[petsc-users] [WARNING: UNSCANNABLE EXTRACTION FAILED]GMRES plus BlockJacobi behave differently for seemlingy identical matrices

[Nils Schween]

Dear PETSc users, Dear PETSc developers,

in our software we are solving a linear system with PETSc using GMRES
in conjunction with a BlockJacobi preconditioner, i.e. the default of
the KSP object.

We have two versions of the system matrix, say A and B. The difference
between them is the non-zero pattern. The non-zero pattern of matrix B
is a subset of the one of matrix A. Their values should be identical.

We solve the linear system, using A yields a solution after some
iterations, whereas using B does not converge.

I created binary files of the two matrices, the right-hand side, and
wrote a small PETSc programm, which loads them and demonstrates the
issue. I attach the files to this email.

We would like to understand why the solver-preconditioner combination
works in case A and not in case B. Can you help us finding this out?

To test if the two matrices are identical, I substracted them and
computed the Frobenius norm of the result. It is zero.

To give you more context, we solve a system of partial differential
equations that models astrophysical plasmas. It is essentially a system
of advection-reaction equations. We use a discontinuous Galerkin (dG)
method. Our code relies on the finite element library library deal.ii
and its PETSc interface. The system matrices A and B are the result of
the (dG) discretisation. We GMRES with a BlockJaboci preconditioner,
because we do not know any better.

I tested the code I sent with PETSc 3.24.0 and 3.19.1 on my workstation, i.e.
Linux home-desktop 6.17.2-arch1-1 #1 SMP PREEMPT_DYNAMIC Sun, 12 Oct 2025 12:45:18 +0000 x86_64 GNU/Linux
I use OpenMPI 5.0.8 and I compiled with mpicc, which in my cases use
gcc.

In case you need more information. Please let me know.
Any help is appreciated.

Thank you,
Nils 
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-- 
Nils Schween

Phone: +49 6221 516 557
Mail: nils.schween at mpi-hd.mpg.de
PGP-Key: 4DD3DCC0532EE96DB0C1F8B5368DBFA14CB81849

Max Planck Institute for Nuclear Physics
Astrophysical Plasma Theory (APT)
Saupfercheckweg 1, D-69117 Heidelberg
https://www.mpi-hd.mpg.de/mpi/en/research/scientific-divisions-and-groups/independent-research-groups/apt
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