Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Debian, fgl_glxgears: Using GLX_SGIX_pbuffer… Segmentation fault

    1st October 2008

    If you get Segmentation fault when trying to run fgl_glxgears in your Debian desktop environment, most often this would mean that 3D acceleration isn’t enabled.

    For the case of ATI (and ATI Mobility) Radeon series, the easiest procedure would be (doing all as root, or prepending sudo to all commands):

    1. aptitude update, to ensure you’ve got the list of latest packages
    2. aptitude install fglrx-driver fglrx-control fglrx-kernel-src, for the actual driver; I also installed fglrx-atieventsd and fglrx-glx (these are driver-recommended packages)
    3. aptitude install module-assistant, required for building the kernel module
    4. module-assistant prepare, to verify that you have everything needed for the module build procedure
    5. module-assistant update
    6. module-assistant auto-install fglrx, to build and install the fglrx kernel module
    7. depmod -a
    8. modprobe fglrx, to load the fglrx kernel module
    9. aticonfig ––initial, to configure ATI’s device section in /etc/X11/xorg.conf (for more options, see aticonfig ––help)
    10. reboot

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    Posted in *nix | 5 Comments »

    Which Hosting Control Panel to use for a Debian server?

    27th September 2008

    To cut the long story short: for the final evaluation, I had this line of control panels:

    SysCP: looks good to me (though demo isn’t functional), has customer billing module. Unsure as to where it is used, but most probably sponsors are also the users of SysCP. Majority of support forums are in German.

    DTC: has no demo, only some screenshots. Has a set of packages for Debian lenny (which is a huge plus for maintenance and future upgrades). DTC is being developed by GPLHost, and is also used by GPLHost – so this is a live (used) distribution. Seems quite feature-rich.

    Virtualmin claims to be the “world’s most powerful and flexible web server control panel”. Virtualmin offers 4 means to control it: Web, mobile device, command line, and remote API. There are both screenshots and demo. Has both GPL and Professional versions. GPL version has a number of limitations, comparing to Pro version. From what I’ve read about Webmin (all three – Virtualmin, Webmin, Usermin – are just different “layers” of server control), it is a framework with a number of “interface scripts”, which allow to control various services. As such, it is easily extendible, but is not monolithic – in the sense of module inter-dependencies and action triggers.

    RavenCore was a promising CP.

    GNUPanel is a year-old control panel, but has a news item on the front page (dated August, 17) promising new, completely rewritten release somewhere in October. By the feature list, looks promising. However, I need the panel right now, and even in October, that will be quite a rough release, not really used/tested anywhere, so not a good option as well. But GNUPanel is a panel to check in half a year for progress.

    As the final choice, I had ISPConfig (which seems to be the best by people’s comments), and which is also quite widely used, and is easy to install onto Debian (at least the Perfect setup: Debian Etch says so), and DTC. I discarded Virtualmin (for the poor functionality of the GPLed version), RavenCore (for the lack of current descriptions and non-functioning demo), GNUPanel (which just isn’t ready yet), and SysCP (because ISPConfig seems better ;) ).

    As DTC has Debian packages (and will be easier to maintain/upgrade), I decided to try it first. I already have it installed (that’s easy, esp. if you first read the DTC Debian Express Setup). Later I might post my impressions from using DTC.

    Update: DTC is indeed easy and pleasant to use. I had problems allowing FTP and SSH access using MySQL authorization, but at least FTP was an easy one to fix (SSH access with MySQL authorization is still unconfigured, but that’s a low priority for me). There is a minor concern about the files and directory permissions setup, but thanks to chrooted environment that is only minor concern. Use of a single Apache installation for hosting admin and serving user sites might be a sub-optimal decision, but it works. Traffic and disk space accounting are plain superb! Server memory use for the dtc-toaster installation is troublesome, but for a powerful RAM-my server that is not a problem (I now have about 800-900MiB RAM occupied, but that includes the XCache’s cache, quite big MySQL cache, and loads of Apache and PHP modules).

    But I’m still willing to try other control panels. As I expected, GNUPanel hasn’t released anything yet; Ravencore‘s online demo is still unfunctional; ISPConfig has recently released RC (and their demo is working as it should and as it used to); SysCP is also up and running fast. If my little hosting service starts pouring in some cash, then I’ll try SysCP on my second server – to compare it with DTC, and choose one of them for further support/extension/localization.

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    Posted in *nix, Notepad, Software, Web | 17 Comments »

    Debian-Med Project

    3rd September 2008

    There’s a Debian-Med project, aiming to

    develop Debian into an operating system that is particularly well fit for the requirements for medical practice and research

    Debian-Med has several web sites/pages: one at Debian.org (descriptive), and the actual project’s website at debian-med.alioth.debian.org. There’s also debian-med wiki (for developers).

    As of nowadays, Debian-Med has released a number of Debian packages, which are grouped into respective Debian Med Tasks. The Biology-dev task, for example, contains MCL and libsbml packages (among many others).

    Check this project out – you might find that the software you need is already available as Debian package.

    This post was stimulated by Steffen’s comment.

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    Posted in *nix, Links, Science, Software | No Comments »

    Installing libsbml on Debian (to make iBioSim start)

    30th August 2008

    There’s a troubleshooter for Ubuntu, which (expectedly) works quite the same for Debian (lenny in my case).

    I’m installing libsbml to make the iBioSim tool work under Debian GNU/Linux. First thing I had to do was to make Sun’s java interpreter do all the java interpretation work instead of gcj: sudo update-java-alternatives -s java-6-sun (this assumes you do have java-6-sun installed).

    Installing libsbml moved me one step further, now I’m getting another error from iBioSim:

    Exception in thread "main" java.lang.NoClassDefFoundError: biomodelsim/BioSim
    Caused by: java.lang.ClassNotFoundException: biomodelsim.BioSim
            at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
            at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
            at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
            at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
            at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
    

    This yet has to be fixed somehow.

    If Zhou Xin’s blog becomes for any reason inaccessible (or moves to his own domain), below is the extract of the instructions from his post on how to install libsbml on Debian/Ubuntu Linux:
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    Posted in *nix, Links, Science, Software, Systems Biology | 3 Comments »

    debian.org.ua: universal Ukrainian Debian mirror

    15th July 2008

    http://debian.org.ua/ and ftp://debian.org.ua/

    What is on offer (mirrors):

    • backports.org
    • cygwin
    • deb.opera.com
    • debian – stable, testing, sid
    • debian-archive (starting from 1.1!)
    • debian-multimedia
    • installation media (CDs/DVDs)
    • debian-security
    • even debian-volatile is here!

    All this goodness is only 3 hops away from my DSL modem…. (ISP UkrTelecom)

    Gone editing /etc/apt/sources.list :)

    P.S. For non-ukrainian IPs, access might be slow/bandwidth-limited; for Ukrainian IPs, speed might be up to 100MBit/sec.

    Update: some time after publishing this post, debian.org.ua was down for some reason. When it was up, it was serving me packages with a mere 3 kb/sec :( . I found that ftp2.debian.org.ua mirror is faster at the moment.

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    Posted in *nix, Links | No Comments »

    Concise guide to CPU frequency scaling in Linux

    11th July 2008

    Debian HOW-TO: CPU power management / frequency scaling

    Also as a PDF: Debian how-to: CPU frequency scaling and power management.

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    Posted in *nix, how-to, Links | No Comments »

    Fresh install of Debian Etch 4.0r1 hangs/freezes dead after boot: solution

    24th October 2007

    Recently, I installed Debian Etch 4.0r1 onto my laptop. However, after the first boot into plain console, computer was dead-frozen after some console usage. I rebooted using the Power button – this time to gdm; and again, after some keyboard input system was hanging dead.

    I found the reason at debianhelp.org forums. Basically, it’s the PC speaker module (pcspr) not functioning correctly. I suspect this problem manifests itself only on some types of laptops. The solution is either to somehow reconfigure the pcspkr module, or just disable it. More on how to disable the module below.
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    Posted in *nix, Links | 1 Comment »