VMD-L Mailing List

From: Anoop Krishnan (anoopnm007_at_gmail.com)
Date: Sat Sep 20 2014 - 01:43:04 CDT

Also, in the crash report, the file is mentioned as -
usr/lib/xorg/modules/extensions/libglx.so which corresponds to the package
xserver-xorg-core.
It will be great if you can tell me whether I have installed the graphics
card driver wrong or any other such mistakes.

Thanking you
Regards

On Sat, Sep 20, 2014 at 11:12 AM, Anoop Krishnan <anoopnm007_at_gmail.com>
wrote:

> Hi,
>
> Thank you for the reply. I installed the latest VMD. I'm still struggling
> with the issue that the pc crashes when I click on any of the options in
> the Extension tab. The title of the error report is 'Xorg crashed with
> SIGABRT'.
>
> This is the VMD startup message.
>
> Info) VMD for LINUX, version 1.9.2beta1 (September 12, 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, 2 CPUs detected.
> Info) Free system memory: 3291MB (81%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator:
> Info) [0] GeForce GTX 750 Ti 5 SM_5.0 @ 1.11 GHz, 2.0GB RAM, KTO, AE1, ZCP
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this X server option. Most OpenGL drivers
> Warning) disable stereoscopic display when 'Composite' is enabled.
> Info) OpenGL renderer: GeForce GTX 750 Ti/PCIe/SSE2
> Info) Features: STENCIL MSAA(4) 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/vmd1_2b/plugins/LINUX/molfile
>
>
> Regards
>
> On Sat, Sep 20, 2014 at 10:15 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>> Hi,
>> Try running the new VMD 1.9.2 beta 1 version, that should cure the
>> warnings
>> you get about CUDA on your GeForce 750 Ti.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Thu, Aug 21, 2014 at 10:00:37AM +0530, Anoop Krishnan wrote:
>> > The startup messages in the terminal are as follows:
>> >
>> > Info) VMD for LINUX, version 1.9.1 (February 1, 2012)
>> > Info)
>> > [1]http://www.ks.uiuc.edu/Research/vmd/A A A A A A A A A A A A A A
>> A A A A A A A A A A
>> > Info) Email questions and bug reports to
>> > [2]vmd_at_ks.uiuc.eduA A A A A A A A A A
>> > Info) Please include this reference in published work using VMD:A A
>> > Info)A A A Humphrey, W., Dalke, A. and Schulten, K., `VMD - VisualA
>> A
>> > Info)A A A Molecular Dynamics', J. Molec. Graphics 1996, 14.1,
>> 33-38.
>> > Info) -------------------------------------------------------------
>> > Info) Multithreading available, 2 CPUs detected.
>> > Info) Free system memory: 2712MB (67%)
>> > 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 750 TiA 5 SM_5.0 @ 1.11 GHz, 2.0GB 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 750 Ti/PCIe/SSE2
>> > Info)A A Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS
>> GLSL(OVFGS)
>> > Info)A A Full GLSL rendering mode is available.
>> > Info)A A Textures: 2-D (16384x16384), 3-D (2048x2048x2048),
>> Multitexture
>> > (4)
>> > Info) Dynamically loaded 2 plugins in directory:
>> > Info) /usr/local/lib/vmd/plugins/LINUX/molfile
>> >
>> > I ignored the CUDA error because, I was using VMD only for
>> visualization
>> > and post processing or creating the input coordinates. Since, I'm not
>> > using VMD for any computation, I thought it is fine to ignore it. I
>> > reinstalled the driver, now. However, the error is still persisting.
>> Can
>> > you please guide me through the steps to install the graphics card
>> and VMD
>> > if it is any different from what is mentioned in:
>> > [3]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21891.html
>> >
>> > Regards
>> >
>> > On Wed, Aug 20, 2014 at 10:34 AM, John Stone <[4]johns_at_ks.uiuc.edu>
>> wrote:
>> >
>> > Can you cut/paste the VMD startup messages that are printed in the
>> > text console and send them in email?A That may be informative.
>> >
>> > I have run VMD on a GeForce GTX 750 on Linux without trouble, but
>> > I used a different minor rev of the video driver than the one
>> you're
>> > using.
>> >
>> > Cheers,
>> > A John
>> > On Wed, Aug 20, 2014 at 10:21:35AM +0530, Anoop Krishnan wrote:
>> > >A A Thanks for the clarification. Let me try to trouble shoot it
>> > then.
>> > >A A I'm running the latest NVIDIA driver which I installed with
>> -
>> > >A A NVIDIA-Linux-x86-340.24.run
>> > >A A I followed the instructions ion the VMD mailing list
>> exactly.
>> > Still I was
>> > >A A finding the same trouble.
>> > >
>> > >A A Regards
>> > >
>> > >A A On Wed, Aug 20, 2014 at 1:56 AM, John Stone
>> > <[1][5]johns_at_ks.uiuc.edu> wrote:
>> > >
>> > >A A A Hi,
>> > >A A A AA If the whole windowing system crashes, that would be
>> an
>> > indication of
>> > >A A A problems with your video driver, not VMD.AA Are you
>> running
>> > the
>> > >A A A latest NVIDIA driver, or are you using one fo the open
>> source
>> > >A A A video drivers such as nouveau?
>> > >
>> > >A A A Cheers,
>> > >A A A AA John Stone
>> > >A A A AA [2][6]vmd_at_ks.uiuc.edu
>> > >
>> > >A A A On Thu, Aug 14, 2014 at 05:19:57PM +0530, Anoop Krishnan
>> > wrote:
>> > >A A A >AA AA I have been using VMD for past four years in my
>> > Pentium Dual-Core
>> > >A A A CPU
>> > >A A A >AA AA (E5300_at_2.6 GHz * 2) with 4 GB RAM and Ubuntu
>> 12.04 -
>> > 32 bit.
>> > >A A A Recently, I
>> > >A A A >AA AA added a graphics card NVIDIA GeForce GTX 750 Ti
>> to
>> > the system.
>> > >A A A Once, I
>> > >A A A >AA AA have installed the graphics card VMD is working
>> > smoothly.
>> > >A A A However, I'm
>> > >A A A >AA AA unable to access the Extensions tab in VMD.
>> Once I
>> > click on any
>> > >A A A of the
>> > >A A A >AA AA options in Extension such as Movie maker or
>> Nanotube
>> > builder,
>> > >A A A system
>> > >A A A >AA AA instantly crashes and goes to the login screen.
>> > >A A A >
>> > >A A A >AA AA I have been unable to figure out the problem as
>> the
>> > graphics card
>> > >A A A and VMD
>> > >A A A >AA AA are otherwise working smooth. It would be great
>> if
>> > someone can
>> > >A A A suggest any
>> > >A A A >AA AA solution to this issue.
>> > >A A A >
>> > >A A A >AA AA Thank you
>> > >A A A >AA AA Regards
>> > >A A A >AA AA --
>> > >A A A >AA AA Anoop Krishnan N M
>> > >A A A --
>> > >A A A NIH Center for Macromolecular Modeling and Bioinformatics
>> > >A A A Beckman Institute for Advanced Science and Technology
>> > >A A A University of Illinois, 405 N. Mathews Ave, Urbana, IL
>> 61801
>> > >A A A [3][7]http://www.ks.uiuc.edu/~johns/AA AA AA AA AA
>> A
>> > Phone: [4]217-244-3349
>> > >A A A [5][8]http://www.ks.uiuc.edu/Research/vmd/
>> > >
>> > >A A --
>> > >A A Anoop Krishnan N M
>> > >A A Research Student
>> > >A A Department of Civil Engineering
>> > >A A IISc Bangalore
>> > >A A INDIA
>> > >A A Ph: [9]09945191019
>> > >
>> > > References
>> > >
>> > >A A Visible links
>> > >A A 1. mailto:[10]johns_at_ks.uiuc.edu
>> > >A A 2. mailto:[11]vmd_at_ks.uiuc.edu
>> > >A A 3. [12]http://www.ks.uiuc.edu/~johns/
>> > >A A 4. tel:[13]217-244-3349
>> > >A A 5. [14]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
>> > [15]http://www.ks.uiuc.edu/~johns/A A A A A A Phone:
>> > [16]217-244-3349
>> > [17]http://www.ks.uiuc.edu/Research/vmd/
>> >
>> > --
>> > Anoop Krishnan N M
>> > Research Student
>> > Department of Civil Engineering
>> > IISc Bangalore
>> > INDIA
>> > Ph: 09945191019
>> >
>> > References
>> >
>> > Visible links
>> > 1. http://www.ks.uiuc.edu/Research/vmd/
>> > 2. mailto:vmd_at_ks.uiuc.edu
>> > 3. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21891.html
>> > 4. mailto:johns_at_ks.uiuc.edu
>> > 5. mailto:johns_at_ks.uiuc.edu
>> > 6. mailto:vmd_at_ks.uiuc.edu
>> > 7. http://www.ks.uiuc.edu/~johns/A
>> > 8. http://www.ks.uiuc.edu/Research/vmd/
>> > 9. tel:09945191019
>> > 10. mailto:johns_at_ks.uiuc.edu
>> > 11. mailto:vmd_at_ks.uiuc.edu
>> > 12. http://www.ks.uiuc.edu/~johns/
>> > 13. tel:217-244-3349
>> > 14. http://www.ks.uiuc.edu/Research/vmd/
>> > 15. http://www.ks.uiuc.edu/~johns/
>> > 16. tel:217-244-3349
>> > 17. 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/
>>
>
>
>
> --
> Anoop Krishnan N M
> Research Student
> Department of Civil Engineering
> IISc Bangalore
> INDIA
> Ph: 09945191019
> 

-- 
Anoop Krishnan N M
Research Student
Department of Civil Engineering
IISc Bangalore
INDIA
Ph: 09945191019