VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 14 2016 - 20:34:31 CDT

Hi,
  Perhaps I should revise the README to mention this specifically so
others don't run into this problem with permissions getting changed prior
to the final step. I'll see about updating the README to make this more clear.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 15, 2016 at 12:05:25AM +0000, Vermaas, Joshua wrote:
> For those searching for a link in the near future, this link: http://www.ks.uiuc.edu/Research/vmd/current/README.html should work. As a general rule, configuring and compiling should be done in user-land, and sudo should only be needed for the last step, when installation actually occurs into folders that root should own.
>
> Thus, after untarring the binary distribution of vmd, this ought to be the sequence of steps:
>
> cd vmd-1.9.2
> ./configure
> cd src
> sudo make install
>
> -Josh
>
>
> On Jul 14, 2016, at 3:32 PM, Axel Kohlmeyer <akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>> wrote:
>
> On Thu, Jul 14, 2016 at 5:08 PM, anu chandra <anu80125_at_gmail.com<mailto:anu80125_at_gmail.com>> wrote:
> Dear Axel,
>
> Thanks for noting this down. I have used the following steps to install VMD.
>
> $ sudo cp -r vmd-1.9.2 /usr/local/
> $ cd /usr/local/
> $ cd vmd-1.9.2
> $ sudo ./configure
> $ cd src/
> $ sudo make install
>
> Can you please correct me with the installation steps here.
>
> this is *exactly* the kind of *excessive* and *unnecessary* use of
> sudo that i am criticizing. if you do this everywhere and as
> frequently, it is no wonder your machine gets messed up. i am
> convinced that you have similar issues elsewhere, e.g. with OpenGL
> libraries, that contribute to your problems.
>
> the correct procedure is listed in the installation instructions that
> come with VMD.
>
> axel.
>
>
> Many thanks
> Anu
>
> On Thu, Jul 14, 2016 at 10:23 PM, anu chandra <anu80125_at_gmail.com<mailto:anu80125_at_gmail.com>> wrote:
>
>
> Dear Axel,
>
> Thanks for noting this down. I have used the following steps to install
> VMD.
>
> $ sudo cp -r vmd-1.9.2 /usr/local/
> $ cd /usr/local/
> $ cd vmd-1.9.2
> $ sudo ./configure
> $ cd src/
> $ sudo make install
>
> Can you please correct me with the installation steps here.
>
> Many thanks
> Anu
>
>
> On Thu, Jul 14, 2016 at 4:59 PM, Axel Kohlmeyer <akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>>
> wrote:
>
> On Thu, Jul 14, 2016 at 11:51 AM, anu chandra <anu80125_at_gmail.com<mailto:anu80125_at_gmail.com>> wrote:
> Hello,
>
> Thanks for the replies.
>
> @John,
>
> I do have /tmp and /usr/tmp exist in the system. I have the following
> file
> in the VMD installation directory, and stride_LINUXAMD64 is present in
> it
>
> $ ls -l /usr/local/lib/vmd/
> total 49220
> -rw-------. 1 acn root 2020 Jul 11 17:09 Announcement
> drwxr-xr-x. 2 acn root 19 Jul 11 17:09 doc
> -rw-------. 1 acn root 143336 Jul 11 17:07 libexpat.so.0
> -rw-------. 1 acn root 131599 Jul 11 17:07 libhdf5_hl.so.7
> -rw-------. 1 acn root 2963577 Jul 11 17:07 libhdf5.so.7
> -rw-------. 1 acn root 14562968 Jul 11 17:07 liboptix.so.1
> -rw-------. 1 acn root 1696378 Jul 11 17:07 liboptixu.so.1
> -rw-------. 1 acn root 7605784 Jul 11 17:07 libprotobuf.so.7
> -rw-------. 1 acn root 652249 Jul 11 17:07 libsqlite3.so.0
> -rw-------. 1 acn root 7754 Jul 11 17:09 LICENSE
> drwx------. 5 acn root 50 Jul 11 17:07 plugins
> -rw-------. 1 acn root 15893 Jul 11 17:09 README
> drwx------. 8 acn root 88 Jul 11 17:09 scripts
> drwx------. 3 acn root 4096 Jul 11 17:09 shaders
> -rw-------. 1 acn root 160424 Jul 11 17:09 stride_LINUXAMD64
> -rw-------. 1 acn root 2184618 Jul 11 17:09 surf_LINUXAMD64
> -rw-------. 1 acn root 210440 Jul 11 17:09 tachyon_LINUXAMD64
> -rw-------. 1 acn root 3166 Jul 11 17:09 vmd_completion.dat
> -rwxr-xr-x. 1 root root 20028968 Jul 11 17:09 vmd_LINUXAMD64
>
>
> @Axel, thanks for the information. As you mentioned, I do understand
> the
> risk involved in using sudo. Since glxinfo and OpenGL application like
> VMD,
> pymol etc. was not working with regular user, I was just trying to find
> out
> the whether this happens with root user. As you suggested, I am looking
> around to find out the where things going wrong.
>
> just look at the listing above. this is all wrong!!
> you are missing executable and read permissions on pretty much
> anything that matters.
> ...and this is *exactly* what can go wrong through too liberal use of
> sudo.
>
> please see below how it should look like.
>
> [akohlmey_at_ws18 ]$ ls -l ~/.local/lib/vmd/
> total 49232
> -rw-r--r-- 1 akohlmey klein 2020 Jan 29 2015 Announcement
> drwxr-xr-x 2 akohlmey klein 4096 Jan 29 2015 doc
> -rwxr-xr-x 1 akohlmey klein 143336 Mar 1 2011 libexpat.so.0
> -rwxr-xr-x 1 akohlmey klein 131599 Feb 29 2012 libhdf5_hl.so.7
> -rwxr-xr-x 1 akohlmey klein 2963577 Feb 29 2012 libhdf5.so.7
> -rwxr-xr-x 1 akohlmey klein 14562968 Oct 7 2014 liboptix.so.1
> -rwxr-xr-x 1 akohlmey klein 1696378 Oct 7 2014 liboptixu.so.1
> -rwxr-xr-x 1 akohlmey klein 7605784 Feb 29 2012 libprotobuf.so.7
> -rwxr-xr-x 1 akohlmey klein 652249 Mar 5 2011 libsqlite3.so.0
> -rw-r--r-- 1 akohlmey klein 7754 Jan 29 2015 LICENSE
> drwxr-xr-x 5 akohlmey klein 4096 Dec 30 2014 plugins
> -rw-r--r-- 1 akohlmey klein 15893 Jan 29 2015 README
> drwxr-xr-x 8 akohlmey klein 4096 Jan 29 2015 scripts
> drwxr-xr-x 3 akohlmey klein 4096 Jan 29 2015 shaders
> -rwxr-xr-x 1 akohlmey klein 160424 Jan 29 2015 stride_LINUXAMD64
> -rwxr-xr-x 1 akohlmey klein 2184618 Jan 29 2015 surf_LINUXAMD64
> -rwxr-xr-x 1 akohlmey klein 210440 Jan 29 2015 tachyon_LINUXAMD64
> -rw-r--r-- 1 akohlmey klein 3166 Jan 29 2015 vmd_completion.dat
> -rwxr-xr-x 1 akohlmey klein 20028968 Jan 29 2015 vmd_LINUXAMD64
>
> the best approach now is to completely remove VMD and install it
> again, but correctly.
>
> axel.
>
>
>
> Many thanks
> Anu
>
> On Thu, Jul 14, 2016 at 4:31 PM, Axel Kohlmeyer <akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>>
> wrote:
>
> On Thu, Jul 14, 2016 at 7:30 AM, anu chandra <anu80125_at_gmail.com<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<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
> [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<mailto:akohlmey_at_gmail.com> http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA,
> USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com> http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com> http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
> 

-- 
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/