Thanks for reporting the problem and testing the fix. I have an MR to fix the problem https://gitlab.com/petsc/petsc/-/merge_requests/9089

   Barry


On Mar 3, 2026, at 3:44 AM, Matteo Semplice via petsc-users <petsc-users@mcs.anl.gov> wrote:

Dear Barry,

    indeed your suggestion fixes things! (I assume that you meant PetscCall(MatDuplicate(A, MAT_DO_NOT_COPY_VALUES, &B));)

Now I get a consistent output.

Hand-coded Jac:

   row 84:     (84, 60.)      (85, 0.)      (3446, -80.)      (3447, 0.)      (6808, 20.)      (6809, 0.)      
   row 85:     (84, 0.00914434)      (85, 1.)      (3446, 0.)      (3447, 0.)      (6808, 0.)      (6809, 0.)     

Finite-difference Jac:

   row 84:     (84, 60.)      (85, 0.)      (3446, -80.)      (3447, 0.)      (6808, 20.)      (6809, 0.)      
   row 85:     (84, 0.)      (85, 0.999971)      (3446, 0.)      (3447, 0.)      (6808, 0.)      (6809, 0.) 

Difference of the two matrices:
   row 84:     (84, 0.)      (85, 0.)      (3446, 0.)      (3447, 0.)      (6808, 0.)      (6809, 0.)      
   row 85:     (84, 0.00914434)      (85, 2.9293e-05)      (3446, 0.)      (3447, 0.)      (6808, 0.)      (6809, 0.)

I have applied your suggestion on the top of the release branch and I had to fix also the creation of matrix C. Here below is the complete diff, in case you want to apply it to the official repository:

diff --git a/src/snes/interface/snes.c b/src/snes/interface/snes.c
index f66c23a1417..eee3d070d4c 100644
--- a/src/snes/interface/snes.c
+++ b/src/snes/interface/snes.c
@@ -2768,8 +2768,6 @@ PetscErrorCode SNESTestJacobian(SNES snes, PetscReal *Jnorm, PetscReal *diffNorm
  Vec               x = snes->vec_sol, f;
  PetscReal         nrm, gnorm;
  PetscReal         threshold = 1.e-5;
-  MatType           mattype;
-  PetscInt          m, n, M, N;
  void             *functx;
  PetscBool         complete_print = PETSC_FALSE, threshold_print = PETSC_FALSE, flg, istranspose;
  PetscBool         silent = diffNorm != PETSC_NULLPTR ? PETSC_TRUE : PETSC_FALSE;
@@ -2832,14 +2830,7 @@ PetscErrorCode SNESTestJacobian(SNES snes, PetscReal *Jnorm, PetscReal *diffNorm
      PetscCall(MatComputeOperator(jacobian, MATAIJ, &A));
    }
 
-    PetscCall(MatGetType(A, &mattype));
-    PetscCall(MatGetSize(A, &M, &N));
-    PetscCall(MatGetLocalSize(A, &m, &n));
-    PetscCall(MatCreate(PetscObjectComm((PetscObject)A), &B));
-    PetscCall(MatSetType(B, mattype));
-    PetscCall(MatSetSizes(B, m, n, M, N));
-    PetscCall(MatSetBlockSizesFromMats(B, A, A));
-    PetscCall(MatSetUp(B));
+    PetscCall(MatDuplicate(A, MAT_DO_NOT_COPY_VALUES, &B));
    PetscCall(MatSetOption(B, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE));
 
    PetscCall(SNESGetFunction(snes, NULL, NULL, &functx));
@@ -2865,11 +2856,7 @@ PetscErrorCode SNESTestJacobian(SNES snes, PetscReal *Jnorm, PetscReal *diffNorm
      const PetscInt    *bcols;
      const PetscScalar *bvals;
 
-      PetscCall(MatCreate(PetscObjectComm((PetscObject)A), &C));
-      PetscCall(MatSetType(C, mattype));
-      PetscCall(MatSetSizes(C, m, n, M, N));
-      PetscCall(MatSetBlockSizesFromMats(C, A, A));
-      PetscCall(MatSetUp(C));
+      PetscCall(MatDuplicate(A, MAT_DO_NOT_COPY_VALUES, &C));
      PetscCall(MatSetOption(C, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE));
 
      PetscCall(MatAYPX(B, -1.0, A, DIFFERENT_NONZERO_PATTERN));

Thanks a lot!

Matteo

On 03/03/2026 03:28, Barry Smith wrote:
   Stefano hit the nail on the head!

   The matrices are of the same type it is just that MatView() for DMDA AIJ matrices MatView_MPI_DA()  causes them to printed out in “natural ordering” related to the grid instead of PETSc parallel ordering.  It is perhaps a case of Barry being too clever for his own good.

   SNESTestJacobian() has the code:

```
    PetscCall(MatGetType(A, &mattype));
    PetscCall(MatGetSize(A, &M, &N));
    PetscCall(MatGetLocalSize(A, &m, &n));
    PetscCall(MatCreate(PetscObjectComm((PetscObject)A), &B));
    PetscCall(MatSetType(B, mattype));
    PetscCall(MatSetSizes(B, m, n, M, N));
    PetscCall(MatSetBlockSizesFromMats(B, A, A));
    PetscCall(MatSetUp(B));
    PetscCall(MatSetOption(B, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE));

    PetscCall(SNESGetFunction(snes, NULL, NULL, &functx));
    PetscCall(SNESComputeJacobianDefault(snes, x, B, B, functx));
```

    It does not use MatDuplicate() hence the B (finite difference matrix) does not inherit the MatView_MPI_DA()  function.

    Could you please try the following. Edit src/snes/interface/snes.c and locate the routine SNESTestJacobian()  and replace the block of code  that creates the B matrix above with 

```
   PetscCall(MatDuplicate(B, MAT_DO_NOT_COPY_VALUES, &D));
```

   Then run make all in the PETSc home directory. Then rerun your program. The plan is now both matrices will be displayed in the same ordering (natural ordering on the multidimensional grid) and so the three matrices displayed should make sense.

   Barry




On Mar 2, 2026, at 6:00 PM, Matteo Semplice via petsc-users <petsc-users@mcs.anl.gov> wrote:

It's indeed a DMDA (with 2 dofs per point), but the code is run with

-snes_test_jacobian -snes_test_jacobian_view

Would the hand-coded and the f.d. jacobian be different matrix type in this case?

Matteo

Il 02/03/26 21:32, Stefano Zampini ha scritto:
Maybe you are using a DMDA, with one matrix coming from it and the other not? DMDA changes the View to dump in natural ordering. 

Il giorno lun 2 mar 2026 alle ore 18:10 Matteo Semplice via petsc-users <petsc-users@mcs.anl.gov> ha scritto:

Dear all,

    the following output from -snes_test_jacobian_view lokks clear enough to pinpoint my mistake (I must be putting jacobian elements in the wrong place), but it nevertheless left me suprised.

0 SNES Function norm 2.945516399303e-01
  ---------- Testing Jacobian -------------
  Testing hand-coded Jacobian, if (for double precision runs) ||J - Jfd||_F/||J||_F is
    O(1.e-8), the hand-coded Jacobian is probably correct.
  ||J - Jfd||_F/||J||_F = 0.000121529, ||J - Jfd||_F = 0.395752
  Hand-coded Jacobian ----------
Mat Object: 4 MPI processes
  row 84:     (84, 60.)      (85, 0.)      (3446, -80.)      (3447, 0.)      (6808, 20.)      (6809, 0.)     
  row 85:     (84, 0.00914434)      (85, 1.)      (3446, 0.)      (3447, 0.)      (6808, 0.)      (6809, 0.)    
    
   Finite difference Jacobian ----------
Mat Object: 4 MPI processes
  type: mpiaij
  row 84:   (84, 60.)    (1806, -80.)    (3528, 20.)   
  row 85:   (85, 0.999971)

  Hand-coded minus finite-difference Jacobian with tolerance 1e-05 ----------
Mat Object: 4 MPI processes
  type: mpiaij
  row 84:  
  row 85:   (84, 0.00914434)    (85, 2.9293e-05)

The difference of the two matrices shoudl be nonzero in row 84 for all elements 1806, 3528, 3446, 6808. Is it intended that the difference is shown only for matrix elements that are present in both the hand-coded and the FD jacobian?

I would have expected an output like

row 84: (1806,80.)   (3446,-80.), etc

(This was on  PETSc Release Version 3.24.2)

Thanks

    Matteo

-- 
Prof. Matteo Semplice
Università degli Studi dell’Insubria
Dipartimento di Scienza e Alta Tecnologia – DiSAT
Professore Associato
Via Valleggio, 11 – 22100 Como (CO) – Italia
tel.: +39 031 2386316


--
Stefano
-- 
---
Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como

-- 
Prof. Matteo Semplice
Università degli Studi dell’Insubria
Dipartimento di Scienza e Alta Tecnologia – DiSAT
Professore Associato
Via Valleggio, 11 – 22100 Como (CO) – Italia
tel.: +39 031 2386316