VMD-L Mailing List

From: Stipe Mustać (stipe.mustac_at_pharma.unizg.hr)
Date: Mon Jan 27 2025 - 05:09:49 CST

Hi Robin,

First of all I want to apologize for answering a bit later, I was really
away for the weekend. I really didn't expect to get the answer from the
creator himself, thank you very much for finding some time to answer.

When I use tcl interpreter i am also able to write some tcl scripts
which I can after that use inside the vmd to manipulate my system
(writing script and then sourcing with vmd tcl interpreter). I believe
in some cases that i also used some features or packages which weren't
inherently built into vmd. Can't I do the same with python interpreter?
I mean write some script which uses some other python package (e.g.
numpy) and run that script using vmd python interpreter?

As for the error, I knew I had to change the same things as I did with
regular build. But some parts of code still aren't the same which causes
new errors to arise. I will open up an issue on github, but despite of
that i will also write it here once again in case someone with the same
issue looking here for the answer finds it.

---error:---

py_atomsel.C:2138:24: error: invalid conversion from ‘PyTypeObject*’
{aka ‘_typeobject*’} to ‘Py_ssize_t’ {aka ‘long int’} [-fpermissive]
  2138 |     PyObject_HEAD_INIT(&PyType_Type)
/usr/include/python3.13/object.h:138:10: note: in definition of macro
‘PyObject_HEAD_INIT’
   138 |         (type)                      \
       |          ^~~~
In file included from PluginMgr.h:31,
                  from VMDApp.h:23,
                  from py_atomsel.C:21:
ResizeArray.h: In instantiation of ‘void ResizeArray<T>::append(const
T&) [with T = Matrix4]’:
BaseMolecule.h:460:55:   required from here
   460 |   void add_instance(Matrix4 & inst) { instances.append(inst); }
       | ~~~~~~~~~~~~~~~~^~~~~~
ResizeArray.h:108:13: warning: ‘void* memcpy(void*, const void*,
size_t)’ writing to an object of type ‘class Matrix4’ with no trivial
copy-assignment; use copy-assignment or copy-initialization instead
[-Wclass-memaccess]
   108 |       memcpy(newdata, data, currSize * sizeof(T));
       |       ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from Timestep.h:29,
                  from BaseMolecule.h:36,
                  from DrawMolecule.h:26,
                  from Molecule.h:27,
                  from MoleculeList.h:26,
                  from py_atomsel.C:22:
Matrix4.h:26:7: note: ‘class Matrix4’ declared here
    26 | class Matrix4 {
       |       ^~~~~~~
make: *** [Makefile:536: py_atomsel.o] Error 1
Traceback (most recent call last):

---code downloaded from your website:---

#if PY_MAJOR_VERSION >= 3
   PyTypeObject itertype = {
     PyObject_HEAD_INIT(&PyType_Type)
     "atomsel.iterator",
     sizeof(atomsel_iterobject), 0, // basic, item size
     (destructor)iter_dealloc, // dealloc
     0, //tp_print
     0, 0, // tp get and setattr
     0, // tp_as_async
     0, // tp_repr
     0, 0, 0, // as number, sequence, mapping
     0, 0, 0, // hash, call, str
     PyObject_GenericGetAttr, 0, // getattro, setattro
     0, // tp_as_buffer
     Py_TPFLAGS_DEFAULT, // flags
     0, // docstring
     0, 0, 0, // traverse, clear, richcompare
     0, // tp_weaklistoffset
     PyObject_SelfIter, // tp_iter
     (iternextfunc)iter_next, // tp_iternext
     iter_methods, // tp_methods
     0, 0, 0, // members, getset, base
};

PyTypeObject Atomsel_Type = {
     PyObject_HEAD_INIT(0)
     "atomsel",
     sizeof(PyAtomSelObject), 0, // basic, item size
     (destructor)atomsel_dealloc, //dealloc
     0, // tp_print
     0, 0, // tp get and set attr
     0, // tp_as_async
     (reprfunc)atomsel_repr, // tp_repr
     0, 0, &atomsel_mapping, // as number, sequence, mapping
     0, 0, (reprfunc)atomsel_str, // hash, call, str
     (getattrofunc) atomsel_getattro, // getattro
     (setattrofunc) atomsel_setattro, // setattro
     0, // tp_as_buffer
     Py_TPFLAGS_DEFAULT|Py_TPFLAGS_BASETYPE, // flags
     atomsel_doc, // docstring
     0, 0, 0, // traverse, clear, richcompare
     0, // tp_weaklistoffset
     atomsel_iter, // tp_iter
     0, // tp_iternext
     atomselection_methods, // tp_methods,
     0, atomsel_getset, 0, // members, getset, base
     0, 0, 0, // tp_dict, descr_get, descr_set
     0, 0, // dictoffset, init
     PyType_GenericAlloc, // tp_alloc
     atomsel_new, // tp_new
     PyObject_Del, // tp_free
};

---source code downloaded from the official site:---

#if PY_MAJOR_VERSION >= 3
   PyTypeObject itertype = {
     // XXX Clang++ doesn't like this initializer, see PEP 3123:
     // https://urldefense.com/v3/__https://www.python.org/dev/peps/pep-3123/__;!!DZ3fjg!7qfoWAWo4aV1_SZjGRPzOLjMgDM52ekr5V2QxkTo6101gQdbj8SOAlLerUcUqlBOIZeASvHsLjF0W_E2EmS-WhcLIkV6xbY$
     //     See also:
     // https://urldefense.com/v3/__http://python3porting.com/cextensions.html*module-initialization__;Iw!!DZ3fjg!7qfoWAWo4aV1_SZjGRPzOLjMgDM52ekr5V2QxkTo6101gQdbj8SOAlLerUcUqlBOIZeASvHsLjF0W_E2EmS-WhcLACxGrY8$
     // https://urldefense.com/v3/__https://docs.python.org/3.7/extending/newtypes.html__;!!DZ3fjg!7qfoWAWo4aV1_SZjGRPzOLjMgDM52ekr5V2QxkTo6101gQdbj8SOAlLerUcUqlBOIZeASvHsLjF0W_E2EmS-WhcLN42r7DI$
     // PyObject_HEAD_INIT(&PyType_Type)
     PyVarObject_HEAD_INIT(NULL, 0)
     "atomsel.iterator",
     sizeof(atomsel_iterobject), 0, // basic, item size
     (destructor)iter_dealloc, // dealloc
     0, //tp_print
     0, 0, // tp get and setattr
     0, // tp_as_async
     0, // tp_repr
     0, 0, 0, // as number, sequence, mapping
     0, 0, 0, // hash, call, str
     PyObject_GenericGetAttr, 0, // getattro, setattro
     0, // tp_as_buffer
     Py_TPFLAGS_DEFAULT, // flags
     0, // docstringHi Robin,
     0, 0, 0, // traverse, clear, richcompare
     0, // tp_weaklistoffset
     PyObject_SelfIter, // tp_iter
     (iternextfunc)iter_next, // tp_iternext
     iter_methods, // tp_methods
     0, 0, 0, // members, getset, base
   };

   PyTypeObject Atomsel_Type = {
     // XXX Clang++ doesn't like this initializer:
     // https://urldefense.com/v3/__https://www.python.org/dev/peps/pep-3123/__;!!DZ3fjg!7qfoWAWo4aV1_SZjGRPzOLjMgDM52ekr5V2QxkTo6101gQdbj8SOAlLerUcUqlBOIZeASvHsLjF0W_E2EmS-WhcLIkV6xbY$
     //     See also:
     // https://urldefense.com/v3/__http://python3porting.com/cextensions.html*module-initialization__;Iw!!DZ3fjg!7qfoWAWo4aV1_SZjGRPzOLjMgDM52ekr5V2QxkTo6101gQdbj8SOAlLerUcUqlBOIZeASvHsLjF0W_E2EmS-WhcLACxGrY8$
     // https://urldefense.com/v3/__https://docs.python.org/3.7/extending/newtypes.html__;!!DZ3fjg!7qfoWAWo4aV1_SZjGRPzOLjMgDM52ekr5V2QxkTo6101gQdbj8SOAlLerUcUqlBOIZeASvHsLjF0W_E2EmS-WhcLN42r7DI$
     // PyObject_HEAD_INIT(0)
     PyVarObject_HEAD_INIT(NULL, 0)
     "atomsel",
     sizeof(PyAtomSelObject), 0, // basic, item size
     (destructor)atomsel_dealloc, //dealloc
     0, // tp_print
     0, 0, // tp get and set attr
     0, // tp_as_async
     (reprfunc)atomsel_repr, // tp_repr
     0, 0, &atomsel_mapping, // as number, sequence, mapping
     0, 0, (reprfunc)atomsel_str, // hash, call, str
     (getattrofunc) atomsel_getattro, // getattro
     (setattrofunc) atomsel_setattro, // setattro
     0, // tp_as_buffer
     Py_TPFLAGS_DEFAULT|Py_TPFLAGS_BASETYPE, // flags
     atomsel_doc, // docstring
     0, 0, 0, // traverse, clear, richcompare
     0, // tp_weaklistoffset
     atomsel_iter, // tp_iter
     0, // tp_iternext
     atomselection_methods, // tp_methods,
     0, atomsel_getset, 0, // members, getset, base
     0, 0, 0, // tp_dict, descr_get, descr_set
     0, 0, // dictoffset, init
     PyType_GenericAlloc, // tp_alloc
     atomsel_new, // tp_new
     PyObject_Del, // tp_free
   };

Is it safe to replace this code chunk by the official one to solve this
error?

Best,
Stipe

On 1/23/25 5:33 AM, Robin Betz wrote:
> Hi Stipe,
>
> vmd-python is an importable Python module that is used from other
> scripts that run in the Python interpreter. It's useful for running
> analyses, etc, using Python scripts that may use other packages, and
> doesn't have the visualization window. "Regular" VMD is a standalone
> executable that embeds an interpreter (either Python or TCL) that can
> be used to interact with the program. I use "regular" VMD for
> visualizing and exploring MD systems and trajectories, and then write
> scripts that use vmd-python to perform analyses and generate plots.
>
> You'll get the same compilation errors you had for Python 3.13 + VMD
> trying to build vmd-python. If you open up an issue on the github
> (https://urldefense.com/v3/__https://github.com/Eigenstate/vmd-python__;!!DZ3fjg!7qfoWAWo4aV1_SZjGRPzOLjMgDM52ekr5V2QxkTo6101gQdbj8SOAlLerUcUqlBOIZeASvHsLjF0W_E2EmS-WhcLvF01wTU$
> <https://urldefense.com/v3/__https://github.com/Eigenstate/vmd-python__;!!DZ3fjg!5l7DtkIA3Lqg2MdXtD8UY3aLIy28zM-7rOJ848KJ80dXS_OJK0A15h2_C0NIVhN-chZtPN9sR-23dBJ9UA$>)
> I'll try to get to it. There's conda builds available but only through
> Python 3.1-- that's also something I've been meaning to fix.
>
> Best,
> Robin
>
> On Wed, Jan 22, 2025 at 4:20 PM Stipe Mustać
> <stipe.mustac_at_pharma.unizg.hr> wrote:
>
> Dear Josh,
>
> Thanks for your help (and after some additional struggles) I
> finally managed to compile the vmd with python interpreter. I
> didn't install any programs listed in the documentation as
> dependencies (surf, stride, tachyon) but the software seems to run
> normally?
>
> I tried to compile vmd-python by Robin Betz, but i have some other
> compilation errors too which for now I can't solve. Should I open
> a new topic or can I go on here with that compilation error here?
> I also don't understand what are the advantages of vmd-python over
> just using vmd with python interpreter regularly?
>
> Thank you very much once again, I would never be able to solve
> this struggle without your assistance.
> Sincerely,
> Stipe
>
> On 1/21/25 8:04 PM, Josh Vermaas wrote:
>> 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!7qfoWAWo4aV1_SZjGRPzOLjMgDM52ekr5V2QxkTo6101gQdbj8SOAlLerUcUqlBOIZeASvHsLjF0W_E2EmS-WhcLst6wNyw$
>>>> <https://urldefense.com/v3/__https://gcc.gnu.org/bugzilla/show_bug.cgi?id=106416__;!!HXCxUKc!0gXBBlCKD1JmI3G9yQRw9h2LyV4GBDdHs2sBsXyx7GpOMLrJpvzrRPhrE04oA2ru5H0Y-ZlIirL-qdqS7TgRr7NCaBz5NQ$>
>>>> 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> <mailto:vermaasj_at_msu.edu>:
>>>>> >
>>>>> > Hi Stipe,
>>>>> >
>>>>> > How did you install VMD? The default VMD installations that
>>>>> you can download from the ks.uiuc.edu <http://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
>>>>> <https://urldefense.com/v3/__http://vermaaslab.github.io__;!!DZ3fjg!5l7DtkIA3Lqg2MdXtD8UY3aLIy28zM-7rOJ848KJ80dXS_OJK0A15h2_C0NIVhN-chZtPN9sR-3j4Yzeaw$>
>>>>> >
>>>>> >
>>>>
>>>> --
>>>> Josh Vermaas
>>>>
>>>> vermaasj_at_msu.edu
>>>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>>>> Michigan State University
>>>> vermaaslab.github.io <https://urldefense.com/v3/__http://vermaaslab.github.io__;!!DZ3fjg!5l7DtkIA3Lqg2MdXtD8UY3aLIy28zM-7rOJ848KJ80dXS_OJK0A15h2_C0NIVhN-chZtPN9sR-3j4Yzeaw$>
>>
>> --
>> Josh Vermaas
>>
>> vermaasj_at_msu.edu
>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>> Michigan State University
>> vermaaslab.github.io <https://urldefense.com/v3/__http://vermaaslab.github.io__;!!DZ3fjg!5l7DtkIA3Lqg2MdXtD8UY3aLIy28zM-7rOJ848KJ80dXS_OJK0A15h2_C0NIVhN-chZtPN9sR-3j4Yzeaw$>
>