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

[Eric Chamberland]

Thanks Matthew!

I hope you're doing well.

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:

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 -> 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 -> 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!eq26UN2CarzUz7T9WGteIHDXqp5w7VVjasgK6Vd1QKhEZ2DgW9eB1ibuO_ba7ZyquQVtToW81IARavsFIj_RRgdYXowj80Dz3tMpJzHH$  
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!eq26UN2CarzUz7T9WGteIHDXqp5w7VVjasgK6Vd1QKhEZ2DgW9eB1ibuO_ba7ZyquQVtToW81IARavsFIj_RRgdYXowj80Dz3rS6d7R8$ >

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