Search Results: "ana"

22 July 2011

Clint Adams: More template flexibility

As of deets 0.1, you can now also populate Cosmo template variables through Lua code. For example: /tmp/silly.lua:
require("utils-grep")
local intel = grep_program_output("VGA.*Intel","lspci")
file.file( "/tmp/garbage" ,  
    ensure = "present",
    owner = "root",
    group = "root",
    mode = "755",
    source = file.cosmotemplate("/tmp/silly.cosmo", intel)
 )
/tmp/silly.cosmo:
# On $systeminfo hostname, we might have used the following information
# to populate this config file.
#
# We did not.
$map $v 1 [[# $it]]
Then run sudo luau --rectify /tmp/silly.lua and your /tmp/garbage should be equally useless whether or not you have an Intel video card.

Brett Parker: Things that annoy me #31294

I use rss2maildir.py to read rss feeds, it has a nifty feature whereby if a post is changed, it just gets tacked on to a thread for that post. There are 2 things that really annoy me with rss feeds, though - 1 is the people that don't include the full post in the rss feed, and the other is people that include a comment count in the rss feed. I don't care how many comments are on the post, dammit. I'd deliberately go follow the post if I did, but having that comment count means that I get another one in the thread for NO REASON, the content of the post hasn't changed, dammit. This means that until that post drops out of the feed, every 30 minutes if the comment count has changed (and so the "content" of the feed changes) I get that post yet again and marked as new in my mailbox. Why does anyone put the comment count in the feed, does anyone really care?! If you want to link to comments from the feed, that's fine, just drop the count from it, and the content of the post wouldn't change, and I'd be happy. Erm, comments are currently turned off here, until I manage to get round to turning on all the little spam prevention fun... just thought I'd have a whinge, really!

21 July 2011

Stefano Zacchiroli: Test Driven Development in Debian

... or TDDD and DEP8 context As a nice byproduct of the huge "rolling" discussion we had back in April/May, various people have brainstormed about applying Test-Driven Development (TDD) techniques to Debian development. Here is a brief summary of some opinions on the matter: ... and hey, they've also coined the cool TDDD acronym, which I hereby took the freedom to re-target to Test-Driven Development in Debian. Having a cool acronym, we are already half-way to actually having the process up and running *g*. more testing I believe Debian needs more testing and I've been advocating for that since quite a while e.g. at DebConf10, as one of the main goals we should pursue in the near future. Of course advocating alone is not enough in Debian to make things happen and that is probably why this goal has been (thus far) less successful that others we have put forward, such as welcoming non-packaging contributors as Debian Project members. There are important reasons for increasing testing in Debian. quality assurance Quality Assurance has always been, and still is, one of the distinctive traits of Debian. I often say that Debian has a widespread culture of technical excellence and that is visible in several places: the Debian Policy process, lintian, piuparts, periodic full archive rebuilds, the EDOS/Mancoosi QA tools, the cultural fact that maintainers tend to know a lot about the software they're packaging rather than only about packaging, the we release when it's ready mantra, etc. But caring about quality is not a boolean, it's rather something that should be continuously cherished, refining quality requirements over time. By simply maintaining the status quo in its QA tools and processes, Debian won't remain for long a distribution who could claim to care about package quality. Others will catch up and are in fact already doing that. In particular, we surely have room for improvements in our quality tools and processes for: reducing inertia Inertia is a recurring topic among Debian lovers (and haters). It is often argued how difficult it is to make changes in Debian, both small and large, due to several (alleged) hindrances such as the size of the archive, the number of ports, the number of maintainers that should agree before proceeding with a cross-package change, etc. It's undeniable that the more code/ports/diversity you have, the more difficult is to apply "global" changes. But at least for what concerns the archive size, I believe that for the most part it's just FUD: simply debunking the self-inflicted culture about how "dangerous" doing NMUs is might go and has already gone, imho a long way to fight inertia. Adding per-package and integration tests will make us go another long way in reducing inertia when it comes to performing archive-wide changes. Indeed if a package you are not entirely familiar with has extensive test suites, and if they still pass after your changes, you can be more confident in your changes. The barrier to contribution, possibly via NMU, gets reduced as a result. And if your change will turn out to be bad but still not spot by the test suites, then you can NMU (or otherwise contribute) again to extend the test suite and make the life easier for future contributors to that package. It smells a lot like an useful virtuous cycle to me. autopkgtest / DEP8 how you can help Of all the above, the topic that intrigues me the most is as-installed package testing. Work on that front has been started a few years ago by Ian Jackson when he was working for Canonical. The status quo is embodied by the autopkgtest package. At present, the package contains of various tools and the following two specs:
  1. README.package-tests provides a standard format to declare per-package tests using the new debian/tests/control file. Tests come as executable files which will be run by the adt-run tool in a testbed where the package(s) to be tested is already installed. This part of the specs has been reified as DEP8 which I'm (supposedly) co-driving with Iustin Pop and Ian (for well-deserved credits).
  2. README.virtualisation-sever describes the interface among the test runner and the testbed. A nice separation is provided among the runner and the testbed, enabling different testbed environments with a varying degree of isolation: you can have a "null" testbed which runs tests on your real machines (needless to say, this is highly discouraged, but is provided by the adt-virt-null tool), a chroot testbed (adt-chroot), or a XEN/LVM based testbed (adt-virt-xenlvm).
The specs allow for several runtime testing scenarios and look quite flexible. The tools on the other hand suffer a bit of bitrot, which is unsurprisingly given they haven't been used much for several years. At the very minimum the following Python development tasks are in need of some love: If you are both interested in TDDD and grok Python, the above and many others tasks might whet your appetite. If this is the case don't hesitate to contact me, I'll be happy to provide some guidance.
Note: this post is the basis for the TDDD BoF that I will co-host with Tom Marble at DebConf11. If you plan to come, we will appreciate your thoughts on this matter as well as your help in getting the autopkgtest toolchain up and running again.

Clint Adams: 950 continued

% ssh root@192.168.2.15
root@192.168.2.15's password: 
BusyBox v1.19.0.git (Maemo 3:1.19-7+0m6) built-in shell (ash)
Enter 'help' for a list of built-in commands.
RM680-22-6_PR_RM680:~# cat /proc/cpuinfo 
Processor       : ARMv7 Processor rev 2 (v7l)
BogoMIPS        : 298.32
Features        : swp half thumb fastmult vfp edsp neon vfpv3 
CPU implementer : 0x41
CPU architecture: 7
CPU variant     : 0x3
CPU part        : 0xc08
CPU revision    : 2
Hardware        : Nokia RM-680 board
Revision        : 1124
Serial          : 0000000000000000
SoC Info        : OMAP3630 ES1.2-hs
        IDCODE  : 2b89102f
        Pr. ID  : 00000000 00000000 000000cc cafeb891
RM680-22-6_PR_RM680:~# uname -a
Linux RM680 2.6.32.39-dfl61-20112201 #1 PREEMPT Wed Jun 1 18:17:45 EEST 2011 armv7l GNU/Linux
RM680-22-6_PR_RM680:~# dpkg --version   head -n 1
Debian  dpkg' package management program version 1.15.8.8 (armel).
RM680-22-6_PR_RM680:~# apt-get --version   head -n 1
apt 0.7.25.3 for armel compiled on Mar 28 2011 23:31:47

Kai Wasserb ch: pbuilder: building a source package

From time to time I get e-mails about my wine-unstable packages being uninstallable. Most often it turns out, that the problem stems from using e.g. oldstable (Lenny) instead of at least stable (Squeeze). The same problem arises, if you wish to install the wine-unstable packages on a platform for which I don't offer binaries. In either case you need to build the package from source, which isn't as difficult, as many think. This entry in my ongoing tips mini-series of posts is thus going to detail how you setup pbuilder and afterwards use it to build a package. Please note, that I'm just focusing on pbuilder here and ignore things like cowbuilder. Preparations The following steps are needed just once, in general. Some would be needed again, if you want to create a second base.tgz, e.g. for a different distribution.
  1. Install pbuilder with your favourite package manager, e.g. aptitude: aptitude install pbuilder
  2. Become root
  3. Configure pbuilder. Have a look at /etc/pbuilderrc, /usr/share/doc/pbuilder/examples/pbuilderrc and the manual page for pbuilderrc for reference. If you want to change some settings made in /etc/pbuilderrc, create a /root/.pbuilderrc and override any settings you don't like.
  4. Create the base.tgz (the chroot environment for your builds). In the easiest case all your settings are made in the configuration files and you just need to run pbuilder --create, which creates the base.tgz in /var/cache/pbuilder, unless you changed the configuration.
    You should also note, that you can override certain settings, like the distribution or the path to (and name of) the base.tgz file created. See the manual page for pbuilder for all options and when they can be used.
Build a package The following steps are needed for every build:
  1. Download the source package, you want to build. No matter how you fetch them (dget, apt-get source, ), you should end up with three files, one of them ending in .dsc.
  2. Become root.
  3. Update your base.tgz file: pbuilder --update. Again, see the manual page for further options. (You can skip this step, if you just created the base.tgz or you just updated it for another build.)
  4. Build the source package: run pbuilder --build /path/to/source-package.dsc (obviously you need to replace the last argument with a real path)
  5. If you haven't changed the configuration of pbuilder in that regard, then your binaries end up in /var/cache/pbuilder/result. Install the binaries, you want, from there (with dpkg -i).
Now you should be able to build your own packages from source! And to answer one question, that some of you might have now ("Why use pbuilder at all and not just build the package with dpkg-buildpackage directly?"): because pbuilder allows you to reliably build in a clean environment. That can safe you a lot of trouble, especially if you modified the source package. And it helps to keep the number of installed packages on your system down.

Raphaël Hertzog: People behind Debian: Martin Michlmayr, former Debian Project Leader

Martin Michlmayr is a Debian developer since 2000 and I share quite a few things with him, starting with his age and involvement in the quality assurance team. He managed to be elected Debian Project Leader in 2003 and 2004. He s no longer as active as he used to be but his input is always very valuable and he continues to do very interesting things in particular concerning the support of NAS devices. Read on for the details. Raphael: Who are you? Martin: I m Martin Michlmayr. I m 32, originally from Austria, and currently living in the UK. I ve contributed to various free software projects over the years but Debian is without doubt the one I m most passionate about. I joined Debian in 2000 when I was a student. I worked on Debian more or less full time for a few years while I was pretending to study. Later I started a PhD to do research about quality and management aspects of volunteer free software projects. I investigated the release process in several free software projects, in particular looking at time-based releases. After finishing my PhD in 2007, I joined Hewlett-Packard. I m part of HP s Open Source Program Office and work on various free software and open source activities, both internally and within the community. Raphael: How did you start contributing to Debian? Martin: I first used Debian in the days of 0.93R6, some time around the end of 1995. The 0.93R6 release was still based on a.out but I needed an ELF-based system for some application, so I moved to Slackware. I then quickly moved to Red Hat Linux where I stayed for several years. I rediscovered Debian in 2000 and quickly decided to join the project. I cannot recall how I rediscovered Debian but when I did, it was clear to me that Debian was the ideal project for me: I could identify with its philosophy, I liked the volunteer nature of the project, and I found the size and diversity of Debian interesting since a large project offers a lot of different challenges and opportunities. I remember how many new things there were to learn and back then the documentation and other resources for new contributors were nowhere as good as they are today. My application manager, Julian Gilbey, was a great help he was incredibly friendly and passionate about Debian. I also remember meeting up with Peter Palfrader (weasel) for key signing when we were both in the New Maintainer queue. I was incredibly lucky with my New Maintainer process and soon became an official Debian Developer. Because there was a shortage of application managers, my first major contribution in Debian was to become an application manager myself and help other people join the project. Debian is a large project with a long history and a rich culture, so new contributors should expect that it will take some time to become familiar with everything. Fortunately, there are many resources, such as documentation and the debian-mentors list, for new contributors. Another great way to become familiar with the way things are done in Debian is to subscribe to various Debian mailing lists and ideally to read some mailing list archives. It s also a great idea to attend the Debian Conference or other conferences since meeting people in real life is a great way to integrate. I remember attending Debian Conference 1 in Bordeaux where I gave my first public talk. Finally, new contributors should find an area where they can make a unique contribution. Most people in Debian maintain packages but there are so many other ways to contribute. For example, most of my contributions were not technical but were about coordination and other organizational activities. Raphael: What s your biggest achievement within Debian? Martin: I m particularly proud of a number of achievements: Raphael: Speaking about NAS devices: what exactly are you doing on this topic and how can people help? Martin: There are plenty of instructions on the Internet to install Linux distributions on NAS or various embedded devices by connecting a serial console and then typing in hundreds of commands. What I found is that such instructions significantly limit the user base because they are way too complicated for most users. There are just too many steps that can go wrong. So instead, in Debian, we provide a solution that just works: usually, you download a firmware image for your NAS device from Debian and when you upgrade you get the Debian installer. You connect to the installer via SSH and perform a normal installation. The installer knows about the device and will prepare everything for you automatically for example, it knows if the device has requirements for the partition layout and it will install the kernel where the device expects to find it; unfortunately, NAS devices are not like PCs, so the requirements are different for almost every device and therefore you need special code to support a new device. Finally, there are detailed installation guides and we provide help on our mailing lists. There are a number of technical areas for improvement. The installation could be made even easier, and it would be nice to support new platforms and devices. A bigger problem is that while we ve implemented a great solution for NAS devices, we haven t really extended this work to support other classes of devices. For example, tablets and mobile phones are getting incredibly popular and we don t have a compelling solution for such devices, mostly because of the lack of an appropriate GUI. Raphael: What are your plans for Debian Wheezy? Martin: I ve recently been asked by Stefano Zacchiroli, our current Debian Project Leader, to coordinate the care-taking of Debian finances. Debian, as a volunteer project, relies on donations and in-kind gifts (e.g. hardware) to maintain its infrastructure and to support various development efforts, such as funding sprints and other developer gatherings. Debian s money and other assets are held by affiliate organizations around the world. My responsibility will be to keep track of money and other assets (e.g. hardware and trademarks), work with the DPL to establish procedures related to the use of Debian s assets, and make sure that the procedures are followed. Finally, we want to publish public statements so our donors know how we use their donations to further improve Debian. I just started working on this and this will be my main activity in Debian in the coming months. Raphael: Speaking of money, I plan to run a fundraising to get the Debian book I wrote with Roland Mas translated (cf. http://debian-handbook.info). Is this something Debian should support? Martin: First of all, I should make it clear that I don t decide how Debian spends its money. This is up to the DPL to decide together with the project at a whole. I ll just make sure that procedures are followed and expenses tracked and reported properly. Having said that, in my opinion, it s unlikely that Debian as a project will fund this effort. It would be inconsistent with the position of the project not to fund work directly (only some related expenses, such as travel costs to allow Debian teams to organize face-to-face meetings). Whether Debian should support the fundraising effort by helping to promote it is another question and that s probably not as clear cut. It looks like a worthwhile effort, but on the other hand it would be unfair for authors of other Debian books for Debian to put its weight behind one and there are many other efforts that are worth promoting if you promote one, where do you stop? So while it sounds worthwhile, it s probably better for Debian to stay out of it. But somehow related to this, I sometimes worry about the fact that there are so few paid opportunities around Debian. If you contribute to the Linux kernel for a while, you have an excellent chance to get hired by someone and to work on the kernel full time. The kernel may be an extreme example but there are a lot of projects that have more paid opportunities than Debian, e.g. Mono, GNOME, OpenOffice/LibreOffice and KDE. Obviously, there are some Debian Developers who can spend some time on Debian as part of their job. I know that some Canonical employees contribute to Debian, that support companies like credativ improve Debian as part of their work, and that system administrators fix bugs or package new software as they deploy Debian. But I think this is a minority of contributors and even they don t work full time on Debian. Instead what I see is that a lot of people leave university, get a job and then no longer have time for Debian or people start a family and no longer have time. I can take myself as an example since I don t have nearly as much time as I did in the past when I was a student. I guess there are different ways to deal with this problem one would be to create more paid opportunities around Debian outside the project, another one might be to make it easier for new volunteers to join the project. I don t have the answers to these questions but it s something I wonder about, and I also wonder whether pure volunteer projects can still keep up with projects with a lot of full time contributors. Raphael: What motivates you to continue to contribute year after year? Martin: Debian is a great project with a great mission, goals and people. I contribute to make Debian a better solution and to promote the free software philosophy. Finally, the community around Debian provides a lot of motivation. It s amazing how much I ve learned about other cultures because of my involvement in Debian and how many friends I ve made over the years all around the world. Raphael: Do you have wishes for Debian Wheezy? Martin: Not really. I m pretty happy with the way things are going at the moment. We have made a lot of organizational changes in the last few years from which the project has greatly benefited. I m particularly pleased about the plans to adopt a time-based freeze. Raphael: Is there someone in Debian that you admire for their contributions? Martin: There are many people I admire greatly. I d like to mention Joey Hess because he s a great example to follow. He doesn t get involved in politics, is easy to work with and does great technical work. In fact, he has made not one but several contributions that have completely changed Debian (debconf, debhelper, and debian-installer). Furthermore, Debian has a lot of contributors who have done great work over the years but who are not very vocal about it. People like Colin Watson or Peter Palfrader. Debian has many unique contributors and the list of people I admire is much longer than the few people I just mentioned.
Thank you to Martin for the time spent answering my questions. I hope you enjoyed reading his answers as I did. He raised some interesting questions. Subscribe to my newsletter to get my monthly summary of the Debian/Ubuntu news and to not miss further interviews. You can also follow along on Identi.ca, Twitter and Facebook.

No comment Liked this article? Click here. My blog is Flattr-enabled.

20 July 2011

Andrew Pollock: [life/americania] 4th of July in the Grand Canyon

Our adventurous friends Eric and Katie had invited us to join them on a hike in the Grand Canyon over the 4th of July weekend. As this struck us as something we'd never have considered doing otherwise, we thought we'd accept their kind offer. We're so glad we did. It was quite a bit of traveling just to get there. We flew out of San Jose on Thursday night, got into Las Vegas, rented a car, and then drove to Peach Springs, Arizona, where we stayed the night. We didn't get in at the Grand Canyon Caverns Inn until around midnight, and we had to get up again for a 5:00am departure (I think we actually got away by more like 5:30am), to drive to the Hualapai Hilltop, where the trail head was. Zoe handled all of this very well. She didn't end up falling asleep in the car until about 10:30pm I think, and dealt with the transfer out of the car at midnight very well and went back to sleep. The drive to the Hualapai Hilltop, along Indian Road 18, took about an hour. We had to dodge a bit of livestock on the road. The road itself was sealed and of good quality. We remarked on the way back out that as soon as you left the Havasupai Reservation and entered the Hualapai Reservation that there was a distinct degradation in the quality of the road. We parked at the Hilltop, and got ourselves organised, and commenced our descent by about 7:10am. The first 1.5 miles was very steep. There were a bunch of switchbacks and there was a fair few people coming up the other way already. There were also a few mule trains coming in the opposite direction that we had to dodge. The mule trains have right of way, so we had to stop and get out of the way to let them pass. Zoe thought they were pretty cool because they invariably had a few dogs with them as well, and she thinks dogs are awesome. The remaining 6.5 miles (it was an 8 mile/13 kilometre hike in total) were fairly easy. There was a lot of variety in terrain. Rocks, sand, dirt. It wasn't all in the sun, which was made it more comfortable. Heat wise, I think it was in the high 30's Celsius, with pretty much no humidity, so it didn't feel too uncomfortable. Towards the end, as we got near the water, there was a distinct change in the canyon. There was more greenery, and we started hearing insects and seeing bird life. When we first saw the water, it was hard not to just jump in, it looked so inviting. The total hiking time was about 4 hours 45 minutes, which included a reasonable stop to give Zoe some breakfast. We arrived in the village at around midday. Unfortunately the lodge wasn't ready for check ins until 1pm, so we had to twiddle our thumbs for a little bit. Zoe handled the hike incredibly well. We used a Macpac Possum child carrier that Nigel had passed down to us, and she didn't complain the whole time. She even took a nap in it. We were very relieved that it wasn't a problem for her. Sarah carried her, and I carried everything else. (I'm so glad I didn't see the photo of how I looked until well afterwards). In hindsight we probably brought too much stuff, but we didn't really know what to expect down there, so we'd rather have too much than too little. The village completely exceeded my expectations. I had this (silly) mental picture of it being just the lodge and not much else, but somewhere between 450 and 700 people live in the village. It had two general-type stores, a cafe that was pretty much like a fast food/takeaway place, an elementary school, and some sort of basic medical clinic. There was also a small general purpose community centre of some sort. The main store had pretty much everything you'd need in the food department. The cafe frequently ran out of various different things, but you weren't going to go hungry. For the remainder of Friday, we just stayed put in the village and let Zoe stretch her legs. Eric and Katie and their kids explored the first set of falls down from the village, unofficially named Rock Falls. On Saturday, we all hiked down to Havasu Falls. We met a couple of other families (amusingly both from the Bay Area) along the way, so we had some interesting conversations. I have no idea how long the hike was. Havasu Falls was impressive. Quite tall and narrow at the top, and quite loud. Zoe was impressed. We took her for a bit of a swim in the pools in the bottom. We had lunch there, and then Zoe and Sarah stayed there (Zoe took a nap in the KinderKot (also courtesy of Nigel) in the shade by the falls, and I took the Macpac with a water bladder in it to refill it at the spring in the campground, which was further down stream, and to check out Mooney Falls with Eric and Katie (and their kids), which was further downstream again from the campground. Mooney Falls was pretty insane. A lot taller than Havasu Falls, and a lot more treacherous to get to the bottom of. Parts of it were vertical. Chains and rickety ladders were involved. Caves were involved. I'm so glad I didn't have Zoe in the Macpac, because on multiple occasions, the top of it got bashed into rocks, so without having Sarah with me also to act as a guide, there's no way I could have safely descended with Zoe in the backpack. My favourite photo illustrating how crazy this was is this one that I took of Eric and Katie. This photo highlights some of the craziness involved to get down. I pretty much got to the bottom, had a quick look around and left Eric and Katie to it, because I figured Zoe would have woken up by now, and was probably bored. Turned out I had all of the sunscreen with me as well. So I climbed back up, and trekked back to the campground, refilled at the spring, and headed back up to Havasu Falls. After we reunited, we then hiked back up to the village, which to be honest, was the hardest bit of hiking we did. I was carrying Zoe in the Macpac, and it was hot, and it was mostly loose sand all the way. We were very glad to get back to the village. Zoe started showing signs of coming down with a cold and a cough, so we decided to cut short our stay in the village and leave on Sunday instead of Monday. We'd been tossing up between getting a helicopter or horses out. We ended up opting for the helicopter after learning that the horses still took about 3.5 hours, and you basically had no control over the animal. We were dubious as to how Zoe would go being bounced around on the back of a horse for that long. The helicopter ride also took all of about 5 minutes. The tribal members get first dibs on the helicopter, and there had been a death in the village, and I think a lot of people had come to the village for the viewing (the casket itself was flown out earlier on Sunday morning for a burial out of the village), so I suspect there was a higher number of tribal passengers than usual. We didn't get out until 2pm. Again, Zoe was incredibly good. She just hung out with us while we waiting for a flight out. There were plenty of dogs for her to be entertained by, and some other kids. She also took a pretty decent nap. So we finally got out, and got back to our car, and then the heavens opened. It absolutely poured down with rain. Sarah was keen to check out Hoover Dam, so we decided to stay near Boulder City in Nevada, and got a suite in the Hacienda Hotel and Casino for cheap. The next day was the Monday public holiday for Independence Day, and we were tossing up whether or not to take Zoe to a doctor to get her checked to see if she had bronchitis (we've been a bit gun-shy about bronchitis since the time she came down with it when we were in Australia). She ended up falling asleep in the car while we were hunting around for an Urgent Care facility that was open, so we decided to let her sleep and drove to Las Vegas. After she woke up, we took her to see the flamingos at Flamingo and the lions at MGM Grand. Zoe absolutely loved all the lights, sights and sounds of Las Vegas. In the afternoon, we took her to a doctor, and got the "first child, huh?" from the doctor (she didn't have bronchitis). After that, we went and briefly checked out Hoover Dam (just walked half way across the bridge in front of it and walked across the dam itself). The following day, we packed up and spent the morning on the Las Vegas strip again. This time we went to the Venetian (Zoe thought the gondolas were pretty cool) and then we flew out in the afternoon. So it was a lovely little family vacation. We ended up spending about as much time in Las Vegas as we did in the Grand Canyon, but that was okay. I'd really like to go back to Supai again, but I'm not sure if the stars will align themselves appropriately. If we did, knowing what I know now, I'd take a lot less food and put all of the luggage on a horse, and just hike in with the minimum of stuff. I'd probably be game to hike out as well if the bulk of the luggage was on a horse. Photos from the trip are here.

Aigars Mahinovs: Debconf11 the arrival and Debcamp

Short version arrival was quite easy, the arrival wiki page is now up-to-date and my photos are uploaded every day to this Flickr set. I had a small problem departing from CDG to Zagreb after scanning my suit twice and complaining that it had too many electronic devices, they had me remove my Nexus S, Nokia N950 and Kindle 3 from the suit pockets and then scanned that all lot again. After that another security guy asked me to open my suitcase and started squishing my Ligo cheese and declaring in a grave voice that it was too soft to be legal . As I kept calm and explained the DebConf cheese party to him, he looked around, put the cheese back in the bag and said ok, ok, off you go . So I still have that softness for the party. I heard an even better anecdote from our next years hosts when they were travelling trough Germany, a border official asked a typical so, what are you here for? question. They answered that they were in transit for an IT conference and gave him the invitation letter. He read the letter, nodded and then said: DebConf, huh? So, who was the author of the Linux kernel? and when after the initial shock they gave the right answer, they were immediately waved trough. Now that s what I call good border security. :) Meeting point - cafe at the Zagreb airport I met up with the guys in the Zagreb airport caf , which was immediately after exiting the secure zone. We waited for dkg to arrive and get his baggage. The passport check too a couple of minutes, but the baggage claim looked to be taking almost a half an hour. The airport bus After that was sorted out, we took out some local money in one of the 5 ATMs around and went to the bus. We were waived to just put our bags into the bus luggage space and get on, the driver went around to sell us tickets just before we drove off. It was one of the most comfortable and well air-conditioned buses I have been on in a long time. We were in the Zagreb bus station in less than half an hour. Non-official bus that tried to lure us Then a funny part started an old man came up to dkg and immediately asked Are you going to Banja Luka? , and when he said yes, the man started dragging us along to the bus station saying that there is a bus to there that will leave in a couple minutes, but we were in luck, so we should follow him right to the bus. Driven by curiosity, we went on. The man dragged us to the far side of the bus terminal bus stops where there was a minibus with Bosnian number plates, but no official designation as a passenger transit bus and no other passengers. They asked a reasonable 120 kuna for the trip, but they looked very shady to me, so we refused. I think that if we agreed and we were lucky enough that they actually did get us to Banja Luka, the price would have risen along the way, for example using the highway tolls as an excuse. Bus ticket to Banja Luka After getting cursed at by the old man and being demanded to buy him a beer for his efforts, we went upstairs to the real bus station where we were told that there were two buses to Banja Luka: one at 15:00 and another at 16:30, but that those two buses arrive in Banja Luka almost at the same time, so we got us tickets for the latter bus and went to a local bar to get some food and drinks. I somehow managed to get sausages in deepfried bread that for some reason cost almost triple of a hamburger and fries that others got, but it sure helped to pass the time and after all those 9 was not a bad price for a good meal. Bus to Banja Luka at Zagreb bus station We were a bit surprised by the bus drivers asking us to pay 1 (or 8 kuna) for bags to be put into bus bag storage, especially as we for several minutes could not quite understand what they want of us as neither of them spoke either English, Russian or German. Border crossing I don t remember when was the last time I crossed a real (i.e. non-Shengen) border in a bus, so getting out of the bus and walking one-by-one to the border official was a new experience. On the other border of two bus drivers collected the passports an then brought them back later, so that was less painful. And by then we were in Bosnia! And of the things that greeted us was a billboard for the casino in Banja Luka Hotel Bosna. :) By the time we got to Banja Luka, dkg had already made friends with an official from Croatian ministry of regional development that sat behind us on the bus and knew English very well (after living in Canada for some time). The bus station in Banja Luka looked almost abandoned like the bus stopped in the field with only a few taxi drivers and a bunch of buildings some distance away showing that this was indeed part of civilization. Banja Luka taxis The taxi drivers would take you to the venue for 8-10 KM 5 or 50-100 kuna (if their meter is broken and you look to be really ignorant of the exchange rates). If you walk on a bit, there is a bus station with an ATM taking Visa cards and a bit further on a bus stop that will take you to the centre of the city for 1.5 KM. The train station looked fully abandoned when we went there, only a news kiosk was working there. The bus driver reacted well to the name Hotel Bosna and wave toward it when we passed by it. Central bus stop - get off here Meeting first Debian peoples at the hotel It is hard to miss, especially the blinking Casino sign or the white pillars with black letters Hotel Bosna on top. You just get off at the bus station Central and walk back a couple hundred meters. Then see all you Debian friends drinking in the cool bar and walk around the corner to the main entrance of the hotel to check in. Church at sunset Main event location Hotel room The rooms are looking really great this is the best DebConf location that I have been to (I was not in Argentina). Soft beds with linens changed daily, nice air conditioning, towels (changed daily, if used), good shower, It is lacking in the speed and power of its free WiFi and in some place there is a clear impression that the hotel was built as a top of the line hotel a couple decades ago, but somehow has fallen into a disrepair since. Or it is simply used much more than expected. IMG_4973 So far I would say that the DebCamp is running full steam two hacklabs have desks, chairs, power and network connection, one of them even has sufficient air conditioning. The network works great for me so far, at least in the venue. The hotel wireless is barely usable to read a blog post, preferably without photos. Dinner buffet The food is being served well and on time. So far for lunch and dinner you walk up to the reception and get a food ticket based on your room number and go to the M level for the food (the M level is between the ground floor, labelled as PR , and first floor) where for breakfast and dinner there is a buffet, but for lunch you sit at a table and they bring you food. Vegetarians should clearly say vegetarian while pointing at themselves to get the special vegetarian option. So far food has been very good, except that that they often run out of popular items, such as fries, in the buffet. You can also ask for beer and other extra drinks with your food, but know that they cost extra up to 2.5KM for a beer, for example.

Clint Adams: Things I clearly won't have time to do this week

19 July 2011

Olivier Berger: Migrating mail from Evolution local storage to Evolution + local Imap (dovecot with Maildir) 1/X

I ve been fed up with Evolution being so buggy and slow, which was making managing my mail ever more painful as time passes. Still, one of the advantages of Evolution over other MUAs is the vfolders feature, which I ve been using intensively for years. Would there be some alternate way of managing my mail ? I ve been reading about notmuch s progress in becoming a very powerful mail management / retrieval tool (it could very well replace the vfolder feature of Evolution), but unfortunately, it is not (yet) integrated with Evolution. Others have documented their mail setup, and it seems that I could achieve a middle ground solution by migrating all my mail folders, currently stored inside Evolution s local storage, into Maildir folders managed by a local dovecot IMAP server. Evolution would still be my MUA, but it would store my mail inside Maildirs through dovecot. I ve been told that Evolution may be less buggy with IMAP than with local folders, which could solve my main annoyances. Also, it would make it possible to index mail with notmuch, as it supports the Maildir storage format. I ve then decided to take the opportunity of a holiday period to start the migration attempt. I ll document it in another post.

John Goerzen: Trains and Birthdays

This weekend, the boys got what they ve been waiting for: another trip on Amtrak. For the last week or so, Jacob has had a morning ritual. He ll look at the calendar, figure out what today is, figure out when we ll get on the train, and then figure out how many days it will be. As the number gets lower, the excitement gets higher, of course. Friday morning, we woke the boys at 2:30AM to get to the train station. The only Amtrak trains through our area are middle of the night departures. Jacob is normally hard to wake up, but when I tell him that I m waking him up to go to the train station, he wakes up faster than I ve ever seen him before. It takes about 3 seconds for him to process that in his groggy state, and then he sits up straight, throws off the covers, and is instantly ready to go. Both boys were excited even in the station waiting room. Oliver has been on an Amtrak train before, but it s been awhile and he probably doesn t remember it. He constantly talked about it, jabbering as much as his vocabulary lets him. Once we were on the train, Terah and I would have liked to get some more sleep. The boys, on the other hand, were now wide awake, and didn t fall back asleep until about 5:30. That means Terah and I didn t, either. Here s what it usually looks like: When it came time for breakfast, we went to the dining car as usual. Jacob had already been telling us for days what he would eat for breakfast on the train: I always have French toast on the train, dad. And so he did. A few minutes later, I heard the waitress telling other people they were out of French toast, so I was glad I didn t have to disappoint Jacob over that! But it was Oliver that really came alive on this trip. I don t think I ve ever seen him so excited. It was almost constant. He happily talked about anything he could see or touch. But he also listened to other conversations, and would frequently pick out one word from a sentence and try to say it. He does that at home too, but not nearly so often as on the train. Both boys wanted to go exploring a lot my word for taking them for a walk in the train and seeing what they might find. We walked up and down the train several times, Jacob excited over opening the doors between the cars, and Oliver excited just to be there. Oliver s excitement kept him from sleeping well. He did eventually get a short nap, but that wasn t quite enough to avert a couple of tantrums later in the day. The reason for the trip was the 80th birthday party for Terah s grandpa. And it so happened that Oliver s 2nd birthday would be over the same time. So, Saturday morning, we all went for breakfast at Das Dutchman Essenhaus, one of the favorite local restaurants in northern Indiana. After that, it was over to a relative s place for some birthday festivities. The children got mini cakes to decorate as rail cars. There was frosting and all sorts of toppings. Great fun was had by all, and it was wise that this activity took place in a garage rather than indoors. Yes, that is a marshmallow stuck to Jacob s nose. Then in the evening, it was off to another relative s place for some more family time. Jacob had a great time all day, and was in high spirits. He asked me to sit by him at dinner, and started one of the longest conversations I ve had with him in some time. We just talked about the things that happened in the day, but it was nice when I told him, I like sitting by you, Jacob, and he said, Dad, me too! The big highlight for the day happened in the evening. We were gathered around a fire with a guitar to do some singing. Jacob was happily perched in his lawn chair, but got very excited when he saw some lightweight airplanes flying overhead. These kept flying at some distance, and he kept pointing them out to us. But that wasn t even the most exciting part. That came when the fireflies came out. Jacob ran around, catching them in his hands, and excitedly showing them to whatever person happened to be closest. He was laughing with joy for such a long time. At one point, someone asked him if the bugs were tickling his hands. He said, evidentally just realizing it, Oh yes, they ARE tickling my hands! He was one very happy boy. Sunday I had to leave to get back home, while Terah and the boys will return a couple of days later. Although I do sort of look forward to a train trip that I can relax without having to manage two young boys, I do miss them already and will be happy to have everyone back home in a few days. (This post written during the trip and posted a week later after arriving home)

18 July 2011

Wouter Verhelst: About the beard...

I'm someone who sometimes has a beard, and sometimes doesn't. Today, I'm someone with a fairly long beard, although it's not (yet?) one of the likes of andrew or maddog. I don't think it looks very well on me, but you can blame the government (or lack thereof) in Belgium. How?! What?! Yes, the government. A while back, a movie critic working for the RTL (a Francophone Belgian TV station) decided to keep his beard until the Belgian government took the oath of office. He was quickly joined by an actor, and then by a Flemish radio presenter (dutch, with pictures). And then by a whole bunch of people. I didn't join them, initially. But after a while, when my beard was starting to get long again, people started asking me, 'is that for the government?' And initially I said no. But people kept asking. Since it seemed like a good excuse for not having shaven that long, after a while I just decided to say 'yes' for the heck of it. And now, after having said so for quite a while, I've kindof grown to the idea. Which, I guess, means that if the impossible happens, and someone back home manages to form a government that will take the oath while I'm still in Bosnia and Herzegovina, I'll have to go out and buy some razor equipment. But I don't expect that to happen. Today, exactly 400 days after the previous election (yes, it's really been that long), it still doesn't look as if there's going to be an agreement on anything. I wish there was something positive or funny that I could report on in this whole thing, but it doesn't look like it. Sigh.

Jelmer Vernooij: Summer of Code 2011

The Samba team is once again participating in the Summer of Code this year. This year we have 4 students working on various projects related to Samba. This year I am mentoring Dhananjay Sathe, who is improving the GTK+ frontends for Samba. In particular, he is making it possible to manage shares and users of a remote Samba or Windows machine. Dhananjay is also blogging about his progress.

17 July 2011

Wouter Verhelst: Mechlin to Banja Luka in statistics

I decided to go to DebConf11 by car. Not willing to do this alone, I asked for volunteers to join me in my car trip. One such volunteer showed up, and the car trip happened. Now, since I remembered to push the correct buttons on my dashboard after I completely fueled up the car and checked the tire tension and other things, I am now proud to be able to present you with the following statistics on this trip:
  1. Total distance travelled: 1466.8 km
  2. Average driving speed: 95.9 km/h [0]
  3. Total number of kilometers wasted on 'oh, crap, we forgot something': 10 (approx) [1][2]
  4. Total amount of fuel used: 81.3l
  5. Average fuel consumption rate: 5.5l/100km [3]
  6. Total amount of kilometers spent behind the wheel by Jeremy: 50 (approx)
  7. Total amount of kilometers spent behind the wheel by Wouter: the rest.[4]
  8. Time of departure: 2011-07-16 21:00
  9. Time of departure after point three and making sure we had everything: 2011-07-16 22:00
  10. Time of arrival: 2011-07-17 15:15 (approx) [5]
  11. Outside temperature at departure: 12 celcius
  12. Outside temperature at arrival: 35 celcius
  13. Longest (voluntary) break: 1 hour (approx; breakfast, tanking, bathroom visit, watching the sun rise)
  14. Longest (involuntary) break: 45 minutes (approx; customs check) [6]
  15. Last fueling stop: 4 AM.
  16. Amount of kilometers left to go before the car said bleep, you need to tank soon: less than one.
  17. Most tense moment: on crossing the slovenia->croatia border, confusing the border police officer ("no, I'm Wouter, that is Jeremy" yes, we both had photo-ID), who then promptly holds on to our documents, asks the car's papers, and tells us to please park over there and wait a moment while he gets us to be handled by guy in a somewhat more military-looking uniform.[7]
  18. Biggest "uh-oh" moment: after crossing the croatia->bosnia and herzegovina border, watching the very, very, very, very, very[8] long line of trucks queueing to cross the border. In the other direction. And then realizing that you probably need to go through that very same queue on the way back
  19. Largest single toll fee: 15 [9]
  20. Last bit of time spent asleep before this trip: the minutes surrounding 2011-07-16 05:00:00 [10]
  21. Time wasted writing this blog post when I really should've gone to bed instead: 45 minutes
  22. Time now: 21:02:54
But it was fun. And that's all that matters. Those who've shown up at debconf already, or who will arrive soon: see you tomorrow. Those who will arrive later: see you soon. And those who won't arrive: better luck next time, I hope. [0] this includes times when the car isn't moving with the engine running, but not times when the car is turned off, locked, alone and forgotten, in the rain, while those idiots who were supposed to be its drivers were inside having a drink.
[1] Which is surprisingly little. Usually I manage to need more.
[2] Jeremy forgot his^Wa Debian banner. I forgot something, I can't recall what. I decided to bring some CD's to enjoy during the trip, and a 3.5mm audio connection cable which we end up not using
[3] According to the dash. I'm too tired right now to check it. Also see the next two points. [4] This could incorrectly be interpreted as a criticism on Jeremy. It's not his fault that I only told him a day before we left that I have a manual transmission. And in fact, if anything, I'm unhappy with the fact that I even had to hand him the wheel for those 50 km. I would've loved to be able to say "I went all the way from Mechlin to Banja Luka, all by myself".
[5] I forgot to check the clock, to be honest.
[6] What, you think I have a chronometer?
[7] The last four points could really have been written as two. Figuring out which goes with which is left as an exercise to the reader.
[8] very, very, very
[9] 7-day Slovenian road tax vignet
[10] Once I wake up, I hardly ever manage to fall asleep again. Esecially if it's light outside.

Lars Wirzenius: rm is too slow

Some weeks ago I noticed that one of my backup servers was not removing the old backup generations it was making. It had over 18 months worth of daily backups, done with rsync and "cp -al". This is not the world's greatest backup system, but that's entirely irrelevant for this rant. The cron job that would do that did not exist: I had forgotten to enable it. So I ran it by hand. Then fixed it, when I noticed it was buggy, and didn't remove any old generations prior to 2010. After that I removed years-old backups of machines that haven't existed for years. Disk usage:
       Size  Used Avail Use% 
before 5.4T  2.6T  2.6T  51% 
after  5.4T  892G  4.3T  18% 
Inodes:
          Inodes    IUsed     IFree IUse%
before 732577792 77645915 654931877   11%
after  732577792 16871789 715706003    3%
That's about 61 million files removed, over the course of three weeks, of which the machine was down due to crashes for about one week. It should not take two weeks to copy a couple of terabytes (it's less than two megabytes per second). It should definitely not take two weeks to delete it. Almost all the time it was up, it was removing files. There were a couple of times when it finished one run and was idle until I woke up and started the next run. Say a day in total. Why is "sudo rm -rf" on a large directory tree, or set of large directory trees, so slow? I suspect part of the problem is that the system call API is beautiful, but simplistic: you need to call unlink or rmdir on every file separately, and that means doing an inode lookup separately for each file. Having a system call to delete everything in a directory would have a chance of removing things more efficiently, I suspect. However, since I've not done any profiling, nor even analyzed the relevant source code in the kernel, I might be entirely wrong. I wonder if anyone else needs to remove large directory trees frequently? I do that a lot, because of my backup software development hobby. But I may be in a unique position, and nobody else would benefit from fast removal. (I'll note that my backup server is using ext3, and that ext4 is much faster at removing files, particularly large files, but it's still not fast enough.)

Daniel Baumann: Debian Live Autobuilds

Right now I am sitting in the train to the airport for going to DebCamp/DebConf 11 in Banja Luka, Bosnia and Herzegovina. During DebCamp amongst other things I am going to work on finishing up the last bits on getting daily/weekly Debian Live autobuilds back for wheezy. This spring Jimmy Kaplowitz offered to help with the task of overseeing the debian-live autobuilder and to coordinate necessary bits with cdimage.debian.org. Having them on cdimage.d.o became recently possible as Steve McIntyre offered to make a VM available for us (live-build requires root privileges, and naturally, you would not want to let that run on the host system itself, that is why in the past it was not possible to build them on cdimage.d.o). The remaining issues are, and this is why the autobuilds are not yet back since spring, that live-build still needs two things: a couple of tweeks for wheezy, and the autobuild stuff need to be properly integrated into live-build itself. That will happen as an additional binary package live-build-cron with a bunch of debconf questions, so that everyone and his dog can setup a debian-live autobuild server on his own machine. The initial upload (which will not yet work, do not bother to try) was uploaded to experimental this week and cleared the new queue, now looking forward to get this all finished up and resulting in a live-build uploaded to unstable by the end of the week. In the second week, Jimmy arrives, I will be introducing him to live-build and the various little things to watch for and hopefully manage to persuade him to take over the autobuilds maintenance. Having all images that are based on packages solely from the stable/testing/unstable archives moved to cdimage.d.o is freeing up ressources on live.debian.net which did the job in the past since etch. Ben Armstrong volunteered to help with overseeing the live.d.n instance of live-build-cron that will build more then once per day images for si, with the only difference that they will not use live-* from the archive but the latest snapshots from our git snapshots repository. This will be a big help for the development as eventually we will be autotesting these images for various things. Last but not least, thanks to both Jimmy and Ben for all your kindness, patience and help with this during the last couple of months. We have interesting times ahead.

Thorsten Glaser: mksh R40b; joe 3.1jupp16 and 2.8jupp2 released

mksh R40b (nowadays with filled in user s caveats (for R40, too!) and packager s upgrade hints) has just been released. This is a should-have upgrade, fixing a number of admittedly some obscure bugs, changing things begun in R40, improving upon others. Thanks to the PLD Linux guys for spotting all these errors; thanks to them and phpnet.org both for adopting mksh so well. I have also fixed a bug in nroff(1) which will lead to an even nicer looking HTML manpage mksh(1) (after the next rebuild and upload of a MirBSD snapshot scheduled RSN). jupp 3.1.16 took on the task of merging Debian joe changes (aiming at an upload). I also split the jupprc file into three versions (2.8 generic/DOS, 3.1+jupp and 3.7/Unix) because of the differences in the baseline executables making rc files partially mutually incompatible (think Insert key), annoyingly warning (think syntax, hmsg), or less usable (joe s new menu system). jupp 2.8.2 is a companion to jupp 3.1.16 mostly because of the new help window character map Binaries for jupp should be updated RSN too. Considering Banja Luka is arriving quickly, the r in RSN should be taken with a few grains of salt. I ve also scheduled working on the pcc Debian package for the next future; updating lynx and maybe others like OpenSSH in MirBSD is also due; cvs(1) will receive more of my time, but before the next Upload I d like to fix LP#12230 once verified. Builds for Debian/m68k are also still running. I note I did in fact not manage to make a new base image, yet (but 2.6.39 kernels miss a patch, anyway, so waiting for 3.0 is ok). It s still using gcc-4.4 because nobody tests gcc-4.6 and gcj-4.6 FTBFS due to SIGSEGV, but that s ok in my books. rsyslog is broken but sysklogd works. The #ksh Freenode page finally got a well-deserved link to Planet Commandline. Throw more my way! Acronyms and translations, too. (Got Norwegian and Rumanian covered in the meantime. No idea whether any RTL languages will work in that beast. But I m young and need the money) Since I m writing a wlog entry anyway let me thank Gunnar for a nice summary on the current Free Culture discussion; my comments on Nina s site seem to be eaten, but let me support it fully, although, of course, I normally use a copycenter style licence, which is specifically written for general works of authorship under copyright law, not limited to software. I did in fact have that in mind. Maybe some people will like it (it s less than one Kibibyte long) either generally or just for their everyday random musings (they can then keep CC-BY-SA for the big works if they so desire). Wouter, grass background makes green headlines illegible. I ve never liked, and never installed manually, cups either. (Benny tells me that Apple s new version refuses to talk with a non-Apple cups, kinda defeating the whole idea I think.) Port 9100 is JetDirect (probably with an HP in front and some subset of trailing) and just nice. (Being able to talk ESC/P with your printer like print '\033K\x07\0\x3E\x81\x99\xA5\xA5\x81\x3E' >/dev/lpa too rocks though, IMHO. Yes, mine can, and I still can. /dev/lpa is BSD.)

Kai, thanks for your vimrc lines:

	:highlight TrailWhitespace ctermbg=red guibg=red
	:match TrailWhitespace /\s\+$\  \+\ze\t/
 

Automatic removal is harmful, though I just fell into the trap since jupprc contains needed whitespace at EOL but manual removal (bound to ^K] in jupp) rocks. And I like that your solution uses such strong a colour vim users are the single most represented offender group for actually leaving the redundant whitespace at EOL there, and it should hurt their eyes. (Sadly there is some vehement disagreement preventing them from inclusion in grml-etc-core but that s why I re-post them here.) Ah, and jupp can of course display whitespace visibly (although it uses / , replacing the arrow with if no UTF-8, not ), accessible with ^Ov. Steve, want to put up a checklist for sites? We can crowdsource the testing to maybe get some interesting results Some other people would get more comments if they were idling in IRC (Freenode) or allow comments on their blog, specifically without too high an entrance barrier OpenID is ok, but many other things, and ECMAscript, are not; but I can t really say that loud because our wlog is static HTML compiled from a flat plaintext data source so it doesn t allow such either. I often forget what I wanted to add if I can t get it out quickly enough (especially at work). Sowwy Me like the cat picture postings (Amayita, Tiago, Gracias!).

16 July 2011

Clint Adams: Nokia N950

I am holding a device running MeeGo 1.2 Harmattan 1.2011.22-6PRRM680, courtesy of the good folks at Nokia.

Matthew Palmer: MySQL replication and crash recovery

The question was recently asked, How do I perform crash recovery on a MySQL master/slave database cluster? Because replication is async, a transaction that has been committed to the master may not be able to leave the master before the crash happens. The short answer is, you don t. Asynchronous replication, by it s very nature, is prone to these sorts of issues, and MySQL doesn t make life easier in general by using query replay. Some of the issues aren t massive: for instance, if a slave crashes, the master will keep replication logs for the slave until it comes back up (as long as the slave comes back before the master decides some of the replogs are too old and starts deleting them, of course), so as long as you can live without a master for a while, you can recover and continue along your merry way. Promoting a slave to be a master, on the other hand, is a situation frought with peril. Here, you ve just got to hope hope that your chosen slave is consistent with the master s state at death (because it s async, you have no guarantees about that), and that all the other slaves have the same ideas about what counts as the current state of the data. If your newly-promoted slave managed to apply an update that another slave didn t, that slave will be out of sync with reality (until such time as the now-dead master comes back and replays all those queries hahahaha). To even guarantee that any slaves have a consistent view of the data as compared to the new master, you ve got to rereplicate everything from the new master, because MySQL s where are you up to? counter is master-specific. I ve heard people who have to deal with this sort of thing these days say that the Maatkit tools are handy for dealing with various issues of this type (monitoring, repairing the database when it gets inconsistent). However, I prefer to keep right the hell away from MySQL replication altogether, after a year of having to gently coax an insane MySQL tree replication setup to do the right thing for any extended period, and watching a group of DBAs at Engine Yard go slowly insane. My preferred alternatives are: Never discount the value of the Jaws approach to scaling ( we re gonna need a bigger boat^Wmachine ) hardware is so ridiculously cheap, relative to the clueful sysadmin time needed to make (and keep) MySQL replication running, that you really need to be at the huge end of town (where other scaling issues are going to bite you in the arse first) before spending too much time on your database is worth the investment. Even then, you ll get more bang for your buck from: than you ever will from the constant, mind-numbing grind that is keeping MySQL replication going.
  1. The term comes from a time when a colleague near-screamed This slave cluster keeps fucking me! at a particularly intransigent set of MySQL slaves.

15 July 2011

Dirk Eddelbuettel: MCMC and faster Gibbs Sampling using Rcpp

Sanjog Misra, who uses Rcpp for Monte Carlo Markov Chain (MCMC) analyses in quantitative marketing, kindly set me a short example of Rcpp use. The example is based on a blog post by Darren Wilkinson which itself discusses and compares the suitability of R, Python, Java or C for MCMC analysis, using the Gibbs sampler as a concrete example. Darren's post is worth checking out: he stresses the rather pragmatic aspects of how fast and/or easy it is to write the code, rather than just the mere runtime. As such, he is not too concerned with a speed advantage of Python over R which he sees at a factor of around 2.4, leaving him to continue to prototype in R. Similarly, with C 'only' being faster than Java by a factor of two, he prefers Java for the numerically more demanding parts. We do of course advocate the use of Rcpp to combine the best aspects of R and C++, respectively. This Gibbs sampler example provides a nice backdrop. So working with Darren's example, consider the same Gibbs sampler for a bivariate distribution (and apologies for the lack of latex typesetting on my blog)
f(x,y) = k x^2 exp( -x y^2 - y^2 + 2y - 4x)
where the conditional distributions are
f(x y) = (x^2)*exp(-x*(4+y*y))               ## a Gamma density kernel
f(y x) = exp(-0.5*2*(x+1)*(y^2 - 2*y/(x+1))  ## a Gaussian kernel
Sanjog then spotted and corrected a small error in the variance expression in Darren's derivation; this is now acknowledged on Darren's website. Full details are in the R script now committed in SVN. The R code for the Gibbs sample can therefore be written as follows below. Note that this uses thinning to minimize serial correlation in the conditional densities--which renders the computation more demanding as 'N times thin' draws have to be generated:
## Here is the actual Gibbs Sampler
## This is Darren Wilkinsons R code (with the corrected variance)
## But we are returning only his columns 2 and 3 as the 1:N sequence
## is never used below
Rgibbs <- function(N,thin)  
    mat <- matrix(0,ncol=2,nrow=N)
    x <- 0
    y <- 0
    for (i in 1:N)  
        for (j in 1:thin)  
            x <- rgamma(1,3,y*y+4)
            y <- rnorm(1,1/(x+1),1/sqrt(2*(x+1)))
         
        mat[i,] <- c(x,y)
     
    mat
 
A second variant can be computed using the R bytecode compiler which appeared with the recent release of R 2.13.0 (and which we analysed in this blog post from April). This is as easy as
## We can also try the R compiler on this R function
RCgibbs <- cmpfun(Rgibbs)
Thanks to Rcpp and the inline package, we can also write a C++ variant that can be built and launched from R with ease. The C++ code is assigned to an R text variable gibbscode. (And we used to typeset such code on the blog as a character string, ie in a faint red color---but have now switched to highlight it as if it were freestanding C++ code. It really is passed as a single string to R which then uses the cxxfunction() to compile, link and load a C++ function built around the code. See previous posts on the inline package for more.)
## Now for the Rcpp version -- Notice how easy it is to code up!
gibbscode <- '

  using namespace Rcpp;   // inline does that for us already
  // n and thin are SEXPs which the Rcpp::as function maps to C++ vars
  int N   = as<int>(n);
  int thn = as<int>(thin);
  int i,j;
  NumericMatrix mat(N, 2);
  RNGScope scope;         // Initialize Random number generator
  // The rest of the code follows the R version
  double x=0, y=0;
  for (i=0; i<N; i++)  
    for (j=0; j<thn; j++)  
      x = ::Rf_rgamma(3.0,1.0/(y*y+4));
      y = ::Rf_rnorm(1.0/(x+1),1.0/sqrt(2*x+2));
     
    mat(i,0) = x;
    mat(i,1) = y;
   
  return mat;             // Return to R
'
# Compile and Load
RcppGibbs <- cxxfunction(signature(n="int", thin = "int"),
                         gibbscode, plugin="Rcpp")
It is noteworthy how the code logic is essentially identical between the basic R version, and the C++ version. Two nested loops control draws of x from a Gamma distribution, conditional on y, as well as draws of y from a Normal, conditional on x. Add a small amount of parameter passing to obtain the parameters N and thin, allocation of a results matrix and setup of the random number generator state to remain consistent with R, as well as a return of the matrix---and that is all. As Darren's code uses the GNU GSL in its C variant, I also became interested in seeing how a C/C++ hybrid variant using our RcppGSL package would fare. The code is below.
gslgibbsincl <- '
  #include <gsl/gsl_rng.h>
  #include <gsl/gsl_randist.h>
  using namespace Rcpp;  // just to be explicit
'
gslgibbscode <- '
  int N = as<int>(ns);
  int thin = as<int>(thns);
  int i, j;
  gsl_rng *r = gsl_rng_alloc(gsl_rng_mt19937);
  double x=0, y=0;
  NumericMatrix mat(N, 2);
  for (i=0; i<N; i++)  
    for (j=0; j<thin; j++)  
      x = gsl_ran_gamma(r,3.0,1.0/(y*y+4));
      y = 1.0/(x+1)+gsl_ran_gaussian(r,1.0/sqrt(2*x+2));
     
    mat(i,0) = x;
    mat(i,1) = y;
   
  gsl_rng_free(r);
  return mat;           // Return to R
'
## Compile and Load
GSLGibbs <- cxxfunction(signature(ns="int", thns = "int"),
                        body=gslgibbscode, includes=gslgibbsincl,
                        plugin="RcppGSL")
This code is similar to the version using just Rcpp, but we need to allocate space for the GSL random generator object (and later release that memory allocation), and we do of course call the GSL functions. This also necessitates declaring the function using the two header files listed as arguments for the include argument of cxxfunction(). So how is the performance? The script (now committed in Rcpp's SVN repo as examples/RcppGibbs/RcppGibbs.R, and also part of the next release) creates the output below when running in non-interactive mode (whereas interactive mode creates a few charts too):
edd@max:~/svn/rcpp/pkg/Rcpp/inst/examples/RcppGibbs$ r RcppGibbs.R
Replication # 1 complete 
Replication # 2 complete 
Replication # 3 complete 
Replication # 4 complete 
                    N=1000 N=5000 N=10000 N=20000
Elasped Time (R)     0.124  2.650  10.511  41.773
Elasped Time (RC)    0.081  1.916   7.594  30.280
Elapsed Time (Rcpp)  0.003  0.076   0.306   1.221
Elapsed Time (Rgsl)  0.002  0.049   0.196   0.784
SpeedUp Rcomp.       1.530  1.380   1.380   1.380
SpeedUp Rcpp        41.330 34.870  34.350  34.210
SpeedUp GSL         62.000 54.080  53.630  53.280
               test replications elapsed  relative user.self sys.self
4  GSLGibbs(N, thn)           10   7.845  1.000000      7.84        0
3 RcppGibbs(N, thn)           10  12.218  1.557425     12.22        0
2   RCgibbs(N, thn)           10 312.296 39.808286    311.98        0
1    Rgibbs(N, thn)           10 420.953 53.658764    420.59        0
The first block is a hand-computed comparison using four sets of parameters; the second block uses the excellent rbenchmark package to compare ten runs at twenty-thousand draws. We see a nominal increase in performance due to the bytecode compiler, saving roughly 38 percent which seems appropriate given that the R code mostly controls the loops; actual work in undertaken in the already compiled RNG functions. The Rcpp variant is about 34 times faster than the pure R code. Sanjog reported higher increases on his OS X machines (and Darren's post echos a similar order of magnitude). However, on my i7 running Linux I always obtained an improvement in the mid- to high thirties. That is certainly already a rather pleasant result. What surprised and stunned me at first was that the GSL solution scores an improvement of around 53 times (close to the factor of 60 reported by Darren). A closer look at the code (shown above) makes it clear that there are very few compute-intensive operations outside of the RNG draws. I validated this further with a second study timing just one million draws each from a Gaussian and Gamma using R via Rcpp, and using the GSL. It turns out that the R code is about 2.5 times slower for random draws from the Gamma distribution than the GSL. Inspection of the source code---in files src/nmath/rgamma.c for R and randist/gamma.c for the GSL shows why. R uses a much more complex (and presumably more precise) algorithm. I may follow up with Martin Maechler to see if we can illustrative the numerical benefits of this more expensive approach---this blog entry is getting long enough already. So to sum up: Gibbs sampling is a somewhat resource-heavy Monte Carlo Markov Chain method for investigating multivariate distributions. R excels at quick and simple explorations, albeit at somewhat slower execution speed. The Rcpp package can help by providing easy means to accelerate simulations by a significant factor. The example discussed here is now in SVN repository for Rcpp and will be part of the next release.

Updated 2011-07-16: Darren has just updated his comparison; fixed two typos here too.

Next.

Previous.