<div dir="ltr">Hi Jesus,<div><br></div><div>I think you are on main. Did everything you have get rebuilt? Toby just rewrote large sections of logging</div><div>and this is right where it fails for you. It should be easy to see what is wrong by running in the debugger.</div><div><br></div><div>  Thanks,</div><div><br></div><div>     Matt</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jul 17, 2023 at 3:11 PM Pierre Jolivet <<a href="mailto:pierre.jolivet@lip6.fr">pierre.jolivet@lip6.fr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><br><div><blockquote type="cite"><div>On 17 Jul 2023, at 9:00 PM, Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" target="_blank">FERRANJ2@my.erau.edu</a>> wrote:</div><br><div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">Pierre:</div><div style="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;text-decoration:none">Setting the environment variable allows make check to complete without errors.</div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">It only seems to run three checks.</div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">I recall that in the past, make check would run 100+ tests.</div></div></blockquote><div><br></div><div>You are probably thinking of make test, which is running thousands of tests indeed.</div><br><blockquote type="cite"><div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">This is what I get from make check:</div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">=========================================================================<br></div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt"><span style="font-family:monospace"><span style="background-color:rgb(255,255,255)">Running check examples to verify correct installation<span> </span></span><br>Using PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc and PETSC_ARCH=arch-linux-c-debug<span> </span><br>C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process<span> </span><br>C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes<span> </span><br>C/C++ example src/vec/vec/tests/ex47 run successfully with hdf5<span> </span><br>Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process<span> </span><br>Completed test examples<br></span>=========================================================================<br></div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt"><br></div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">Anyhow, some of the APIs that worked before now break.</div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">For example "<span style="font-family:monospace">DMPlexCreateGmshFromFile()</span>" breaks when I read simple test mesh.</div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">I tried configuring and installing both the newest release of PETSc and that tarball of version 3.18.3.</div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">Both seem to be breaking APIs that used to work in the older OS.</div></div></blockquote><div><br></div><div>There has been some internal changes to the behavior of DMPlex, they should be documented in the change log.</div><div>But you are saying that with the same version, just by switching OS, you get a different behavior?</div><div>Do as Satish suggested then, because it’s unlikely that the root cause is in the library itself.</div><div><br></div><div>Thanks,</div><div>Pierre</div><br><blockquote type="cite"><div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">=========================================================================<br></div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt"><span style="font-family:monospace"><span style="background-color:rgb(255,255,255)">[0]PETSC ERROR: ------------------------------------------------------------------------<span> </span></span><br>[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<span> </span><br>[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<span> </span><br>[0]PETSC ERROR: or see<span> </span><a href="https://petsc.org/release/faq/#valgrind" target="_blank">https://petsc.org/release/faq/#valgrind</a><span> </span>and<span> </span><a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><span> </span><br>[0]PETSC ERROR: ---------------------  Stack Frames ------------------------------------<span> </span><br>[0]PETSC ERROR: The line numbers in the error traceback are not always exact.<span> </span><br>[0]PETSC ERROR: #1 DMPlexSetMigrationSF() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/ple<br>xnatural.c:21<span> </span><br>[0]PETSC ERROR: #2 JAF_DMPlexCreateFromMesh() at /home/jesus/Desktop/JAF_NML/ApplicationCode/PETSc/PETScCGH5.c:5865<span> </span><br>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<span> </span><br>[unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59)<br>- process 0<span> </span><br>:<span> </span><br>system msg for write_line failure : Bad file descriptor<span> </span><br>[0]PETSC ERROR: ------------------------------------------------------------------------<span> </span><br>[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<span> </span><br>[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<span> </span><br>[0]PETSC ERROR: or see<span> </span><a href="https://petsc.org/release/faq/#valgrind" target="_blank">https://petsc.org/release/faq/#valgrind</a><span> </span>and<span> </span><a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><span> </span><br>[0]PETSC ERROR: ---------------------  Stack Frames ------------------------------------<span> </span><br>[0]PETSC ERROR: The line numbers in the error traceback are not always exact.<span> </span><br>[0]PETSC ERROR: #1 DMPlexSetMigrationSF() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/ple<br>xnatural.c:21<span> </span><br>[0]PETSC ERROR: #2 JAF_DMPlexCreateFromMesh() at /home/jesus/Desktop/JAF_NML/ApplicationCode/PETSc/PETScCGH5.c:5865<span> </span><br>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<span> </span><br>[unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59)<br>- process 0<span> </span><br>:<span> </span><br>system msg for write_line failure : Bad file descriptor<span> </span><br>--------------------------------------------------------------------------<span> </span><br>Primary job  terminated normally, but 1 process returned<span> </span><br>a non-zero exit code. Per user-direction, the job has been aborted.<span> </span><br>--------------------------------------------------------------------------<span> </span><br>[0]PETSC ERROR: ------------------------------------------------------------------------<span> </span><br>[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end<span> </span><br>[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<span> </span><br>[0]PETSC ERROR: or see<span> </span><a href="https://petsc.org/release/faq/#valgrind" target="_blank">https://petsc.org/release/faq/#valgrind</a><span> </span>and<span> </span><a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><span> </span><br>[0]PETSC ERROR: ---------------------  Stack Frames ------------------------------------<span> </span><br>[0]PETSC ERROR: The line numbers in the error traceback are not always exact.<span> </span><br>[0]PETSC ERROR: #1 PetscEventRegLogGetEvent() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/logging/u<br>tils/eventlog.c:622<span> </span><br>[0]PETSC ERROR: #2 PetscLogEventRegister() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/logging/plog<br>.c:802<span> </span><br>[0]PETSC ERROR: #3 VecInitializePackage() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/interface<br>/dlregisvec.c:187<span> </span><br>[0]PETSC ERROR: #4 VecCreate() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/interface/veccreate.<br>c:32<span> </span><br>[0]PETSC ERROR: #5 DMCreateLocalVector_Section_Private() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm<br>/interface/dmi.c:80<span> </span><br>[0]PETSC ERROR: #6 DMCreateLocalVector_Plex() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex<br>/plexcreate.c:4432<span> </span><br>[0]PETSC ERROR: #7 DMCreateLocalVector() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/interface/dm.c:<br>1056<span> </span><br>[0]PETSC ERROR: #8 DMPlexCreateGmsh() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/plexgms<br>h.c:1933<span> </span><br>[0]PETSC ERROR: #9 DMPlexCreateGmshFromFile() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex<br>/plexgmsh.c:1433<span> </span><br>[0]PETSC ERROR: #10 JAF_DMPlexCreateFromMesh() at /home/jesus/Desktop/JAF_NML/ApplicationCode/PETSc/PETScCGH5.c:5845<span> </span><br>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<span> </span><br>[unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59)<br>- process 0<span> </span><br>:<span> </span><br>system msg for write_line failure : Bad file descriptor<span> </span><br>[0]PETSC ERROR: ------------------------------------------------------------------------<span> </span><br>[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end<span> </span><br>[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<span> </span><br>[0]PETSC ERROR: or see<span> </span><a href="https://petsc.org/release/faq/#valgrind" target="_blank">https://petsc.org/release/faq/#valgrind</a><span> </span>and<span> </span><a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><span> </span><br>[0]PETSC ERROR: ---------------------  Stack Frames ------------------------------------<span> </span><br>[0]PETSC ERROR: The line numbers in the error traceback are not always exact.<span> </span><br>[0]PETSC ERROR: #1 PetscStrcasecmp() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/utils/str.c:285<span> </span><br>[0]PETSC ERROR: #2 PetscEventRegLogGetEvent() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/logging/u<br>tils/eventlog.c:622<span> </span><br>[0]PETSC ERROR: #3 PetscLogEventRegister() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/logging/plog<br>.c:802<span> </span><br>[0]PETSC ERROR: #4 VecInitializePackage() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/interface<br>/dlregisvec.c:188<span> </span><br>[0]PETSC ERROR: #5 VecCreate() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/interface/veccreate.<br>c:32<span> </span><br>[0]PETSC ERROR: #6 DMCreateLocalVector_Section_Private() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm<br>/interface/dmi.c:80<span> </span><br>[0]PETSC ERROR: #7 DMCreateLocalVector_Plex() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex<br>/plexcreate.c:4432<span> </span><br>[0]PETSC ERROR: #8 DMCreateLocalVector() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/interface/dm.c:<br>1056<span> </span><br>[0]PETSC ERROR: #9 DMPlexCreateGmsh() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/plexgms<br>h.c:1933<span> </span><br>[0]PETSC ERROR: #10 DMPlexCreateGmshFromFile() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/ple<br>x/plexgmsh.c:1433<span> </span><br>[0]PETSC ERROR: #11 JAF_DMPlexCreateFromMesh() at /home/jesus/Desktop/JAF_NML/ApplicationCode/PETSc/PETScCGH5.c:5845<span> </span><br>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<span> </span><br>[unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59)<br>- process 0<span> </span><br>:<span> </span><br>system msg for write_line failure : Bad file descriptor<span> </span><br>--------------------------------------------------------------------------<span> </span><br>mpiexec detected that one or more processes exited with non-zero status, thus causing<span> </span><br>the job to be terminated. The first process to do so was:<span> </span><br><br> Process name: [[33478,1],2]<span> </span><br> Exit code:    15<br>===========================================================================</span></div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt"><br></div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">Here are the options I give ./configure:</div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt"><br></div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">./configure --download-mpich=yes --download-viennacl=yes --download-hdf5=yes --download-chaco=yes --download-metis=yes --download-parmetis=yes --download-cgns=yes<br></div><div id="m_-9020343707798443473appendonsend" style="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;text-decoration:none"></div><hr style="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;text-decoration:none;display:inline-block;width:1116.22px"><span style="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;text-decoration:none;float:none;display:inline"></span><div id="m_-9020343707798443473divRplyFwdMsg" dir="ltr" style="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;text-decoration:none"><font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b><span> </span>Pierre Jolivet <<a href="mailto:pierre.jolivet@lip6.fr" target="_blank">pierre.jolivet@lip6.fr</a>><br><b>Sent:</b><span> </span>Monday, July 17, 2023 1:58 PM<br><b>To:</b><span> </span>Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu" target="_blank">FERRANJ2@my.erau.edu</a>><br><b>Cc:</b><span> </span><a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><span> </span><<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br><b>Subject:</b><span> </span>[EXTERNAL] Re: [petsc-users] PETSc Installation Assistance</font><div> </div></div><div style="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;text-decoration:none"><table width="100%" border="0" cellpadding="0" cellspacing="0" role="presentation" style="min-width:100%;background-color:rgb(255,235,156);border:1px solid rgb(136,136,136);font-size:14px;line-height:1.5;font-family:Arial,sans-serif;text-align:left"><tbody><tr><td style="padding:5px 10px"><span style="color:rgb(214,0,0)"><b>CAUTION:</b></span><span> </span>This email originated outside of Embry-Riddle Aeronautical University. Do not click links or open attachments unless you recognize the sender and know the content is safe.</td></tr></tbody></table><br><div><a href="https://petsc.org/release/faq/#what-does-the-message-hwloc-linux-ignoring-pci-device-with-non-16bit-domain-mean" target="_blank">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. <<a href="mailto:FERRANJ2@my.erau.edu" target="_blank">FERRANJ2@my.erau.edu</a>> wrote:</div><br><div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">Greetings.</div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt"><br></div><div 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;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 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;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="m_-9020343707798443473LPlnk513721" target="_blank">https://petsc.org/release/install/download/#recommended-obtain-release-version-with-git</a>):</div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt"><ul><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>==============================================================================</div><div><span style="font-family:monospace"><span style="background-color:rgb(255,255,255)">Running check examples to verify correct installation<span> </span></span><br>Using PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc and PETSC_ARCH=arch-linux-c-debug<span> </span><br>Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process<span> </span><br>See<span> </span><a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><span> </span><br>hwloc/linux: Ignoring PCI device with non-16bit domain.<span> </span><br>Pass --enable-32bits-pci-domain to configure to support such devices<span> </span><br>(warning: it would break the library ABI, don't enable unless really needed).<span> </span><br>lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<span> </span><br>Number of SNES iterations = 2<span> </span><br>Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes<span> </span><br>See<span> </span><a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><span> </span><br>hwloc/linux: Ignoring PCI device with non-16bit domain.<span> </span><br>Pass --enable-32bits-pci-domain to configure to support such devices<span> </span><br>(warning: it would break the library ABI, don't enable unless really needed).<span> </span><br>lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<span> </span><br>Number of SNES iterations = 2<span> </span><br>0a1,3<span> </span><br>> hwloc/linux: Ignoring PCI device with non-16bit domain.<span> </span><br>> Pass --enable-32bits-pci-domain to configure to support such devices<span> </span><br>> (warning: it would break the library ABI, don't enable unless really needed).<span> </span><br>/home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/tests<span> </span><br>Possible problem with ex47 running with hdf5, diffs above<span> </span><br>=========================================<span> </span><br>Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process<span> </span><br>See<span> </span><a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><span> </span><br>hwloc/linux: Ignoring PCI device with non-16bit domain.<span> </span><br>Pass --enable-32bits-pci-domain to configure to support such devices<span> </span><br>(warning: it would break the library ABI, don't enable unless really needed).<span> </span><br>Number of SNES iterations =     3<span> </span><br>Completed test examples<span> </span><br>Error while running make check<span> </span><br>gmake[1]: *** [makefile:123: check] Error 1<span> </span><br>make: *** [GNUmakefile:17: check] Error 2</span><br></div><div>==============================================================================</div><div><br></div><div><br></div><div>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 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt">==============================================================================<br></div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt"><span style="font-family:monospace"><span style="background-color:rgb(255,255,255)">make PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_P</span><br>arty/newPETSC/petsc-3.18.3 PETSC_ARCH=arch-linux-c-debug check<span> </span><br>Running check examples to verify correct installation<span> </span><br>Using PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_Party/newPETSC/petsc-3.18.3 and PETSC_ARCH=arch-linux-c-debug<span> </span><br>Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process<span> </span><br>See<span> </span><a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><span> </span><br>hwloc/linux: Ignoring PCI device with non-16bit domain.<span> </span><br>Pass --enable-32bits-pci-domain to configure to support such devices<span> </span><br>(warning: it would break the library ABI, don't enable unless really needed).<span> </span><br>lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<span> </span><br>Number of SNES iterations = 2<span> </span><br>Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes<span> </span><br>See<span> </span><a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><span> </span><br>hwloc/linux: Ignoring PCI device with non-16bit domain.<span> </span><br>Pass --enable-32bits-pci-domain to configure to support such devices<span> </span><br>(warning: it would break the library ABI, don't enable unless really needed).<span> </span><br>hwloc/linux: Ignoring PCI device with non-16bit domain.<span> </span><br>Pass --enable-32bits-pci-domain to configure to support such devices<span> </span><br>(warning: it would break the library ABI, don't enable unless really needed).<span> </span><br>lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<span> </span><br>Number of SNES iterations = 2<span> </span><br>0a1,3<span> </span><br>> hwloc/linux: Ignoring PCI device with non-16bit domain.<span> </span><br>> Pass --enable-32bits-pci-domain to configure to support such devices<span> </span><br>> (warning: it would break the library ABI, don't enable unless really needed).<span> </span><br>/home/jesus/Desktop/JAF_NML/3rd_Party/newPETSC/petsc-3.18.3/src/vec/vec/tests<span> </span><br>Possible problem with ex47 running with hdf5, diffs above<span> </span><br>=========================================<span> </span><br>Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process<span> </span><br>See<span> </span><a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a><span> </span><br>hwloc/linux: Ignoring PCI device with non-16bit domain.<span> </span><br>Pass --enable-32bits-pci-domain to configure to support such devices<span> </span><br>(warning: it would break the library ABI, don't enable unless really needed).<span> </span><br>Number of SNES iterations =     3<span> </span><br>Completed test examples<span> </span><br>Error while running make check<span> </span><br>gmake[1]: *** [makefile:149: check] Error 1<span> </span><br>make: *** [GNUmakefile:17: check] Error 2<br>==============================================================================</span><br></div><div 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;text-decoration:none;font-family:"Times New Roman",Times,serif;font-size:12pt"><br></div><div style="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;text-decoration:none"><div style="font-family:"Times New Roman",Times,serif;font-size:12pt"><br></div><div 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="m_-9020343707798443473LPlnk436746" target="_blank">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="m_-9020343707798443473LPlnk774935" target="_blank">https://petsc.org/release/faq/#what-does-it-mean-when-make-check-hangs-or-errors-on-petscoptionsinsertfile</a>) to no avail.</div><div style="font-family:"Times New Roman",Times,serif;font-size:12pt"><ul><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 style="font-family:"Times New Roman",Times,serif;font-size:12pt"><br></div><div 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> </span><br></div><div 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="m_-9020343707798443473x_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="m_-9020343707798443473x_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></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> </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> </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> </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> </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> </span><a href="mailto:ferranj2@my.erau.edu" target="_blank">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> </span></span></span><span style="margin:0px;font-family:"Times New Roman",Times,serif;font-size:12pt"><a href="mailto:jesus.ferrand@gmail.com" target="_blank">jesus.ferrand@gmail.com</a></span></div></div></div></div></div></div></div></div></blockquote></div></div></div></div></blockquote></div><br></div></blockquote></div><br clear="all"><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="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div>