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

[Nils Schween]

Thank you very much Pierre!

I was not aware of the fact that the fill-in in the ILU decides about
its quality. But its clear now. I will just test what level of fill we
need for our application.

Once more thanks,
Nils


Pierre Jolivet <pierre at joliv.et> writes:

>> On 24 Oct 2025, at 1:52 PM, Nils Schween <nils.schween at mpi-hd.mpg.de> wrote:
>> 
>> 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.
>
> The default subdomain solver is ILU(0).
> By definition, this won’t allow fill-in.
> So when you are not storing the zeros in B, the quality of your PC is much worse.
> You can check this yourself with -A_ksp_view -B_ksp_view:
> […]
>     0 levels of fill
>     tolerance for zero pivot 2.22045e-14
>     matrix ordering: natural
>     factor fill ratio given 1., needed 1.
>       Factored matrix follows:
>         Mat Object: (A_) 1 MPI process
>           type: seqaij
>           rows=1664, cols=1664
>           package used to perform factorization: petsc
>           total: nonzeros=117760, allocated nonzeros=117760
>             using I-node routines: found 416 nodes, limit used is 5
> […]
>     0 levels of fill
>     tolerance for zero pivot 2.22045e-14
>     matrix ordering: natural
>     factor fill ratio given 1., needed 1.
>       Factored matrix follows:
>         Mat Object: (B_) 1 MPI process
>           type: seqaij
>           rows=1664, cols=1664
>           package used to perform factorization: petsc
>           total: nonzeros=49408, allocated nonzeros=49408
>             not using I-node routines
>
> Check the number of nonzeros of both factored Mat.
> With -B_pc_factor_levels 3, you’ll get roughly similar convergence speed (and density in the factored Mat of both PC).
>
> Thanks,
> Pierre
>
>> 
>> 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 
>> <example.tar.gz>
>> 
>> -- 
>> 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

-- 
Nils Schween
PhD Student

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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