Chroot workaround for fslview (HOWTO)

Note

With the release of FSLView 4.0.0b this workaround should no longer be necessary. However, the technology is stil equally useful to work around similar problems with other software.

Preamble

Sometimes research software lags behind developments in libraries it relies upon, because necessary changes to the code might require considerable effort, and thus time. That leads to difficulties building those tools using up-to-date library versions due API incompatibility.

That is what happened with fslview from the FSL suite. Today, at the end of 2011, it still relies on Qt3 and VTK GUI support for it.

Note

Last version of Qt3, 3.3.8, was released in February 2007, with official support by Trolltech terminated later that year.

Qt4 was first released in 2005, and current stable series 4.7 released appeared in September 2010.

Because of its age and discontinued upstream support, Qt3 was orphaned in Debian, and tools relying on it were encouraged to migrate to use Qt4. As a result, although Qt3 itself is still present in Debian (and thus Ubuntu), VTK GUI support for Qt3 (package libvtk5.4-qt3) which fslview uses, was removed from Debian due to Qt3 deprecation. It should be made clear that it was not removed to annoy people, but rather because it became unfeasible to maintain its robust building and functioning. So nowadays fslview is present only in those previous releases of Debian and Ubuntu which carry the libvtk5.4-qt3 library. Those are – Debian squeeze (stable), Ubuntu nutty and maverick. If you upgraded your system from one of those releases, chances are that you still have fslview (and required libraries) installed although not they are not available from the APT repository anymore. Therefore fresh systems installations will not have them at all.

Workaround

While everyone is waiting for a new release of fslview compatible with Qt4 there are possible workarounds to keep research going on bleeding edge Debian-based operating systems. The first, obvious choice for a FOSS enthusiast, is to build fslview from source by first building VTK Qt3 bindings, possibly after building Qt3 itself. While it might be educationally valuable and exciting, we are afraid in the end it might be more frustrating than useful.

Therefore we would like to suggest another, much more straightforward and hopefully painless approach – lightweight virtualization, or chroot jailing, which exists in Unix-land since 1970s. With this exercise in 4 simple steps we will install a complete (minimalistic) installation of Debian stable into a separate directory – without harming the original system installation. We will provide a convenience wrapper to run fslview as if it was installed on the “main” system. So your system will stay intact while you would enhance it with additional software in a stable Debian environment. Moreover if security or critical fixes to any components of that installation become available, this chroot environment, being a complete Debian installation, could be as easily upgraded as your main system, thus guaranteeing robust performance.

Although we demonstrate this setup with fslview in mind, such approach is generally useful for various use cases. For example, we have used it in the opposite situation – on stable Debian systems we needed to run some software available only from Debian unstable or testing, and backporting of all required dependencies was either cumbersome or just impossible without sacrificing stability of the system.

Prerequisites

For this exercise you would need

  • 3–20 minutes depending on the bandwidth to the Debian mirror and efficiency in cut/paste operations

  • root access to the system while performing this setup, although end-users of fslview would not need root access after everything is set up

  • 2 additional tools – debootstrap to install Debian in a directory and a convenience utility schroot to “enable” such an environment

Procedure

  • Install the tools:

    sudo apt-get install debootstrap schroot

  • Choose a location with enough space (600 MB should be enough) and install a complete Debian squeeze installation with fslview:

    sudo debootstrap --include=fslview squeeze /srv/chroots/squeeze http://ftp.us.debian.org/debian

    Note

    You might like to adjust the URL to a Debian mirror closer to you

  • Create schroot configuration file /etc/schroot/chroot.d/squeeze with the following content:

    [squeeze]
description=Debian squeeze (6.x stable)
type=directory
directory=/srv/chroots/squeeze
users=YOURLOGIN
aliases=debian,default

    Replace YOURLOGIN with a comma separated list of users who should be allowed to access this chroot environment (see man schroot.conf for more options, e.g. how to specify whole groups with groups=..., etc.)

  • At this point you should already be able to invoke any command within the chroot environment, so just create a little shell script /usr/local/bin/fslview, make it executable and be all set:

    echo -e '#!/bin/sh\nexport FSLDIR=/usr/share/fsl\nschroot -p -c squeeze /usr/bin/fslview "$@"' > /usr/local/bin/fslview
chmod a+x /usr/local/bin/fslview

    Note

    You might need to become root for the above.

Optional steps

Although at this point you can run fslview from the chroot-ed environment, we would suggest a few additional steps. For some of them (marked with chroot-root) you would need to become root in a chroot environment via following steps:

  • enter chroot using schroot -c squeeze -p

  • become root (via su command, root password should be the same as on the main system)

So here are recommended optional additions:

  • chroot-root: Enable NeuroDebian repository. Choose squeeze release and mirror of preference (remove sudo from provided cmdline).

  • chroot-root: Enable security and functionality updates:

    sed -e 's,squeeze,squeeze-updates,g' /etc/apt/sources.list > /etc/apt/sources.list.d/updates.list
echo 'deb http://security.debian.org/ squeeze/updates main' > /etc/apt/sources.list.d/security.list
apt-get update
apt-get upgrade

  • Make fsl atlases accessible within the chroot environment. There are two ways and you must choose only one of them, otherwise you might damage your “main” system installation.

    • chroot-root: Install atlases packages in the chroot-ed environment:

      apt-get install fsl-atlases

      Although this is the best/correct way it would require additional 200MB of space, possibly duplicating what you already have installed in the main system. Also it requires enabling of NeuroDebian repository in chroot environment.

    • Alternatively you can bind-mount those directories with atlases installed on the “main” system within chroot. For that edit (as root on the “main” system) /etc/schroot/default/fstab and add following entries:

      /usr/share/fsl/data/atlases /usr/share/fsl/data/atlases none rw,bind 0 0
/usr/share/data             /usr/share/data             none rw,bind 0 0

      You need to be aware of the potential consequences of this second approach: Any package that installs files under /usr/share/data will modify files in the same directory outside the chroot as well. If you don’t want to risk that don’t use this method and simply install the necessary data packages inside the chroot environment too, as describe before.

      Note

      Similarly you can bind-mount any other directory you would like to make visible in chroot. Just be careful to not “overlap” with system directories in chroot which already carry something.

Also you might like to read man schroot on how to enable persistent sessions so that chroot initiation could be done ones during boot instead of per each fslview invocation

If you have any comments (typos, improvements, etc) – feel welcome to leave a comment below, or just email us@NeuroDebian .

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