<html><head><meta http-equiv="content-type" content="text/html; charset=us-ascii"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><a href="https://petsc.org/release/faq/#what-does-the-message-hwloc-linux-ignoring-pci-device-with-non-16bit-domain-mean">https://petsc.org/release/faq/#what-does-the-message-hwloc-linux-ignoring-pci-device-with-non-16bit-domain-mean</a><br><div><br></div><div>Thanks,</div><div>Pierre</div><div><br><blockquote type="cite"><div>On 17 Jul 2023, at 7:51 PM, Ferrand, Jesus A. <FERRANJ2@my.erau.edu> wrote:</div><br class="Apple-interchange-newline"><div><meta charset="UTF-8"><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;">Greetings.</div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><br></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;">I recently changed operating systems (Ubuntu 20.04 -> Debian 12 "Bookworm") and tried to reinstall PETSc.</div><div class="elementToProof ContentPasted0" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;">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><div class="elementToProof ContentPasted0" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><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 class="ContentPasted8" style="font-family: monospace;"><span class="ContentPasted8" style="background-color: rgb(255, 255, 255);">Running check examples to verify correct installation<span class="Apple-converted-space"> </span></span><br class="ContentPasted8">Using PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc and PETSC_ARCH=arch-linux-c-debug<span class="Apple-converted-space"> </span><br class="ContentPasted8">Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process<span class="Apple-converted-space"> </span><br class="ContentPasted8">See<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="Apple-converted-space"> </span><br class="ContentPasted8">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="Apple-converted-space"> </span><br class="ContentPasted8">Pass --enable-32bits-pci-domain to configure to support such devices<span class="Apple-converted-space"> </span><br class="ContentPasted8">(warning: it would break the library ABI, don't enable unless really needed).<span class="Apple-converted-space"> </span><br class="ContentPasted8">lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<span class="Apple-converted-space"> </span><br class="ContentPasted8">Number of SNES iterations = 2<span class="Apple-converted-space"> </span><br class="ContentPasted8">Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes<span class="Apple-converted-space"> </span><br class="ContentPasted8">See<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="Apple-converted-space"> </span><br class="ContentPasted8">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="Apple-converted-space"> </span><br class="ContentPasted8">Pass --enable-32bits-pci-domain to configure to support such devices<span class="Apple-converted-space"> </span><br class="ContentPasted8">(warning: it would break the library ABI, don't enable unless really needed).<span class="Apple-converted-space"> </span><br class="ContentPasted8">lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<span class="Apple-converted-space"> </span><br class="ContentPasted8">Number of SNES iterations = 2<span class="Apple-converted-space"> </span><br class="ContentPasted8">0a1,3<span class="Apple-converted-space"> </span><br class="ContentPasted8">> hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="Apple-converted-space"> </span><br class="ContentPasted8">> Pass --enable-32bits-pci-domain to configure to support such devices<span class="Apple-converted-space"> </span><br class="ContentPasted8">> (warning: it would break the library ABI, don't enable unless really needed).<span class="Apple-converted-space"> </span><br class="ContentPasted8">/home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/tests<span class="Apple-converted-space"> </span><br class="ContentPasted8">Possible problem with ex47 running with hdf5, diffs above<span class="Apple-converted-space"> </span><br class="ContentPasted8">=========================================<span class="Apple-converted-space"> </span><br class="ContentPasted8">Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process<span class="Apple-converted-space"> </span><br class="ContentPasted8">See<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="Apple-converted-space"> </span><br class="ContentPasted8">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="Apple-converted-space"> </span><br class="ContentPasted8">Pass --enable-32bits-pci-domain to configure to support such devices<span class="Apple-converted-space"> </span><br class="ContentPasted8">(warning: it would break the library ABI, don't enable unless really needed).<span class="Apple-converted-space"> </span><br class="ContentPasted8">Number of SNES iterations = 3<span class="Apple-converted-space"> </span><br class="ContentPasted8">Completed test examples<span class="Apple-converted-space"> </span><br class="ContentPasted8">Error while running make check<span class="Apple-converted-space"> </span><br class="ContentPasted8">gmake[1]: *** [makefile:123: check] Error 1<span class="Apple-converted-space"> </span><br class="ContentPasted8">make: *** [GNUmakefile:17: check] Error 2</span><br></div><div class="ContentPasted6 ContentPasted7">==============================================================================</div><div class="ContentPasted6 ContentPasted7"><br></div><div class="ContentPasted6 ContentPasted7"><br></div><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></div></div><div class="elementToProof ContentPasted0" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;">==============================================================================<br></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><span class="ContentPasted1 ContentPasted2" style="font-family: monospace;"><span class="ContentPasted1" style="background-color: rgb(255, 255, 255);">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<span class="Apple-converted-space"> </span><br class="ContentPasted1">Running check examples to verify correct installation<span class="Apple-converted-space"> </span><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<span class="Apple-converted-space"> </span><br class="ContentPasted1">Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process<span class="Apple-converted-space"> </span><br class="ContentPasted1">See<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="Apple-converted-space"> </span><br class="ContentPasted1">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="Apple-converted-space"> </span><br class="ContentPasted1">Pass --enable-32bits-pci-domain to configure to support such devices<span class="Apple-converted-space"> </span><br class="ContentPasted1">(warning: it would break the library ABI, don't enable unless really needed).<span class="Apple-converted-space"> </span><br class="ContentPasted1">lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<span class="Apple-converted-space"> </span><br class="ContentPasted1">Number of SNES iterations = 2<span class="Apple-converted-space"> </span><br class="ContentPasted1">Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes<span class="Apple-converted-space"> </span><br class="ContentPasted1">See<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="Apple-converted-space"> </span><br class="ContentPasted1">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="Apple-converted-space"> </span><br class="ContentPasted1">Pass --enable-32bits-pci-domain to configure to support such devices<span class="Apple-converted-space"> </span><br class="ContentPasted1">(warning: it would break the library ABI, don't enable unless really needed).<span class="Apple-converted-space"> </span><br class="ContentPasted1">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="Apple-converted-space"> </span><br class="ContentPasted1">Pass --enable-32bits-pci-domain to configure to support such devices<span class="Apple-converted-space"> </span><br class="ContentPasted1">(warning: it would break the library ABI, don't enable unless really needed).<span class="Apple-converted-space"> </span><br class="ContentPasted1">lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<span class="Apple-converted-space"> </span><br class="ContentPasted1">Number of SNES iterations = 2<span class="Apple-converted-space"> </span><br class="ContentPasted1">0a1,3<span class="Apple-converted-space"> </span><br class="ContentPasted1">> hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="Apple-converted-space"> </span><br class="ContentPasted1">> Pass --enable-32bits-pci-domain to configure to support such devices<span class="Apple-converted-space"> </span><br class="ContentPasted1">> (warning: it would break the library ABI, don't enable unless really needed).<span class="Apple-converted-space"> </span><br class="ContentPasted1">/home/jesus/Desktop/JAF_NML/3rd_Party/newPETSC/petsc-3.18.3/src/vec/vec/tests<span class="Apple-converted-space"> </span><br class="ContentPasted1">Possible problem with ex47 running with hdf5, diffs above<span class="Apple-converted-space"> </span><br class="ContentPasted1">=========================================<span class="Apple-converted-space"> </span><br class="ContentPasted1">Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process<span class="Apple-converted-space"> </span><br class="ContentPasted1">See<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="Apple-converted-space"> </span><br class="ContentPasted1">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="Apple-converted-space"> </span><br class="ContentPasted1">Pass --enable-32bits-pci-domain to configure to support such devices<span class="Apple-converted-space"> </span><br class="ContentPasted1">(warning: it would break the library ABI, don't enable unless really needed).<span class="Apple-converted-space"> </span><br class="ContentPasted1">Number of SNES iterations = 3<span class="Apple-converted-space"> </span><br class="ContentPasted1">Completed test examples<span class="Apple-converted-space"> </span><br class="ContentPasted1">Error while running make check<span class="Apple-converted-space"> </span><br class="ContentPasted1">gmake[1]: *** [makefile:149: check] Error 1<span class="Apple-converted-space"> </span><br class="ContentPasted1">make: *** [GNUmakefile:17: check] Error 2<br class="ContentPasted1">==============================================================================</span><br></div><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><br></div><div class="elementToProof" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div class="ContentPasted3" style="font-family: "Times New Roman", Times, serif; font-size: 12pt;"><br></div><div class="ContentPasted3 ContentPasted4" style="font-family: "Times New Roman", Times, serif; font-size: 12pt;">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><div class="ContentPasted3 ContentPasted4" style="font-family: "Times New Roman", Times, serif; font-size: 12pt;"><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></div><div class="ContentPasted3" style="font-family: "Times New Roman", Times, serif; font-size: 12pt;"><br></div><div class="ContentPasted3" style="font-family: "Times New Roman", Times, serif; font-size: 12pt;">Surprisingly, I can compile my PETSc programs using a makefile, and run them.<span class="Apple-converted-space"> </span><br></div><div class="ContentPasted3" style="font-family: "Times New Roman", Times, serif; font-size: 12pt;">However, the programs are now broken (I get SIGSEGV originating from within DM/DMPlex APIs).<br></div><div id="Signature"><div><div style="font-family: "Times New Roman", Times, serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><br></div><div></div><div></div><div id="divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;"><p style="margin-top: 0px; margin-bottom: 0px;"></p><div><div style="margin: 0px 0px 10.66px;"><br class="webkit-block-placeholder"></div><div><p style="margin: 0px 0px 11px; background: repeat white; line-height: normal;"><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt;">Sincerely:</span></p><div style="margin: 0px; background: repeat white; line-height: normal;"><u><span style="margin: 0px; font-family: "Courier New", monospace; font-size: 14pt; color: red;"><b><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></div><div style="margin: 0px; background: repeat white; line-height: normal;"><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt;">Embry-Riddle Aeronautical University - Daytona Beach - FL<br>Ph.D. Candidate, Aerospace Engineering<br></span></div><div style="margin: 0px; background: repeat white; 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;">M.Sc.</span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><span class="Apple-converted-space"> </span>Aerospace Engineering<br></span></div><div style="margin: 0px; background: repeat white; 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;">B.Sc.</span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><span class="Apple-converted-space"> </span>Aerospace Engineering</span></div><div style="margin: 0px; background: repeat white; 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;">B.Sc.</span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><span class="Apple-converted-space"> </span>Computational Mathematics</span></div><div style="margin: 0px; background: repeat white; 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;"><br></span></div><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt;"></span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt;"></span><div style="margin: 0px; background: repeat white; 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;">Phone:</span></u><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><span class="Apple-converted-space"> </span>(386)-843-1829</span></div><div style="margin: 0px; background: repeat white; 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;">Email(s):</span></u><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><span class="Apple-converted-space"> </span><a href="mailto:ferranj2@my.erau.edu">ferranj2@my.erau.edu</a></span></div><div style="margin: 0px; background: repeat white; 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;"><span style="margin: 0px; font-family: "Times New Roman", Times, serif;"> <span class="Apple-converted-space"> </span></span></span><span style="margin: 0px; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><a href="mailto:jesus.ferrand@gmail.com">jesus.ferrand@gmail.com</a></span></div></div></div></div></div></div></div></div></blockquote></div><br></body></html>