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<p>Hi Matthew,<br>
</p>
<div class="moz-cite-prefix">On 2025-03-14 13:09, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAMYG4Gk=dOdKnYHgbX9XHK5aERy49LBO0HvS-tD-scU+fV9Hyw@mail.gmail.com">
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<div dir="ltr">On Fri, Mar 14, 2025 at 12:53 PM Eric Chamberland
<<a href="mailto:Eric.Chamberland@giref.ulaval.ca"
moz-do-not-send="true" class="moz-txt-link-freetext">Eric.Chamberland@giref.ulaval.ca</a>>
wrote:</div>
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<p>Thanks Matthew!</p>
<p>I hope you're doing well.<br>
</p>
</div>
</blockquote>
<div><br>
</div>
<div>Hi! I know there is still a Plex bug submitted, but this
is the busiest time of the year. I will fix it soon.</div>
</div>
</div>
</blockquote>
No rush, we are working on 2D examples for now, take your time!<br>
<blockquote type="cite"
cite="mid:CAMYG4Gk=dOdKnYHgbX9XHK5aERy49LBO0HvS-tD-scU+fV9Hyw@mail.gmail.com">
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<div class="gmail_quote gmail_quote_container">
<div> </div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>I have a question regarding a change I did on our code:
I modified the code to call <code>PetscPythonInitialize(PETSC_NULLPTR,
PETSC_NULLPTR)</code> after <code>SlepcInitialize</code>.</p>
<p>Our CI ran successfully across 20 different
environments (including Valgrind), but we encountered a
segmentation fault on Ubuntu 24.04 when calling <code>PetscPythonInitialize</code>
within our Python module (built using Pybind11
bindings).</p>
<p>On Ubuntu, calling <code>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:rgb(0,0,0);background-color:rgb(255,255,255)"></span></span></p>
</div>
</blockquote>
<div>This is weird. When I have seen things like this before,
it is because someone is not dynamically linking properly,
so that</div>
<div>static variables are duplicated, and they get out of
sync.</div>
<div><br>
</div>
<div>This is why I always use -python to have PETSc do that
initialization automatically, and it guaranteed to be linked
to the same</div>
<div>libpython that the SNESPYTHON is using.</div>
</div>
</div>
</blockquote>
<p>Ok, my colleague René and I have built a reproducer, see
<a class="moz-txt-link-freetext" href="https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/issues/1717__;!!G_uCfscf7eWS!Y9u6eJnvOw3IsoL2l2NE4TRAuerg63WS_QF4KnevrJSvCcetF4dyqWweHkPeGbZJ27D_p1cH1cvdr5RhjeMhZ82J5axUqPoNQMXT6pFI$">https://gitlab.com/petsc/petsc/-/issues/1717</a>.</p>
<p>Thanks,</p>
<p>Eric<br>
</p>
<blockquote type="cite"
cite="mid:CAMYG4Gk=dOdKnYHgbX9XHK5aERy49LBO0HvS-tD-scU+fV9Hyw@mail.gmail.com">
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<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p><span style="font-family:monospace"><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)">Thread 1
"python3" received signal SIGSEGV, Segmentation
fault. </span><br>
<span
style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x00001555339b372a</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span
style="color:rgb(178,104,24);background-color:rgb(255,255,255)">PyList_New</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> () from </span><span
style="color:rgb(24,178,24);background-color:rgb(255,255,255)">/lib/x86_64-linux-gnu/libpython3.12.so.1.0</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> </span><br>
(gdb) bt <br>
#0 <span
style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x00001555339b372a</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span
style="color:rgb(178,104,24);background-color:rgb(255,255,255)">PyList_New</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> () from </span><span
style="color:rgb(24,178,24);background-color:rgb(255,255,255)">/lib/x86_64-linux-gnu/libpython3.12.so.1.0</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> </span><br>
#1 <span
style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x0000155533ad89d7</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span
style="color:rgb(178,104,24);background-color:rgb(255,255,255)">PyImport_Import</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> () from </span><span
style="color:rgb(24,178,24);background-color:rgb(255,255,255)">/lib/x86_64-linux-gnu/libpython3.12.so.1.0</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> </span><br>
#2 <span
style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x0000155533ad8c80</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span
style="color:rgb(178,104,24);background-color:rgb(255,255,255)">PyImport_ImportModule</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> () from </span><span
style="color:rgb(24,178,24);background-color:rgb(255,255,255)">/lib/x86_64-linux-gnu/libpython3.12.so.1.0</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> </span><br>
#3 <span
style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x000015553f437c0c</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span
style="color:rgb(178,104,24);background-color:rgb(255,255,255)">PetscPythonInitialize</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span
style="color:rgb(24,178,178);background-color:rgb(255,255,255)">pyexe</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x0, </span><span
style="color:rgb(24,178,178);background-color:rgb(255,255,255)">pylib</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x0) at </span><span
style="color:rgb(24,178,24);background-color:rgb(255,255,255)">/tmp/build_openmpi-4.1.6-opt/petsc-3.21.6-debug/src/sys/python/pythonsys.c</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)">: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:rgb(0,0,0);background-color:rgb(255,255,255)">grep -r
PETSC_PYTHON_EXE
/opt/petsc-3.21.6_debug_openmpi-4.1.6/include/ </span><br>
<span
style="color:rgb(178,24,178);background-color:rgb(255,255,255)">/opt/petsc-3.21.6_debug_openmpi-4.1.6/include/petscconf.h</span><span
style="color:rgb(24,178,178);background-color:rgb(255,255,255)">:</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)">#define </span><span
style="font-weight:bold;color:rgb(255,84,84);background-color:rgb(255,255,255)">PETSC_PYTHON_EXE</span><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)">
"/usr/bin/python3"</span></span></p>
<p><span style="font-family:monospace"><span
style="color:rgb(0,0,0);background-color:rgb(255,255,255)">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/<a href="https://urldefense.us/v3/__http://libpython3.12d.so__;!!G_uCfscf7eWS!Y9u6eJnvOw3IsoL2l2NE4TRAuerg63WS_QF4KnevrJSvCcetF4dyqWweHkPeGbZJ27D_p1cH1cvdr5RhjeMhZ82J5axUqPoNQHADXm5h$" target="_blank" moz-do-not-send="true">libpython3.12d.so</a> ->
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/<a href="https://urldefense.us/v3/__http://libpython3.12.so__;!!G_uCfscf7eWS!Y9u6eJnvOw3IsoL2l2NE4TRAuerg63WS_QF4KnevrJSvCcetF4dyqWweHkPeGbZJ27D_p1cH1cvdr5RhjeMhZ82J5axUqPoNQI5lkBGY$" target="_blank" moz-do-not-send="true">libpython3.12.so</a> ->
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>(I installed the debug ("d") versions to get debug
symbols, but the segfault occurs even without them.)</p>
<p>Interestingly, on the same Ubuntu setup, calling <code>PetscPythonInitialize</code>
within our <em>pure C++</em> code works fine, and the <code>"pc_type
python"</code> example runs successfully.</p>
<p>This issue only occurs when calling <code>PetscPythonInitialize</code>
from our <em>Python module</em>.</p>
<p>Any ideas?</p>
<p>Could this be something that has already been fixed in
PETSc 3.22.x?</p>
<p>Thanks,</p>
<p>Eric</p>
<p><br>
</p>
<div>On 2025-03-12 16:48, Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<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"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">petsc-users@mcs.anl.gov</a>>
wrote:</div>
<div class="gmail_quote">
<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>
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<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!Y9u6eJnvOw3IsoL2l2NE4TRAuerg63WS_QF4KnevrJSvCcetF4dyqWweHkPeGbZJ27D_p1cH1cvdr5RhjeMhZ82J5axUqPoNQC9gNDOK$" target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
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<pre 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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<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!Y9u6eJnvOw3IsoL2l2NE4TRAuerg63WS_QF4KnevrJSvCcetF4dyqWweHkPeGbZJ27D_p1cH1cvdr5RhjeMhZ82J5axUqPoNQC9gNDOK$" target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
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<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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