From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Wed Dec 03 2014 - 14:36:38 CST

Hi John,

Thanks for all research... For the moment, I see this only with VMD .. I will look into it tomorrow or on Friday and let you know

Best
Vlad

On December 3, 2014 9:34:31 PM CET, John Stone <johns_at_ks.uiuc.edu> wrote:
>Vlad,
> Here is further discussion of the XOpenIM() stuff in FLTK, pertaining
>to some potential performance problems with certain locales and the
>most recent versions of FLTK:
> https://groups.google.com/forum/#!topic/fltkgeneral/X1heD2dWaOw
>
>Do you get the same XOpenIM() error/warning if you run some of the
>FLTK example/demo applications, or only when running VMD?
>
>Cheers,
> John
>
>On Wed, Dec 03, 2014 at 02:31:20PM -0600, John Stone wrote:
>> 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/
>
>--
>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/

-- 
Sent from my Android device with K-9 Mail. Please excuse my brevity.