From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Jun 03 2009 - 08:16:06 CDT

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/%
> 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.