VMD-L Mailing List

From: Rich Cook (rcook_at_llnl.gov)
Date: Thu Dec 17 2009 - 18:05:34 CST

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