VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 18 2017 - 10:14:00 CDT

Hi,
  I assume that these are startup errors caused by "VolArea", so if
inserting the "after idle" prior to the the VolArea package inclusion
doesn't cure the problem, I would determine whether just commenting
out the VolArea-related extra startup commands alleviates those
errors or not. If it does, then you know that the issue is purely
related to VolArea and you can determine what needs to be fixed with
regard to VolArea to make the startup errors go away.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 18, 2017 at 12:39:09PM +0000, João Ribeiro wrote:
> Dear Rahul,
> make sure that the scripts in your .vmdrc are inside the "after idle"
> command (e.g. after idle {scripts}) and the paths that you have defined in
> your vmdrc file are valid.
> I hope this helps
> Best
> João
> On Mon, Sep 18, 2017 at 5:08 AM RAHUL SURESH <[1]drrahulsuresh_at_gmail.com>
> wrote:
>
> I have my VMD for CUDA downloaded and installed using he folowing
> commands
>
> ./configure
> cd src/
> sudo make install
>
> and on caling VMD i get the following message
>
> viji_at_viji-X10SRA-F-Invalid-entry-length-16-Fixed-up-to-11:~/Downloads/VMD-CUDA/vmd-1.9.3/src$
> vmd
> /usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/nvidia-375/libGL.so.1: no
> version information available (required by
> /usr/local/lib/vmd/vmd_LINUXAMD64)
> Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
> Info)
> [2]http://www.ks.uiuc.edu/Research/vmd/Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
> Info) Email questions and bug reports to
> [3]vmd_at_ks.uiuc.edu         Â
> Info) Please include this reference in published work using VMD:Â Â
> Info)   Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Â
> Info)Â Â Â Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 16 CPUs detected.
> Info)Â Â CPU features: SSE2 AVX AVX2 FMA
> Info) Free system memory: 61GB (96%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator:
> Info) [0] Quadro K1200Â Â Â Â Â Â Â 4 SM_5.0 @ 1.03 GHz, 3.9GB RAM,
> KTO, AE1, ZCP
> 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 K1200/PCIe/SSE2
> Info)Â Â Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> Info)Â Â Full GLSL rendering mode is available.
> Info)Â Â Textures: 2-D (16384x16384), 3-D (4096x4096x4096),
> Multitexture (4)
> Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> Info)Â Â Compiling 1 OptiX shaders on 1 target GPU...
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> couldn't load file
> "/home/viji/Downloads/vmd-1.9.3/plugins/LINUXAMD64/Routines/Other/sqlite/64B/libtclsqlite3.so":
> /home/viji/Downloads/vmd-1.9.3/plugins/LINUXAMD64/Routines/Other/sqlite/64B/libtclsqlite3.so:
> cannot open shared object file: No such file or directory
> /usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
> /usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
> /usr/local/lib/vmd/scripts/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
> /usr/local/lib/vmd/plugins/noarch/tcl
> /home/viji/Downloads/vmd-1.9.3/plugins/LINUXAMD64/
> /usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
> /usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
> /usr/local/lib/vmd/scripts/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
> /usr/local/lib/vmd/plugins/noarch/tcl
> /home/viji/Downloads/vmd-1.9.3/plugins/LINUXAMD64/
> /home/viji/Downloads/vmd-1.9.3/plugins/LINUXAMD64/Routines/Lib
> /usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
> /usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
> /usr/local/lib/vmd/scripts/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
> /usr/local/lib/vmd/plugins/noarch/tcl
> /home/viji/Downloads/vmd-1.9.3/plugins/LINUXAMD64/
> /home/viji/Downloads/vmd-1.9.3/plugins/LINUXAMD64/Routines/Lib
> /home/viji/Downloads/vmd-1.9.3/plugins/LINUXAMD64/Routines/Other
> /usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
> /usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
> /usr/local/lib/vmd/scripts/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
> /usr/local/lib/vmd/plugins/noarch/tcl
> /home/viji/Downloads/vmd-1.9.3/plugins/LINUXAMD64/
> /home/viji/Downloads/vmd-1.9.3/plugins/LINUXAMD64/Routines/Lib
> /home/viji/Downloads/vmd-1.9.3/plugins/LINUXAMD64/Routines/Other
> /home/viji/Downloads/vmd-1.9.3/plugins/LINUXAMD64/Routines/Other/graph
> The VolArea package could not be loaded:
>
> vmd >
>
> What does the above thing suggests?
> Any post regarding this would be really hellpful
> --
> Regards,
> Rahul Suresh
> Research Scholar
> Bharathiar University
> Coimbatore
>
> --
> â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦â*¦...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> [4]jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
>
> References
>
> Visible links
> 1. mailto:drrahulsuresh_at_gmail.com
> 2. http://www.ks.uiuc.edu/Research/vmd/
> 3. mailto:vmd_at_ks.uiuc.edu
> 4. mailto:jribeiro_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
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/