VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jun 05 2009 - 11:09:59 CDT

On Fri, 2009-06-05 at 11:04 -0500, John Stone wrote:
> Hi,
> From what you're saying, it sounds like you get correct behavior
> with the "nv" driver, but not with the NVIDIA provided display driver,
> is that correct? If the "nv" driver works (but would obviously be
> very slow and low on features), then that does seem to indicate that
> this is an OpenGL driver issue. Can you try using a newer or older
> version of the NVIDIA driver available from the nvidia web site
> and see if the problem goes away:
> http://www.nvidia.com/

FWIW, nvidia just today released a new driver. version 185.18.14

cheers,
   axel.

>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jun 05, 2009 at 05:56:04PM +0200, lucie delemotte wrote:
> > Hi,
> >
> > >i would thus suspect that there is some problem or incompatibility
> > >with your OpenGL library relative to your Xserver. since you have
> > >a very new distribution, and it seems to contain somewhat experimental
> > >software (you mentioned Tk8.6, which is not even officially released),
> > >i would suggest you try a few more steps to narrow down the possible
> > >causes. one option to try would be to disable some advanced OpenGL
> > >features via using: env VMDSIMPLEGRAPHICS=1 vmd -e state.vmd
> > >and see if that makes a difference.
> >
> > It makes no difference. Regrding the tk/tcl version, this is the only
> > version available on this distribution (tcl-8.6-0.b1.1mdv2009.1.i586.rpm and
> > tk-8.6-0.b1.2mdv2009.1.i586.rpm)
> >
> > >the second, more drastic option would be to uninstall the nvidia
> > >driver and try the (limited functionality) "nv" driver that ships
> > >with the distribution instead.
> > >i would also make sure that you have all patches and updates installed.
> > >new distributions, particularly those that are willing to ship beta
> > >software, tend to have a lot of updates in the first few months.
> >
> > The OS is newly installed and all updates are done but it does not change
> > anything. Changing the graphical to "nv" in the xorg file permits the state
> > file to load but as it does not activate GL functions (or other stuff like
> > that), using vmd in this configuration is painful. I also tried to use the
> > version given by the mandriva distribution and gives the same behavior as
> > with the drivers taken from the nivdia website.
> >
> > >Do you have Compiz or other
> > >desktop special effects features enabled on this machine?
> >
> > Compiz is deactivated for the moment but if activated, it changes nothing
> > regarding vmd.
> > Besides, compiz works well when activated, and glxgears also gives good fps.
> >
> > >If all else fails,
> > >trying alternative non-vendor drivers may be worthwhile to narrow down the
> > >source of trouble.
> >
> > Can you be more specific on this information ?
> >
> > Thanks again,
> > Lucie
> >
> > On Wed, Jun 3, 2009 at 9:05 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > >
> > > Hi,
> > > Yeah, I think Axel's suggestions here are probably on the mark.
> > > I've never encountered the problem you're describing with the
> > > NVIDIA's drivers however, so I'm somewhat surprised that you're
> > > having this problem on your particular combination of hardware
> > > and software. If changing the drivers affects the behavior, then
> > > we may need to file a bug to NVIDIA. Do you have Compiz or other
> > > desktop special effects features enabled on this machine? That's
> > > another thing that may be worth checking on in addition to what
> > > Axel already suggested. I would try and solve the problem while
> > > retaining the use of the NVIDIA-provided OpenGL drivers if possible,
> > > either by using an older driver version or by enabling/disabling various
> > > options, since they will give the best performance. If all else fails,
> > > trying alternative non-vendor drivers may be worthwhile to narrow down the
> > > source of trouble.
> > >
> > > Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Wed, Jun 03, 2009 at 09:16:06AM -0400, Axel Kohlmeyer wrote:
> > > > On Wed, 2009-06-03 at 09:36 +0200, lucie delemotte wrote:
> > > > > Hi,
> > > >
> > > > lucie,
> > > >
> > > > i tried your input as well on a variety of linux machines
> > > > (32-bit, 64-bit, "old" linux, "new" linux, nvidia, non-nvidia)
> > > > and it always worked.
> > > >
> > > > [...]
> > > >
> > > > > After that, I get no vmd> prompt. The openGL window opens but doesn't
> > > > > show anything and no main window appears. I then have to kill the
> > > > > process to quit.
> > > >
> > > > i would thus suspect that there is some problem or incompatibility
> > > > with your OpenGL library relative to your Xserver. since you have
> > > > a very new distribution, and it seems to contain somewhat experimental
> > > > software (you mentioned Tk8.6, which is not even officially released),
> > > > i would suggest you try a few more steps to narrow down the possible
> > > > causes. one option to try would be to disable some advanced OpenGL
> > > > features via using: env VMDSIMPLEGRAPHICS=1 vmd -e state.vmd
> > > > and see if that makes a difference.
> > > >
> > > > the second, more drastic option would be to uninstall the nvidia
> > > > driver and try the (limited functionality) "nv" driver that ships
> > > > with the distribution instead.
> > > > i would also make sure that you have all patches and updates installed.
> > > > new distributions, particularly those that are willing to ship beta
> > > > software, tend to have a lot of updates in the first few months.
> > > >
> > > > since it was working with -debug, it could be some sort of race
> > > > condition somewhere (debugging slows down execution).
> > > >
> > > > > I also forgot to mention that every script I have works well in the
> > > > > -dispdev text mode.
> > > >
> > > > which just confirms that this is an X-related problem.
> > > >
> > > > cheers,
> > > > axel.
> > > > > Cheers again,
> > > > > Lucie
> > > > >
> > > > > On Tue, Jun 2, 2009 at 9:01 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> > > > >
> > > > > Lucie,
> > > > > After fixing an invalid filename for the .coor file (was
> > > > > looking
> > > > > in a directory
> > > > > "'/media/disk/LUCIE/ionchannels/kv1/kv1.5/kv1.5.26/"
> > > > > which obviously doesn't exist on my machine), the state file
> > > > > you provided loads fine for me with both VMD 1.8.7 beta 5 and
> > > > > VMD 1.8.6.
> > > > > If you run VMD 1.8.7 beta 5 and load the saved state via the
> > > > > command
> > > > > line -e flag, how far does it get? Can you mail me the
> > > > > output from
> > > > > that test? (no -debug)
> > > > >
> > > > > Cheers,
> > > > > John Stone
> > > > > vmd_at_ks.uiuc.edu
> > > > >
> > > > >
> > > > >
> > > > > On Tue, Jun 02, 2009 at 06:42:38PM +0200, lucie delemotte
> > > > > wrote:
> > > > > > Hi,
> > > > > > I uploaded the files to biocore (called state.tar.gz).
> > > > > > Thanks again.
> > > > > >
> > > > > > Lucie
> > > > > >
> > > > > > On Tue, Jun 2, 2009 at 6:15 PM, John Stone
> > > > > <johns_at_ks.uiuc.edu> wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > > Can you tar up the saved state and related files, gzip
> > > > > it, and
> > > > > > > either post it on biocore or email it to me (if it is
> > > > > small enough)?
> > > > > > > I'd like to try loading it for myself so I can see what's
> > > > > going on there.
> > > > > > >
> > > > > > > Cheers,
> > > > > > > John Stone
> > > > > > > vmd_at_ks.uiuc.edu
> > > > > > >
> > > > > > > On Tue, Jun 02, 2009 at 05:48:19PM +0200, lucie delemotte
> > > > > wrote:
> > > > > > > > Thanks for the quick answer!
> > > > > > > > Yes, vmd works fine when not loading a script (all
> > > > > windows open and I can
> > > > > > > > load things from the graphical menu).
> > > > > > > > Secondly, the script is supposed to load a pdb file plus
> > > > > a namdbin file.
> > > > > > > > (With the other computer or in the debug mode, I get the
> > > > > same text as
> > > > > > > above
> > > > > > > > plus :
> > > > > > > >
> > > > > > > > Info) Using plugin pdb for coordinates from file
> > > > > > > > kv1.5.26.0.pdb
> > > > > > > > Info) Finished with coordinate file
> > > > > > > > kv1.5.26.0.pdb.
> > > > > > > > 0
> > > > > > > >
> > > > > > > > Info) Using plugin namdbin for coordinates from file ...
> > > > > > > > ..........
> > > > > > > > ........
> > > > > > > > ........
> > > > > > > > ........
> > > > > > > > [New Thread 0xa8914b90 (LWP
> > > > > > > > 25252)]
> > > > > > > > [Thread 0xa8914b90 (LWP 25252)
> > > > > > > > exited]
> > > > > > > > [New Thread 0xa8113b90 (LWP
> > > > > > > > 25253)]
> > > > > > > > [Thread 0xa8113b90 (LWP 25253)
> > > > > > > > exited]
> > > > > > > > [New Thread 0xa8113b90 (LWP
> > > > > > > > 25254)]
> > > > > > > > [Thread 0xa8113b90 (LWP 25254)
> > > > > > > > exited]
> > > > > > > > [New Thread 0xa8914b90 (LWP
> > > > > > > > 25255)]
> > > > > > > > [Thread 0xa8914b90 (LWP 25255)
> > > > > > > > exited]
> > > > > > > > [New Thread 0xa8914b90 (LWP
> > > > > > > > 25256)]
> > > > > > > > [New Thread 0xa8113b90 (LWP
> > > > > > > > 25257)]
> > > > > > > > [Thread 0xa8914b90 (LWP 25256)
> > > > > > > > exited]
> > > > > > > > [Thread 0xa8113b90 (LWP 25257)
> > > > > > > > exited]
> > > > > > > > {{1 0 0 0.654825} {0 1 0 -0.0264271} {0 0 1 -9.97098} {0
> > > > > 0 0 1}}
> > > > > > > {{-0.728706
> > > > > > > > -0.681299 -0.0693803 0} {-0.060971 -0.0363649 0.997481
> > > > > 0} {-0.682102
> > > > > > > > 0.731099 -0.01504 0} {0 0 0 1}} {{0.0266042 0 0 0} {0
> > > > > 0.0266042 0 0} {0 0
> > > > > > > > 0.0266042 0} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0}
> > > > > {0 0 0
> > > > > > > > 1}}
> > > > > > > > 0
> > > > > > > >
> > > > > > > > 0
> > > > > > > >
> > > > > > > > [New Thread 0xa8113b90 (LWP
> > > > > > > > 25258)]
> > > > > > > > [New Thread 0xa8914b90 (LWP
> > > > > > > > 25259)]
> > > > > > > > [Thread 0xa8914b90 (LWP 25259)
> > > > > > > > exited]
> > > > > > > > [Thread 0xa8113b90 (LWP 25258)
> > > > > > > > exited]
> > > > > > > >
> > > > > > > > vmd >
> > > > > > > >
> > > > > > > >
> > > > > > > > and the graphical window works fine.
> > > > > > > >
> > > > > > > > Lucie
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > On Tue, Jun 2, 2009 at 5:39 PM, John Stone
> > > > > <johns_at_ks.uiuc.edu> wrote:
> > > > > > > >
> > > > > > > > >
> > > > > > > > > Hi,
> > > > > > > > > Does VMD run correctly for you by itself? The main
> > > > > menu should
> > > > > > > > > appear if it was installed correctly and you don't
> > > > > have an empty .vmdrc
> > > > > > > > > in your home directory. Once you've verified that VMD
> > > > > itself is
> > > > > > > working
> > > > > > > > > fine, the next question I'd ask is whether you're
> > > > > loading any
> > > > > > > coordinates
> > > > > > > > > with that PSF file or just the PSF file. Unless you
> > > > > load coordinates
> > > > > > > as
> > > > > > > > > well, nothing will be displayed in the VMD graphics
> > > > > window. VMD needs
> > > > > > > > > the atomic coordinates to be able to draw anything.
> > > > > The PSF file only
> > > > > > > > > contains the structure data (e.g.
> > > > > bonds/angles/dihedrals/etc). When
> > > > > > > you
> > > > > > > > > loaded it in VMD 1.8.6, did the saved state also load
> > > > > a PDB file or
> > > > > > > some
> > > > > > > > > other coordinate file, or not?
> > > > > > > > >
> > > > > > > > > Cheers,
> > > > > > > > > John Stone
> > > > > > > > > vmd_at_ks.uiuc.edu
> > > > > > > > >
> > > > > > > > > On Tue, Jun 02, 2009 at 05:31:26PM +0200, lucie
> > > > > delemotte wrote:
> > > > > > > > > > Hi all,
> > > > > > > > > >
> > > > > > > > > > I have a vmd state script (state.vmd) that was
> > > > > working properly with
> > > > > > > vmd
> > > > > > > > > > 1.8.6.
> > > > > > > > > > After upgrading from mandriva 2008.0 to mandriva
> > > > > 2009.1 and changing
> > > > > > > to
> > > > > > > > > vmd
> > > > > > > > > > 1.8.7, the script stopped loading (either in command
> > > > > line with vmd -e
> > > > > > > > > > state.vmd or in the Tkconsole with the play
> > > > > command). The openGL
> > > > > > > window
> > > > > > > > > pops
> > > > > > > > > > up but nothing appears in it while the vmd main
> > > > > window doesn't open.
> > > > > > > In
> > > > > > > > > the
> > > > > > > > > > console, the regular vmd stuff appears :
> > > > > > > > > >
> > > > > > > > > > Info) VMD for LINUX, version 1.8.7beta5 (June 1,
> > > > > 2009)
> > > > > > > > > >
> > > > > > > > > > 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: 326MB (16%)
> > > > > > > > > >
> > > > > > > > > > Info) No CUDA accelerator devices available.
> > > > > > > > > >
> > > > > > > > > > Info) OpenGL renderer: Quadro FX 3450/4000
> > > > > SDI/PCI/SSE2
> > > > > > > > > >
> > > > > > > > > > Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT
> > > > > PP PS GLSL(OVF)
> > > > > > > > > >
> > > > > > > > > > Info) Full GLSL rendering mode is available.
> > > > > > > > > >
> > > > > > > > > > Info) Textures: 2-D (4096x4096), 3-D
> > > > > (512x512x512), Multitexture
> > > > > > > (4)
> > > > > > > > > >
> > > > > > > > > > psfplugin) Detected a Charmm31 PSF file
> > > > > > > > > >
> > > > > > > > > > Info) Using plugin psf for structure file
> > > > > kv1.5.26.0.psf
> > > > > > > > > >
> > > > > > > > > > Info) Analyzing structure ...
> > > > > > > > > >
> > > > > > > > > > Info) Atoms: 305464
> > > > > > > > > >
> > > > > > > > > > Info) Bonds: 221738
> > > > > > > > > >
> > > > > > > > > > Info) Angles: 172116 Dihedrals: 117638
> > > > > Impropers: 4748
> > > > > > > Cross-terms:
> > > > > > > > > > 1552
> > > > > > > > > > Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes:
> > > > > 0
> > > > > > > Impropertypes:
> > > > > > > > > > 0
> > > > > > > > > > Info) Residues:
> > > > > > > > > > 85614
> > > > > > > > > > Info) Waters:
> > > > > > > > > > 83392
> > > > > > > > > > Info) Segments:
> > > > > > > > > > 21
> > > > > > > > > > Info) Fragments: 84058 Protein: 4 Nucleic:
> > > > > > > > > > 0
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > I tested versions beta.2, beta.3 and beta.5
> > > > > unsuccessfully. I also
> > > > > > > > > checked
> > > > > > > > > > that the script is still working on another
> > > > > computer. It also appears
> > > > > > > > > that
> > > > > > > > > > vmd 1.8.6 is not working at all (vmd main window not
> > > > > appearing) on
> > > > > > > the
> > > > > > > > > new
> > > > > > > > > > installation.
> > > > > > > > > > The Nvidia drivers are well installed with the
> > > > > latest version :
> > > > > > > 180.51
> > > > > > > > > > Tcl/Tk version 8.6
> > > > > > > > > > gcc (GCC) 4.3.2
> > > > > > > > > >
> > > > > > > > > > I tried the debug mode to check what was wrong and
> > > > > interstingly, my
> > > > > > > > > > state.vmd file loads properly (gdb version :
> > > > > 6.8-6mdv2009.1).
> > > > > > > > > >
> > > > > > > > > > Any help would be greatly appreciated.
> > > > > > > > > > Lucie
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > > NIH Resource for Macromolecular Modeling and
> > > > > Bioinformatics
> > > > > > > > > Beckman Institute for Advanced Science and Technology
> > > > > > > > > University of Illinois, 405 N. Mathews Ave, Urbana, IL
> > > > > 61801
> > > > > > > > > Email: johns_at_ks.uiuc.edu Phone:
> > > > > 217-244-3349
> > > > > > > > > WWW:
> > > > > http://www.ks.uiuc.edu/~johns/>
> > > <http://www.ks.uiuc.edu/%
> > > > > 7Ejohns/><
> > > > > > > http://www.ks.uiuc.edu/%7Ejohns/>
> > > > > > > > > Fax: 217-244-6078
> > > > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > NIH Resource for Macromolecular Modeling and
> > > > > Bioinformatics
> > > > > > > Beckman Institute for Advanced Science and Technology
> > > > > > > University of Illinois, 405 N. Mathews Ave, Urbana, IL
> > > > > 61801
> > > > > > > Email: johns_at_ks.uiuc.edu Phone:
> > > > > 217-244-3349
> > > > > > > WWW: http://www.ks.uiuc.edu/~johns/>
> > > > > <http://www.ks.uiuc.edu/%7Ejohns/>
> > > > > > > Fax: 217-244-6078
> > > > > > >
> > > > >
> > > > > --
> > > > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > > > Beckman Institute for Advanced Science and Technology
> > > > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > > > WWW: http://www.ks.uiuc.edu/~johns/> Fax: 217-244-6078
> > > > >
> > > > >
> > > >
> > > > --
> > > > =======================================================================
> > > > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > > > Center for Molecular Modeling -- University of Pennsylvania
> > > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > > > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > > > =======================================================================
> > > > If you make something idiot-proof, the universe creates a better idiot.
> > >
> > > --
> > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > Beckman Institute for Advanced Science and Technology
> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > > WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > > Fax: 217-244-6078
> > > 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.