On 27 Jan 2025, at 6:53 PM, medane.tchako...@univ-fcomte.fr wrote:
Re:
This is a small reproductible example using MatDenseGetSubMatrix
Command: petscmpiexec -n 4 ./example
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PetscInt nlines = 8; // lines PetscInt ncolumns = 3; // columns PetscInt random_size = 12; PetscInt rank; PetscInt size;
// Initialize PETSc PetscInitialize(&argc, &args, NULL, NULL);
MPI_Comm_rank(MPI_COMM_WORLD, &rank); MPI_Comm_size(MPI_COMM_WORLD, &size);
// R_full with all values to zero Mat R_full; MatCreateDense(PETSC_COMM_WORLD, PETSC_DECIDE, PETSC_DECIDE, nlines, ncolumns, NULL, &R_full); MatZeroEntries(R_full); MatView(R_full, PETSC_VIEWER_STDOUT_WORLD);
// Creating and setting A and S to rand values Mat A, S; MatCreateDense(PETSC_COMM_WORLD, PETSC_DECIDE, PETSC_DECIDE, nlines / 2, random_size, NULL, &A); MatCreateDense(PETSC_COMM_WORLD, PETSC_DECIDE, PETSC_DECIDE, random_size, ncolumns, NULL, &S); MatSetRandom(A, NULL); MatSetRandom(S, NULL);
// Computing R_part Mat R_part; MatDenseGetSubMatrix(R_full, PETSC_DECIDE, nlines / 2, PETSC_DECIDE, PETSC_DECIDE, &R_part); MatMatMult(A, S, MAT_REUSE_MATRIX, PETSC_DECIDE, &R_part);
// Visualizing R_full MatDenseRestoreSubMatrix(R_full, &R_part); MatView(R_full, PETSC_VIEWER_STDOUT_WORLD);
// Destroying matrices MatDestroy(&R_part); MatDestroy(&R_full);
PetscFinalize(); return 0;
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Part of the error output contains….:
"Cannot change/reset row sizes to 1 local 4 global after previously setting them to 2 local 4 global ….”
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PetscInt nlines = 8; // lines PetscInt ncolumns = 3; // columns PetscInt random_size = 12; PetscInt rank; PetscInt size;
// Initialize PETSc PetscInitialize(&argc, &args, NULL, NULL);
MPI_Comm_rank(MPI_COMM_WORLD, &rank); MPI_Comm_size(MPI_COMM_WORLD, &size);
// R_full with all values to zero Mat R_full; MatCreateDense(PETSC_COMM_WORLD, PETSC_DECIDE, PETSC_DECIDE, nlines, ncolumns, NULL, &R_full); MatZeroEntries(R_full); MatView(R_full, PETSC_VIEWER_STDOUT_WORLD);
// Creating and setting A and S to rand values Mat A, S; MatCreateDense(PETSC_COMM_WORLD, PETSC_DECIDE, PETSC_DECIDE, nlines / 2, random_size, NULL, &A); MatCreateDense(PETSC_COMM_WORLD, PETSC_DECIDE, PETSC_DECIDE, random_size, ncolumns, NULL, &S); MatSetRandom(A, NULL); MatSetRandom(S, NULL);
// Computing R_part Mat R_part; MatMatMult(A, S, MAT_INITIAL_MATRIX, PETSC_DECIDE, &R_part); MatView(R_part, PETSC_VIEWER_STDOUT_WORLD);
Mat R_sub; MatDenseGetSubMatrix(R_full, PETSC_DECIDE, nlines / 2, PETSC_DECIDE, PETSC_DECIDE, &R_sub);
PetscScalar *storage = NULL; MatDenseGetArray(R_part, &storage); PetscScalar *storage_sub = NULL; MatDenseGetArray(R_sub, &storage_sub);
PetscArraycpy(storage_sub, storage, (nlines / 2) * ncolumns);
MatDenseRestoreArray(R_part, &storage); MatDenseRestoreArray(R_sub, &storage_sub);
MatDenseRestoreSubMatrix(R_full, &R_sub);
MatView(R_full, PETSC_VIEWER_STDOUT_WORLD);
// Destroying matrices MatDestroy(&R_part); MatDestroy(&R_full);
PetscFinalize(); return 0; ==========================================================
Now Using MatDenseGetArray
Please let me know if I need to clarify something.
Thanks Medane
On 27 Jan 2025, at 16:26, Pierre Jolivet <pie...@joliv.et> wrote:
On 27 Jan 2025, at 3:52 PM, Matthew Knepley <knep...@gmail.com> wrote:
Re:
MatDenseGetSubMatrix in fact could be the best alternative (cleaner code), but as mentioned earlier, I would like to use the smaller matrix R_part to get the result of a MatMatMult operation.
MatMatMult(A, S, MAT_INITIAL_MATRIX, PETSC_DECIDE, &R_part);
When trying to use MAT_REUSE_MATRIX, this gave an error (expected error I think). On the other side, I mentionned on MatDenseGetSubMatrix page, "The output matrix is not redistributed by PETSc”. So will R_part be a valid output matrix for MatMatMult?
I believe it is, but I am not the expert.
Pierre, can the SubMatrix be used as the output of a MatMatMult()?
It should be, but there may be some limitations due to leading dimensions and what not. By looking at just the single line of code we got from you, I can see at least one issue: it should be MAT_REUSE_MATRIX, not MAT_INITIAL_MATRIX (assuming you got R_part from MatDenseGetSubMatrix). Feel free to share a (minimal) reproducer.
Thanks, Pierre Thanks,
Matt Thanks
> On 27 Jan 2025, at 2:23 PM, medane.tchako...@univ-fcomte.fr wrote:
>
> Dear PETSc users,
>
> I hope this message finds you well. I don’t know If my question is relevant, but I’am currently working with DENSE type matrix, and would like to copy one matrix R_part [ n/2 x m] (resulted from a MatMatMult operation) into another dense matrix R_full [n x m].
> Both matrices being on the same communicator, I would like to efficiently copy R_part in the first half of R_full.
> I have being using MatSetValues, but for large matrices, the subsequent assembling operation is costly.
Could you please share the output of -log_view as well as a single file that will be generated with -info dump (e.g., dump.0, the file associated to process #0)?
This shouldn’t be that costly, so there may be an option missing, like MAT_NO_OFF_PROC_ENTRIES.
Anyway, if you want to optimize this, the fastest way would be to call MatDenseGetArray[Read,Write]() and then do the necessary PetscArraycpy().
The other alternative (which I think makes cleaner code) is to use
to create your R_part matrix. Then you are directly acting on the memory you want when assemble the smaller matrix.
THanks,
Matt Thanks,
Pierre
> Please could you suggest me some strategies or functions to do this efficiently.
>
> Thank you for your time and assistance.
>
> Best regards,
> Tchakorom Medane
>
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener
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ex1234.c