[petsc-users] PETSc Installation Assistance

[Pierre Jolivet]

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. <FERRANJ2 at my.erau.edu> 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): ferranj2 at my.erau.edu <mailto:ferranj2 at my.erau.edu>
>     jesus.ferrand at gmail.com <mailto:jesus.ferrand at gmail.com>
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