VMD-L Mailing List

From: Matthew J. Comstock (comstock_at_pa.msu.edu)
Date: Wed May 28 2014 - 16:07:29 CDT

Ah, excellent! VMD 1.9.2a39 -64 runs perfectly so far with my graphics
card in Linux. No troubles at all.

Though I now notice that the behavior of the NewCartoon rep has changed
when displaying my dsDNA. The previous version, though I don＊t know why,
showed only every ~5 bases, whereas the new version is showing every base?
Perhaps the older version had a display bug?

Thanks!

Matt Comstock

On 5/28/14, 3:35 PM, "John Stone" <johns_at_ks.uiuc.edu> wrote:

>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
>> > can易t 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. Here易s 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 I易ve looked around the list and elsewhere to try to figure
>>out
>> > what I might be doing wrong, but I易m 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 couldn易t 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/