VMD-L Mailing List

From: anu chandra (anu80125_at_gmail.com)
Date: Thu Jul 14 2016 - 06:30:11 CDT

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 of protein fails with
following error,

$ sudo vmd OPM.pdb
[sudo] password :
Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) 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 K4200 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. Most OpenGL drivers
Warning) disable stereoscopic display when 'Composite' is enabled.
Info) OpenGL renderer: Quadro K4200/PCIe/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
Info) Full GLSL rendering mode is available.
Info) 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) Atoms: 6290
Info) Bonds: 5398
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 2448
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1902 Protein: 4 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) Frishman,D & Argos,P. (1995) Knowledge-based secondary structure
Info) 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 <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 <johns_at_ks.uiuc.edu> wrote:
>
>> Hi,
>> 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. 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. You should revisit the graphics
>> driver installation, potentially removing and reinstalling them to
>> cure the problem if necessary. Until 'glxinfo' works correctly,
>> apps like VMD won't work right either.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Tue, Jul 12, 2016 at 05:32:50PM +0100, anu chandra wrote:
>> > Dear John,
>> >
>> > I have noticed that VMD as well as glxinfo works fine as sudo user
>> and
>> > root user. Unfortunately, glxinfo showed following error with
>> regular user
>> > and the VMDA also failed. It looks the issue is with environment
>> > variable. Can you please advice me how to set this up?
>> >
>> > As regular user:
>> >
>> > $ glxinfo
>> > name of display: :0.0
>> > libGL error: No matching fbConfigs or visuals found
>> > libGL error: failed to load driver: swrast
>> > X Error of failed request:A GLXBadContext
>> > A Major opcode of failed request:A 153 (GLX)
>> > A Minor opcode of failed request:A 6 (X_GLXIsDirect)
>> > A Serial number of failed request:A 46
>> > A Current serial number in output stream:A 45
>> >
>> > As sudo:
>> >
>> > sudo glxinfo
>> > [sudo] password :
>> > name of display: :0.0
>> > display: :0A screen: 0
>> > direct rendering: Yes
>> > server glx vendor string: NVIDIA Corporation
>> > server glx version string: 1.4
>> > server glx extensions:
>> > A A A GLX_ARB_context_flush_control, GLX_ARB_create_context,
>> > A A A GLX_ARB_create_context_profile,
>> GLX_ARB_create_context_robustness,
>> > A A A GLX_ARB_fbconfig_float, GLX_ARB_multisample,
>> GLX_EXT_buffer_age,
>> > A A A GLX_EXT_create_context_es2_profile,
>> > GLX_EXT_create_context_es_profile,
>> > A A A GLX_EXT_framebuffer_sRGB, GLX_EXT_libglvnd,
>> GLX_EXT_stereo_tree,
>> > A A A GLX_EXT_swap_control, GLX_EXT_swap_control_tear,
>> > A A A GLX_EXT_texture_from_pixmap, GLX_EXT_visual_info,
>> > GLX_EXT_visual_rating,
>> > A A A GLX_NV_copy_buffer, GLX_NV_copy_image,
>> GLX_NV_delay_before_swap,
>> > A A A GLX_NV_float_buffer, GLX_NV_multisample_coverage,
>> > A A A GLX_NV_robustness_video_memory_purge, GLX_NV_swap_group,
>> > A A A GLX_NV_video_capture, GLX_SGIX_fbconfig, GLX_SGIX_pbuffer,
>> > A A A GLX_SGI_swap_control, GLX_SGI_video_sync
>> > client glx vendor string: NVIDIA Corporation
>> >
>> > Many thanks
>> > Anu
>> > On Tue, Jul 12, 2016 at 1:19 PM, anu chandra <[1]anu80125_at_gmail.com>
>> > wrote:
>> >
>> > Dear John,
>> >
>> > Thanks for the reply. Unfortunately, reinstalling the graphics
>> driver
>> > didn't help me to solve the issue. I have following driver
>> installed,
>> >
>> > $ rpm -qa | grep nvidia
>> > xorg-x11-drv-nvidia-352.93-1.el7.x86_64
>> > nvidia-uvm-kmod-352.93-3.el7.x86_64
>> > yum-plugin-nvidia-1.0.2-1.el7.elrepo.noarch
>> > xorg-x11-drv-nvidia-gl-352.93-1.el7.x86_64
>> > xorg-x11-drv-nvidia-libs-352.93-1.el7.x86_64
>> > xorg-x11-drv-nvidia-devel-352.93-1.el7.x86_64
>> > nvidia-detect-367.27-1.el7.elrepo.x86_64
>> > nvidia-kmod-352.93-2.el7.x86_64
>> >
>> > Any help would be highly appreciated
>> >
>> > Many thanks
>> > Aneesh
>> > On Mon, Jul 11, 2016 at 6:00 PM, John Stone <[2]johns_at_ks.uiuc.edu>
>> > wrote:
>> >
>> > Hi,
>> > A Most likely what has occured here is that during your install
>> of
>> > FFTW, the system also updated your graphics driver and reverted
>> it to
>> > a
>> > Mesa software rasterizer.A If you reinstall your graphics
>> driver I
>> > would
>> > expect it to correct the problems you're seeing.
>> >
>> > Cheers,
>> > A John Stone
>> > A [3]vmd_at_ks.uiuc.edu
>> > On Mon, Jul 11, 2016 at 05:37:34PM +0100, anu chandra wrote:
>> > >A A Dear VMD users,
>> > >
>> > >A A The VMD was working fine in my system all of these days.
>> > Unfortunately,
>> > >A A after I installed FFTW (that was for Gromacs
>> installation), VMD
>> > failed to
>> > >A A show the display window and showed the following message,
>> > >
>> > >A A $ vmd
>> > >A A Info) VMD for LINUXAMD64, version 1.9.2 (December 29,
>> 2014)
>> > >A A Info)
>> > >A A [1][4]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 Info) Email questions and bug reports to
>> > >A A [2]vmd_at_ks.uiuc.eduA A A A A A A A A A
>> > >A A Info) Please include this reference in published work
>> using
>> > VMD:A A
>> > >A A Info)A A AA Humphrey, W., Dalke, A. and Schulten, K.,
>> `VMD -
>> > VisualA A
>> > >A A Info)A A AA Molecular Dynamics', J. Molec. Graphics 1996,
>> > 14.1, 33-38.
>> > >A A Info)
>> > -------------------------------------------------------------
>> > >A A Info) Multithreading available, 16 CPUs detected.
>> > >A A Info) Free system memory: 31139MB (97%)
>> > >A A Info) Creating CUDA device pool and initializing
>> hardware...
>> > >A A Info) Detected 1 available CUDA accelerator:
>> > >A A Info) [0] Quadro K4200A A A A A A AA 7 SM_3.0 @ 0.78 GHz,
>> > 4.0GB RAM, KTO,
>> > >A A AE2, ZCP
>> > >A A Info) Detected 1 available TachyonL/OptiX ray tracing
>> > accelerator
>> > >A A Warning) Detected X11 'Composite' extension: if incorrect
>> > display occurs
>> > >A A Warning) try disabling this X server option.AA Most
>> OpenGL
>> > drivers
>> > >A A Warning) disable stereoscopic display when 'Composite' is
>> > enabled.
>> > >A A libGL error: No matching fbConfigs or visuals found
>> > >A A libGL error: failed to load driver: swrast
>> > >A A XRequest.153: BadValue (integer parameter out of range for
>> > operation) 0x0
>> > >A A XRequest.153: GLXBadContext 0x2e00001
>> > >A A XRequest.153: 0 0x0
>> > >A A Info) OpenGL renderer: ErrorUnknown
>> > >A A Info)A AA Features: STENCIL
>> > >A A Info)A AA GLSL rendering mode is NOT available.
>> > >A A XRequest.153: GLXBadDrawable 0x2e00091
>> > >A A Info) Dynamically loaded 2 plugins in directory:
>> > >A A Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
>> > >A A XRequest.153: GLXBadContext 0x2e00001
>> > >A A XRequest.153: 0 0x0
>> > >A A XRequest.153: GLXBadDrawable 0x2e00091
>> > >A A XRequest.153: GLXBadContext 0x2e00001
>> > >A A XRequest.153: 0 0x0
>> > >
>> > >A A I wonder what went wrong when I installed FFTW. A
>> > re-installation of the
>> > >A A nvidia drivers also didn't help me to rectify the problem.
>> > >
>> > >A A My nvidia drivers shows,
>> > >
>> > >A A $ cat /proc/driver/nvidia/version
>> > >A A NVRM version: NVIDIA UNIX x86_64 Kernel ModuleAA
>> 352.93AA Tue
>> > AprAA 5
>> > >A A 18:18:24 PDT 2016
>> > >A A GCC version:AA gcc version 4.8.5 20150623 (Red Hat
>> 4.8.5-4)
>> > (GCC)
>> > >
>> > >A A I am using RHEL 7 workstation. Unfortunately, a successful
>> > system update
>> > >A A and reboot also didn't help me to solve the problem.
>> > >
>> > >A A Any help here would be highly appreciated.
>> > >
>> > >A A Many thanks in advance
>> > >A A Anu
>> > >
>> > > References
>> > >
>> > >A A Visible links
>> > >A A 1. [5]http://www.ks.uiuc.edu/Research/vmd/
>> > >A A 2. mailto:[6]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
>> > [7]http://www.ks.uiuc.edu/~johns/A A A A A A Phone:
>> > [8]217-244-3349
>> > [9]http://www.ks.uiuc.edu/Research/vmd/
>> >
>> > References
>> >
>> > Visible links
>> > 1. mailto:anu80125_at_gmail.com
>> > 2. mailto:johns_at_ks.uiuc.edu
>> > 3. mailto:vmd_at_ks.uiuc.edu
>> > 4. http://www.ks.uiuc.edu/Research/vmd/A
>> > 5. http://www.ks.uiuc.edu/Research/vmd/
>> > 6. mailto:vmd_at_ks.uiuc.edu
>> > 7. http://www.ks.uiuc.edu/~johns/
>> > 8. tel:217-244-3349
>> > 9. 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/
>>
>>
>