<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><br><div><blockquote type="cite"><div>On 17 Jul 2023, at 9:00 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;">Pierre:</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;">Setting the environment variable allows make check to complete without errors.</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;">It only seems to run three checks.</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 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 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;">This is what I get from make check:</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;"><span class="ContentPasted1" style="font-family: monospace;"><span class="ContentPasted1" style="background-color: rgb(255, 255, 255);">Running check examples to verify correct installation<span class="Apple-converted-space"> </span></span><br class="ContentPasted1">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="ContentPasted1">C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process<span class="Apple-converted-space"> </span><br class="ContentPasted1">C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes<span class="Apple-converted-space"> </span><br class="ContentPasted1">C/C++ example src/vec/vec/tests/ex47 run successfully with hdf5<span class="Apple-converted-space"> </span><br class="ContentPasted1">Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process<span class="Apple-converted-space"> </span><br class="ContentPasted1">Completed test examples<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="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;">Anyhow, some of the APIs that worked before now break.</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;">For example "<span class="ContentPasted0 ContentPasted2" style="font-family: monospace;">DMPlexCreateGmshFromFile()</span>" breaks when I read simple test mesh.</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 tried configuring and installing both the newest release of PETSc and that tarball of version 3.18.3.</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;">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 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;"><span class="ContentPasted0" style="font-family: monospace;"><span class="ContentPasted0" style="background-color: rgb(255, 255, 255);">[0]PETSC ERROR: ------------------------------------------------------------------------<span class="Apple-converted-space"> </span></span><br class="ContentPasted0">[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: or see<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/#valgrind">https://petsc.org/release/faq/#valgrind</a><span class="Apple-converted-space"> </span>and<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="ContentPasted0">[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: The line numbers in the error traceback are not always exact.<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #1 DMPlexSetMigrationSF() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/ple<br class="ContentPasted0">xnatural.c:21<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #2 JAF_DMPlexCreateFromMesh() at /home/jesus/Desktop/JAF_NML/ApplicationCode/PETSc/PETScCGH5.c:5865<span class="Apple-converted-space"> </span><br class="ContentPasted0">application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<span class="Apple-converted-space"> </span><br class="ContentPasted0">[unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59)<br class="ContentPasted0">- process 0<span class="Apple-converted-space"> </span><br class="ContentPasted0">:<span class="Apple-converted-space"> </span><br class="ContentPasted0">system msg for write_line failure : Bad file descriptor<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: ------------------------------------------------------------------------<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: or see<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/#valgrind">https://petsc.org/release/faq/#valgrind</a><span class="Apple-converted-space"> </span>and<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="ContentPasted0">[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: The line numbers in the error traceback are not always exact.<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #1 DMPlexSetMigrationSF() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/ple<br class="ContentPasted0">xnatural.c:21<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #2 JAF_DMPlexCreateFromMesh() at /home/jesus/Desktop/JAF_NML/ApplicationCode/PETSc/PETScCGH5.c:5865<span class="Apple-converted-space"> </span><br class="ContentPasted0">application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<span class="Apple-converted-space"> </span><br class="ContentPasted0">[unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59)<br class="ContentPasted0">- process 0<span class="Apple-converted-space"> </span><br class="ContentPasted0">:<span class="Apple-converted-space"> </span><br class="ContentPasted0">system msg for write_line failure : Bad file descriptor<span class="Apple-converted-space"> </span><br class="ContentPasted0">--------------------------------------------------------------------------<span class="Apple-converted-space"> </span><br class="ContentPasted0">Primary job terminated normally, but 1 process returned<span class="Apple-converted-space"> </span><br class="ContentPasted0">a non-zero exit code. Per user-direction, the job has been aborted.<span class="Apple-converted-space"> </span><br class="ContentPasted0">--------------------------------------------------------------------------<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: ------------------------------------------------------------------------<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: or see<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/#valgrind">https://petsc.org/release/faq/#valgrind</a><span class="Apple-converted-space"> </span>and<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="ContentPasted0">[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: The line numbers in the error traceback are not always exact.<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #1 PetscEventRegLogGetEvent() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/logging/u<br class="ContentPasted0">tils/eventlog.c:622<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #2 PetscLogEventRegister() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/logging/plog<br class="ContentPasted0">.c:802<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #3 VecInitializePackage() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/interface<br class="ContentPasted0">/dlregisvec.c:187<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #4 VecCreate() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/interface/veccreate.<br class="ContentPasted0">c:32<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #5 DMCreateLocalVector_Section_Private() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm<br class="ContentPasted0">/interface/dmi.c:80<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #6 DMCreateLocalVector_Plex() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex<br class="ContentPasted0">/plexcreate.c:4432<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #7 DMCreateLocalVector() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/interface/dm.c:<br class="ContentPasted0">1056<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #8 DMPlexCreateGmsh() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/plexgms<br class="ContentPasted0">h.c:1933<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #9 DMPlexCreateGmshFromFile() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex<br class="ContentPasted0">/plexgmsh.c:1433<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #10 JAF_DMPlexCreateFromMesh() at /home/jesus/Desktop/JAF_NML/ApplicationCode/PETSc/PETScCGH5.c:5845<span class="Apple-converted-space"> </span><br class="ContentPasted0">application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<span class="Apple-converted-space"> </span><br class="ContentPasted0">[unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59)<br class="ContentPasted0">- process 0<span class="Apple-converted-space"> </span><br class="ContentPasted0">:<span class="Apple-converted-space"> </span><br class="ContentPasted0">system msg for write_line failure : Bad file descriptor<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: ------------------------------------------------------------------------<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: or see<span class="Apple-converted-space"> </span><a href="https://petsc.org/release/faq/#valgrind">https://petsc.org/release/faq/#valgrind</a><span class="Apple-converted-space"> </span>and<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="ContentPasted0">[0]PETSC ERROR: --------------------- Stack Frames ------------------------------------<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: The line numbers in the error traceback are not always exact.<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #1 PetscStrcasecmp() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/utils/str.c:285<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #2 PetscEventRegLogGetEvent() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/logging/u<br class="ContentPasted0">tils/eventlog.c:622<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #3 PetscLogEventRegister() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/sys/logging/plog<br class="ContentPasted0">.c:802<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #4 VecInitializePackage() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/interface<br class="ContentPasted0">/dlregisvec.c:188<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #5 VecCreate() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/interface/veccreate.<br class="ContentPasted0">c:32<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #6 DMCreateLocalVector_Section_Private() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm<br class="ContentPasted0">/interface/dmi.c:80<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #7 DMCreateLocalVector_Plex() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex<br class="ContentPasted0">/plexcreate.c:4432<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #8 DMCreateLocalVector() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/interface/dm.c:<br class="ContentPasted0">1056<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #9 DMPlexCreateGmsh() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/plexgms<br class="ContentPasted0">h.c:1933<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #10 DMPlexCreateGmshFromFile() at /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/ple<br class="ContentPasted0">x/plexgmsh.c:1433<span class="Apple-converted-space"> </span><br class="ContentPasted0">[0]PETSC ERROR: #11 JAF_DMPlexCreateFromMesh() at /home/jesus/Desktop/JAF_NML/ApplicationCode/PETSc/PETScCGH5.c:5845<span class="Apple-converted-space"> </span><br class="ContentPasted0">application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0<span class="Apple-converted-space"> </span><br class="ContentPasted0">[unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59)<br class="ContentPasted0">- process 0<span class="Apple-converted-space"> </span><br class="ContentPasted0">:<span class="Apple-converted-space"> </span><br class="ContentPasted0">system msg for write_line failure : Bad file descriptor<span class="Apple-converted-space"> </span><br class="ContentPasted0">--------------------------------------------------------------------------<span class="Apple-converted-space"> </span><br class="ContentPasted0">mpiexec detected that one or more processes exited with non-zero status, thus causing<span class="Apple-converted-space"> </span><br class="ContentPasted0">the job to be terminated. The first process to do so was:<span class="Apple-converted-space"> </span><br class="ContentPasted0"><br class="ContentPasted0"> Process name: [[33478,1],2]<span class="Apple-converted-space"> </span><br class="ContentPasted0"> Exit code: 15<br class="ContentPasted0">===========================================================================</span></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;">Here are the options I give ./configure:</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 ContentPasted3" 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;">./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="appendonsend" 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><hr tabindex="-1" 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; display: inline-block; width: 1116.21875px;"><span 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; float: none; display: inline !important;"></span><div id="divRplyFwdMsg" dir="ltr" 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;"><font face="Calibri, sans-serif" style="font-size: 11pt;"><b>From:</b><span class="Apple-converted-space"> </span>Pierre Jolivet <<a href="mailto:pierre.jolivet@lip6.fr">pierre.jolivet@lip6.fr</a>><br><b>Sent:</b><span class="Apple-converted-space"> </span>Monday, July 17, 2023 1:58 PM<br><b>To:</b><span class="Apple-converted-space"> </span>Ferrand, Jesus A. <<a href="mailto:FERRANJ2@my.erau.edu">FERRANJ2@my.erau.edu</a>><br><b>Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><span class="Apple-converted-space"> </span><<a href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>><br><b>Subject:</b><span class="Apple-converted-space"> </span>[EXTERNAL] Re: [petsc-users] PETSc Installation Assistance</font><div> </div></div><div 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; line-break: after-white-space;"><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 class="Apple-converted-space"> </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">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">FERRANJ2@my.erau.edu</a>> wrote:</div><br class="x_Apple-interchange-newline"><div><div class="x_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; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;">Greetings.</div><div class="x_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; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><br></div><div class="x_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; 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="x_elementToProof x_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; 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="x_elementToProof x_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; 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="x_ContentPasted6">==============================================================================</div><div class="x_ContentPasted6"><span class="x_ContentPasted8" style="font-family: monospace;"><span class="x_ContentPasted8" style="background-color: rgb(255, 255, 255);">Running check examples to verify correct installation<span class="x_Apple-converted-space"> </span></span><br class="x_ContentPasted8">Using PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc and PETSC_ARCH=arch-linux-c-debug<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">See<span class="x_Apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">Pass --enable-32bits-pci-domain to configure to support such devices<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">(warning: it would break the library ABI, don't enable unless really needed).<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">Number of SNES iterations = 2<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">See<span class="x_Apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">Pass --enable-32bits-pci-domain to configure to support such devices<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">(warning: it would break the library ABI, don't enable unless really needed).<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">Number of SNES iterations = 2<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">0a1,3<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">> hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">> Pass --enable-32bits-pci-domain to configure to support such devices<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">> (warning: it would break the library ABI, don't enable unless really needed).<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">/home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/tests<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">Possible problem with ex47 running with hdf5, diffs above<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">=========================================<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">See<span class="x_Apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">Pass --enable-32bits-pci-domain to configure to support such devices<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">(warning: it would break the library ABI, don't enable unless really needed).<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">Number of SNES iterations = 3<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">Completed test examples<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">Error while running make check<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">gmake[1]: *** [makefile:123: check] Error 1<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted8">make: *** [GNUmakefile:17: check] Error 2</span><br></div><div class="x_ContentPasted6 x_ContentPasted7">==============================================================================</div><div class="x_ContentPasted6 x_ContentPasted7"><br></div><div class="x_ContentPasted6 x_ContentPasted7"><br></div><div class="x_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="x_elementToProof x_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; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;">==============================================================================<br></div><div class="x_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; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><span class="x_ContentPasted1 x_ContentPasted2" style="font-family: monospace;"><span class="x_ContentPasted1" style="background-color: rgb(255, 255, 255);">make PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_P</span><br class="x_ContentPasted1">arty/newPETSC/petsc-3.18.3 PETSC_ARCH=arch-linux-c-debug check<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Running check examples to verify correct installation<span class="x_Apple-converted-space"> </span><br class="x_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="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">See<span class="x_Apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Pass --enable-32bits-pci-domain to configure to support such devices<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">(warning: it would break the library ABI, don't enable unless really needed).<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Number of SNES iterations = 2<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">See<span class="x_Apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Pass --enable-32bits-pci-domain to configure to support such devices<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">(warning: it would break the library ABI, don't enable unless really needed).<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Pass --enable-32bits-pci-domain to configure to support such devices<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">(warning: it would break the library ABI, don't enable unless really needed).<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">lid velocity = 0.0016, prandtl # = 1., grashof # = 1.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Number of SNES iterations = 2<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">0a1,3<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">> hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">> Pass --enable-32bits-pci-domain to configure to support such devices<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">> (warning: it would break the library ABI, don't enable unless really needed).<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">/home/jesus/Desktop/JAF_NML/3rd_Party/newPETSC/petsc-3.18.3/src/vec/vec/tests<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Possible problem with ex47 running with hdf5, diffs above<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">=========================================<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">See<span class="x_Apple-converted-space"> </span><a href="https://petsc.org/release/faq/">https://petsc.org/release/faq/</a><span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">hwloc/linux: Ignoring PCI device with non-16bit domain.<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Pass --enable-32bits-pci-domain to configure to support such devices<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">(warning: it would break the library ABI, don't enable unless really needed).<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Number of SNES iterations = 3<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Completed test examples<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">Error while running make check<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">gmake[1]: *** [makefile:149: check] Error 1<span class="x_Apple-converted-space"> </span><br class="x_ContentPasted1">make: *** [GNUmakefile:17: check] Error 2<br class="x_ContentPasted1">==============================================================================</span><br></div><div class="x_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; text-decoration: none; font-family: "Times New Roman", Times, serif; font-size: 12pt;"><br></div><div class="x_elementToProof" 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 class="x_ContentPasted3" style="font-family: "Times New Roman", Times, serif; font-size: 12pt;"><br></div><div class="x_ContentPasted3 x_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="x_ContentPasted3 x_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="x_ContentPasted3" style="font-family: "Times New Roman", Times, serif; font-size: 12pt;"><br></div><div class="x_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="x_Apple-converted-space"> </span><br></div><div class="x_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="x_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="x_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="x_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="x_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="x_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="x_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="x_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="x_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="x_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></div></div></div></blockquote></div><br></body></html>