y linux-headers-2.6-amd64 # or -686 for 32bit
280 sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-dkms \
281 virtualbox-ose-guest-utils virtualbox-ose-guest-x11