VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 17 2009 - 19:20:35 CST

Rich,
  Just remove the "TK" option and see what happens.

Cheers,
  John

On Thu, Dec 17, 2009 at 05:17:47PM -0800, Rich Cook wrote:
> Hmm, I didn't know you could do that! ....
> I assume I just leave off the TCL option to the configure script in
> vmd directory.
>
> On Dec 17, 2009, at 5:05 PM, John Stone wrote:
>
> >Rich,
> > What happens if you compile without Tk enabled?
> >The crash you encountered before looked like it was
> >specific to Tk, rather than Tcl itself, so testing
> >with Tk turned off may be useful.
> >
> >Cheers,
> > John
> >
> >On Thu, Dec 17, 2009 at 04:05:34PM -0800, Rich Cook wrote:
> >>Hmm, I'm thinking I accidentally used the plugins from the tarball
> >>mixed with the CVS vmd build directory.
> >>I rebuilt from CVS and found a bug in plugins/volutil/Makefile:
> >>
> >>echo "Copying volutil 1.3 files to"
> >>gmake[1]: *** Recursive variable `CXXFLAGS' references itself
> >>(eventually). Stop.
> >>gmake[1]: Leaving directory `/usr/global/tools/vmd/1.8.7/
> >>aix_5_64_fed/
> >>src/plugins/volutil'
> >>gmake: *** [distrib] Error 1
> >>
> >>Caused by this in the volutil/Makefile:
> >>
> >>CXXFLAGS=${CXXFLAGS} -DDEBUG -g -Wall -pedantic
> >>
> >>should be:
> >>CXXFLAGS += -DDEBUG -g -Wall -pedantic
> >>
> >>So I fixed that and it now compiles, but I'm back to the exact same
> >>segfault as from the tarball. Sigh.
> >>
> >>Info) VMD for AIX5_64, version 1.8.8a6 (December 17, 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, 16 CPUs detected.
> >>Info) Free system memory: 6308MB (20%)
> >>Info) OpenGL renderer: NVIDIA GeForce 7300 GT OpenGL Engine
> >>Info) Features: STENCIL MTX
> >>Info) Textures: 2-D (4096x4096), Multitexture (4)
> >>Segmentation fault (core dumped)
> >>
> >>
> >>On Dec 17, 2009, at 3:03 PM, John Stone wrote:
> >>
> >>>
> >>>Rich,
> >>>Show me your configuration options, it looks to me like
> >>>you may not have compiled with the right combination of
> >>>configuration options. In particular the "Starting VMD text
> >>>interpreter..."
> >>>message indicates to me that Tcl didn't startup and you fell through
> >>>to a default catch-all case that's basically a stub text interpreter
> >>>we only ever use for testing purposes.
> >>>
> >>>Cheers,
> >>>John Stone
> >>>vmd_at_ks.uiuc.edu
> >>>
> >>>On Thu, Dec 17, 2009 at 02:45:07PM -0800, Rich Cook wrote:
> >>>>Hello again,
> >>>>I got CVS 1.8.8a6 to build on AIX, but it now hangs in the main
> >>>>event
> >>>>loop with no window.
> >>>>
> >>>>rcook_at_up041 (src): vmd
> >>>>Info) VMD for AIX5_64, version 1.8.8a6 (December 17, 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, 1 CPU detected.
> >>>>Info) Free system memory: 6187MB (19%)
> >>>>Info) Starting VMD text interpreter...
> >>>>
> >>>>(hang)
> >>>>
> >>>>Any thoughts? Thanks.
> >>>>
> >>>>On Dec 16, 2009, at 10:14 PM, John Stone wrote:
> >>>>
> >>>>>
> >>>>>Rich,
> >>>>>For CVS builds the easiest thing to do is put a copy of your
> >>>>>vmd/lib directory from the tarball source into your cvs area
> >>>>>and use that. We don't currently put the lib directory into
> >>>>>CVS due to the large file sizes and issues that would create.
> >>>>>
> >>>>>Regarding the vmd_initial_tcl error you're getting sounds
> >>>>>like a compiler bug to me. If you look at vmd.C, you can
> >>>>>see that vmd_initialize_tcl() is quite obviously in the code.
> >>>>>I have one suggestion for you to try though, try changing this
> >>>>>line:
> >>>>>const char *argv0 = vmd_initialize_tcl(argv[0]);
> >>>>>to this:
> >>>>>const char *argv0 = vmd_initialize_tcl((const char *) argv[0]);
> >>>>>
> >>>>>If that cures the problem then some compiler engineer at IBM
> >>>>>needs a boot in the rear, otherwise I'm not sure why it is
> >>>>>complaining.
> >>>>>
> >>>>>Cheers,
> >>>>>John Stone
> >>>>>vmd_at_ks.uiuc.edu
> >>>>>
> >>>>>
> >>>>>On Wed, Dec 16, 2009 at 05:33:15PM -0800, Rich Cook wrote:
> >>>>>>I tried to build from source on AIX, but it has problems.
> >>>>>>There is
> >>>>>>no
> >>>>>>pdflatex command on AIX, which I worked around by faking it up
> >>>>>>for
> >>>>>>now, but then there is a part of my build where I try to build
> >>>>>>SURF
> >>>>>>and there is no longer a surf directory in vmd. Is that OK?
> >>>>>>Apparently there are some different build instructions for CVS...
> >>>>>>can
> >>>>>>you point me to them?
> >>>>>>
> >>>>>>So I just kept going, and the build fails here:
> >>>>>>
> >>>>>>xlC -D_H_ACCESS=1 -DAIXUSEPERFSTAT -DARCH_AIX5_64 -DVMDORBITALS -
> >>>>>>DVMDWITHORBITALS -DVMDWITHCARBS -DVMDPOLYHEDRA -DVMDSURF -
> >>>>>>DVMDMSMS -
> >>>>>>DVMDFIELDLINES -DVMDPBCSMOOTH -DVMDSTATICPLUGINS -I../plugins/
> >>>>>>include -I../plugins/AIX5_64/molfile -I. -c vmd.C -o ../AIX5_64/
> >>>>>>vmd.o
> >>>>>>Compiling vmd.C --> vmd.o ...
> >>>>>>"vmd.C", line 261.23: 1540-0274 (S) The name lookup for
> >>>>>>"vmd_initialize_tcl" did not find a declaration.
> >>>>>>"vmd.C", line 407.3: 1540-0274 (S) The name lookup for
> >>>>>>"vmd_finalize_tcl" did not find a declaration.
> >>>>>>
> >>>>>>
> >>>>>>On Dec 16, 2009, at 2:18 PM, Rich Cook wrote:
> >>>>>>
> >>>>>>>Thanks, seems straightforward, unless there is a different
> >>>>>>>source
> >>>>>>>layout or other gotchas -- I'm certainly conversant with CVS
> >>>>>>>
> >>>>>>>On Dec 16, 2009, at 1:49 PM, John Stone wrote:
> >>>>>>>
> >>>>>>>>
> >>>>>>>>Richard,
> >>>>>>>>I've added your VMD CVS access, let me know if you need
> >>>>>>>>any help using it.
> >>>>>>>>
> >>>>>>>>Cheers,
> >>>>>>>>John Stone
> >>>>>>>>vmd_at_ks.uiuc.edu
> >>>>>>>>
> >>>>>>>>On Wed, Dec 16, 2009 at 02:49:51PM -0600, Web Form wrote:
> >>>>>>>>>Richard Cook <rcook_at_llnl.gov>
> >>>>>>>>>requests anonymous CVS access to VMD because
> >>>>>>>>>In order to build on AIX
> >>>>>>>>
> >>>>>>>>--
> >>>>>>>>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
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>/* A function that takes a single integer argument and returns
> >>>>>>>a pointer to a function that takes two integer arguments and
> >>>>>>>returns a floating-point number. */
> >>>>>>>float (*func2(int a))(int, int);
> >>>>>>>Rich Cook
> >>>>>>>rcook_at_llnl.gov
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>>/* A function that takes a single integer argument and returns
> >>>>>>a pointer to a function that takes two integer arguments and
> >>>>>>returns a floating-point number. */
> >>>>>>float (*func2(int a))(int, int);
> >>>>>>Rich Cook
> >>>>>>rcook_at_llnl.gov
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>--
> >>>>>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
> >>>>>
> >>>>
> >>>>
> >>>>/* A function that takes a single integer argument and returns
> >>>>a pointer to a function that takes two integer arguments and
> >>>>returns a floating-point number. */
> >>>>float (*func2(int a))(int, int);
> >>>>Rich Cook
> >>>>rcook_at_llnl.gov
> >>>>
> >>>>
> >>>>
> >>>
> >>>--
> >>>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
> >>>
> >>
> >>
> >>/* A function that takes a single integer argument and returns
> >> a pointer to a function that takes two integer arguments and
> >> returns a floating-point number. */
> >>float (*func2(int a))(int, int);
> >>Rich Cook
> >>rcook_at_llnl.gov
> >>
> >>
> >>
> >
> >--
> >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
> >
>
>
> /* A function that takes a single integer argument and returns
> a pointer to a function that takes two integer arguments and
> returns a floating-point number. */
> float (*func2(int a))(int, int);
> Rich Cook
> rcook_at_llnl.gov
>
>
> 

-- 
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