VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 14 2016 - 10:31:15 CDT

On Thu, Jul 14, 2016 at 7:30 AM, anu chandra <anu80125_at_gmail.com> 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 of protein fails with following
> error,
>
> $ sudo vmd OPM.pdb

you shouldn't need to be using sudo to run VMD. in fact, it is a very,
*very* bad idea. one little typo in a VMD plugin and your whole system
may become unusable or worse.
that and the other symptoms you describe suggest, that you have messed
up ownership/permissions on some shared libraries and possible
executables, too.
these kind of things often happen when people use "sudo" without
thinking and whenever something doesn't work.

axel.

> [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/
>>>
>>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.