From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 28 2014 - 14:35:00 CDT

Oops, I somehow missed that your machine is setup dual-boot, I thought you were
running Windows. If you're running Linux, you can get a test build following
the URL below right now:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 28, 2014 at 02:33:45PM -0500, John Stone wrote:
> You'll need to run one of the new pre-release versions of VMD 1.9.2 in order
> to use CUDA on the latest GPUs, because the VMD 1.9.1 builds were done
> using an older CUDA toolkit and at that time we didn't know how to ensure
> forward binary compatibility. I expect to have a new CUDA-enabled Windows
> build posted in the next few days, accessible by the steps outlined here:
> http://www.ks.uiuc.edu/Research/vmd/alpha/
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, May 28, 2014 at 07:06:23PM +0000, Matthew J. Comstock wrote:
> > Hello,
> >
> > I am having trouble getting CUDA to work with my new desktop graphics card
> > in Linux.
> >
> > I just recently assembled a desktop for fairly basic manipulation and
> > visualization of protein structures in VMD. I have been doing these tasks
> > (fairly well) on a MB Air. I have been making movies from trajectories
> > using the quick surf rep and the Tachyon internal ray tracer. The movies
> > look awesome (at least I think so) but take a lot of time. My goal with
> > the desktop was to speed up the process in part with more main RAM (I have
> > 32 GB now) and a discrete graphics card with CUDA processing. I see that
> > both quick surf and Tachyon are sped up with CUDA.
> >
> > I bought components and assembled the desktop with seemingly no trouble. I
> > have Win7 installed on a partition without issues. The latest NVIDIA
> > drivers (337.88) are installed along with VMD 1.9.1. The graphics card is
> > a Gigabyte Geforce GTX770. In windows, VMD correctly identifies my
> > graphics card, including the CUDA processor, and runs without error. I do
> > in fact see great speed up playing trajectories with quick surf using the
> > gpu (beautifully smooth high speed playback now - thanks!). But of course
> > in Windows I am limited to only 4 GB of my RAM (only a 32-bit VMD build
> > seems to be available). And who wants to run VMD in Windows anyway?
> >
> > I have also installed Fedora (both versions 18 and 20) and Ubuntu. For
> > unknown reasons no version of Fedora I install can see my ethernet card. I
> > canšt solve that mysterious problem (and not related to VMD) - hence the
> > Ubuntu (has no such problems). On Ubuntu I have installed the latest
> > (current - 304.117, also a few older versions from packages, and the
> > drivers downloaded directly from NVIDIA included in the CUDA 6.0 install)
> > NVIDIA drivers, which all appear to run just fine. I installed VMD 1.9.1
> > 64-bit, which also runs just fine, recognizing my card and the CUDA
> > processor. EXCEPT on startup it gives a CUDA error. Herešs the startup
> > output:
> >
> > Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> > 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, 8 CPUs detected.
> > Info) Free system memory: 31023MB (96%)
> > Info) Creating CUDA device pool and initializing hardware...
> > CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
> > Info) Detected 1 available CUDA accelerator:
> > Info) [0] GeForce GTX 770 8 SM_3.0 @ 1.19 GHz, 4.0GB RAM, KTO, OIO, ZCP
> > Warning) Detected X11 'Composite' extension: if incorrect display occurs
> > Warning) try disabling this optional X server feature.
> > Info) OpenGL renderer: GeForce GTX 770/PCIe/SSE2
> > Info) Features: STENCIL MSAA(16) 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
> >
> >
> > If I try to do a QuickSurf rep I get the following error:
> >
> > QuickSurf: R*1.0, I=0.5, H=1.0 Pad: 3.6 minR: 1.5 maxR: 1.8)
> > GridSZ: ( 115 155 134) BBox: (-29.7 -10.8 -32.4)->(84.3 143.2 100.6)
> > CUDA error: invalid device function , CUDAQuickSurf.cu line 783
> > Computing density map grid on CPUs .Running marching cubes on CPU...
> > Info) QuickSurf: 0.126 [pre:0.001 vol:0.065 gr:0.015 mc:0.03 mcv:0.012]
> >
> >
> > On a Tachyon internal render I get no errors, but also no indication it is
> > using either the GPU or the CPU.
> >
> > Of course Išve looked around the list and elsewhere to try to figure out
> > what I might be doing wrong, but Išm at a loss now. Has anyone else
> > encountered and solved a similar problem? Did I just pick a bad graphics
> > card with a CUDA driver problem? That would be frustrating. I tried to
> > find a note somewhere about recently verified builds (i.e., hardware known
> > to have no issues) but couldnšt find anything like that.
> >
> > Any advice would be greatly appreciated. Thank you.
> >
> > Matt Comstock
> >
> >
> >
> >
>
> --
> 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/

-- 
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/