[petsc-users] PetscPythonInitialize, KSPPYTHON, PCPYTHON, etc

Eric Chamberland Eric.Chamberland at giref.ulaval.ca
Sun Mar 16 09:31:53 CDT 2025 

Hi Matthew,

On 2025-03-14 13:09, Matthew Knepley wrote:
> On Fri, Mar 14, 2025 at 12:53 PM Eric Chamberland 
> <Eric.Chamberland at giref.ulaval.ca> wrote:
>
>     Thanks Matthew!
>
>     I hope you're doing well.
>
>
> Hi! I know there is still a Plex bug submitted, but this is the 
> busiest time of the year. I will fix it soon.
No rush, we are working on 2D examples for now, take your time!
>
>     I have a question regarding a change I did on our code: I modified
>     the code to call |PetscPythonInitialize(PETSC_NULLPTR,
>     PETSC_NULLPTR)| after |SlepcInitialize|.
>
>     Our CI ran successfully across 20 different environments
>     (including Valgrind), but we encountered a segmentation fault on
>     Ubuntu 24.04 when calling |PetscPythonInitialize| within our
>     Python module (built using Pybind11 bindings).
>
>     On Ubuntu, calling |PetscPythonInitialize| from within our Python
>     3 module results in a segfault with the following backtrace:
>
> This is weird. When I have seen things like this before, it is because 
> someone is not dynamically linking properly, so that
> static variables are duplicated, and they get out of sync.
>
> This is why I always use  -python to have PETSc do that initialization 
> automatically, and it guaranteed to be linked to the same
> libpython that the SNESPYTHON is using.

Ok, my colleague René and I have built a reproducer, see 
https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/issues/1717__;!!G_uCfscf7eWS!Y9u6eJnvOw3IsoL2l2NE4TRAuerg63WS_QF4KnevrJSvCcetF4dyqWweHkPeGbZJ27D_p1cH1cvdr5RhjeMhZ82J5axUqPoNQMXT6pFI$ .

Thanks,

Eric

>
>   Thanks,
>
>      Matt
>
>     Thread 1 "python3" received signal SIGSEGV, Segmentation fault.
>     0x00001555339b372ain PyList_New() from
>     /lib/x86_64-linux-gnu/libpython3.12.so.1.0
>     (gdb) bt
>     #0 0x00001555339b372ain PyList_New() from
>     /lib/x86_64-linux-gnu/libpython3.12.so.1.0
>     #1 0x0000155533ad89d7in PyImport_Import() from
>     /lib/x86_64-linux-gnu/libpython3.12.so.1.0
>     #2 0x0000155533ad8c80in PyImport_ImportModule() from
>     /lib/x86_64-linux-gnu/libpython3.12.so.1.0
>     #3 0x000015553f437c0cin PetscPythonInitialize(pyexe=0x0,
>     pylib=0x0) at
>     /tmp/build_openmpi-4.1.6-opt/petsc-3.21.6-debug/src/sys/python/pythonsys.c:242
>
>     I am puzzled by this segfault...
>
>     Some relevant details:
>
>     grep -r PETSC_PYTHON_EXE
>     /opt/petsc-3.21.6_debug_openmpi-4.1.6/include/
>     /opt/petsc-3.21.6_debug_openmpi-4.1.6/include/petscconf.h:#define
>     PETSC_PYTHON_EXE"/usr/bin/python3"
>
>     ls -la /lib/x86_64-linux-gnu/libpython3.12*
>     lrwxrwxrwx 1 root root       58 Feb  4 09:48
>     /lib/x86_64-linux-gnu/libpython3.12.a ->
>     ../python3.12/config-3.12-x86_64-linux-gnu/libpython3.12.a
>     lrwxrwxrwx 1 root root       60 Feb  4 09:48
>     /lib/x86_64-linux-gnu/libpython3.12d.a ->
>     ../python3.12/config-3.12d-x86_64-linux-gnu/libpython3.12d.a
>     lrwxrwxrwx 1 root root       19 Feb  4 09:48
>     /lib/x86_64-linux-gnu/libpython3.12d.so <https://urldefense.us/v3/__http://libpython3.12d.so__;!!G_uCfscf7eWS!Y9u6eJnvOw3IsoL2l2NE4TRAuerg63WS_QF4KnevrJSvCcetF4dyqWweHkPeGbZJ27D_p1cH1cvdr5RhjeMhZ82J5axUqPoNQHADXm5h$ >
>     -> libpython3.12d.so.1
>     lrwxrwxrwx 1 root root       21 Feb  4 09:48
>     /lib/x86_64-linux-gnu/libpython3.12d.so.1 -> libpython3.12d.so.1.0
>     -rw-r--r-- 1 root root 34018416 Feb  4 09:48
>     /lib/x86_64-linux-gnu/libpython3.12d.so.1.0
>     lrwxrwxrwx 1 root root       18 Feb  4 09:48
>     /lib/x86_64-linux-gnu/libpython3.12.so <https://urldefense.us/v3/__http://libpython3.12.so__;!!G_uCfscf7eWS!Y9u6eJnvOw3IsoL2l2NE4TRAuerg63WS_QF4KnevrJSvCcetF4dyqWweHkPeGbZJ27D_p1cH1cvdr5RhjeMhZ82J5axUqPoNQI5lkBGY$ >
>     -> libpython3.12.so.1
>     lrwxrwxrwx 1 root root       20 Feb  4 09:48
>     /lib/x86_64-linux-gnu/libpython3.12.so.1 -> libpython3.12.so.1.0
>     -rw-r--r-- 1 root root  9055112 Feb  4 09:48
>     /lib/x86_64-linux-gnu/libpython3.12.so.1.0
>
>     (I installed the debug ("d") versions to get debug symbols, but
>     the segfault occurs even without them.)
>
>     Interestingly, on the same Ubuntu setup, calling
>     |PetscPythonInitialize| within our /pure C++/ code works fine, and
>     the |"pc_type python"| example runs successfully.
>
>     This issue only occurs when calling |PetscPythonInitialize| from
>     our /Python module/.
>
>     Any ideas?
>
>     Could this be something that has already been fixed in PETSc 3.22.x?
>
>     Thanks,
>
>     Eric
>
>
>     On 2025-03-12 16:48, Matthew Knepley wrote:
>>     On Wed, Mar 12, 2025 at 4:34 PM Eric Chamberland via petsc-users
>>     <petsc-users at mcs.anl.gov> wrote:
>>
>>         Hi,
>>
>>         just a naive question: looking at KSPPYTHON and PCPYTHON, we
>>         saw that
>>         there is only 1 example available.
>>
>>         We are asking ourself: is it still supported and can we start
>>         developping ou PCs and KSPs on top of it?
>>
>>         Or is there a "new" replacement for these?
>>
>>
>>     I think the reason that there are so few examples is that many
>>     examples exist in other packages, such as Firedrake, and they are
>>     the main consumers. KSPPYTHON is a way to write KSPSHELL using
>>     Python rather than C, and we mostly write C.
>>
>>     I will say that recently we fixed everything so that PETSc errors
>>     and Python exceptions are passed correctly up the stack, and
>>     debugging these things should be easy. I have been debugging the
>>     PyVista visualization, and I can change the Python in one window
>>     and run in the other. It is easy.
>>
>>       Thanks,
>>
>>          Matt
>>
>>         Thanks,
>>
>>         Eric
>>
>>         -- 
>>         Eric Chamberland, ing., M. Ing
>>         Professionnel de recherche
>>         GIREF/Université Laval
>>         (418) 656-2131 poste 41 22 42
>>
>>
>>
>>     -- 
>>     What most experimenters take for granted before they begin their
>>     experiments is infinitely more interesting than any results to
>>     which their experiments lead.
>>     -- Norbert Wiener
>>
>>     https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!Y9u6eJnvOw3IsoL2l2NE4TRAuerg63WS_QF4KnevrJSvCcetF4dyqWweHkPeGbZJ27D_p1cH1cvdr5RhjeMhZ82J5axUqPoNQF9A_dJh$ 
>>     <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!Y9u6eJnvOw3IsoL2l2NE4TRAuerg63WS_QF4KnevrJSvCcetF4dyqWweHkPeGbZJ27D_p1cH1cvdr5RhjeMhZ82J5axUqPoNQC9gNDOK$ >
>
>     -- 
>     Eric Chamberland, ing., M. Ing
>     Professionnel de recherche
>     GIREF/Université Laval
>     (418) 656-2131 poste 41 22 42
>
>
>
> -- 
> What most experimenters take for granted before they begin their 
> experiments is infinitely more interesting than any results to which 
> their experiments lead.
> -- Norbert Wiener
>
> https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!Y9u6eJnvOw3IsoL2l2NE4TRAuerg63WS_QF4KnevrJSvCcetF4dyqWweHkPeGbZJ27D_p1cH1cvdr5RhjeMhZ82J5axUqPoNQF9A_dJh$  
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!Y9u6eJnvOw3IsoL2l2NE4TRAuerg63WS_QF4KnevrJSvCcetF4dyqWweHkPeGbZJ27D_p1cH1cvdr5RhjeMhZ82J5axUqPoNQC9gNDOK$ >

-- 
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42
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