VMD-L Mailing List

From: Rich Cook (rcook_at_llnl.gov)
Date: Thu Dec 17 2009 - 19:17:47 CST

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