VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 14 2016 - 09:35:36 CDT

Is STRIDE missing from your VMD installation? What do you see in
the VMD installation directory, e.g. 'ls -l /usr/local/lib/vmd'
If STRIDE is present, then there may be an issue with /tmp or /usr/tmp
which STRIDE would try to write to. Do both of those directories exist?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 14, 2016 at 12:30:11PM +0100, anu chandra wrote:
> Hello,
>
> Many thanks for the reply. Interestingly, glxinfo and VMD works fine with
> second user as well as with root user. Unfortunately, while using the VMD
> from root user, 'new cartoon' visualization ofA protein fails with
> following error,
>
> $ sudo vmd OPM.pdb
> [sudo] password :
> Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> Info)
> [1]http://www.ks.uiuc.edu/Research/vmd/A A A A A A A A A A A A A A A A A A A A A A A A
> Info) Email questions and bug reports to
> [2]vmd_at_ks.uiuc.eduA A A A A A A A A A
> Info) Please include this reference in published work using VMD:A A
> Info)A A A Humphrey, W., Dalke, A. and Schulten, K., `VMD - VisualA A
> Info)A A A Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 16 CPUs detected.
> Info) Free system memory: 30840MB (96%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator:
> Info) [0] Quadro K4200A A A A A A A 7 SM_3.0 @ 0.78 GHz, 3.9GB RAM, KTO,
> AE2, ZCP
> Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this X server option.A Most OpenGL drivers
> Warning) disable stereoscopic display when 'Composite' is enabled.
> Info) OpenGL renderer: Quadro K4200/PCIe/SSE2
> Info)A A Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> Info)A A Full GLSL rendering mode is available.
> Info)A A Textures: 2-D (16384x16384), 3-D (4096x4096x4096), Multitexture
> (4)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> Info) File loading in progress, please wait.
> Info) Using plugin pdb for structure file OPM.pdb
> Info) Using plugin pdb for coordinates from file OPM.pdb
> Info) Determining bond structure from distance search ...
> Info) Finished with coordinate file OPM.pdb.
> Info) Analyzing structure ...
> Info)A A A Atoms: 6290
> Info)A A A Bonds: 5398
> Info)A A A Angles: 0A Dihedrals: 0A Impropers: 0A Cross-terms: 0
> Info)A A A Bondtypes: 0A Angletypes: 0A Dihedraltypes: 0A
> Impropertypes: 0
> Info)A A A Residues: 2448
> Info)A A A Waters: 0
> Info)A A A Segments: 1
> Info)A A A Fragments: 1902A A Protein: 4A A Nucleic: 0
> vmd > Info) In any publication of scientific results based in part or
> Info) completely on the use of the program STRIDE, please reference:
> Info)A Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
> Info)A assignment. Proteins: structure, function and genetics, 23,
> 566-579.
> ERROR) No STRIDE binary found; please set STRIDE_BIN environment variable
> ERROR) to the location of the STRIDE binary.
> ERROR) Call to Stride program failed.
>
> Any help would be highly appreciated
>
> Many thanks
> Anu
> On Wed, Jul 13, 2016 at 9:49 AM, Sourav Ray <[3]souravray90_at_gmail.com>
> wrote:
>
> Hello Anu
> Assuming you are using Ubuntu, go to "Software & Updates", then go to
> "Additional Drivers", then try the options where the Graphics
> Cards/options are listed (Xorg/NVIDIA/etc). Change to one that might be
> the suitable one (or keep repeating this and next steps with other
> options listed if not sure), hit "Apply Changes". Your VMD should work
> now, it did for me.
> Regards
> Sourav
> On Wed, Jul 13, 2016 at 11:39 AM, John Stone <[4]johns_at_ks.uiuc.edu>
> wrote:
>
> Hi,
> A This is indicative of some kind of problem with the GLX part of
> the X server as is reported by the output from 'glxinfo' that you
> listed below.A I don't know what happened during your installation
> of FFTW etc that you previously mentioned, but it clearly impacted
> your graphics drivers in some way.A You should revisit the graphics
> driver installation, potentially removing and reinstalling them to
> cure the problem if necessary.A Until 'glxinfo' works correctly,
> apps like VMD won't work right either.
>
> Cheers,
> A John Stone
> A [5]vmd_at_ks.uiuc.edu
> On Tue, Jul 12, 2016 at 05:32:50PM +0100, anu chandra wrote:
> >A A Dear John,
> >
> >A A I have noticed that VMD as well as glxinfo works fine as sudo
> user and
> >A A root user. Unfortunately, glxinfo showed following error with
> regular user
> >A A and the VMDAA also failed. It looks the issue is with
> environment
> >A A variable. Can you please advice me how to set this up?
> >
> >A A As regular user:
> >
> >A A $ glxinfo
> >A A name of display: :0.0
> >A A libGL error: No matching fbConfigs or visuals found
> >A A libGL error: failed to load driver: swrast
> >A A X Error of failed request:AA GLXBadContext
> >A A AA Major opcode of failed request:AA 153 (GLX)
> >A A AA Minor opcode of failed request:AA 6 (X_GLXIsDirect)
> >A A AA Serial number of failed request:AA 46
> >A A AA Current serial number in output stream:AA 45
> >
> >A A As sudo:
> >
> >A A sudo glxinfo
> >A A [sudo] password :
> >A A name of display: :0.0
> >A A display: :0AA screen: 0
> >A A direct rendering: Yes
> >A A server glx vendor string: NVIDIA Corporation
> >A A server glx version string: 1.4
> >A A server glx extensions:
> >A A A A AA GLX_ARB_context_flush_control, GLX_ARB_create_context,
> >A A A A AA GLX_ARB_create_context_profile,
> GLX_ARB_create_context_robustness,
> >A A A A AA GLX_ARB_fbconfig_float, GLX_ARB_multisample,
> GLX_EXT_buffer_age,
> >A A A A AA GLX_EXT_create_context_es2_profile,
> >A A GLX_EXT_create_context_es_profile,
> >A A A A AA GLX_EXT_framebuffer_sRGB, GLX_EXT_libglvnd,
> GLX_EXT_stereo_tree,
> >A A A A AA GLX_EXT_swap_control, GLX_EXT_swap_control_tear,
> >A A A A AA GLX_EXT_texture_from_pixmap, GLX_EXT_visual_info,
> >A A GLX_EXT_visual_rating,
> >A A A A AA GLX_NV_copy_buffer, GLX_NV_copy_image,
> GLX_NV_delay_before_swap,
> >A A A A AA GLX_NV_float_buffer, GLX_NV_multisample_coverage,
> >A A A A AA GLX_NV_robustness_video_memory_purge,
> GLX_NV_swap_group,
> >A A A A AA GLX_NV_video_capture, GLX_SGIX_fbconfig,
> GLX_SGIX_pbuffer,
> >A A A A AA GLX_SGI_swap_control, GLX_SGI_video_sync
> >A A client glx vendor string: NVIDIA Corporation
> >
> >A A Many thanks
> >A A Anu
> >A A On Tue, Jul 12, 2016 at 1:19 PM, anu chandra
> <[1][6]anu80125_at_gmail.com>
> >A A wrote:
> >
> >A A A Dear John,
> >
> >A A A Thanks for the reply. Unfortunately, reinstalling the
> graphics driver
> >A A A didn't help me to solve the issue. I have following driver
> installed,
> >
> >A A A $ rpm -qa | grep nvidia
> >A A A xorg-x11-drv-nvidia-352.93-1.el7.x86_64
> >A A A nvidia-uvm-kmod-352.93-3.el7.x86_64
> >A A A yum-plugin-nvidia-1.0.2-1.el7.elrepo.noarch
> >A A A xorg-x11-drv-nvidia-gl-352.93-1.el7.x86_64
> >A A A xorg-x11-drv-nvidia-libs-352.93-1.el7.x86_64
> >A A A xorg-x11-drv-nvidia-devel-352.93-1.el7.x86_64
> >A A A nvidia-detect-367.27-1.el7.elrepo.x86_64
> >A A A nvidia-kmod-352.93-2.el7.x86_64
> >
> >A A A Any help would be highly appreciated
> >
> >A A A Many thanks
> >A A A Aneesh
> >A A A On Mon, Jul 11, 2016 at 6:00 PM, John Stone
> <[2][7]johns_at_ks.uiuc.edu>
> >A A A wrote:
> >
> >A A A A Hi,
> >A A A A AA Most likely what has occured here is that during your
> install of
> >A A A A FFTW, the system also updated your graphics driver and
> reverted it to
> >A A A A a
> >A A A A Mesa software rasterizer.AA If you reinstall your
> graphics driver I
> >A A A A would
> >A A A A expect it to correct the problems you're seeing.
> >
> >A A A A Cheers,
> >A A A A AA John Stone
> >A A A A AA [3][8]vmd_at_ks.uiuc.edu
> >A A A A On Mon, Jul 11, 2016 at 05:37:34PM +0100, anu chandra
> wrote:
> >A A A A >AA AA Dear VMD users,
> >A A A A >
> >A A A A >AA AA The VMD was working fine in my system all of
> these days.
> >A A A A Unfortunately,
> >A A A A >AA AA after I installed FFTW (that was for Gromacs
> installation), VMD
> >A A A A failed to
> >A A A A >AA AA show the display window and showed the following
> message,
> >A A A A >
> >A A A A >AA AA $ vmd
> >A A A A >AA AA Info) VMD for LINUXAMD64, version 1.9.2
> (December 29, 2014)
> >A A A A >AA AA Info)
> >A A A A >AA AA [1][4][9]http://www.ks.uiuc.edu/Research/vmd/A A
> A A A A A A A A A
> >A A A A A A A A A A A A A A A A A
> >A A A A >AA AA Info) Email questions and bug reports to
> >A A A A >AA AA [2]vmd_at_ks.uiuc.eduA A A A A A A A A A
> >A A A A >AA AA Info) Please include this reference in published
> work using
> >A A A A VMD:A A
> >A A A A >AA AA Info)A A AAA Humphrey, W., Dalke, A. and
> Schulten, K., `VMD -
> >A A A A VisualA A
> >A A A A >AA AA Info)A A AAA Molecular Dynamics', J. Molec.
> Graphics 1996,
> >A A A A 14.1, 33-38.
> >A A A A >AA AA Info)
> >A A A A
> -------------------------------------------------------------
> >A A A A >AA AA Info) Multithreading available, 16 CPUs
> detected.
> >A A A A >AA AA Info) Free system memory: 31139MB (97%)
> >A A A A >AA AA Info) Creating CUDA device pool and initializing
> hardware...
> >A A A A >AA AA Info) Detected 1 available CUDA accelerator:
> >A A A A >AA AA Info) [0] Quadro K4200A A A A A A AAA 7 SM_3.0
> @ 0.78 GHz,
> >A A A A 4.0GB RAM, KTO,
> >A A A A >AA AA AE2, ZCP
> >A A A A >AA AA Info) Detected 1 available TachyonL/OptiX ray
> tracing
> >A A A A accelerator
> >A A A A >AA AA Warning) Detected X11 'Composite' extension: if
> incorrect
> >A A A A display occurs
> >A A A A >AA AA Warning) try disabling this X server option.AAA
> Most OpenGL
> >A A A A drivers
> >A A A A >AA AA Warning) disable stereoscopic display when
> 'Composite' is
> >A A A A enabled.
> >A A A A >AA AA libGL error: No matching fbConfigs or visuals
> found
> >A A A A >AA AA libGL error: failed to load driver: swrast
> >A A A A >AA AA XRequest.153: BadValue (integer parameter out of
> range for
> >A A A A operation) 0x0
> >A A A A >AA AA XRequest.153: GLXBadContext 0x2e00001
> >A A A A >AA AA XRequest.153: 0 0x0
> >A A A A >AA AA Info) OpenGL renderer: ErrorUnknown
> >A A A A >AA AA Info)A AAA Features: STENCIL
> >A A A A >AA AA Info)A AAA GLSL rendering mode is NOT
> available.
> >A A A A >AA AA XRequest.153: GLXBadDrawable 0x2e00091
> >A A A A >AA AA Info) Dynamically loaded 2 plugins in directory:
> >A A A A >AA AA Info)
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> >A A A A >AA AA XRequest.153: GLXBadContext 0x2e00001
> >A A A A >AA AA XRequest.153: 0 0x0
> >A A A A >AA AA XRequest.153: GLXBadDrawable 0x2e00091
> >A A A A >AA AA XRequest.153: GLXBadContext 0x2e00001
> >A A A A >AA AA XRequest.153: 0 0x0
> >A A A A >
> >A A A A >AA AA I wonder what went wrong when I installed FFTW.
> A
> >A A A A re-installation of the
> >A A A A >AA AA nvidia drivers also didn't help me to rectify
> the problem.
> >A A A A >
> >A A A A >AA AA My nvidia drivers shows,
> >A A A A >
> >A A A A >AA AA $ cat /proc/driver/nvidia/version
> >A A A A >AA AA NVRM version: NVIDIA UNIX x86_64 Kernel
> ModuleAAA 352.93AAA Tue
> >A A A A AprAAA 5
> >A A A A >AA AA 18:18:24 PDT 2016
> >A A A A >AA AA GCC version:AAA gcc version 4.8.5 20150623 (Red
> Hat 4.8.5-4)
> >A A A A (GCC)
> >A A A A >
> >A A A A >AA AA I am using RHEL 7 workstation. Unfortunately, a
> successful
> >A A A A system update
> >A A A A >AA AA and reboot also didn't help me to solve the
> problem.
> >A A A A >
> >A A A A >AA AA Any help here would be highly appreciated.
> >A A A A >
> >A A A A >AA AA Many thanks in advance
> >A A A A >AA AA Anu
> >A A A A >
> >A A A A > References
> >A A A A >
> >A A A A >AA AA Visible links
> >A A A A >AA AA 1. [5][10]http://www.ks.uiuc.edu/Research/vmd/
> >A A A A >AA AA 2. mailto:[6][11]vmd_at_ks.uiuc.edu
> >A A A A --
> >A A A A NIH Center for Macromolecular Modeling and Bioinformatics
> >A A A A Beckman Institute for Advanced Science and Technology
> >A A A A University of Illinois, 405 N. Mathews Ave, Urbana, IL
> 61801
> >A A A A [7][12]http://www.ks.uiuc.edu/~johns/AA AA AA AA AA
> A Phone:
> >A A A A [8]217-244-3349
> >A A A A [9][13]http://www.ks.uiuc.edu/Research/vmd/
> >
> > References
> >
> >A A Visible links
> >A A 1. mailto:[14]anu80125_at_gmail.com
> >A A 2. mailto:[15]johns_at_ks.uiuc.edu
> >A A 3. mailto:[16]vmd_at_ks.uiuc.edu
> >A A 4. [17]http://www.ks.uiuc.edu/Research/vmd/A
> >A A 5. [18]http://www.ks.uiuc.edu/Research/vmd/
> >A A 6. mailto:[19]vmd_at_ks.uiuc.edu
> >A A 7. [20]http://www.ks.uiuc.edu/~johns/
> >A A 8. tel:[21]217-244-3349
> >A A 9. [22]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
> [23]http://www.ks.uiuc.edu/~johns/A A A A A A Phone:
> [24]217-244-3349
> [25]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/Research/vmd/
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. mailto:souravray90_at_gmail.com
> 4. mailto:johns_at_ks.uiuc.edu
> 5. mailto:vmd_at_ks.uiuc.edu
> 6. mailto:anu80125_at_gmail.com
> 7. mailto:johns_at_ks.uiuc.edu
> 8. mailto:vmd_at_ks.uiuc.edu
> 9. http://www.ks.uiuc.edu/Research/vmd/A
> 10. http://www.ks.uiuc.edu/Research/vmd/
> 11. mailto:vmd_at_ks.uiuc.edu
> 12. http://www.ks.uiuc.edu/~johns/A
> 13. http://www.ks.uiuc.edu/Research/vmd/
> 14. mailto:anu80125_at_gmail.com
> 15. mailto:johns_at_ks.uiuc.edu
> 16. mailto:vmd_at_ks.uiuc.edu
> 17. http://www.ks.uiuc.edu/Research/vmd/A
> 18. http://www.ks.uiuc.edu/Research/vmd/
> 19. mailto:vmd_at_ks.uiuc.edu
> 20. http://www.ks.uiuc.edu/~johns/
> 21. tel:217-244-3349
> 22. http://www.ks.uiuc.edu/Research/vmd/
> 23. http://www.ks.uiuc.edu/~johns/
> 24. tel:217-244-3349
> 25. 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/