From: Matthew J. Comstock (
Date: Wed May 28 2014 - 14:06:23 CDT


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 anywayŠ

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
canıt 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. Hereıs the startup

Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
Info) Email questions and bug reports to
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, 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) 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 , 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 Iıve looked around the list and elsewhere to try to figure out
what I might be doing wrong, but Iım 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 couldnıt find anything like that.

Any advice would be greatly appreciated. Thank you.

Matt Comstock