VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Tue Jan 21 2025 - 13:04:06 CST

Hi Stipe,

Lets try to keep this in VMD-L, so that future googlers can figure out
what the problem was. I think this is more of the same. Looks like you
are using python 3.13, while my Ubuntu machine uses 3.12. The key line
from your logs are these:

PythonTextInterp.C:105:24: error: ‘PyEval_CallObject’ was not declared
in this scope; did you mean ‘PyObject_CallObject’?
PythonTextInterp.C:177:3: error: ‘PySys_AddWarnOption’ was not declared
in this scope; did you mean ‘PySys_ResetWarnOptions’?

For what I am sure are good reasons, occasionally python deprecates
parts of their API. In this case, VMD is depending on PyEval_CallObject
and PySys_AddWarnOption. PyEval_CallObject was deprecated in 3.9, and
was removed as of 3.13, which is why you are running into issues
compiling it. Based on a bit of googling, it looks like you just use
PyObject_CallObject instead.

For AddWarnOption it looks like the API changed pretty drastically. I'm
not actually sure what happens if we have no warn options, so you may
want to consider just exempting python 3.13 and higher from
AddWarnOption, as we just add the defaults anyway. So something like this:

#if PY_MAJOR_VERSION >= 3 && PY_MINOR_VERSION <= 12
   PySys_AddWarnOption(L"default");
#elif PY_MAJOR_VERSION < 3
   PySys_AddWarnOption((char*) "default");
#endif

I know Diego has been working quite a bit on a "VMD 2.0" that hopefully
has all these deprecations taken care of.

-Josh

On 1/21/25 12:39 PM, Stipe Mustać wrote:
>
> Hi Josh,
>
> I changed the mentioned lines and the compilation finished without
> reporting any errors. Then I went on to compile vmd, and got the
> following:
>
> Compiling  PythonTextInterp.C  -->  PythonTextInterp.o  ...
> PythonTextInterp.C: In function ‘void call_callbacks(const char*,
> PyObject*)’:
> PythonTextInterp.C:105:24: error: ‘PyEval_CallObject’ was not declared
> in this scope; did you mean ‘PyObject_CallObject’?
>   105 |     PyObject *result = PyEval_CallObject(obj, arglist);
>       |                        ^~~~~~~~~~~~~~~~~
>       |                        PyObject_CallObject
> PythonTextInterp.C: In constructor
> ‘PythonTextInterp::PythonTextInterp(VMDApp*)’:
> PythonTextInterp.C:177:3: error: ‘PySys_AddWarnOption’ was not
> declared in this scope; did you mean ‘PySys_ResetWarnOptions’?
>   177 |   PySys_AddWarnOption(L"default");
>       |   ^~~~~~~~~~~~~~~~~~~
>       |   PySys_ResetWarnOptions
> PythonTextInterp.C:199:16: warning: ‘void PySys_SetArgv(int,
> wchar_t**)’ is deprecated [-Wdeprecated-declarations]
>   199 |   PySys_SetArgv(argc, wargv);
>       |   ~~~~~~~~~~~~~^~~~~~~~~~~~~
> In file included from /usr/include/python3.13/Python.h:125,
>                  from py_commands.h:24,
>                  from PythonTextInterp.C:21:
> /usr/include/python3.13/sysmodule.h:10:38: note: declared here
>    10 | Py_DEPRECATED(3.11) PyAPI_FUNC(void) PySys_SetArgv(int,
> wchar_t **);
>       |                                      ^~~~~~~~~~~~~
> make: *** [Makefile:621: PythonTextInterp.o] Error 1
>
> I am not sure if i provided the right directories as libraries or is
> it really some python syntax problem? Log file again in attachment.
>
> Thank you very much once again for your assistance.
>
> Stipe
>
> On 1/21/25 5:53 PM, Josh Vermaas wrote:
>> Hi Stipe,
>>
>> Based on the log you attached, you want to look for compiler errors.
>> I see this in the log you attached:
>>
>> src/qcschemaplugin.c: In function ‘open_qcschema_read’:
>> src/qcschemaplugin.c:162:29: error: assignment to ‘int’ from ‘struct
>> _json_value *’ makes integer from pointer without a cast
>> [-Wint-conversion]
>>   162 |           data->totalcharge =
>> aux_value->u.object.values[j].value;
>>       |                             ^
>> src/qcschemaplugin.c:165:30: error: assignment to ‘int’ from ‘struct
>> _json_value *’ makes integer from pointer without a cast
>> [-Wint-conversion]
>>   165 |           data->multiplicity =
>> aux_value->u.object.values[j].value;
>>
>> To me, this looks like your compiler is pickier than mine, and is
>> treating something that used to be a warning into a full-blown error.
>> See https://urldefense.com/v3/__https://gcc.gnu.org/bugzilla/show_bug.cgi?id=106416__;!!DZ3fjg!_vU_wZI0PEweVBPa5TRtW2yif8SBUaFGrtzTpissBFduCV2t60rrBb8hO_T3ft7SOXgKZLz4eD7Bu5lLfSQ$ which makes
>> this look like the intended behavior nowadays, which is unfortunate
>> since this particular plugin hasn't been changed in YEARS. I think
>> you could make the compiler happy by adding in the cast there:
>>
>> data->totalcharge = (int) aux_value->u.object.values[j].value;
>> data->multiplicity = (int) aux_value->u.object.values[j].value;
>>
>> Or alternatively changing the compiler flags to make that error a
>> warning again.
>>
>> -Josh
>>
>>
>> On 1/21/25 11:18 AM, Stipe Mustać wrote:
>>> Hello Josh!
>>>
>>> Thank you very much for the links you provided. I used them all and
>>> I can compile nothing. Neither vmd nor vmd-python. I actually
>>> realized later i have to compile vmd from source and that is what i
>>> am trying to do the entire day today. I was mostly referring to the
>>> guide posted by Robin Betz. Unfortunately I can‘t even compile the
>>> plugins. The error I get when compiling plugins is:
>>>
>>> make[2]: *** [Makefile:556:
>>> ../compile/lib_LINUXAMD64/molfile/qcschemaplugin.o] Error 1
>>> make[2]: Leaving directory
>>> '/home/stipe/downloads/vmdpackaging/plugins/molfile_plugin'
>>> make[1]: *** [Makefile:164: molfilelibs] Error 1
>>> make[1]: Leaving directory '/home/stipe/downloads/vmdpackaging/plugins'
>>> make: *** [Make-arch:338: LINUXAMD64] Error 2
>>>
>>> I applied that sed command you provided in your guide to switch from
>>> tcl 8.5 to 8.6. I am sending the entire make output in the
>>> attachment. I haven’t still installed surf, stride or tachyon. My os
>>> is arch linux and it uses python 3.13.
>>>
>>> Thank you once again.
>>> Sincerely,
>>> Stipe Mustac
>>>
>>>
>>> > Am 21.01.2025 um 16:23 schrieb Josh Vermaas <vermaasj_at_msu.edu>:
>>> >
>>> > Hi Stipe,
>>> >
>>> > How did you install VMD? The default VMD installations that you
>>> can download from the ks.uiuc.edu website don't come with a python
>>> interpreter built-in. Instead, if you want python and graphics, you
>>> end up needing to compile VMD yourself.
>>> https://urldefense.com/v3/__https://robinbetz.com/blog/2015/01/08/compiling-vmd-with-python-support/__;!!DZ3fjg!5Cp0UHc8gqyWY_z16AWli_FiYQKIyw3BouVGyNUkt9XAZL4zSZdjwo-vEOH5HAHnuSGU33rJAEKLeSGKjP8$
>>> has a blogpost describing the process, and she's also got a way of
>>> installing VMD as a python package
>>> (https://urldefense.com/v3/__https://vmd.robinbetz.com/__;!!DZ3fjg!5Cp0UHc8gqyWY_z16AWli_FiYQKIyw3BouVGyNUkt9XAZL4zSZdjwo-vEOH5HAHnuSGU33rJAEKLw_8HEtI$
>>> ). I've got packaging instructions for alpha versions of VMD that I
>>> use within my lab as well.
>>> https://urldefense.com/v3/__https://github.com/jvermaas/vmd-packaging-instructions__;!!DZ3fjg!5Cp0UHc8gqyWY_z16AWli_FiYQKIyw3BouVGyNUkt9XAZL4zSZdjwo-vEOH5HAHnuSGU33rJAEKL8qbMb2s$
>>> > Hope this helps!
>>> >
>>> > -Josh
>>> >
>>> >
>>> >> On 1/20/25 2:18 PM, Stipe Mustać wrote:
>>> >> Hello! I am trying to use python interpreter in vmd. The error
>>> message I keep getting is:
>>> >>
>>> >> Info) Starting Python...
>>> >> 'import site' failed; use -v for traceback
>>> >> rlwrap: warning: vmd crashed, killed by SIGSEGV (core dumped).
>>> >> rlwrap itself has not crashed, but for transparency,
>>> >> it will now kill itself with the same signal
>>> >>
>>> >> warnings can be silenced by the --no-warnings (-n) option
>>> >> Segmentation fault (core dumped)
>>> >>
>>> >> I saw a person who posted in this mailing list having the same
>>> issue in 2023, tried to reproduce all the tutorials and guides, but
>>> without any success. I would appreciate any help.
>>> >>
>>> >> Sincerely,
>>> >> Stipe Mustac
>>> >>
>>> >
>>> > --
>>> > Josh Vermaas
>>> >
>>> > vermaasj_at_msu.edu
>>> > Assistant Professor, Plant Research Laboratory and Biochemistry
>>> and Molecular Biology
>>> > Michigan State University
>>> > vermaaslab.github.io
>>> >
>>> >
>>
>> --
>> Josh Vermaas
>>
>> vermaasj_at_msu.edu
>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>> Michigan State University
>> vermaaslab.github.io 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io