Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

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    Archive for August, 2007

    Slackware Linux + ATI video drivers: extremely slow fgl_glxgears problem solution

    13th August 2007

    I had just installed the latest ATI video drivers for Linux onto my Slackware 11 (with kernel; I have Radeon Mobility X600 with 64MiB of non-shared memory.

    Running glxgears, I got ~2050 FPS (glxgears window focused) and ~4900 FPS (console window focused, glxgears window out of focus).

    But running fgl_glxgears yielded values as low as 1 FPS! As fgl_glxgears is much more similar to the real-world game visuals, it’s apparent that no game will be playable at e.g. 0.2 FPS.

    Also, there were numerous repetitions of a single error in the console window:

    FGLTexMgr: open of shared memory object failed (Function not implemented) __FGLTexMgrCreateObject: __FGLTexMgrSHMmalloc failed! fglX11AllocateManagedSurface: __FGLTexMgrCreateObject failed!

    I found the solution which worked perfectly for me:
    Read the rest of this entry »


    Posted in *nix, Misc, Notepad | 2 Comments »

    Is the force with you?

    12th August 2007

    Today, after starting ./configure to make one of the programs, I noticed this in the logs:
    is the Force with you? configure will tell!

    I don’t know what is that intended to mean, but this is definitely funny: configure script, able to detect if the Force is with Skywalker…


    Posted in Humour, Programming | No Comments »

    Non-Programmer’s Tutorial for Python

    12th August 2007

    Non-Programmer’s Tutorial for Python


    Posted in Links, Programming, Python | No Comments »

    Python: iterate (and read) all files in a directory (folder)

    12th August 2007

    To iterate through all the files within the specified directory (folder), with ability to use wildcards (*, ?, and [ ]-style ranges), use the following code snippet:
    Read the rest of this entry »


    Posted in Programming, Python | 39 Comments »

    Back to blog

    12th August 2007

    I’ve been away from Internet for quite a long while… but now I’m back, and writing again!

    As I’m moving to Linux as my primary OS, my readers should expect more Linux-related posts in the nearest future. However, this does not mean any changes in the overall blog ideology and priorities – they will be kept as they are now.

    I’m currently completing a DNA sequence-analysis server, which will be announced later; I might post additional details on making an automated pipeline-like analysis web-servers for bioinformatics and/or data analysis; but the decision “to post or not to post” will be made based on “popular demand” (if any…).


    Posted in Misc | No Comments »

    Installing KRename on Slackware: is not a valid libtool archive

    12th August 2007

    When ‘make’ing krename (after ./configure, of course), it failed with an error message like:

    libtool: link: `/usr/’ is not a valid libtool archive

    After reading this topic (in Russian), I found that is a configuration file for
    This configuration file is created when installing ATI or nVidia video drivers – they replace the bundled and create

    The solution to the “absent” file is, thus, either to install ATI/nVidia drivers (if you have ATI/nVidia video card), or to manually create “fake”
    Here is the sample of “fake” (to copy-paste, click the “Plain text” header) :
    Read the rest of this entry »


    Posted in *nix, Software | 1 Comment »

    Geany source installation error: “ file format not recognized; treating as linker script”

    10th August 2007

    Today I was looking for some simple but convenient source-code editor. I came across this post, and decided to try Geany. I’m using Slackware 11 at the moment, and as there were no packages available, I downloaded Geany source to compile and install.

    However, the ‘configure’ script failed. When trying to compile ‘conftest.c’ with gcc, the following error was produced: file format not recognized; treating as linker script

    (Note 1: in the error above, I removed all the paths which were prepended to the actual error message.)
    (Note 2: I suspect that this error is the result of incomplete/failed/erroneous update of glibc slackware package I attempted a while ago. Will have to fix that more properly than described below.)

    Here’s the solution which helped me to install Geany successfully:
    Read the rest of this entry »


    Posted in *nix, Programming, Software | 4 Comments »