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<p>Thanks Matthew!</p>
<p>I hope you're doing well.<br>
</p>
<p data-start="250" data-end="403">I have a question regarding a
change I did on our code: I modified the code to call <code
data-start="323" data-end="376">PetscPythonInitialize(PETSC_NULLPTR,
PETSC_NULLPTR)</code> after <code data-start="383"
data-end="400">SlepcInitialize</code>.</p>
<p data-start="405" data-end="636">Our CI ran successfully across 20
different environments (including Valgrind), but we encountered a
segmentation fault on Ubuntu 24.04 when calling <code
data-start="553" data-end="576">PetscPythonInitialize</code>
within our Python module (built using Pybind11 bindings).</p>
<p data-start="638" data-end="766">On Ubuntu, calling <code
data-start="657" data-end="680">PetscPythonInitialize</code>
from within our Python 3 module results in a segfault with the
following backtrace:</p>
<p><span style="font-family:monospace"><span
style="color:#000000;background-color:#ffffff;">Thread 1
"python3" received signal SIGSEGV, Segmentation fault.
</span><br>
<span style="color:#1818b2;background-color:#ffffff;">0x00001555339b372a</span><span
style="color:#000000;background-color:#ffffff;"> in </span><span
style="color:#b26818;background-color:#ffffff;">PyList_New</span><span
style="color:#000000;background-color:#ffffff;"> () from </span><span
style="color:#18b218;background-color:#ffffff;">/lib/x86_64-linux-gnu/libpython3.12.so.1.0</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
(gdb) bt
<br>
#0 <span style="color:#1818b2;background-color:#ffffff;">0x00001555339b372a</span><span
style="color:#000000;background-color:#ffffff;"> in </span><span
style="color:#b26818;background-color:#ffffff;">PyList_New</span><span
style="color:#000000;background-color:#ffffff;"> () from </span><span
style="color:#18b218;background-color:#ffffff;">/lib/x86_64-linux-gnu/libpython3.12.so.1.0</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
#1 <span style="color:#1818b2;background-color:#ffffff;">0x0000155533ad89d7</span><span
style="color:#000000;background-color:#ffffff;"> in </span><span
style="color:#b26818;background-color:#ffffff;">PyImport_Import</span><span
style="color:#000000;background-color:#ffffff;"> () from </span><span
style="color:#18b218;background-color:#ffffff;">/lib/x86_64-linux-gnu/libpython3.12.so.1.0</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
#2 <span style="color:#1818b2;background-color:#ffffff;">0x0000155533ad8c80</span><span
style="color:#000000;background-color:#ffffff;"> in </span><span
style="color:#b26818;background-color:#ffffff;">PyImport_ImportModule</span><span
style="color:#000000;background-color:#ffffff;"> () from </span><span
style="color:#18b218;background-color:#ffffff;">/lib/x86_64-linux-gnu/libpython3.12.so.1.0</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
#3 <span style="color:#1818b2;background-color:#ffffff;">0x000015553f437c0c</span><span
style="color:#000000;background-color:#ffffff;"> in </span><span
style="color:#b26818;background-color:#ffffff;">PetscPythonInitialize</span><span
style="color:#000000;background-color:#ffffff;"> (</span><span
style="color:#18b2b2;background-color:#ffffff;">pyexe</span><span
style="color:#000000;background-color:#ffffff;">=0x0, </span><span
style="color:#18b2b2;background-color:#ffffff;">pylib</span><span
style="color:#000000;background-color:#ffffff;">=0x0) at </span><span
style="color:#18b218;background-color:#ffffff;">/tmp/build_openmpi-4.1.6-opt/petsc-3.21.6-debug/src/sys/python/pythonsys.c</span><span
style="color:#000000;background-color:#ffffff;">:242</span><br>
</span></p>
<p>I am puzzled by this segfault...</p>
<p>Some relevant details:<br>
</p>
<p><span style="font-family:monospace"><span
style="color:#000000;background-color:#ffffff;">grep -r
PETSC_PYTHON_EXE
/opt/petsc-3.21.6_debug_openmpi-4.1.6/include/
</span><br>
<span style="color:#b218b2;background-color:#ffffff;">/opt/petsc-3.21.6_debug_openmpi-4.1.6/include/petscconf.h</span><span
style="color:#18b2b2;background-color:#ffffff;">:</span><span
style="color:#000000;background-color:#ffffff;">#define </span><span
style="font-weight:bold;color:#ff5454;background-color:#ffffff;">PETSC_PYTHON_EXE</span><span
style="color:#000000;background-color:#ffffff;">
"/usr/bin/python3"</span></span></p>
<p><span style="font-family:monospace"><span
style="color:#000000;background-color:#ffffff;">ls -la
/lib/x86_64-linux-gnu/libpython3.12*<br>
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<br>
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<br>
lrwxrwxrwx 1 root root 19 Feb 4 09:48
/lib/x86_64-linux-gnu/libpython3.12d.so ->
libpython3.12d.so.1<br>
lrwxrwxrwx 1 root root 21 Feb 4 09:48
/lib/x86_64-linux-gnu/libpython3.12d.so.1 ->
libpython3.12d.so.1.0<br>
-rw-r--r-- 1 root root 34018416 Feb 4 09:48
/lib/x86_64-linux-gnu/libpython3.12d.so.1.0<br>
lrwxrwxrwx 1 root root 18 Feb 4 09:48
/lib/x86_64-linux-gnu/libpython3.12.so ->
libpython3.12.so.1<br>
lrwxrwxrwx 1 root root 20 Feb 4 09:48
/lib/x86_64-linux-gnu/libpython3.12.so.1 ->
libpython3.12.so.1.0<br>
-rw-r--r-- 1 root root 9055112 Feb 4 09:48
/lib/x86_64-linux-gnu/libpython3.12.so.1.0<br>
</span></span></p>
<p data-start="2568" data-end="2673">(I installed the debug ("d")
versions to get debug symbols, but the segfault occurs even
without them.)</p>
<p data-start="2675" data-end="2842">Interestingly, on the same
Ubuntu setup, calling <code data-start="2724" data-end="2747">PetscPythonInitialize</code>
within our <em data-start="2759" data-end="2769">pure C++</em>
code works fine, and the <code data-start="2795" data-end="2813">"pc_type
python"</code> example runs successfully.</p>
<p data-start="2844" data-end="2931">This issue only occurs when
calling <code data-start="2880" data-end="2903">PetscPythonInitialize</code>
from our <em data-start="2913" data-end="2928">Python module</em>.</p>
<p data-start="2933" data-end="2945">Any ideas?</p>
<p data-start="2947" data-end="3017">Could this be something that
has already been fixed in PETSc 3.22.x?</p>
<p data-start="2947" data-end="3017">Thanks,</p>
<p data-start="2947" data-end="3017">Eric</p>
<p data-start="2947" data-end="3017"><br>
</p>
<div class="moz-cite-prefix">On 2025-03-12 16:48, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAMYG4GkLze3Oma-PiuRVzdH5VRh-y9cQuxbDp9Hh3+LNd0sWWw@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">
<div dir="ltr">On Wed, Mar 12, 2025 at 4:34 PM Eric Chamberland
via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov"
moz-do-not-send="true" class="moz-txt-link-freetext">petsc-users@mcs.anl.gov</a>>
wrote:</div>
<div class="gmail_quote gmail_quote_container">
<blockquote class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi,<br>
<br>
just a naive question: looking at KSPPYTHON and PCPYTHON, we
saw that <br>
there is only 1 example available.<br>
<br>
We are asking ourself: is it still supported and can we
start <br>
developping ou PCs and KSPs on top of it?<br>
<br>
Or is there a "new" replacement for these?<br>
</blockquote>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Thanks,<br>
<br>
Eric<br>
<br>
-- <br>
Eric Chamberland, ing., M. Ing<br>
Professionnel de recherche<br>
GIREF/Université Laval<br>
(418) 656-2131 poste 41 22 42<br>
<br>
</blockquote>
</div>
<div><br clear="all">
</div>
<div><br>
</div>
<span class="gmail_signature_prefix">-- </span><br>
<div dir="ltr" class="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>What most experimenters take for granted before
they begin their experiments is infinitely more
interesting than any results to which their
experiments lead.<br>
-- Norbert Wiener</div>
<div><br>
</div>
<div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!eq26UN2CarzUz7T9WGteIHDXqp5w7VVjasgK6Vd1QKhEZ2DgW9eB1ibuO_ba7ZyquQVtToW81IARavsFIj_RRgdYXowj80Dz3rS6d7R8$" target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<pre class="moz-signature" cols="72">--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42</pre>
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