NeuroDebian Virtual Machine
===========================
+`Installation`_ | `Working with the virtual machine`_ | `Troubleshooting`_ |
+`What has changed`_
+
.. quotes::
:random: 1
:tags: vm
-Those, who are not yet running a Debian-based operating system, but are already
-tired of fiddling with dozens of neuro-software packages, can get a glimpse of
-neuroscience research in a Debian environment via a `virtual machine`_.
+For all systems running a non-Debian-based operation system, such as MS Windows
+or Mac OS X, we offer a `virtual machine`_ that can be equipped with a large
+variety of neuroscience software with just a few mouse clicks (e.g. AFNI_,
+FSL_, PyMVPA_).
.. _virtual machine: http://en.wikipedia.org/wiki/Virtual_machine
-NeuroDebian offers a virtual machine that comes preinstalled with a number
-of popular neuroscience packages (e.g. AFNI_, Caret_, FSL_, PyMVPA_).
-
-.. _AFNI: http://afni.nimh.nih.gov/afni/
-.. _Caret: http://brainvis.wustl.edu/wiki/index.php/Caret:About
-.. _FSL: http://www.fmrib.ox.ac.uk/fsl/
-.. _PyMVPA: http://www.pymvpa.org
-
-The virtual machine contains an installation of `Debian 5.0 (lenny)`_ with a
-GNOME_ desktop environment. All installed software comes from standard Debian
-packages, or prospective Debian packages from NeuroDebian -- no custom
-installations whatsoever. 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
-bugfixes provided by the Debian project for the whole operating system, as well
-as from software updates for neuroscience-related packages.
-
-.. _Debian 5.0 (lenny): http://www.debian.org/releases/stable
-.. _GNOME: http://www.gnome.org/
+The virtual machine contains an installation of `Debian 7.0 (wheezy)`_ with a
+XFCE4_ desktop environment. All installed software comes from standard Debian
+packages, or prospective Debian packages from NeuroDebian. The virtual machine
+can be seen as a showcase of what Debian for neuroscience research feels like.
+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.
+
+Even on Debian-based systems this virtual machine is an excellent way to
+maintain an analysis environment that remains identical throughout the lifetime
+of a study and that can be archived alongside acquired data and publications.
+This is a much more practical way than freezing the entire software stack of a
+whole workstation, where it quickly becomes troublesome to combine the desire
+for latest research methodology for new studies and the need for stability for
+ongoing projects.
Installation
-------------
+~~~~~~~~~~~~
-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.
+The following instructions demonstrate how to install the NeuroDebian virtual
+machine -- here shown exemplary for Mac OS X, but the procedure is virtually
+identical on a Windows box. There is also a video tutorial at coffee break
+length. `[Virtual machine setup video tutorial]
+<http://www.youtube.com/watch?v=eqfjKV5XaTE>`_.
-.. _VirtualBox: http://www.virtualbox.org
+If you don't have t already, 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 `download page`_ (about 1GB download size). The machine is distributed as a
-`tar` file. Please extract this file, using appropriate software for your
-operating system. Every Linux system comes with the `tar` commandline utility,
-and potentially other graphical archivers that can extract this format. MacOS X
-users can simply double-click such file to extract it. Windows users can extract
-it with, for example, 7zip_.
+.. _VirtualBox: http://www.virtualbox.org
-Once extracted, you'll find a directory with three files. Now start VirtualBox,
-and select "Import Appliance" from the file menu.
+Obtain the most recent version of the NeuroDebian virtual machine by visiting
+http://neuro.debian.net and selecting your operating system and a download
+server on the frontpage.
-.. _download page: http://neuro.debian.net/debian/vm
-.. _7zip: http://www.7-zip.org/
+Start VirtualBox and select "Import Appliance" from the file menu.
.. image:: pics/vm_import_app.jpg
-Next dialog will ask you to choose a virtual machine. Please navigate to the
-extracted NeuroDebian download and select the `NeuroDebian.ovf` file.
+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.
.. image:: pics/vm_import_wizard.jpg
-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 3.5
-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. If you have a large screen you should
-increase the display memory to 32 MB in the *Display* settings.
+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.
.. image:: pics/vm_add_host_folder.jpg
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. Note, the folder name is simply a label. Your directory will not
-be renamed.
+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.
.. image:: pics/vm_host_folder.jpg
+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
+
+.. image:: pics/vm_settings_display.jpg
+
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. You can now explore the system. The virtual machine is connected
+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.
-.. warning::
+.. image:: pics/vm_settings.jpg
- VirtualBox might offer you to upgrade the "guest additions" to version 3.1.2.
- Do **not** do this, since that version is broken, and after the upgrade you
- will now longer be able to use the mouse inside the virtual machine.
+The virtual machine logs yourself in automatically. This is the default account:
-.. image:: pics/vm_settings.jpg
+:user: brain
+:password: neurodebian
+
+:root password: neurodebian
+
+In most cases you should not be forced to type the password, because ``sudo``
+is configured to work without it.
+
+.. note::
-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.
+ 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.
-Enjoy!
+Working with the virtual machine
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The NeuroDebian virtual machine has very low maintenance demands. We have
+prepared a short video demo that shows most typical procedures that you will
+probably perform while working with NeuroDebian inside a virtual machine:
+use the virtual machine in full-screen and seamless mode, shared folder access,
+software installation, as well as suspending and resuming the
+virtual machine. `[Virtual machine handling video tutorial]
+<http://www.youtube.com/watch?v=OV7fYSEoOeQ>`_
+
+
+.. _chap_vm_troubleshooting:
Troubleshooting
----------------
+~~~~~~~~~~~~~~~
+
+.. container:: foldup
+
+ .. container:: expandinstructions
+
+ Click on an item to expand it
+
+ 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 contrib
+
+ to::
+
+ deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib
+
+ Only modify lines that refer to ``geomirror`` (all of them), but do **not**
+ modify entries for ``security.debian.org``.
+
+ Our proxy setup at work prevents APT from downloading packages
+ APT needs to be told how to access the proxy. Talk to your local sysadmin
+ and ask for the proxy's address (maybe a username and password too), as well
+ as the ports for HTTP and FTP proxies. With this information add the
+ following lines in the file, /etc/apt/apt.conf.d/80proxy. This will ensure
+ that after an upgrade changes won't be lost::
+
+ Acquire::http::proxy "http://<username>:<password>@<proxy>:<port>/";
+ Acquire::ftp::proxy "ftp://<username>:<password>@<proxy>:<port>/";
+ Acquire::https::proxy "https://<username>:<password>@<proxy>:<port>/";
+
+ 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.
+
+ My VM lost mounted host directories after upgrading from VirtualBox from 3.x to 4.x
+ 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-`dpkg --print-architecture`
+ sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-dkms \
+ virtualbox-ose-guest-utils virtualbox-ose-guest-x11
+
+ and reboot VM.
+
+ My VM lost mounted host directories, and display auto-resizing after upgrade
+ NeuroDebian VMs ship without Linux kernel headers pre-installed to
+ minimize distribution/running footprint for one time throw-away
+ usages of the VM. To install headers package(s) just run
+
+ sudo apt-get install -y linux-headers-`dpkg --print-architecture`
+
+ and reboot VM.
+
+ I am still running an older VirtualBox 3.x
+ Download one of the image files listed below. These older releases
+ are distributed as a `zip` file. Please extract all files from the
+ `.zip` file, using appropriate software for your operating system.
+
+ * `NeuroDebian 6.0.2 image (32bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
+
+ * `NeuroDebian 6.0.2 image (64bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
+
+
+What has changed
+----------------
+
+.. container:: foldup
+
+ .. container:: expandinstructions
+
+ Click on an item to expand it
+
+ 7.8.0 -- 2 Feb 2015
+ * VM appliance based on the updated wheezy point release 7.8.0.
+ Should resolve problems with upgrades of the guest additions.
+
+ 7.4.20140423 -- 24 Apr 2014
+ * VM appliance based on the updated wheezy point release 7.4.
+ Should resolve problems with upgrades of the guest additions.
+ See http://neuro.debian.net/faq.html#comment-1351846812
+
+ 7.4.0 -- 28 Feb 2014
+ * VM appliance based on the official wheezy point release 7.4.
+
+ 7.2.0 -- 03 Nov 2013
+ * VM appliance based on the official wheezy point release 7.2.
+ * Ships with updated neurodebian-* packages:
+ - installs ipython notebook and qtconsole for "Scientific Python"
+ and "PyMVPA tutorial" welcome wizard choices.
+
+ 7.0.0 -- 15 May 2013
+ * VM appliance based on the official wheezy release.
+ * Uses xfce4-terminal by default (instead of urxvt/rxvt-unicode as
+ in beta-releases)
+
+ 6.999.b4.20130421 -- 22 Apr 2013
+ * Refreshed VM appliance to avoid lengthy initial upgrade
+
+ 6.999.b4.20121231 -- 31 Dec 2012
+ * Based on beta 4 release of debian-installer_ for wheezy
+ * Comes with XFCE4_ instead of GNOME_
+
+ 6.0.6 -- 01 Oct 2012
+ * Updated core system to Debian squeeze 6.0.6
+
+ 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
-There is no network connectivity.
+ * 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
- If the virtual machine cannot access the internet, but the host computer can,
- it might be necessary to re-establish the network connection. To do this,
- please click on the `network manager` icon in the virtual machine's system
- tray (upper right corner of the desktop) and select `Wired Network`. After a
- few seconds the network should become available.
+ 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
-I cannot hear sounds played in the virtual machine.
+ 6.0.2 -- 08 Feb 2011
+ * Minor update
- Sorry, but audio is not (yet) preconfigured properly. If you want to have that
- fixed, please drop us a note.
+ 6.0.1 -- 01 Dec 2010
+ * Minor update
+.. include:: link_names.txt
projects / neurodebian.git / blobdiff