From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Mar 09 2014 - 09:25:50 CDT

Hi,
  I'm guessing that when you install those fonts and ibus, ibus enables
internationalized input mechanisms by default, and that this is what
causes the crash. There was a documented crash in the Tcl/Tk code that
could be triggered with internationalized input managers were used,
such as with SCIM, or similar mechanisms. Your description below
seems like another version of the same problem. One thing you might
try is to run "wishx" if you have Tcl/Tk installed, and see if it
runs or crashes, and if it runs, let me know which version of Tcl/Tk
you have installed on this system.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Mar 09, 2014 at 02:51:55PM +0100, René Genz wrote:
> Dear all,
>
> on Fedora 20 x86_64 using GNOME as Desktop Environment (DE) VMD 1.9.1
> 'LINUX_64 OpenGL, CUDA' will crash if the following packages are
> installed and the computer has been rebooted:
> yum install -y sazanami-gothic-fonts
> yum install -y sazanami-mincho-fonts
> yum install -y ibus
>
> One of the font packages is sufficient to cause trouble, if ibus is
> installed.
>
>
> Note, if you install KDE:
> yum install -y @kde-desktop && reboot
>
> and use KDE as DE, VMD will start without a problem!
>
> It does not make a difference which terminal emulator (gnome-terminal or
> konsole), which shell (BASH, or TCSH), or which display manager (KDM,
> GDM) I use.
>
>
>
> Description of graphical user interface output after starting VMD until
> crash:
> * "VMD 1.9.1 OpenGL Display" window opens
> * "VMD" Main window is about to open, i.e. in terminal output up to line
> 'Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile'
> * VMD crashes
>
>
> Attached is an archive that contains the output of the commands 'vmd',
> 'vmd -dispdev text', and 'vmd -debug'.
> Note, two different machines were used to test/pinpoint the problem,
> hence different file names:
> vmd-kdm-gnome-*
> => is the machine I encountered the problem on
> => uses Fedora, Fedora-Updates, RPMFusion-{,Non}Free{,-Updates}
> repositories; SELinux disabled; KDE+GNOME installed; using KDM
>
>
> vmd-gdm-gnome-*
> => is the machine I used to pinpoint the problem
> => uses Fedora and Fedora-Updates repositories; SELinux enabled; only
> GNOME installed; using GDM
>
>
>
>
>
> Installation of VMD has been performed with these commands:
> yum install -y svgalib-devel
> yum install -y mesa-libGLU-devel # libGLU.so.1 required for start of vmd
> yum install -y tcsh # csh
> tar xfz vmd-1.9.1.bin.LINUXAMD64.opengl.tar.gz
> cd vmd-1.9.1
> ./configure
> cd src
> make install
>
>
>
>
>
> The 'Automatic Bug Reporting Tool' (ABRT) from Fedora guided me to these
> pages after it detected the crash of VMD:
> https://retrace.fedoraproject.org/faf/reports/57121/
> https://bugzilla.redhat.com/show_bug.cgi?id=911492
> The bug report was closed automatically due to Fedora 18 reaching its
> end-of-life. It did not got fixed, as far as I can see.
>
>
> The latest development version of VMD
> (http://www.ks.uiuc.edu/Research/vmd/vmd-new/) has the same issue.
>
> I did not try to compile VMD from source.
>
>
>
>
> One workaround is:
> yum remove -y sazanami-gothic-fonts sazanami-mincho-fonts
> # no reboot required; vmd immediately will stop to crash
> # there are still some 'bad font:' references to the sazanami font
>
> If you require the fonts, another workaround is:
> yum remove -y ibus && reboot
> # reboot is required
>
>
>
> I will try test builds, if you want me to.
>
> Is more information required?
>
> Shall I file a bug report downstream at Fedora bug tracker?
> To which component shall I file the bug report?
> In the new bug report I will mention this thread and the other bug
> report, if you think the problems are related.
>
>
> Thanks for your help :)
> --
> Kind regards,
> René

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/