VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 05 2017 - 09:54:32 CDT

Hi,
  Thanks for the note. From your symptoms, it seems that there's
still an unresolved issue with the latest version of OptiX and some machines
that don't have GPUs installed. I will see if I can reproduce it here
and report that this is still not fixed to the OptiX developers at NVIDIA.

Best regards,
  John Stone
  johns_at_ks.uiuc.edu

On Sun, Sep 03, 2017 at 10:39:39PM -0400, sooraj achar wrote:
> Yup setting the bash environment variable ended up fixing the problem.
> Thanks for the help.
> On Sun, Sep 3, 2017 at 9:52 PM, John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Â Try setting this environment variable before you try running VMD
> and let me know if it cures your problem or not:
> /bin/bash:
> Â export VMDNOOPTIX=1
> /bin/csh:
> Â setenv VMDNOOPTIX 1
>
> Best regards,
> Â John Stone
> Â [2]vmd_at_ks.uiuc.edu
>
> On Sun, Sep 03, 2017 at 06:19:26PM -0400, sooraj achar wrote:
> >Â Â Hi, I recently installed VMD on my linux partition but am unable
> to get it
> >Â Â to start up in either the gui or text (with -dispdev text) modes,
> as they
> >Â Â both return segmentation faults before loading the program. I've
> also
> >Â Â attempted to run VMD through the debug mode: I've copied the
> output below.
> >Â Â My laptop's graphics are handled by a Kaby Lake integrated
> graphics card
> >Â Â so I don't think I have CUDA drivers installed, but that
> shouldn't make a
> >Â Â difference. Let me know if you need more information from me.
> Thanks.
> >Â Â ***
> >Â Â *** Running VMD in debugger, type 'run' at debugger prompt
> >Â Â ***
> >Â Â GNU gdb (GDB) Fedora 8.0-13.fc26
> >Â Â Copyright (C) 2017 Free Software Foundation, Inc.
> >Â Â License GPLv3+: GNU GPL version 3 or later
> >Â Â <[1][3]http://gnu.org/licenses/gpl.html>
> >Â Â This is free software: you are free to change and redistribute
> it.
> >Â Â There is NO WARRANTY, to the extent permitted by law.Ã*Â Type
> "show
> >Â Â copying"
> >Â Â and "show warranty" for details.
> >Â Â This GDB was configured as "x86_64-redhat-linux-gnu".
> >Â Â Type "show configuration" for configuration details.
> >Â Â For bug reporting instructions, please see:
> >Â Â <[2][4]http://www.gnu.org/software/gdb/bugs/>.
> >Â Â Find the GDB manual and other documentation resources online at:
> >Â Â <[3][5]http://www.gnu.org/software/gdb/documentation/>.
> >Â Â For help, type "help".
> >Â Â Type "apropos word" to search for commands related to "word"...
> >Â Â Reading symbols from /usr/local/lib/vmd/vmd_LINUXAMD64...(no
> debugging
> >Â Â symbols found)...done.
> >Â Â (gdb) run
> >Â Â Starting program: /usr/local/lib/vmd/vmd_LINUXAMD64Ã*
> >Â Â /usr/local/lib/vmd/vmd_LINUXAMD64: /lib64/libGL.so.1: no version
> >Â Â information available (required by
> /usr/local/lib/vmd/vmd_LINUXAMD64)
> >Â Â [Thread debugging using libthread_db enabled]
> >Â Â Using host libthread_db library "/lib64/libthread_db.so.1".
> >Â Â Info) VMD for LINUXAMD64, version 1.9.4a8 (August 30, 2017)
> >Â Â Info) [4][6]http://www.ks.uiuc.edu/Research/vmd/ Ã*Â Ã*Â Ã*Â
> Ã*Â Ã*Â Ã*Â Ã*Â Ã*Â Ã*
> >Â Â Ã*Â Ã*Â Ã* Ã*
> >Â Â Info) Email questions and bug reports to [5][7]vmd_at_ks.uiuc.edu
> Ã*Â Ã*Â Ã*Â Ã*
> >Â Â Ã* Ã*
> >Â Â Info) Please include this reference in published work using VMD:
> Ã* Ã*
> >Â Â Info) Ã*Â Ã* Humphrey, W., Dalke, A. and Schulten, K., `VMD -
> Visual Ã* Ã*
> >Â Â Info) Ã*Â Ã* Molecular Dynamics', J. Molec. Graphics 1996, 14.1,
> 33-38.
> >Â Â Info)
> -------------------------------------------------------------
> >Â Â Info) Multithreading available, 4 CPUs detected.
> >Â Â Info) Ã*Â CPU features: SSE2 AVX AVX2 FMAÃ*
> >Â Â Info) Free system memory: 5826MB (74%)
> >Â Â [New Thread 0x7fffe96a5700 (LWP 3635)]
> >Â Â [New Thread 0x7fffe8ea4700 (LWP 3636)]
> >Â Â [New Thread 0x7fffe86a3700 (LWP 3637)]
> >Â Â [New Thread 0x7fffe7ea2700 (LWP 3638)]
> >Â Â Info) No CUDA accelerator devices available.
> >Â Â Warning) Detected X11 'Composite' extension: if incorrect display
> occurs
> >Â Â Warning) try disabling this X server option.Ã*Â Most OpenGL
> drivers
> >Â Â Warning) disable stereoscopic display when 'Composite' is
> enabled.
> >Â Â Info) OpenGL renderer: Mesa DRI Intel(R) HD Graphics 620 (Kaby
> Lake GT2)Ã*
> >Â Â Info) Ã*Â Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVFS)Ã*
> >Â Â Info) Ã*Â Full GLSL rendering mode is available.
> >Â Â Info) Ã*Â Textures: 2-D (16384x16384), 3-D (512x512x512),
> Multitexture (8)
> >Â Â Thread 1 "vmd_LINUXAMD64" received signal SIGSEGV, Segmentation
> fault.
> >Â Â 0x00007ffff527ad20 in ?? () from /usr/local/lib/vmd/liboptix.so.1
> >
> > References
> >
> >Â Â Visible links
> >Â Â 1. [8]http://gnu.org/licenses/gpl.html
> >Â Â 2. [9]http://www.gnu.org/software/gdb/bugs/
> >Â Â 3. [10]http://www.gnu.org/software/gdb/documentation/
> >Â Â 4. [11]http://www.ks.uiuc.edu/Research/vmd/
> >Â Â 5. mailto:[12]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
> [13]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone:
> [14]217-244-3349
> [15]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. http://gnu.org/licenses/gpl.html
> 4. http://www.gnu.org/software/gdb/bugs/
> 5. http://www.gnu.org/software/gdb/documentation/
> 6. http://www.ks.uiuc.edu/Research/vmd/
> 7. mailto:vmd_at_ks.uiuc.edu
> 8. http://gnu.org/licenses/gpl.html
> 9. http://www.gnu.org/software/gdb/bugs/
> 10. http://www.gnu.org/software/gdb/documentation/
> 11. http://www.ks.uiuc.edu/Research/vmd/
> 12. mailto:vmd_at_ks.uiuc.edu
> 13. http://www.ks.uiuc.edu/~johns/
> 14. file:///tmp/tel:217-244-3349
> 15. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/