[petsc-users] PetscSF Fortran interface

Wed Jan 11 08:16:01 CST 2023

Hi, Nicholas,
  See
https://petsc.org/release/developers/contributing/#starting-a-new-feature-branch
on how to contribute.

  You will need to create your own fork of petsc,  then create a feature
branch and your code, and then ask for a merge request to merge your branch
to the petsc repo.

  Once you have the MR, we can figure out why it could not compile.

  Thanks for the contribution!

--Junchao Zhang

On Wed, Jan 11, 2023 at 12:58 AM Nicholas Arnold-Medabalimi <
narnoldm at umich.edu> wrote:

> Hi Junchao
>
>  Apologies for not seeing that. Usually, the fortran90-specific functions
> have notes on the original C version, and I also can't
> see PetscSFCreateSectionSFF90 on the function list on the doc site. Thanks
> so much, and I saw your notes on the merge request.
>
> I don't suppose PetscSFReduceBegin and End are likewise hidden somewhere.
> I'm moving between distributions, and I can go forward with
> PetscSFBcastBegin, but I also need to go backward with Reduce.
>
> I feel like this is a one-to-one change from Bcast to Reduce, and I've
> added the relevant lines in src/vec/is/sf/interface/ftn-custom/zsf.c and
> src/vec/f90-mod/petscvec.h90 and it compiles fine, but I'm still getting a
> linking error for the Reduce routines.
>
> I need some input on what I'm missing here. I hope I didn't miss that this
> routine exists elsewhere.
>
> I've attached the two files, but it's not an ideal way to transmit
> changes.
>
> If I get some instructions on contributing, I can make a merge request for
> the changes if they are helpful.
>
>
> Thanks
>
> Nicholas
>
> On Tue, Jan 10, 2023 at 4:42 PM Junchao Zhang <junchao.zhang at gmail.com>
> wrote:
>
>> Hi, Nicholas,
>>    It seems we have implemented it, but with another name,
>> PetscSFCreateSectionSFF90, see
>> https://gitlab.com/petsc/petsc/-/merge_requests/5386
>>    Try it to see if it works!
>>
>> --Junchao Zhang
>>
>>
>> On Tue, Jan 10, 2023 at 11:45 AM Nicholas Arnold-Medabalimi <
>> narnoldm at umich.edu> wrote:
>>
>>> Er to be honest I still can't get my stub to compile properly, and I
>>> don't know how to go about making a merge request. But here is what I am
>>> attempting right now. Let me know how best to proceed
>>>
>>>
>>> Its not exactly clear to me how to setup up the remote offset properly.
>>>
>>> in src/vec/is/sf/interface/ftn-custom/zsf.c
>>>
>>> PETSC_EXTERN void petscsfcreatesectionsf(PetscSF *sf, PetscSection
>>> *rootSection, F90Array1d *aremoteOffsets, PetscSection *leafSection,
>>> PetscSF *sectionSF, int * ierr PETSC_F90_2PTR_PROTO(remoteoffsetsd))
>>> {
>>>
>>>   int * remoteOffsets;
>>>   *ierr = F90Array1dAccess(aremoteOffsets, PETSC_INT, (void**)
>>> &remoteOffsets PETSC_F90_2PTR_PARAM(remoteoffsetsd));if (*ierr) return;
>>>   *ierr = PetscSFCreateSectionSF(*sf,*rootSection,
>>> &remoteOffsets,*leafSection,*sectionSF);if (*ierr) return;
>>>
>>> }
>>>
>>> This is the sticking point.
>>>
>>> Sincerely
>>> Nicholas
>>>
>>>
>>> On Tue, Jan 10, 2023 at 12:38 PM Junchao Zhang <junchao.zhang at gmail.com>
>>> wrote:
>>>
>>>> Hi, Nicholas,
>>>>   Could you make a merge request to PETSc and then our Fortran experts
>>>> can comment on your MR?
>>>>   Thanks.
>>>>
>>>> --Junchao Zhang
>>>>
>>>>
>>>> On Tue, Jan 10, 2023 at 11:10 AM Nicholas Arnold-Medabalimi <
>>>> narnoldm at umich.edu> wrote:
>>>>
>>>>> Hi Junchao
>>>>>
>>>>> I think I'm almost there, but I could use some insight into how to use
>>>>> the PETSC_F90_2PTR_PROTO and F90Array1dAccess for the remoteOffset
>>>>> parameter input so if another function comes up, I can add it myself
>>>>> without wasting your time.
>>>>> I am very grateful for your help and time.
>>>>>
>>>>> Sincerely
>>>>> Nicholas
>>>>>
>>>>> On Tue, Jan 10, 2023 at 10:55 AM Junchao Zhang <
>>>>> junchao.zhang at gmail.com> wrote:
>>>>>
>>>>>> Hi, Nicholas,
>>>>>>    I am not a fortran guy, but I will try to add
>>>>>> petscsfcreatesectionsf.
>>>>>>
>>>>>>    Thanks.
>>>>>> --Junchao Zhang
>>>>>>
>>>>>>
>>>>>> On Tue, Jan 10, 2023 at 12:50 AM Nicholas Arnold-Medabalimi <
>>>>>> narnoldm at umich.edu> wrote:
>>>>>>
>>>>>>> I think it should be something like this, but I'm not very fluent in
>>>>>>> Fortran C interop syntax. Any advice would be appreciated. Thanks
>>>>>>>
>>>>>>> PETSC_EXTERN void petscsfcreatesectionsf(PetscSF *sf, PetscSection *
>>>>>>> rootSection, F90Array1d *aremoteOffsets, PetscSection *leafSection,
>>>>>>> PetscSF *sectionSF, int * ierr PETSC_F90_2PTR_PROTO(remoteoffsetsd))
>>>>>>> {
>>>>>>>
>>>>>>>   int * remoteOffsets;
>>>>>>>   *ierr = F90Array1dAccess(aremoteOffsets, PETSC_INT, (void**) &
>>>>>>> remoteOffsets PETSC_F90_2PTR_PARAM(remoteoffsetsd));if (*ierr)
>>>>>>> return;
>>>>>>>   *ierr = PetscSFCreateSectionSF(*sf,*rootSection, &remoteOffsets,*
>>>>>>> leafSection,*sectionSF);if (*ierr) return;
>>>>>>>
>>>>>>> }
>>>>>>>
>>>>>>> On Mon, Jan 9, 2023 at 11:41 PM Nicholas Arnold-Medabalimi <
>>>>>>> narnoldm at umich.edu> wrote:
>>>>>>>
>>>>>>>> Hi Junchao
>>>>>>>>
>>>>>>>> Thanks again for your help in November. I've been using the your
>>>>>>>> merge request branch quite heavily. Would it be possible to add a
>>>>>>>> petscsfcreatesectionsf interface as well?
>>>>>>>> I'm trying to write it myself using your commits as a guide but I
>>>>>>>> have been struggling with handling the section parameter properly.
>>>>>>>>
>>>>>>>> Sincerely
>>>>>>>> Nicholas
>>>>>>>>
>>>>>>>> On Sat, Nov 19, 2022 at 9:44 PM Junchao Zhang <
>>>>>>>> junchao.zhang at gmail.com> wrote:
>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Sat, Nov 19, 2022 at 8:05 PM Nicholas Arnold-Medabalimi <
>>>>>>>>> narnoldm at umich.edu> wrote:
>>>>>>>>>
>>>>>>>>>> Hi
>>>>>>>>>>
>>>>>>>>>> Thanks, this is awesome. Thanks for the very prompt fix. Just one
>>>>>>>>>> question: will the array outputs on the fortran side copies (and need to be
>>>>>>>>>> deallocated) or direct access to the dmplex?
>>>>>>>>>>
>>>>>>>>> Direct access to internal data;  no need to deallocate
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Sincerely
>>>>>>>>>> Nicholas
>>>>>>>>>>
>>>>>>>>>> On Sat, Nov 19, 2022 at 8:21 PM Junchao Zhang <
>>>>>>>>>> junchao.zhang at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi, Nicholas,
>>>>>>>>>>>   See this MR,
>>>>>>>>>>> https://gitlab.com/petsc/petsc/-/merge_requests/5860
>>>>>>>>>>>   It is in testing, but you can try branch
>>>>>>>>>>> jczhang/add-petscsf-fortran to see if it works for you.
>>>>>>>>>>>
>>>>>>>>>>>   Thanks.
>>>>>>>>>>> --Junchao Zhang
>>>>>>>>>>>
>>>>>>>>>>> On Sat, Nov 19, 2022 at 4:16 PM Nicholas Arnold-Medabalimi <
>>>>>>>>>>> narnoldm at umich.edu> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Junchao
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks. I was wondering if there is any update on this. I may
>>>>>>>>>>>> write a small interface for those two routines myself in the interim but
>>>>>>>>>>>> I'd appreciate any insight you have.
>>>>>>>>>>>>
>>>>>>>>>>>> Sincerely
>>>>>>>>>>>> Nicholas
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, Nov 16, 2022 at 10:39 PM Junchao Zhang <
>>>>>>>>>>>> junchao.zhang at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi, Nicholas,
>>>>>>>>>>>>>   I will have a look and get back to you.
>>>>>>>>>>>>>   Thanks.
>>>>>>>>>>>>> --Junchao Zhang
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Wed, Nov 16, 2022 at 9:27 PM Nicholas Arnold-Medabalimi <
>>>>>>>>>>>>> narnoldm at umich.edu> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Petsc Users
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I'm in the process of adding some Petsc for mesh management
>>>>>>>>>>>>>> into an existing Fortran Solver. It has been relatively straightforward so
>>>>>>>>>>>>>> far but I am running into an issue with using PetscSF routines. Some like
>>>>>>>>>>>>>> the PetscSFGetGraph work no problem but a few of my routines require the
>>>>>>>>>>>>>> use of PetscSFGetLeafRanks and PetscSFGetRootRanks and those don't seem to
>>>>>>>>>>>>>> be in the fortran interface and I just get a linking error. I also don't
>>>>>>>>>>>>>> seem to see a PetscSF file in the finclude. Any clarification or assistance
>>>>>>>>>>>>>> would be appreciated.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Sincerely
>>>>>>>>>>>>>> Nicholas
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> Nicholas Arnold-Medabalimi
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>>>>> Computational Aeroscience Lab
>>>>>>>>>>>>>> University of Michigan
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Nicholas Arnold-Medabalimi
>>>>>>>>>>>>
>>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>>> Computational Aeroscience Lab
>>>>>>>>>>>> University of Michigan
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Nicholas Arnold-Medabalimi
>>>>>>>>>>
>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>> Computational Aeroscience Lab
>>>>>>>>>> University of Michigan
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Nicholas Arnold-Medabalimi
>>>>>>>>
>>>>>>>> Ph.D. Candidate
>>>>>>>> Computational Aeroscience Lab
>>>>>>>> University of Michigan
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Nicholas Arnold-Medabalimi
>>>>>>>
>>>>>>> Ph.D. Candidate
>>>>>>> Computational Aeroscience Lab
>>>>>>> University of Michigan
>>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Nicholas Arnold-Medabalimi
>>>>>
>>>>> Ph.D. Candidate
>>>>> Computational Aeroscience Lab
>>>>> University of Michigan
>>>>>
>>>>
>>>
>>> --
>>> Nicholas Arnold-Medabalimi
>>>
>>> Ph.D. Candidate
>>> Computational Aeroscience Lab
>>> University of Michigan
>>>
>>
>
> --
> Nicholas Arnold-Medabalimi
>
> Ph.D. Candidate
> Computational Aeroscience Lab
> University of Michigan
>
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