VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 28 2014 - 16:09:48 CDT

Matt,
  If you send me your structure file, I could have a look, but most likely
this is because we have made changes so that VMD recognizes more atom names
used in recent versions of tools like AMBER etc.

Cheers,
  John

On Wed, May 28, 2014 at 09:07:29PM +0000, Matthew J. Comstock wrote:
> 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
> >> > 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/
> 

-- 
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/