VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 04 2010 - 13:54:49 CST

Hi,
  The existing VMD code checks both for computeModeProhibited and
for the kernel execution timeout flag (used for display), so unless
the nvidia-smi tool and driver 'forgot' the setting by the time you
ran VMD (there was a bug of this sort some time back), this should not
affect the behavior at all. If setting the VMDCUDANODISPLAYGPUS
environment variable makes a difference, please let me know, as that
would be an unexpected behavior given how I wrote the code.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 04, 2010 at 02:16:58PM -0500, Axel Kohlmeyer wrote:
> On Thu, 2010-03-04 at 19:54 +0200, Filippo Federici Canova wrote:
> > Hi,
> >
> > I actually tried both with the Quadro on and off,
> > and by off i mean i disabled it with the
> > nvidia-smi command line program to set it on
> > 'prohibited'. the driver is 190.53 and the
> > latest cuda sdk was installed.
>
> that may explain the error message. you see.
>
> try setting VMDCUDANODISPLAYGPUS instead or
> at the same time to exclude the NVS from
> within VMD.
>
> cheers,
> axel.
>
> >
> > cheers
> >
> > Filippo
> >
> > Quoting John Stone <johns_at_ks.uiuc.edu>:
> >
> > >
> > > Hi,
> > > I suspect what is happening there is that the Quadro NVS 295 is
> > > running out of memory. I would suggest excluding it from your pool
> > > of CUDA GPUs. Also, what driver version are you running on your machine?
> > >
> > > Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Thu, Mar 04, 2010 at 06:29:44PM +0200, Filippo Federici wrote:
> > >> Hi,
> > >> I just tried to plot some isosurfaces of molecular orbitals,
> > >> with a very fine grid. Since the CPU is also very fast
> > >> (Core i7) is hard to tell if there is a performance improvement.
> > >> I still get that error on startup:
> > >>
> > >> Info) Detected 3 available CUDA accelerators:
> > >> Info) [0] Tesla C1060 30 SM_1.3 @ 1.30 GHz, 4095MB RAM, OIO,
> > >> ZCP
> > >> Info) [1] Quadro NVS 295 1 SM_1.1 @ 1.30 GHz, 255MB RAM, KTO
> > >> Info) [2] Tesla C1060 30 SM_1.3 @ 1.30 GHz, 4095MB RAM, OIO,
> > >> ZCP
> > >> Info) Creating CUDA device pool and initializing hardware...
> > >> CUDA error: no CUDA-capable device is available, line 62
> > >>
> > >> so why 2 Tesla C1060 are not CUDA capable devices according to line 62?
> > >>
> > >> thanks
> > >>
> > >> Filippo
> > >>
> > >> On Thu, 2010-03-04 at 08:11 -0600, John Stone wrote:
> > >> > Hi,
> > >> > Only the electrostatics, molecular orbital rendering, and
> > >> implicit ligand
> > >> > sampling features are accelerated by CUDA in VMD 1.8.7, so those are the
> > >> > only VMD tests that are meaningful for measuring CUDA performance.
> > >> >
> > >> > Try using the commands "volmap coulombmsm", "volmap ils" or the "Orbital"
> > >> > representation, all of these will use CUDA automatically.
> > >> >
> > >> > Please see this page for more information:
> > >> > http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.7/cuda.html
> > >> >
> > >> > Let me know if you have questions.
> > >> >
> > >> > Cheers,
> > >> > John
> > >> >
> > >> >
> > >> >
> > >> > On Thu, Mar 04, 2010 at 09:18:14AM +0200, Filippo Federici wrote:
> > >> > > Good morning,
> > >> > >
> > >> > > we have installed a CUDA workstation and we are done
> > >> > > testing it, but we have some issues with VMD.
> > >> > > I downloaded the binary (LINUX64 CUDA) and apparently
> > >> > > it starts but i see no GPU improvements.
> > >> > > On startup the output tells:
> > >> > >
> > >> > > Info) -------------------------------------------------------------
> > >> > > Info) Multithreading available, 8 CPUs detected.
> > >> > > Info) Free system memory: 5269MB (66%)
> > >> > > Info) Detected 3 available CUDA accelerators:
> > >> > > Info) [0] Tesla C1060 30 SM_1.3 @ 1.30 GHz, 4095MB RAM, OIO,
> > >> > > ZCP
> > >> > > Info) [1] Quadro NVS 295 1 SM_1.1 @ 1.30 GHz, 255MB RAM, KTO
> > >> > > Info) [2] Tesla C1060 30 SM_1.3 @ 1.30 GHz, 4095MB RAM, OIO,
> > >> > > ZCP
> > >> > > Info) Creating CUDA device pool and initializing hardware...
> > >> > > CUDA error: no CUDA-capable device is available, line 62
> > >> > > Warning) Detected X11 'Composite' extension: if incorrect display occurs
> > >> > > Warning) try disabling this optional X server feature.
> > >> > > Info) OpenGL renderer: Quadro NVS 295/PCI/SSE2
> > >> > > Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF)
> > >> > > Info) Full GLSL rendering mode is available.
> > >> > > Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture
> > >> > > (4)
> > >> > > vmd > Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
> > >> > > ---------------------------------------------------------------------
> > >> > > as you can see we have 2 Tesla GPUs and a Quadro NVS 295 for rendering.
> > >> > > The quadro is set to 'prohibited', but I tried to leave it on too with
> > >> > > no luck.
> > >> > > The driver is 190.53, the CUDA SDK samples run correctly, and I can run
> > >> > > some piece of code I wrote with no problem.
> > >> > > Any suggestion?!
> > >> > >
> > >> > > thanks in advance
> > >> > >
> > >> > > Filippo
> > >> > >
> > >> > >
> > >> >
> > >
> > > --
> > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > Beckman Institute for Advanced Science and Technology
> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > >
> >
> >
> >
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078