NI-VISA final fail

In a previous blog post, I already pointed out that using the NI-VISA library to control lab devices with Linux is becoming more and more painful - especially when you heavily rely on National Instrument's high speed USB-GPIB adapters. But hey, supporting kernels newer than 2.6.24 is luxury anyway, right?
Yesterday I tried to update my "test box" for Linux lab software, just in case I can maybe convince one of my colleagues to work with that strange OS for a change. Then, I realized that for us the NI-VISA package has finally become totally useless:

(meas) pc5xxxx ~ # emerge -uDNav --keep-going world

Performing Global Updates:
(Could take a couple of minutes if you have a lot of binary packages.)
  .='update pass'  *='binary update'  #='/var/db update'  @='/var/db move'
  s='/var/db SLOT move'  %='binary move'  S='binary SLOT move'
  p='update /etc/portage/package.*'
/var/lib/layman/n4g/profiles/updates/4Q-2009..........

These are the packages that would be merged, in order:

Calculating dependencies... done!

!!! All ebuilds that could satisfy ">=sys-fs/udev-151[extras]" have been masked.
!!! One of the following masked packages is required to complete your request:
- sys-fs/udev-9999 (masked by: package.mask, missing keyword)
- sys-fs/udev-168-r2 (masked by: package.mask, ~x86 keyword)
- sys-fs/udev-168-r1 (masked by: package.mask, ~x86 keyword)
- sys-fs/udev-168 (masked by: package.mask, ~x86 keyword)
- sys-fs/udev-167-r1 (masked by: package.mask, ~x86 keyword)
- sys-fs/udev-167 (masked by: package.mask, ~x86 keyword)
- sys-fs/udev-164-r2 (masked by: package.mask, ~x86 keyword)
- sys-fs/udev-164-r1 (masked by: package.mask, ~x86 keyword)
- sys-fs/udev-164 (masked by: package.mask, ~x86 keyword)
- sys-fs/udev-163 (masked by: package.mask, ~x86 keyword)
- sys-fs/udev-162 (masked by: package.mask, ~x86 keyword)
- sys-fs/udev-151-r4 (masked by: package.mask)

(dependency required by "sys-power/upower-0.9.9" [ebuild])
(dependency required by "kde-base/kdelibs-4.6.2-r3" [ebuild])
(dependency required by "kde-base/khelpcenter-4.6.2" [ebuild])
For more information, see the MASKED PACKAGES section in the emerge
man page or refer to the Gentoo Handbook.

(meas) pc5xxxx ~ #

The age-old kernel requires old udev (<=142 if I remember correctly), which I enforced with a package.mask and now is incompatible with other recent stuff. Ah well... >:| no more VISA on Linux for us.

A letter for a lot of money

Starting up a new experimental physics research group is again and again interesting. Last time I was really nervous was when I for the first time signed the paperwork to hire someone (in case you're from the US, in Germany and many other European countries PhD students are in the sciences paid employees). Today, another lengthy process came to its (momentary) conclusion; I'll have however to explain this a bit.
Our research is focussing on electronic and mechanical processes at extremely low temperatures. "Extremely low" means in that case something like 20mK, or 0.02 degrees above absolute zero, or -272.95°C. To reach such temperatures, several steps of cooling have to be employed. First, the entire experimental assembly is submerged in a dewar (something like a thermos flask) filled with liquid helium, boiling away at 4.2K. Then, inside another vacuum chamber, evaporation cooling with again liquid helium is used to lower the temperature even further to somewhere around 1.5K. Lastly a closed cooling cycle with a mixture of the two isotopes of helium, helium-3 and helium-4, is used to lower the temperature even further to the base temperature of 0.02K. This entire machinery is called a dilution refrigerator; it was invented in 1951, and is by now available commercially from several companies worldwide.
So what happened today? Well, after getting a grant for buying one of them beasties, writing up the specifications, starting the Europe-wide call for tenders, awaiting and carefully evaluating the quotes, finally I've sent off the decision letter. "Please buy this one." Phew. I hope all works out, this thing costs about as much as a top-range Ferrari...

Hunting the glib-networking / libproxy mystery bug

Just when we wanted to stabilize KDE-4.6, an unpleasant surprise appeared out of nowhere. For no apparent reason, polkit was failing to make DBUS connections. As one consequence, some users could not log into KDE; the desktop would simply hang during the session initialization. After upgrading and downgrading packages, and after a lot of communication on bugzilla (since noone from the Gentoo KDE team could reproduce the bug), a pattern emerged: net-libs/glib-networking-2.28.6.1 was somehow causing the problem, force-unmerging it with "emerge -C" restored correct behaviour. Later, this was narrowed down to net-libs/glib-networking[libproxy].

Minus docs and debug info, this is what is installed by glib-networking:

/usr/lib/gio/modules/libgiolibproxy.so
/usr/lib/gio/modules/libgiognutls.so
/usr/lib/gio/modules/libgiognomeproxy.so
/usr/share/dbus-1/services/org.gtk.GLib.PACRunner.service
/usr/libexec/glib-pacrunner

Which leads to the question, how can these seemingly unrelated libraries
cause DBUS hangs. Let's just say, the Gnome guys did not know either, but obviously the most intrusive part is the proxy autoconfiguration service registered in dbus.

As KDE-4.6.2 stabilization was pending, one way to temporarily get around the problem was to block concurrent installation of net-libs/glib-networking[libproxy]. After all that package appeared only on 24 Apr 2011 (one week before the bug report was filed) as ~arch in the main tree, and is hard-required in exactly one package (net-voip/telepathy-gabble). Yes, we checked that thoroughly before. User responses however were not so, err, welcoming.

"Anyway it is high time ppl start thinking before committing any changes in the main tree... even if we are talking about an unstable ~ stuff..." (bug 365479, comment 38)

"Now we have repeat with strange blocker... and all because some guy forgotten (or didnt want to) try it before pushing into tree... Sometimes i think that Gentoo developers comes from the round-up." (bug 365479, comment 43)

Ah well. Now the blocker is gone again and we won't hinder people from shooting themselves in the foot, but we still dont know what actually the problem is. In any case, libproxy seems to be prone to more misbehaviour (what the %$&%$ is it doing in NVidia OpenGL code??!!). So far the reports of various details do not really add up to a coherent picture.

Finished something, finally

The last weeks were actually a busy time for several reasons. Well, there's one less now: at work, yesterday Friday evening at around 21:00 I finally submitted a manuscript (5Mbyte pdf) for publication that we have been preparing for ages.
The whole story started with measurements done in our lab last year, where we look among other things at electrical currents through single carbon nanotubes at very low temperatures of a few millidegrees above absolute zero. In this particular case, the metallic contacts to the nanotube were made of a magnetic PdNi alloy, which means that you have to take into account the magnetic moment (the spin) of the electrons in the contacts and of the electrons passing through the nanotube. Models for such systems have been developed and measurements done for some time already, but together with our theory colleagues from Chonnam, Poznan, and München we have shown for the first time that even quantitatively these models can be reduced to the non-magnetic case with a rather straightforward transformation, and that still the calculations fit the data very well. That is a pretty nice result, since for the emerging technology field of spintronics control of all these current transport effects is quite important.
Now it's time for new projects (and for awaiting the referee reports)...

Things I always wanted to do... :)

Andreas K. Hüttel changed:

           What    |Removed              |Added
-------------------------------------------------------------
                 CC|                     |alpha@gentoo.org,
                   |                     |amd64@gentoo.org,
                   |                     |arm@gentoo.org,
                   |                     |hppa@gentoo.org,
                   |                     |ia64@gentoo.org,
                   |                     |ppc64@gentoo.org,
                   |                     |ppc@gentoo.org,
                   |                     |sparc@gentoo.org,
                   |                     |x86@gentoo.org

--- Comment #4 from Andreas K. Hüttel 2011-04-27 21:31:53 UTC ---
Here comes the big one. On behalf of the Qt and KDE teams:
Arches, please test and stabilize the ebuilds listed in the
attached text file. The list includes core KDE and Qt packages,
their depedencies and extragear/misc KDE/Qt apps as well

:)

KDE 4.6.2 news & upgrade guide

Just to give everyone a quick heads up, the stable request for KDE SC 4.6.2 plus KDEPIM 4.4.11.1 is likely going to be filed soon. On the whole, the upgrade should go very smooth. In case there are problems, we now have a Gentoo KDE 4.4 - 4.6 Upgrade Guide, covering the most frequent issues. In addition, it probably never hurts to look at the general Gentoo KDE Guide.
If you want to test before the actual stabilization takes place, just grab the keyword file... Cheers!

KDE 4.6.2 - looking for testers!

You may already have heard that a new version of the desktop environment came out today. (No, not the other one.) I'm talking about KDE 4.6.2. It is in my opinion shaping up rather well, and we in the Gentoo KDE team consider it a candidate for stabilization in a while. (It's about time, since upstream considers our "stable" KDE 4.4 rather "dead".) You can look up the list of important known issues on our bugzilla; some of this definitely has to be fixed before stabilization, but on the whole the list looks manageable.
So, we need testers. Especially since we all from the KDE team have been running newer KDE versions for ages by now and have never tried the direct step from 4.4 to 4.6. If you are brave - sync your portage tree, grab the keyword file, place it in /etc/portage/package.keywords - and update your system! As additional bonus, you will get also updates for QT, koffice, digikam, and some more packages...
If there are dependencies missing in the keyword file, please file a bug! If you encounter any build problems, please file a bug! If you see any misbehaviour after the upgrade, please file a bug! Thanks a lot in advance!
Oh yes, one last note. The kdepim guys obviously don't feel like releasing at all, so everything from kmail to blogilo will remain at trusty version 4.4. This is, however, nothing to worry about. (I'd worry a lot more about the kdepim update should it ever happen...)