From: Dallas Warren (dallas.warren_at_monash.edu)
Date: Tue Feb 28 2017 - 19:08:46 CST

>From what I can tell, the no version information error is due to fact
vmd was complied with a latter (or different) version of libGL than
which I have installed on my machine. In order to solve that issue,
meant to compile vmd, so that it uses the local libraries etc.

Instructions on how to compile vmd here:
http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html

Have following installed, so that appears to tick the boxes of what is required.
tcl 8.6.1-4.2.1
FLTK 1.33-1.6
Mesa-libGL 11.2.2-166.1

Next step is to compile the plugins, as documented here:
http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/compiling.html

Issue I have here is where exactly are TCLINC and TCLLIB meant to be
pointing to? From what the instructions say, initially thought was
within what comes with vmd, but no .../lib/tcl or ..../lib/tcl/include
directories.

There is a tcl.h file in /usr/include so set TCLINC to that location.
But stumped where TCLLIB should be pointing to. There is a
/usr/lib64/tcl/tcl8.6 directory but pointing to that get a "file not
recognized: Is a directory" error when run "gmake LINUXAMD64
TCLINC=$TCLINC TCLLIB=$TCLLIB"

I can normally work my way through compiling things, but it's beyond
me this time.
Catch ya,

Dr. Dallas Warren

Drug Delivery, Disposition and Dynamics

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren_at_monash.edu

+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On 28 February 2017 at 11:32, Dallas Warren <dallas.warren_at_monash.edu> wrote:
> Suspect they are all related? A point in the direction of what I
> should be looking at, updating, compiling etc would be appreciated.
> Thank you.
>
> Seen mentioned on the list that the CUDA message came up for older
> versions of vmd (1.9.1), but it was being fixed in 1.9.2
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22958.html
>
> The libGL issue something about old versions of the nvidia driver left
> hanging around?
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22907.html
>
> Opensuse: 42.1
> Kernel: 4.1.36-44
> NVIDIA Driver: 375.26
>
> Upon starting vmd:
> /usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib64/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) 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, 12 CPUs detected.
> Info) CPU features: SSE2 AVX
> Info) Free system memory: 35GB (97%)
> Info) Creating CUDA device pool and initializing hardware...
> CUDA error: invalid device symbol, CUDAClearDevice.cu line 56
> Info) Detected 1 available CUDA accelerator:
> Info) [0] GeForce GTX 550 Ti 4 SM_2.1 @ 1.80 GHz, 956MB 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: GeForce GTX 550 Ti/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 (2048x2048x2048), Multitexture (4)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> after#0
>
> Upon selecting QuickSurf, other representations appear to work fine:
> terminate called after throwing an instance of 'thrust::system::system_error'
> what(): after cub_::DeviceRadixSort::SortPairs(0): invalid device function
> Abort
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Drug Delivery, Disposition and Dynamics
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.warren_at_monash.edu
>
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
>