VMD-L Mailing List

From: Anoop Krishnan (anoopnm007_at_gmail.com)
Date: Sat Sep 20 2014 - 00:42:51 CDT

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