VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 06 2018 - 13:49:16 CST

Hi,
  This looks to me like a failure with Tcl/Tk's support for internationalized
input handlers (e.g. SCIM and the like). I see that the fault appears to
occur at the point where the Tk international input handler is triggered:

> Thread 1 "vmd_LINUXAMD64" received signal SIGSEGV, Segmentation fault.
> XGetICValues (ic=0x0) at ICWrap.c:288
> 288 ICWrap.c: No such file or directory.

The best workaround in the short term is to disable international input
handling when running VMD in interactive mode with Tk. I'm working toward
VMD 1.9.4 builds using a different Tk version that should not exhibit
this problem, as I believe it is a bug in Tk itself.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 06, 2018 at 02:12:01PM -0500, iamcool777able . wrote:
> Hello, I am having issues running VMD on Fedora 27. Running VMD in debug
> mode produces the following output:Â
> Starting program: /usr/local/lib/vmd/vmd_LINUXAMD64Â
> /usr/local/lib/vmd/vmd_LINUXAMD64: /lib64/libGL.so.1: no version
> information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/lib64/libthread_db.so.1".
> Info) VMD for LINUXAMD64, version 1.9.4a8 (August 30, 2017)
> Info) [1]http://www.ks.uiuc.edu/Research/vmd/Â Â Â Â Â Â Â Â Â Â
> Â Â Â
> Info) Email questions and bug reports to [2]vmd_at_ks.uiuc.edu    Â
> Â
> Info) Please include this reference in published work using VMD:Â Â
> Info)  Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Â
> Info)Â Â Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 4 CPUs detected.
> Info)Â Â CPU features: SSE2 AVX AVX2 FMAÂ
> Info) Free system memory: 4272MB (54%)
> [New Thread 0x7fffe9621700 (LWP 7152)]
> [New Thread 0x7fffe8e20700 (LWP 7153)]
> [New Thread 0x7fffe861f700 (LWP 7154)]
> [New Thread 0x7fffe7e1e700 (LWP 7155)]
> Info) No CUDA accelerator devices available.
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this X server option. Most OpenGL drivers
> Warning) disable stereoscopic display when 'Composite' is enabled.
> Info) OpenGL renderer: Mesa DRI Intel(R) HD Graphics 620 (Kaby Lake GT2)Â
> Info)Â Â Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVFS)Â
> Info)Â Â Full GLSL rendering mode is available.
> Info)Â Â Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> Thread 1 "vmd_LINUXAMD64" received signal SIGSEGV, Segmentation fault.
> XGetICValues (ic=0x0) at ICWrap.c:288
> 288 ICWrap.c: No such file or directory.
> Missing separate debuginfos, use: dnf debuginfo-install
> libdrm-2.4.89-1.fc27.x86_64 mesa-dri-drivers-17.2.4-3.fc27.x86_64
> mesa-libGL-17.2.4-3.fc27.x86_64 mesa-libglapi-17.2.4-3.fc27.x86_64
> pcre2-10.30-6.fc27.x86_64 sssd-client-1.16.0-5.fc27.x86_64
> I've tried installing the debugging packages VMD asks for but VMD doesn't
> seem to be able to find them even after I've installed the packages.
> Thanks in advance for the help; let me know if you need any further
> information.Â
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/Research/vmd/
> 2. mailto:vmd_at_ks.uiuc.edu 

-- 
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/