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Greetings.</div>
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<br>
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I recently changed operating systems (Ubuntu 20.04 -> Debian 12 "Bookworm") and tried to reinstall PETSc.</div>
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I tried doing the usual as described in (<a href="https://petsc.org/release/install/download/#recommended-obtain-release-version-with-git" id="LPlnk513721">https://petsc.org/release/install/download/#recommended-obtain-release-version-with-git</a>):</div>
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<ul data-editing-info="{"orderedStyleType":1,"unorderedStyleType":2}">
<li style="list-style-type: "- ";"><span>git clone/pull</span></li><li style="list-style-type: "- ";"><span>./configure --<option_1> ... --<option_N></span></li><li style="list-style-type: "- ";"><span>make install</span></li><li style="list-style-type: "- ";"><span>make check</span></li></ul>
<div>Everything proceeds smoothly until the "make check" step, where I get the following error:</div>
<div class="ContentPasted6">==============================================================================</div>
<div class="ContentPasted6"><span style="font-family:monospace" class="ContentPasted8"><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted8">Running check examples to verify correct installation
</span><br class="ContentPasted8">
Using PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc and PETSC_ARCH=arch-linux-c-debug
<br class="ContentPasted8">
Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process <br class="ContentPasted8">
See https://petsc.org/release/faq/ <br class="ContentPasted8">
hwloc/linux: Ignoring PCI device with non-16bit domain. <br class="ContentPasted8">
Pass --enable-32bits-pci-domain to configure to support such devices <br class="ContentPasted8">
(warning: it would break the library ABI, don't enable unless really needed). <br class="ContentPasted8">
lid velocity = 0.0016, prandtl # = 1., grashof # = 1. <br class="ContentPasted8">
Number of SNES iterations = 2 <br class="ContentPasted8">
Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes <br class="ContentPasted8">
See https://petsc.org/release/faq/ <br class="ContentPasted8">
hwloc/linux: Ignoring PCI device with non-16bit domain. <br class="ContentPasted8">
Pass --enable-32bits-pci-domain to configure to support such devices <br class="ContentPasted8">
(warning: it would break the library ABI, don't enable unless really needed). <br class="ContentPasted8">
lid velocity = 0.0016, prandtl # = 1., grashof # = 1. <br class="ContentPasted8">
Number of SNES iterations = 2 <br class="ContentPasted8">
0a1,3 <br class="ContentPasted8">
> hwloc/linux: Ignoring PCI device with non-16bit domain. <br class="ContentPasted8">
> Pass --enable-32bits-pci-domain to configure to support such devices <br class="ContentPasted8">
> (warning: it would break the library ABI, don't enable unless really needed). <br class="ContentPasted8">
/home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/tests <br class="ContentPasted8">
Possible problem with ex47 running with hdf5, diffs above <br class="ContentPasted8">
========================================= <br class="ContentPasted8">
Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process
<br class="ContentPasted8">
See https://petsc.org/release/faq/ <br class="ContentPasted8">
hwloc/linux: Ignoring PCI device with non-16bit domain. <br class="ContentPasted8">
Pass --enable-32bits-pci-domain to configure to support such devices <br class="ContentPasted8">
(warning: it would break the library ABI, don't enable unless really needed). <br class="ContentPasted8">
Number of SNES iterations = 3 <br class="ContentPasted8">
Completed test examples <br class="ContentPasted8">
Error while running make check <br class="ContentPasted8">
gmake[1]: *** [makefile:123: check] Error 1 <br class="ContentPasted8">
make: *** [GNUmakefile:17: check] Error 2</span><br>
</div>
<div class="ContentPasted6 ContentPasted7">==============================================================================</div>
<div class="ContentPasted6 ContentPasted7"><br>
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<div class="ContentPasted6 ContentPasted7"><br>
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<div class="ContentPasted5">I tried reinstalling the same version I was able to use prior to changing OS's (PETSc 3.18.3, via tarball) and get a similar error.<br>
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==============================================================================<br>
</div>
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<span style="font-family:monospace" class="ContentPasted1 ContentPasted2"><span style="color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted1">make PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_P</span><br class="ContentPasted1">
arty/newPETSC/petsc-3.18.3 PETSC_ARCH=arch-linux-c-debug check <br class="ContentPasted1">
Running check examples to verify correct installation <br class="ContentPasted1">
Using PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_Party/newPETSC/petsc-3.18.3 and PETSC_ARCH=arch-linux-c-debug
<br class="ContentPasted1">
Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process <br class="ContentPasted1">
See https://petsc.org/release/faq/ <br class="ContentPasted1">
hwloc/linux: Ignoring PCI device with non-16bit domain. <br class="ContentPasted1">
Pass --enable-32bits-pci-domain to configure to support such devices <br class="ContentPasted1">
(warning: it would break the library ABI, don't enable unless really needed). <br class="ContentPasted1">
lid velocity = 0.0016, prandtl # = 1., grashof # = 1. <br class="ContentPasted1">
Number of SNES iterations = 2 <br class="ContentPasted1">
Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes <br class="ContentPasted1">
See https://petsc.org/release/faq/ <br class="ContentPasted1">
hwloc/linux: Ignoring PCI device with non-16bit domain. <br class="ContentPasted1">
Pass --enable-32bits-pci-domain to configure to support such devices <br class="ContentPasted1">
(warning: it would break the library ABI, don't enable unless really needed). <br class="ContentPasted1">
hwloc/linux: Ignoring PCI device with non-16bit domain. <br class="ContentPasted1">
Pass --enable-32bits-pci-domain to configure to support such devices <br class="ContentPasted1">
(warning: it would break the library ABI, don't enable unless really needed). <br class="ContentPasted1">
lid velocity = 0.0016, prandtl # = 1., grashof # = 1. <br class="ContentPasted1">
Number of SNES iterations = 2 <br class="ContentPasted1">
0a1,3 <br class="ContentPasted1">
> hwloc/linux: Ignoring PCI device with non-16bit domain. <br class="ContentPasted1">
> Pass --enable-32bits-pci-domain to configure to support such devices <br class="ContentPasted1">
> (warning: it would break the library ABI, don't enable unless really needed). <br class="ContentPasted1">
/home/jesus/Desktop/JAF_NML/3rd_Party/newPETSC/petsc-3.18.3/src/vec/vec/tests <br class="ContentPasted1">
Possible problem with ex47 running with hdf5, diffs above <br class="ContentPasted1">
========================================= <br class="ContentPasted1">
Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process
<br class="ContentPasted1">
See https://petsc.org/release/faq/ <br class="ContentPasted1">
hwloc/linux: Ignoring PCI device with non-16bit domain. <br class="ContentPasted1">
Pass --enable-32bits-pci-domain to configure to support such devices <br class="ContentPasted1">
(warning: it would break the library ABI, don't enable unless really needed). <br class="ContentPasted1">
Number of SNES iterations = 3 <br class="ContentPasted1">
Completed test examples <br class="ContentPasted1">
Error while running make check <br class="ContentPasted1">
gmake[1]: *** [makefile:149: check] Error 1 <br class="ContentPasted1">
make: *** [GNUmakefile:17: check] Error 2<br class="ContentPasted1">
==============================================================================</span><br>
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<br>
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<br>
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I checked the FAQs (<a href="https://petsc.org/release/faq/#table-of-contents" id="LPlnk436746">https://petsc.org/release/faq/#table-of-contents</a>) and tried the suggestions there (specifically the points under
<a href="https://petsc.org/release/faq/#what-does-it-mean-when-make-check-hangs-or-errors-on-petscoptionsinsertfile" id="LPlnk774935">
https://petsc.org/release/faq/#what-does-it-mean-when-make-check-hangs-or-errors-on-petscoptionsinsertfile</a>) to no avail.</div>
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<ul data-editing-info="{"orderedStyleType":1,"unorderedStyleType":2}">
<li style="list-style-type: "- ";"><span>I don't use a VPN.</span></li><li style="list-style-type: "- ";"><span>I tried running make check with Wifi disabled.</span></li><li style="list-style-type: "- ";"><span>Ran ./configure with --download-mpich-device=ch3:nemesis --download-mpich<br>
</span></li></ul>
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<br>
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Surprisingly, I can compile my PETSc programs using a makefile, and run them. <br>
</div>
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However, the programs are now broken (I get SIGSEGV originating from within DM/DMPlex APIs).<br>
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<br>
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<span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">Sincerely:</span></p>
<p style="background: white none repeat scroll 0% 0%; margin: 0px; line-height: normal;">
<u><span style="margin: 0px; font-family: "Courier New", monospace; font-size: 14pt; color: red;"><b style=""><span style="font-family: "Courier New", monospace;">J.A. Ferrand</span></b></span><span style="margin: 0px; font-family: "Swis721 BlkCn BT", sans-serif; font-size: 12pt; color: red;"></span></u></p>
<p style="background: white none repeat scroll 0% 0%; margin: 0px; line-height: normal;">
<span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">Embry-Riddle Aeronautical University - Daytona Beach - FL<br>
Ph.D. Candidate, Aerospace Engineering<br>
</span></p>
<p style="background: white none repeat scroll 0% 0%; margin: 0px; line-height: normal;">
<span style="font-family: "Times New Roman", Times, serif;"></span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">M.Sc.</span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">
Aerospace Engineering<br>
</span></p>
<p style="background: white none repeat scroll 0% 0%; margin: 0px; line-height: normal;">
<span style="font-family: "Times New Roman", Times, serif;"></span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">B.Sc.</span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">
Aerospace Engineering</span></p>
<p style="background: white none repeat scroll 0% 0%; margin: 0px; line-height: normal;">
<span style="font-family: "Times New Roman", Times, serif;"></span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">B.Sc.</span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">
Computational Mathematics</span></p>
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<span style="font-family: "Times New Roman", Times, serif;"></span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);"><br>
</span></p>
<span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: rgb(0, 0, 0);"></span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;"></span>
<p style="background: white none repeat scroll 0% 0%; margin: 0px; line-height: normal;">
<span style="font-family: "Times New Roman", Times, serif;"></span><u><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">Phone:</span></u><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">
(386)-843-1829</span></p>
<p style="background: white none repeat scroll 0% 0%; margin: 0px; line-height: normal;">
<span style="font-family: "Times New Roman", Times, serif;"></span><u><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">Email(s):</span></u><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">
ferranj2@my.erau.edu</span></p>
<p style="background: white none repeat scroll 0% 0%; margin: 0px; line-height: normal; text-indent: 0.5in;">
<span style="font-family: "Times New Roman", Times, serif;"></span><span style="margin: 0px; font-family: Courant; font-size: 12pt; color: black;"><span style="margin: 0px; font-family: "Times New Roman", Times, serif;">
</span></span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt; color: black;">jesus.ferrand@gmail.com</span></p>
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