Greetings. I recently changed operating systems (Ubuntu 20.04 -> Debian 12 "Bookworm") and tried to reinstall PETSc. I tried doing the usual as described in (https://petsc.org/release/install/download/#recommended-obtain-release-version-with-git):
* git clone/pull * ./configure --<option_1> ... --<option_N> * make install * make check Everything proceeds smoothly until the "make check" step, where I get the following error: ============================================================================== Running check examples to verify correct installation Using PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc and PETSC_ARCH=arch-linux-c-debug Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process See https://petsc.org/release/faq/ hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). lid velocity = 0.0016, prandtl # = 1., grashof # = 1. Number of SNES iterations = 2 Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes See https://petsc.org/release/faq/ hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). lid velocity = 0.0016, prandtl # = 1., grashof # = 1. Number of SNES iterations = 2 0a1,3 > hwloc/linux: Ignoring PCI device with non-16bit domain. > Pass --enable-32bits-pci-domain to configure to support such devices > (warning: it would break the library ABI, don't enable unless really needed). /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/vec/vec/tests Possible problem with ex47 running with hdf5, diffs above ========================================= Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process See https://petsc.org/release/faq/ hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). Number of SNES iterations = 3 Completed test examples Error while running make check gmake[1]: *** [makefile:123: check] Error 1 make: *** [GNUmakefile:17: check] Error 2 ============================================================================== 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. ============================================================================== make PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_P arty/newPETSC/petsc-3.18.3 PETSC_ARCH=arch-linux-c-debug check Running check examples to verify correct installation Using PETSC_DIR=/home/jesus/Desktop/JAF_NML/3rd_Party/newPETSC/petsc-3.18.3 and PETSC_ARCH=arch-linux-c-debug Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process See https://petsc.org/release/faq/ hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). lid velocity = 0.0016, prandtl # = 1., grashof # = 1. Number of SNES iterations = 2 Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes See https://petsc.org/release/faq/ hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). lid velocity = 0.0016, prandtl # = 1., grashof # = 1. Number of SNES iterations = 2 0a1,3 > hwloc/linux: Ignoring PCI device with non-16bit domain. > Pass --enable-32bits-pci-domain to configure to support such devices > (warning: it would break the library ABI, don't enable unless really needed). /home/jesus/Desktop/JAF_NML/3rd_Party/newPETSC/petsc-3.18.3/src/vec/vec/tests Possible problem with ex47 running with hdf5, diffs above ========================================= Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process See https://petsc.org/release/faq/ hwloc/linux: Ignoring PCI device with non-16bit domain. Pass --enable-32bits-pci-domain to configure to support such devices (warning: it would break the library ABI, don't enable unless really needed). Number of SNES iterations = 3 Completed test examples Error while running make check gmake[1]: *** [makefile:149: check] Error 1 make: *** [GNUmakefile:17: check] Error 2 ============================================================================== I checked the FAQs (https://petsc.org/release/faq/#table-of-contents) and tried the suggestions there (specifically the points under https://petsc.org/release/faq/#what-does-it-mean-when-make-check-hangs-or-errors-on-petscoptionsinsertfile) to no avail. * I don't use a VPN. * I tried running make check with Wifi disabled. * Ran ./configure with --download-mpich-device=ch3:nemesis --download-mpich Surprisingly, I can compile my PETSc programs using a makefile, and run them. However, the programs are now broken (I get SIGSEGV originating from within DM/DMPlex APIs). Sincerely: J.A. Ferrand Embry-Riddle Aeronautical University - Daytona Beach - FL Ph.D. Candidate, Aerospace Engineering M.Sc. Aerospace Engineering B.Sc. Aerospace Engineering B.Sc. Computational Mathematics Phone: (386)-843-1829 Email(s): ferra...@my.erau.edu jesus.ferr...@gmail.com
