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!a4GaRrrHRLjv08cxI4Uh5a74H5DcewdUJ8zWt0i8SiUDMqKoYa1z38JoxkRS12NV5Jrj_3N9wZbLSTA2N55nv1o$
>>>
>>>
>>> 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!a4GaRrrHRLjv08cxI4Uh5a74H5DcewdUJ8zWt0i8SiUDMqKoYa1z38JoxkRS12NV5Jrj_3N9wZbLSTA2vc2y51A$
>>>>
>>>>
>>>> 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
