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Category: Linux (page 5 of 7)

Booting an Ubuntu server with a degraded software RAID array

My home server runs Ubuntu 12.04 with a software RAID 5 array and since a couple of days I’ve been getting e-mails from the SMART daemon warning me of uncorrectable errors on one of the drives. Today I took the time to take the failing drive out and check it with the tools from the manufacturer.

Because I didn’t want to run the risk of unplugging the wrong drive with the system on (and thus losing the whole RAID array) I shut the server down, removed the harddrive and started it again. The idea was that it would boot right back into the OS, but with a degraded RAID array. Unfortunately the server didn’t come up… After connecting a keyboard and monitor to it it turned out that the system was waiting with an initramfs prompt. From there I could check that the RAID array was indeed degraded, but functioning fine as I could manually mount all partitions.

Some Googling later I found out that by default Ubuntu doesn’t boot into a degraded software RAID array. This is to make sure you as administrator know something is wrong. A good idea for a laptop or PC, but not for a standalone server. The solution is the following:

  • From the initramfs prompt mount your original filesystems, for example in /mnt.
  • Use chroot /mnt to change root into your server’s hard disks.
  • In the file /etc/initramfs-tools/conf.d/mdadm add or change the line to
    BOOT_DEGRADED=true
    
  • Then run
    update-initramfs -u

    to regenerate the initial ramdisk.

  • Type exit to exit the chroot environment.
  • Unmount your file systems and reboot

Now your server should continue booting even though it has a degraded RAID array.

Links

ProbABEL v0.3.0 released

On New Year’s day I released version 0.3.0 of ProbABEL, almost two months after the previous release.

This update contains a few small bug fixes, but the most important feature of this new release is that thanks to the work of Maarten Kooyman we have a four to five-fold speed increase for the types of GWAS we run at work. In his e-mail to the GenABEL developers list he explains what he did to achieve this. The take-home-message of it is that you should always look for a suitable library for important tasks of any program you write. The old ProbABEL was based on a self-written matrix class that handled things like matrix multiplication and matrix subsetting. In the new release we make use of the Eigen C++ template library, maintained and developed by people who know much more about fast implementations of linear algebra than we do.

For those of you running Ubuntu Linux (or one of its derivatives and probably also Debian) I have set up the GenABEL PPA (personal package archive) where you can download and install the ProbABEL .deb package and stay up to date with future updates.
ProbABEL is also available for MS Windows, although we don’t have much experience running it on that platform.

Development of ProbABEL (and other members of the GenABEL suite) takes place on this R-forge page. If you are in search of an open source project to contribute to, feel free to contact us!

User support for the GenABEL suite can be found at our forum.

Installing Loggerhead behind Apache on Ubuntu 12.04

I recently noticed that I couldn’t view my Bazaar repositories anymore using the Loggerhead/Apache combination. It turns out that my previous post isn’t completely correct anymore as there seems to be a bug in Loggerhead for Ubuntu 12.04 and 12.10. I’ve updated the old post with a work-around and now everything works as expected again.

The Raspberry Pi runs ProbABEL

One of the first things I tried on my Raspberry Pi was to compile ProbABEL and see if it runs. Since the Raspberry Pi has an ARM processor I wasn’t sure whether our code was portable to it. Apparently it is! Compiling ProbABEL (r.1027 from SVN) took 30 minutes (single threaded of course) compared to 34 seconds on my Desktop (4 threads on an Intel Core i3 processor), but hey, it worked :-). Surprisingly it also passed all the checks in make check.

Once I hook up some more storage to device I will try to run ProbABEL on some real data. It will be interesting to see how much time it takes to run a linear regression on e.g. chromosome 22 of HapMap3 imputated data for a few hundred samples…

Will the Raspberry Pi be the next platform for GWAS ;-)?

Enter the Raspberry Pi!

Two weeks ago I received a Raspberry Pi! The Raspberry Pi is a small computer based not on a “regular” Intel or AMD x86 processor, but on an ARM processor (similar to the ones used in smartphones etc.). The one I ordered is a model B (with ethernet) and 512MB RAM.

The idea behind this nifty little computer is to provide kids with a low-cost but fully functional computer with which they could start learning more about programming. I’m not sure if this goal will be widely met, but for me it worked ;-). Having this little machine (with its case it measures roughly 10 x 6 x 2.5 cm) in my hands and installing Raspbian Linux on an SD card and looking at the terminal as it booted reminded me of the times when I first played with Slackware Linux on a 486. Of course Raspbian (well, Linux in general) is much more advanced than Slackware 7.0 back in 1999/2000 but the not too stellar performance of the graphical desktop is somewhat comparable.

Apart from playing around with it I’m not sure yet what I’m going to use it for. A domotica hub? A small web sserver? Use DosBox to play old games (from even before the 486 era)? We’ll see!

By the way, I order mine on Thursday Novermber 8th and on the Tuesday after that the package landed on my doorstep. Amazing after hearing about people waiting for months for their orders to be shipped. I order mine from New IT. It probably cost a little bit more, but who cares :-).

ProbABEL 0.2.2 released

On November 7th I released version 0.2.2 of ProbABEL, a set of programs that allow scientists (usually geneticists and epidemiologists) to run Genome-wide association studies (GWAS) in a fast and efficient way, even on machines with low amounts of RAM.

ProbABEL is part of the GenABEL suite, wich is a set of open source package for statistical genomics. Its main developer is Yurii Aulchenko, my former supervisor at the Erasmus Medical Centre.

This update contains a few small bug fixes and an update of the probabel.pl wrapper script that enables the use of chunked imputation output files as input. For more detailed changes, check the announcement.
For those of you running Ubuntu Linux (or one of its derivatives and probably also Debian) I have set up the GenABEL PPA (personal package archive) where you can download and install the ProbABEL .deb package and stay up to date with future updates.
ProbABEL is also available for MS Windows, although we don’t have much experience running it on that platform.

Development of ProbABEL (and other members of the GenABEL suite) takes place on this R-forge page. If you are in search of an open source project to contribute to, feel free to contact us!

User support for the GenABEL suite can be found at our forum.

Enabling middle mouse button emulation in Ubuntu 12.10

A few days ago I installed Ubuntu 12.10 on a 2009 laptop (a Dell Latitude D820). This laptop has a trackpoint (the little nib between the G, B and H keys on the keyboard that functions as a mouse). The trackpoint has its own set of mouse buttons, but, unlike my present Thinkpad, it doesn’t have a middle mouse button.
From my early Linux years I remembered that you could use a simultaneous click on the left and right buttons of a mouse to emulate the click of a middle mouse button. This option had to be set in the Xorg configuration file. My guess was that by now this was no longer needed, but I couldn’t find the appropriate option anywhere in Ubuntu’s settings. It’s quite a shame to see that Gnome/Unity/others(?) remove settings like that.
Anyway, looking around the web I found the solution. The middle mouse butten emulation can be enabled in the Gnome configuration by running the following in a terminal:

gsettings set org.gnome.settings-daemon.peripherals.mouse middle-button-enabled true

It worked immediately!

As an aside, I also had to install the packages nvidia-current and nvidia-settings in order to use the nVidia drivers. Without them using the Unity interface was dead slow, even though the laptop has an nVidia Geforce Go 7400.

Testing for the presence of the “Eigen” headers using autoconf

For the ProbABEL project I’m working on I wanted to test for the presence of the Eigen header files using . Eigen is a C++ template library for linear algebra. It basically consists of a bunch of header files. On my PC the Eigen files are installed in /usr/include/eigen3/ since I used the Debian/Ubuntu libeigen3-dev package.

I first tried to test for the headers by simply including

AC_CHECK_HEADERS([eigen3/Eigen/Dense])

in configure.ac, but that didn’t work:

...
checking eigen3/Eigen/Dense usability... no
checking eigen3/Eigen/Dense presence... no
checking for eigen3/Eigen/Dense... no
...

It turns out that you have to add the following lines to configure.ac:

AC_LANG_PUSH([C++])
AC_CHECK_HEADERS([eigen3/Eigen/Dense])
AC_LANG_POP([C++])

Now I get the following output when running ./configure:

...
checking how to run the C++ preprocessor... g++ -E
checking eigen3/Eigen/Dense usability... yes
checking eigen3/Eigen/Dense presence... yes
checking for eigen3/Eigen/Dense... yes
...

To go into a bit more detail, these are the errors in config.log without the AC_LANG options:

...
configure:4877: checking eigen3/Eigen/Dense usability
configure:4877: gcc -c -g -O2 -Wall conftest.c >&5
In file included from /usr/include/eigen3/Eigen/Core:35:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from conftest.c:67:
/usr/include/eigen3/Eigen/src/Core/util/Macros.h:188:5: error: unknown type name 'namespace'
/usr/include/eigen3/Eigen/src/Core/util/Macros.h:188:21: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token
In file included from /usr/include/eigen3/Eigen/Dense:1:0,
                 from conftest.c:67:
/usr/include/eigen3/Eigen/Core:98:12: error: expected identifier or '(' before string constant
In file included from /usr/include/eigen3/Eigen/Dense:1:0,
                 from conftest.c:67:
/usr/include/eigen3/Eigen/Core:144:18: fatal error: cerrno: No such file or directory
...

It seems to be the case that AC_LANG is set to C instead of C++ and consequently compilation of autoconf’s test programme fails. The AC_LANG_PUSH option forces autoconf to use C++.

Thanks to this post on Stack Overflow I could solve this problem.

Paper on using org-mode for reproducible research

I’m an avid user of Emacs and have been using org-mode for a couple of years now to write notes, keep a ToDo list and a few other things.

A couple of days ago I came across an article in the Journal of Statistical Software that describes how to use org-mode for reproducible research. It’s a great read and the source code of the complete article can be downloaded as well!

Using Plugwise adapters with Linux

Yesterday I received a small package I had ordered: the Plugwise Home Start kit. According to the box it is an energy management and control system. The idea is that you insert a sort of adaptor between a power socket and a device and using the Plugwise Source software you can monitor the power usage of the device. Furthermore, you can use the software to create schedule to turn the device on and off at a specific time.

The package contains the following:

  • a USB adapter (called the Stick)
  • a Circle+, the master adaptor that keeps track of the other devices in the network
  • a Circle, the regular members of the Plugwise network

The Circles communicate to each other using the ZigBee protocol in the 2.4GHz range. According to the documentation, the range of each Circle is about 5m.

Unfortunately the Source software only runs on windows. Luckily some people have already analysed the protocol and written some software to control the Plugwise devices (see links below).

First steps

Plugging the USB dongle in gives the following output in /var/log/syslog:

Nov 19 12:20:37 barabas kernel: [  182.855742] usb 1-1.6.1.1.3: new full speed USB device number 14 using ehci_hcd
Nov 19 12:20:37 barabas mtp-probe: checking bus 1, device 14: "/sys/devices/pci0000:00/0000:00:1a.0/usb1/1-1/1-1.6/1-1.6.1/1-1.6.1.1/1-1.6.1.1.3"
Nov 19 12:20:37 barabas mtp-probe: bus: 1, device: 14 was not an MTP device
Nov 19 12:20:37 barabas kernel: [  183.169370] usbcore: registered new interface driver usbserial
Nov 19 12:20:37 barabas kernel: [  183.169389] USB Serial support registered for generic
Nov 19 12:20:37 barabas kernel: [  183.169431] usbcore: registered new interface driver usbserial_generic
Nov 19 12:20:37 barabas kernel: [  183.169434] usbserial: USB Serial Driver core
Nov 19 12:20:37 barabas kernel: [  183.171310] USB Serial support registered for FTDI USB Serial Device
Nov 19 12:20:37 barabas kernel: [  183.171552] ftdi_sio 1-1.6.1.1.3:1.0: FTDI USB Serial Device converter detected
Nov 19 12:20:37 barabas kernel: [  183.171588] usb 1-1.6.1.1.3: Detected FT232RL
Nov 19 12:20:37 barabas kernel: [  183.171591] usb 1-1.6.1.1.3: Number of endpoints 2
Nov 19 12:20:37 barabas kernel: [  183.171595] usb 1-1.6.1.1.3: Endpoint 1 MaxPacketSize 64
Nov 19 12:20:37 barabas kernel: [  183.171598] usb 1-1.6.1.1.3: Endpoint 2 MaxPacketSize 64
Nov 19 12:20:37 barabas kernel: [  183.171602] usb 1-1.6.1.1.3: Setting MaxPacketSize 64
Nov 19 12:20:37 barabas kernel: [  183.171975] usb 1-1.6.1.1.3: FTDI USB Serial Device converter now attached to ttyUSB0
Nov 19 12:20:37 barabas kernel: [  183.171998] usbcore: registered new interface driver ftdi_sio
Nov 19 12:20:37 barabas kernel: [  183.172002] ftdi_sio: v1.6.0:USB FTDI Serial Converters Driver
Nov 19 12:20:37 barabas modem-manager[901]: <info>  (ttyUSB0) opening serial port...
Nov 19 12:20:49 barabas modem-manager[901]: <info>  (ttyUSB0) closing serial port...
Nov 19 12:20:49 barabas modem-manager[901]: <info>  (ttyUSB0) serial port closed
Nov 19 12:20:49 barabas modem-manager[901]: <info>  (ttyUSB0) opening serial port...
Nov 19 12:20:55 barabas modem-manager[901]: <info>  (ttyUSB0) closing serial port...
Nov 19 12:20:55 barabas modem-manager[901]: <info>  (ttyUSB0) serial port closed

lsusb gives:

Bus 001 Device 014: ID 0403:6001 Future Technology Devices International, Ltd FT232 USB-Serial (UART) IC

I couldn’t get the pairing to work under Linux (with the PlugwiseOnLinux scripts), Even though I corrected the MAC address in the python code. I then tried it in Windows where I failed at first also. After resetting the Circle+ and the Circle (removing/inserting them into the power outlet with 3 second intervals, as mentioned in the FAW on the plugwise website) I managed to pair the Circles. Looking back, I think I didn’t wait long enough for the pairing to work under Linux. During the trials in Windows I noticed that the pairing can take up to about 5 minutes…

Back in Linux I used python-plugwise (see links below) to turn the Circles on and off, e.g. this is how I turn my Circle+ off (note that I am a member of the dialout group, which is needed to communicate with /dev/ttyUSB0):

$ plugwise_util -d /dev/ttyUSB0 -m 000D6F0000B1C117 -s off

This is what I want! The only minor downside of python-plugwise is that it depends on the crcmod python library, which apparently is not package for Debian/Ubuntu. So installing using the python-setup framework as mentioned in the README is necessary.

Reading out the current power usage of my Circle works also:

$ plugwise_util -d /dev/ttyUSB0 -m 000D6F0000B85134 -p
power usage: 2.27W

So, no that it works, what am I going to do with the Plugwise modules? I’m going to use them in my backup scripts to switch the power to my external hard drives.

Making a .deb

I used checkinstall to make a package of python-plugwise. In a working directory, first check out the source code of python-plugwise using mercurial, as mentioned on the web site:

$ hg clone https://bitbucket.org/hadara/python-plugwise

Then run checkinstall and don’t forget to fill in the details correctly. For example, the package name is ‘python’ by default, which you definitely don’t want, since that would overwrite Ubuntu’s default ‘python’ package. Also make sure that you remove the crcmod python library if you installed python-plugwise before, otherwise it won’t get packaged. The output below shows the final values, after I changed them.

$ sudo checkinstall -D python setup.py install
 
checkinstall 1.6.2, Copyright 2009 Felipe Eduardo Sanchez Diaz Duran
	      This software is released under the GNU GPL.
 
 
 
*****************************************
**** Debian package creation selected ***
*****************************************
 
This package will be built according to these values:
 
0 -  Maintainer: [ lennart@karssen.org ]
1 -  Summary: [ python-plugwise is used to control the Plugwise power switches as well as read out information on power usage. ]
2 -  Name:    [ python-plugwise ]
3 -  Version: [ 0.2-hg-20111120 ]
4 -  Release: [ 1 ]
5 -  License: [ GPL ]
6 -  Group:   [ checkinstall ]
7 -  Architecture: [ amd64 ]
8 -  Source location: [ python-plugwise ]
9 -  Alternate source location: [  ]
10 - Requires: [ python ]
11 - Provides: [ python-plugwise ]
12 - Conflicts: [  ]
13 - Replaces: [  ]
 
Enter a number to change any of them or press ENTER to continue:

You can check the contents of the package to make sure the crcmod
files are included using dpkg:

$ dpkg --contents python-plugwise_0.2-hg-20111120-1_amd64.deb

An idea for later: make an SNMP module that calls plugwise_util to get the power usage so that I can monitor the power usage of a device using Cacti.

Links

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