Barry,
We are currently using more and more GPU computations and heavily relying on PETSc solvers (through boomeramg, amgx, gamg preconditioners) so yes we will report you any issues or bottlenecks. This leads to my next question: any hope, one day, of a MatGetDiagonal_SeqAIJHIPSPARSE implementation ? We know that there is Kokkos backend as a workaround though. Thanks again, Pierre LEDAC Commissariat à l’énergie atomique et aux énergies alternatives Centre de SACLAY DES/ISAS/DM2S/SGLS/LCAN Bâtiment 451 – point courrier n°41 F-91191 Gif-sur-Yvette +33 1 69 08 04 03 +33 6 83 42 05 79 ________________________________ De : Barry Smith <[email protected]> Envoyé : mardi 21 octobre 2025 16:35:24 À : LEDAC Pierre Cc : Junchao Zhang; [email protected]; BOURGEOIS Rémi Objet : Re: [petsc-users] [GPU] Jacobi preconditioner That is clearly a dramatic amount! Of course, the previous code was absurd, copying all the nonzero entries to the host, finding the diagonal entries, and then copying them back to the GPU. If, through Nsight, you find other similar performance bottlenecks, please let us know, and I can try to resolve them. Barry On Oct 21, 2025, at 5:55 AM, LEDAC Pierre <[email protected]> wrote: Hello, Thanks for the work ! It is ok now, i check with Nsight system, the diagonal is indeed computed on the device. How much time it saves ? I guess it depends of the number of iterations for Gmres, the lower, the more it is significant. In my case, with 5 158 400 rows for the matrix, 45 iterations of GMRES, time to solve decrease 1.160s from to 0.671s on a RTX A6000. So thanks again, Pierre LEDAC Commissariat à l’énergie atomique et aux énergies alternatives Centre de SACLAY DES/ISAS/DM2S/SGLS/LCAN Bâtiment 451 – point courrier n°41 F-91191 Gif-sur-Yvette +33 1 69 08 04 03 +33 6 83 42 05 79 ________________________________ De : Barry Smith <[email protected]> Envoyé : vendredi 17 octobre 2025 23:27:19 À : LEDAC Pierre Cc : Junchao Zhang; [email protected] Objet : Re: [petsc-users] [GPU] Jacobi preconditioner I have updated the MR with what I think is now correct code for computing the diagonal on the GPU, could you please try it again and let me know if it works and how much time it saves (I think it is should be significant). Thankts for your patients, Barry On Oct 2, 2025, at 1:16 AM, LEDAC Pierre <[email protected]> wrote: Yes, probably the reason I saw also a crash in my test case after a quick fix of the integer conversion. Pierre LEDAC Commissariat à l’énergie atomique et aux énergies alternatives Centre de SACLAY DES/ISAS/DM2S/SGLS/LCAN Bâtiment 451 – point courrier n°41 F-91191 Gif-sur-Yvette +33 1 69 08 04 03 +33 6 83 42 05 79 ________________________________ De : Barry Smith <[email protected]<mailto:[email protected]>> Envoyé : jeudi 2 octobre 2025 02:16:40 À : LEDAC Pierre Cc : Junchao Zhang; [email protected]<mailto:[email protected]> Objet : Re: [petsc-users] [GPU] Jacobi preconditioner Sorry about that. The current code is buggy anyways; I will let you know when I have tested it extensively so you can try again. Barry On Oct 1, 2025, at 3:47 PM, LEDAC Pierre <[email protected]<mailto:[email protected]>> wrote: Sorry the correct error is: /export/home/catA/pl254994/trust/petsc/lib/src/LIBPETSC/build/petsc-barry-2025-09-30-add-matgetdiagonal-cuda/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu(3765): error: argument of type "int*" is incompatible with parameter of type "const PetscInt *" GetDiagonal_CSR<<<(int)((n + 255) / 256), 256, 0, PetscDefaultCudaStream>>>(cusparsestruct->rowoffsets_gpu->data().get(), matstruct->cprowIndices->data().get(), cusparsestruct->workVector->data().get(), n, darray); Pierre LEDAC Commissariat à l’énergie atomique et aux énergies alternatives Centre de SACLAY DES/ISAS/DM2S/SGLS/LCAN Bâtiment 451 – point courrier n°41 F-91191 Gif-sur-Yvette +33 1 69 08 04 03 +33 6 83 42 05 79 ________________________________ De : LEDAC Pierre Envoyé : mercredi 1 octobre 2025 21:46:00 À : Barry Smith Cc : Junchao Zhang; [email protected]<mailto:[email protected]> Objet : RE: [petsc-users] [GPU] Jacobi preconditioner Hi all, Thanks for the MR, there is a build issue cause we use --with-64-bit-indices: /export/home/catA/pl254994/trust/petsc/lib/src/LIBPETSC/build/petsc-barry-2025-09-30-add-matgetdiagonal-cuda/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu(3765): error: argument of type "PetscInt" is incompatible with parameter of type "const PetscInt *" GetDiagonal_CSR<<<(int)((n + 255) / 256), 256, 0, PetscDefaultCudaStream>>>(cusparsestruct->rowoffsets_gpu->data().get(), matstruct->cprowIndices->data().get(), cusparsestruct->workVector->data().get(), n, darray); Thanks, Pierre LEDAC Commissariat à l’énergie atomique et aux énergies alternatives Centre de SACLAY DES/ISAS/DM2S/SGLS/LCAN Bâtiment 451 – point courrier n°41 F-91191 Gif-sur-Yvette +33 1 69 08 04 03 +33 6 83 42 05 79 ________________________________ De : Barry Smith <[email protected]<mailto:[email protected]>> Envoyé : mercredi 1 octobre 2025 18:48:37 À : LEDAC Pierre Cc : Junchao Zhang; [email protected]<mailto:[email protected]> Objet : Re: [petsc-users] [GPU] Jacobi preconditioner I have finally created an MR that moves the Jacobi accessing of the diagonal to the GPU, which should improve the GPU performance of your code. https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/8756__;!!G_uCfscf7eWS!Z_bBmSMgZlgbbCnnU95NebK6rq-HthAoBot_aRjN3FrswnW_hUKhHtQEhzaSBDufQF4zdJmuu48OyETmlFE96TeqxaLz$ Please give it a try and let us know if it causes any difficulties or, hopefully, improves your code's performance significantly. Sorry for the long delay, NVIDIA is hiring too many PETSc developers away from us. Barry On Jul 31, 2025, at 6:46 AM, LEDAC Pierre <[email protected]<mailto:[email protected]>> wrote: Thanks Barry, I agree but didn't dare asking for that. Pierre LEDAC Commissariat à l’énergie atomique et aux énergies alternatives Centre de SACLAY DES/ISAS/DM2S/SGLS/LCAN Bâtiment 451 – point courrier n°41 F-91191 Gif-sur-Yvette +33 1 69 08 04 03 +33 6 83 42 05 79 ________________________________ De : Barry Smith <[email protected]<mailto:[email protected]>> Envoyé : mercredi 30 juillet 2025 20:34:26 À : Junchao Zhang Cc : LEDAC Pierre; [email protected]<mailto:[email protected]> Objet : Re: [petsc-users] [GPU] Jacobi preconditioner We absolutely should have a MatGetDiagonal_SeqAIJCUSPARSE(). It's somewhat embarrassing that we don't provide this. I have found some potential code at https://urldefense.us/v3/__https://stackoverflow.com/questions/60311408/how-to-get-the-diagonal-of-a-sparse-matrix-in-cusparse__;!!G_uCfscf7eWS!Z_bBmSMgZlgbbCnnU95NebK6rq-HthAoBot_aRjN3FrswnW_hUKhHtQEhzaSBDufQF4zdJmuu48OyETmlFE96WMfFt-W$ Barry On Jul 28, 2025, at 11:43 AM, Junchao Zhang <[email protected]<mailto:[email protected]>> wrote: Yes, MatGetDiagonal_SeqAIJCUSPARSE hasn't been implemented. petsc/cuda and petsc/kokkos backends are separate code. If petsc/kokkos meet your needs, then just use them. For petsc users, we hope it will be just a difference of extra --download-kokkos --download-kokkos-kernels in configuration. --Junchao Zhang On Mon, Jul 28, 2025 at 2:51 AM LEDAC Pierre <[email protected]<mailto:[email protected]>> wrote: Hello all, We are solving with PETSc a linear system updated every time step (constant stencil but coefficients changing). The matrix is preallocated once with MatSetPreallocationCOO() then filled each time step with MatSetValuesCOO() and we use device pointers for coo_i, coo_j, and coefficients values. It is working fine with a GMRES Ksp solver and PC Jacobi but we are surprised to see that every time step, during PCSetUp, MatGetDiagonal_SeqAIJ is called whereas the matrix is on the device. Looking at the API, it seems there is no MatGetDiagonal_SeqAIJCUSPARSE() but a MatGetDiagonal_SeqAIJKOKKOS(). Does it mean we should use Kokkos backend in PETSc to have Jacobi preconditioner built directly on device ? Or I am doing something wrong ? NB: Gmres is running well on device. I could use -ksp_reuse_preconditioner to avoid Jacobi being recreated each solve on host but it increases significantly the number of iterations. Thanks, <pastedImage.png> Pierre LEDAC Commissariat à l’énergie atomique et aux énergies alternatives Centre de SACLAY DES/ISAS/DM2S/SGLS/LCAN Bâtiment 451 – point courrier n°41 F-91191 Gif-sur-Yvette +33 1 69 08 04 03 +33 6 83 42 05 79
