[Bio-linux-dev] Ubuntu Mir Concerns

Wed Jul 3 10:14:47 EDT 2013

Dear Tim,

thanks for your comments, here are a few further remarks (mostly
technical and not really related to bioinformatics, I hope that's ok).

On Mon, Jul 01, 2013 at 03:15:05PM +0100, Tim Booth wrote:
> Hi Jan,
> 
> Everyone in the know seems to be saying that the transition away from X
> as the core Linux display server is "a good thing", and having dealt
> with X configuration details for many years I would agree.  Running all
> the X apps via a compatibility mode should not be a problem because it
> is the same X display code just connecting to the new Mir system which
> is driving the hardware.  Mac users know that this approach works well.
> 
> The recent controversy has been the split between Mir and Wayland, and
> you can get a flavour of it by looking at some recent Slashdot stories:
> 
> http://slashdot.org/index2.pl?fhfilter=wayland

I've looked at a couple of these slashdot stories and I'm afraid they
have amplified my concerns. Some of the issues with X11 that are cited
by Wayland or Mir evangelists are understandable and a few seem
justified to me. However, their approach to address or resolve these is
based on abstractions and concepts that are problematic. They appear
rather narrowly informed by use cases from multimedia and mobile
computing contexts and seem keenly aware of problems specific to these
contexts (such as difficulties preventing artifacts in animations),
and to be rather unaware of the value of many X11 features and virtues,
such as server-provided fonts (Wayland leaves that to the clients as
far as I understand).

For scientific applications this does not bode too well, e.g. the
occasional flicker upon resizing an R window showing a boxplot is
no big deal for anyone, but having to draw the lines of the barplot
pixel by pixel, without server support for rendering lines and text,
is not going to be nice for whoever gets to write a new graphics
device for R.

> The initial effect of the Mir announcement seems to have been a spurring
> on of the Wayland developers to get the system working.  If Mir and
> Wayland both become viable solutions then this is no bad thing!
> 
> Regarding Ubuntu 14.04, which should form the basis of Bio-Linux 8, I
> don't think there is a need for concern.  If Mir with X compatibility
> works well then we can use it.  If not, then others in the community
> will ensure that X server packages continue to be available because
> many, many users want these things, and I will build Bio-Linux with
> these packages.
> 
> One significant difference between Mir and Wayland is that Wayland aims
> for excellent remote desktop/remote application support while Mir
> currently does not.  Remote X is essential for many Bio-Linux users so
> I'll do whatever is needed to retain this feature.

I'm not too sure about Wayland remoting, according to Wikipedia
(http://en.wikipedia.org/wiki/Wayland_%28display_server_protocol%29)
it doesn't have network transparency currently, and the pixmap
centric concept of Wayland compares unfavourably to the vector
oriented primitives that X11 servers provide for lines etc., and
this is in fact one of my key concerns about Wayland's use of
pixmaps, rather than graphics primitives, as the core abstraction.

> Regarding dropping APT/Dpkg, there's no way that Ubuntu could do this
> for the 14.04 release and I've seen no sign of them reducing support for
> things like the Launchpad PPA service.  If Ubuntu did drop Debian
> packaging then we'd almost certainly switch Bio-Linux back to Debian,
> but I don't think this is any concern right now.  I think you just have
> to regard Ubuntu Touch as a separate Ubuntu-branded Canonical product,
> very much separate from the Ubuntu OS which is still being positioned as
> a server/workstation solution.

Ok, that's a reassuring perspective, thanks.

Best regards, Jan

> Cheers,
> 
> TIM
> 
> On Mon, 2013-07-01 at 11:57 +0100, jan kim via RT wrote:
> 
> >      Subject: Ubuntu Mir Concerns
> >        Owner: Nobody
> 
> > 
> > Dear Tim
> > 
> > I read that Ubuntu plans to dump X11:
> > 
> >     http://fridge.ubuntu.com/2013/06/27/mir-plans-in-13-10/
> > 
> > and I'm concerned that this may result in major disruptions of usability
> > of Ubuntu for bioinformatics and scientific computing in general. No xterm,
> > no x11 device for R, no recognition of xresources in general, no x11
> > forwarding, no fvwm2, ...?
> > 
> > As far as I understand there is some emulation mode or similar to
> > smoothen the transition, but I wonder how well this would work, and
> > whether it will be supported in the long term.
> > 
> > I've seen a demo of "Ubuntu Touch" on a tablet a couple of weeks ago,
> > and was very disappointed to learn that that didn't use the "normal"
> > Debian package management system, instead Canonical has apparently
> > developed something that is like those app markets operated by Apple
> > and Google -- so there was no way to install R, LaTeX, emacs etc. on
> > a tablet running Touch, as I had hoped, and from this perspective I'm
> > concerned that some tension may develop between the direction Canonical
> > seems to pursue with Mir and Touch and the use of Linux for scientific
> > computing.
> > 
> > Do you have any thoughts on this, and how Biolinux will be affected?
> > 
> > Best regards, Jan
> > --
> > Jan T Kim
> > Head of Bioinformatics
> > The Pirbright Institute (formerly IAH)
> > Ash Road, Pirbright, Surrey GU24 0NF, United Kingdom (GB)
> > t: +44 1483 231070
> > e: jan.kim at pirbright.ac.uk (or jttkim at gmail.com)
> > w: http://www.research.pirbright.ac.uk/bioinformatics
> >    http://www.pirbright.ac.uk/
> > 
> > 
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> 
> -- 
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre 
> 
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> 
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-- 
 +- Jan T. Kim -------------------------------------------------------+
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