VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 03 2014 - 14:31:21 CST

Vlad,
  I did some googling, and it appears that FLTK 1.3.x might be the source of
the "XOpenIM() failed" message:
  https://www.mail-archive.com/fltk-bugs@easysw.com/msg04795.html

That email chain indicates they fixed the problem, but perhaps they didn't
fix it in all cases, or some of the changes that were made were either
missing for FLTK 1.3.2, or maybe they were reverted or lost during some
other updates. If you can try a different FLTK version, you might be
able to prove whether or not FLTK is the code that's generating the warning.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 03, 2014 at 09:23:30PM +0100, Vlad Cojocaru wrote:
> 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) [1]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
> RAPntgenstrasse 20, 48149 MA 1/4nster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at][2]mpi-muenster.mpg.de
> [3]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
> RAPntgenstrasse 20, 48149 MA 1/4nster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at][4]mpi-muenster.mpg.de
> [5]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
> RAPntgenstrasse 20, 48149 MA 1/4nster, Germany
> Tel: +49-251-70365-324; Fax:
> +49-251-70365-399
> Email: vlad.cojocaru[at][6]mpi-muenster.mpg.de
> [7]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
> RAPntgenstrasse 20, 48149 MA 1/4nster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at][8]mpi-muenster.mpg.de
>
> --
> Sent from my Android device with K-9 Mail. Please excuse my brevity.
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/Research/vmd
> 2. http://mpi-muenster.mpg.de/
> 3. http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
> 4. http://mpi-muenster.mpg.de/
> 5. http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
> 6. http://mpi-muenster.mpg.de/
> 7. http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
> 8. http://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/