VMD-L Mailing List

From: Rich Cook (rcook_at_llnl.gov)
Date: Thu Dec 17 2009 - 19:35:12 CST

It crashes when I disable Tk in the same place as before. I'm
confused, because you are telling me to disable Tk but it is crashing
in a Tcl call. Is that intentional? I'm recompiling without Tcl and
without Tk just to see what happens...

On Dec 17, 2009, at 5:20 PM, John Stone wrote:

>
> 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
>

/* 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