[petsc-users] PETSc Installation Assistance

[Ferrand, Jesus A.]

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): ferranj2 at my.erau.edu

    jesus.ferrand at gmail.com
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