VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 22 2017 - 12:09:56 CDT

Dallas, Josh,
  Sorry for the late reply, I was away for the eclipse yesterday and
didn't get home until after midnight due to the "carmageddon" on the
highways from huge numbers of people similarly returning home. :-)

The GTX 550 Ti shown in the startup messages is too old for the current
versions of VMD (because they are based on current versions of OptiX,
which no longer support the very old GPUs). Is this machine a laptop,
or is it a desktop system of some kind? If it is a desktop, then
the easiest solution is to get a newer GPU. If it s a laptop, then
you're probably in the same situation I am, where you have a 5+ year
old machine that still works for the most part, and it may be that
you'll need to update it for reasons of modern software compatibility
rather than because it has actually failed in some way. I have a
personal laptop with a GT560M that is no longer supported, so I
know how this goes.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 22, 2017 at 11:59:58AM +1000, Dallas Warren wrote:
> Thank you for the reply Josh.
>
> Okay, looks like a previous issue I have had is coming back to haunt
> me. I had problems with some rendering, and to avoid that issued set
> VMDNOCUDA.
>
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28339.html
>
> When VMDNOCUDA is set, which is how I have been running vmd, I get the
> following.
>
> /usr/local/lib/vmd/vmd_LINUXAMD64: /usr/X11R6/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: 30GB (85%)
> Info) VMDNOCUDA environment variable is set, CUDA support disabled.
> Info) No CUDA accelerator devices available.
> 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
>
> If I don't set VMDNOCUDA then this is what I get, and the optix
> rendering option is still not available on the render drop down menu.
>
> /usr/local/lib/vmd/vmd_LINUXAMD64: /usr/X11R6/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: 30GB (85%)
> 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, 961MB 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
>
> Looks like I need to get a new graphics card, current one is getting a
> bit long in the tooth.
> 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
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
>
>
> On 22 August 2017 at 11:18, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov> wrote:
> > Hi Dallas,
> >
> > The short answer is yes. Based on the configure options of both the precompiled Linux binaries and your configure options, the OptiX renderer ought to show up on your list of available renderers. However, this does depend on VMD finding the graphics card at startup. I've bolded the relevant lines that I get at startup.
> >
> > josh_at_orange:~$ vmd
> > Info) VMD for LINUXAMD64, version 1.9.3 (August 10, 2017)
> > 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, 20 CPUs detected.
> > Info) Free system memory: 53GB (84%)
> > Info) Creating CUDA device pool and initializing hardware...
> > Info) Detected 1 available CUDA accelerator:
> > Info) [0] Quadro M5000 16 SM_5.2 @ 1.04 GHz, 7.9GB RAM, KTO, AE2, 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 M5000/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) Detected 1 available TachyonL/OptiX ray tracing accelerator
> > Info) Compiling 1 OptiX shaders on 1 target GPU...
> >
> > How does this compare with what you see?
> >
> > -Josh
> >
> > On 08/21/2017 07:14 PM, Dallas Warren wrote:
> >
> > Should the TachyonL-OptiX renderer option be visible in the render
> > window drop down options with the default installation of vmd?
> >
> > Here is a screen shot of the drop down options that appear:
> > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpbs.twimg.com%2Fmedia%2FDHywOqPUwAE4trS.jpg%3Alarge&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C6ce0fe430b8f448f428408d4e8fb1010%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636389612389865757&sdata=fOvoj3fVd1dZM7k2jMZRtWaMmrJa58wgii43Ku20vU8%3D&reserved=0
> >
> > My configure options were:
> >
> > using configure.options: LINUXAMD64 OPENGL OPENGLPBUFFER FLTK TK ACTC
> > CUDA IMD LIBSBALL XINERAMA XINPUT LIBOPTIX LIBOSPRAY LIBTACHYON VRPN
> > NETCDF COLVARS TCL PYTHON PTHREADS NUMPY SILENT ICC
> >
> > FYI, I am looking to generate some 3D videos, following instructions
> > here: https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2Fminitutorials%2Fvrmovies%2F&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C6ce0fe430b8f448f428408d4e8fb1010%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636389612389865757&sdata=%2FlzvTFXvwgLO%2F9P4JuLo1CZ%2BIDYkfey2wlIoA9WT3bE%3D&reserved=0
> >
> > 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<mailto:dallas.warren_at_monash.edu>
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to resemble a nail.
> >
> >
> >
> > 

-- 
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/