VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Wed Dec 03 2014 - 14:23:30 CST

Hi John,

I dont remember to have had any issue with the on-the-fly recognition of CUDA devices before on openSUSE-12.X ... I dont remember exactly now if users were automatically added to the "video" group which may explain why I did not have issues (and dont have machines with earlier OS anymore)

As for the XOpenIM issue, I initially thought it is related to the CUDA stuff ... But other than that, I did not see any issue with VMD functionality so far. So, I'll ignore it for now ... If I notice anything again, I will get back to you and the list

Best,
Vlad

On December 3, 2014 9:04:03 PM CET, John Stone <johns_at_ks.uiuc.edu> wrote:
>Vlad,
> Is the device node permission setting behavior different between the
>old revs of OpenSuse you used before and the new one? If so, this is
>an
>interesting thing to note. I still have no idea what to tell you about
>the "XOpenIM()" error you see, since that presumably has nothing to do
>with CUDA or the GPU device permissions and is more likely an issue of
>compatibility between your X11 and the FLTK/Tcl/Tk libraries you're
>compiling against.
>
>Cheers,
> John
>
>On Wed, Dec 03, 2014 at 09:00:49PM +0100, Vlad Cojocaru wrote:
>> Thanks John and Axel, ...
>>
>> Changing permissions on /dev/nvidia* (chmod o+rw /dev/nvidia*) solved
>
>> the issue. The permissions were rw only for the user "root" and group
>
>> "video" .... An alternative solution maybe to add user "vlad" to
>group
>> "video" but did not test yet.
>>
>> Best
>> Vlad
>>
>>
>> On 12/03/2014 08:21 PM, John Stone wrote:
>> >If you get no output when running as vlad, that may explain
>> >what is going wrong with VMD. Are the permissions set correctly
>> >on the GPU device nodes when you login as vlad? If you can't
>> >run 'nvidia-smi' as 'vlad', then you won't be able to get CUDA
>working
>> >as 'vlad' either. You need to figure out what's going wrong there
>and
>> >correct file permissions or whatever it is that's preventing it from
>
>> >working.
>> >
>> >Cheers,
>> > John Stone
>> > vmd_at_ks.uiuc.edu
>> >
>> >On Wed, Dec 03, 2014 at 07:50:06PM +0100, Vlad Cojocaru wrote:
>> >>Sorry John,
>> >>
>> >>I was running as user "vlad" and that did not produce any output ..
>> >>Running as root I get this output below (nothing that I notice to
>be
>> >>wrong):
>> >>
>> >>Best
>> >>Vlad
>> >>
>> >>Wed Dec 3 19:48:41 2014
>> >>+------------------------------------------------------+
>> >>| NVIDIA-SMI 340.46 Driver Version: 340.46 |
>>
>>>|-------------------------------+----------------------+----------------------+
>> >>| GPU Name Persistence-M| Bus-Id Disp.A | Volatile
>> >>Uncorr. ECC |
>> >>| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
>> >>Compute M. |
>>
>>>|===============================+======================+======================|
>> >>| 0 Quadro K4000 Off | 0000:02:00.0 On
>> >>| N/A |
>> >>| 30% 46C P8 23W / 87W | 1448MiB / 3071MiB | 3%
>Default |
>>
>>>+-------------------------------+----------------------+----------------------+
>> >>
>>
>>>+-----------------------------------------------------------------------------+
>> >>| Compute processes: GPU Memory |
>> >>| GPU PID Process name Usage |
>>
>>>|=============================================================================|
>> >>| No running compute processes
>> >>found |
>>
>>>+-----------------------------------------------------------------------------+
>> >>
>> >>
>> >>
>> >>On 12/03/2014 07:47 PM, Vlad Cojocaru wrote:
>> >>>Hi John,
>> >>>
>> >>>NVIDIA driver: 340.46
>> >>>
>> >>>Weirdly, "nvidia-smi" does not produce any output whatsoever ...
>> >>>There shouldn't be any special compute nodes. This is my own
>> >>>workstation ...
>> >>>
>> >>>Best
>> >>>Vlad
>> >>>
>> >>>
>> >>>On 12/03/2014 07:34 PM, John Stone wrote:
>> >>>>Vlad,
>> >>>> Thanks. What NVIDIA driver version is installed on this
>machine?
>> >>>>If you run "nvidia-smi", does it print any warnings or errors,
>and
>> >>>>do you see all of your GPUs listed? Are any set for "prohibited"
>> >>>>or "exclusive" compute mode?
>> >>>>
>> >>>>Cheers,
>> >>>> John Stone
>> >>>> vmd_at_ks.uiuc.edu
>> >>>>
>> >>>>On Wed, Dec 03, 2014 at 07:27:55PM +0100, Vlad Cojocaru wrote:
>> >>>>>Hi John,
>> >>>>>
>> >>>>>These are the options I used (same as for all my previous
>compilations
>> >>>>>that worked just fine on openSUSE 12.X):
>> >>>>>
>> >>>>>LINUXAMD64 OPENGL FLTK TK ACTC CUDA OPENCL IMD XINERAMA XINPUT
>> >>>>>LIBTACHYON NETCDF COLVARS TCL PYTHON PTHREADS NUMPY LP64
>> >>>>>
>> >>>>>My system has a standard openSUSE 13.1 with tcl 8.6 and Fltk
>1.3.2, and
>> >>>>>CUDA 6.5.14 .. I am not aware of any internationalized input
>scheme
>> >>>>>setup ....
>> >>>>>
>> >>>>>Best
>> >>>>>Vlad
>> >>>>>
>> >>>>>On 12/03/2014 05:26 PM, John Stone wrote:
>> >>>>>>Vlad,
>> >>>>>> What do you get when you run this command:
>> >>>>>>vmdinfo options
>> >>>>>>
>> >>>>>>Cheers,
>> >>>>>> John Stone
>> >>>>>>
>> >>>>>>On Wed, Dec 03, 2014 at 01:47:01PM +0100, Vlad Cojocaru wrote:
>> >>>>>>>Dear all,
>> >>>>>>>
>> >>>>>>>I am experiencing some issues with running VMD with CUDA
>> >>>>>>>acceleration on
>> >>>>>>>my machine. I compiled from source on linux x86_64 (openSUSE
>13.1)
>> >>>>>>>against CUDA 6.5.14 ...NVIDIA driver 340.46 ... At
>compilation, no
>> >>>>>>>issues whatsoever. However, every time I try to run VMD I get
>the
>> >>>>>>>error
>> >>>>>>>below. The program runs fine but CUDA acceleration is not
>available.
>> >>>>>>>
>> >>>>>>>Has anybody encountered a similar issue ? If yes, any idea how
>to
>> >>>>>>>fix it ?
>> >>>>>>>
>> >>>>>>>Thanks in advance
>> >>>>>>>
>> >>>>>>>Best wishes
>> >>>>>>>Vlad
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>Info) VMD for LINUXAMD64, version 1.9.2beta1 (October 23,
>2014)
>> >>>>>>>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, 24 CPUs detected.
>> >>>>>>>Info) Free system memory: 56003MB (86%)
>> >>>>>>>XOpenIM() failed
>> >>>>>>>Info) No CUDA accelerator devices available.
>> >>>>>>>Info) OpenGL renderer: Quadro K4000/PCIe/SSE2
>> >>>>>>>Info) Features: STENCIL STEREO MSAA(4) MDE MTX NPOT PP PS
>> >>>>>>>GLSL(OVFG)
>> >>>>>>>Info) Full GLSL rendering mode is available.
>> >>>>>>>Info) Textures: 2-D (16384x16384), 3-D (4096x4096x4096),
>> >>>>>>>Multitexture
>> >>>>>>>(4)
>> >>>>>>>
>> >>>>>>>--
>> >>>>>>>Dr. Vlad Cojocaru
>> >>>>>>>Computational Structural Biology Laboratory
>> >>>>>>>Department of Cell and Developmental Biology
>> >>>>>>>Max Planck Institute for Molecular Biomedicine
>> >>>>>>>Röntgenstrasse 20, 48149 Münster, Germany
>> >>>>>>>Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> >>>>>>>Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>
>>>>>>>>http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>> >>>>>--
>> >>>>>Dr. Vlad Cojocaru
>> >>>>>Computational Structural Biology Laboratory
>> >>>>>Department of Cell and Developmental Biology
>> >>>>>Max Planck Institute for Molecular Biomedicine
>> >>>>>Röntgenstrasse 20, 48149 Münster, Germany
>> >>>>>Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> >>>>>Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> >>>>>http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>> >>--
>> >>Dr. Vlad Cojocaru
>> >>Computational Structural Biology Laboratory
>> >>Department of Cell and Developmental Biology
>> >>Max Planck Institute for Molecular Biomedicine
>> >>Röntgenstrasse 20, 48149 Münster, Germany
>> >>Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> >>Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> >>http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>>
>> --
>> Dr. Vlad Cojocaru
>> Max Planck Institute for Molecular Biomedicine
>> Department of Cell and Developmental Biology
>> Röntgenstrasse 20, 48149 Münster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>
>--
>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/ 

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