https://petsc.org/release/faq/#what-does-the-message-hwloc-linux-ignoring-pci-device-with-non-16bit-domain-mean
Thanks, Pierre > On 17 Jul 2023, at 7:51 PM, Ferrand, Jesus A. <[email protected]> wrote: > > 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 > underhttps://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): [email protected] <mailto:[email protected]> > [email protected] <mailto:[email protected]>
