VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 14 2016 - 16:32:26 CDT

On Thu, Jul 14, 2016 at 5:08 PM, anu chandra <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> 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>
>> wrote:
>>>
>>> On Thu, Jul 14, 2016 at 11:51 AM, anu chandra <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>
>>> > wrote:
>>> >>
>>> >> 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.
>>> >
>>> >
>>>
>>>
>>>
>>> --
>>> 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.
>>
>>
> 

-- 
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.