Hi Matthew,
On 2025-03-14 13:09, Matthew Knepley wrote:
On Fri, Mar 14, 2025 at 12:53 PM Eric Chamberland
<eric.chamberl...@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@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
