[petsc-users] DMLabel Synchronize
Nicholas Arnold-Medabalimi
narnoldm at umich.edu
Sun Sep 4 16:50:00 CDT 2022
Thank you. I'm able to access the label functions. Can you clarify what the
Begin and End functions are doing?
To clarify the behavior I am trying to achieve, I have identified the blue
cell in the attached figure using metrics during the solve. I have already
created a label across all the partitions I'm using to tag the identified
and adjacent cells however I need the Root cell label to be updated to one
when the initial identified cell is adjacent to its corresponding leaf.
That doesn't seem to be happening with I use the propagate command, but I
may be misusing them. I appreciate the assistance.
[image: image.png]
Sincerely
Nicholas
On Fri, Sep 2, 2022 at 7:27 AM Matthew Knepley <knepley at gmail.com> wrote:
> On Fri, Sep 2, 2022 at 12:53 AM Nicholas Arnold-Medabalimi <
> narnoldm at umich.edu> wrote:
>
>> I've been trying to update from the snapshot to the main branch on the
>> gitlab but I'm having one issue. This does not occur using the snapshot
>> petsc mentioned previously.
>>
>> I use a PetscViewer to read in a file. The appended function is used to
>> fast-forward to the locations in the file. Looking at the error message, I
>> thought maybe the file wasn't opening properly. However, I am able to read
>> in and print the first line of the file using PetscViewerRead. As far as I
>> can tell, the error is only due to the version change and I see something
>> about the viewer in the compatibility notes, but I'm not sure how to
>> resolve it. Any assistance would be appreciated since I can't use the
>> gitlab version for the label functions without fixing this.
>>
>
> You are missing "PetscFunctionBeginUser;" at the start of your function.
> This must be paired with all PetscFunctionReturn() calls since we keep
> track of the stack. We added this check in the new version.
>
> Thanks,
>
> Matt
>
>
>>
>> PetscErrorCode FileFastForward(PetscViewer viewer, char delim, bool &eof)
>> {
>> int i = 0, ret = 0;
>> char buffer;
>> do
>> PetscViewerRead(viewer, &(buffer), 1, &ret, PETSC_CHAR);
>> while (ret > 0 && buffer != delim);
>> if (ret == 0)
>> {
>> printf("End of file reached before delimiter found\n");
>> eof = false;
>> }
>> else
>> eof = true;
>> PetscFunctionReturn(0);
>> }
>> The viewer is opened using
>> PetscViewerCreate(PETSC_COMM_WORLD, &viewer);
>> PetscViewerSetType(viewer, PETSCVIEWERASCII);
>> PetscViewerFileSetMode(viewer, FILE_MODE_READ);
>> PetscViewerFileSetName(viewer, meshfile);
>> The error that is thrown is
>>
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [0]PETSC ERROR: Petsc has generated inconsistent data
>> [0]PETSC ERROR: Invalid stack size 0, pop FileFastForward
>> /home/narnoldm/code/solver-playground/version_upgrade/version_debug.cpp:35.
>> (Note this line is the PetscFunctionReturn)
>>
>> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
>> [0]PETSC ERROR: Petsc Development GIT revision: unknown GIT Date: unknown
>> [0]PETSC ERROR: /home/narnoldm/code/solver-playground/build/bin/version
>> on a named Dragoon by narnoldm Fri Sep 2 00:34:02 2022
>> [0]PETSC ERROR: Configure options
>> --prefix=/home/narnoldm/code/solver-playground/build/external/PETSc
>> --with-hdf5-dir=/home/narnoldm/code/solver-playground/build/external/HDF5
>> --download-triangle --download-parmetis --download-metis --with-debugging=1
>> [0]PETSC ERROR: #1 FileFastForward() at
>> /home/narnoldm/code/solver-playground/version_upgrade/version_debug.cpp:35
>> application called MPI_Abort(MPI_COMM_SELF, 77) - process 0
>> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=77
>> :
>> system msg for write_line failure : Bad file descriptor
>>
>>
>>
>> On Thu, Sep 1, 2022 at 5:32 AM Matthew Knepley <knepley at gmail.com> wrote:
>>
>>> On Wed, Aug 31, 2022 at 9:30 PM Nicholas Arnold-Medabalimi <
>>> narnoldm at umich.edu> wrote:
>>>
>>>> Hi
>>>>
>>>> Thanks, this looks like what I need, but I don't seem to have it in my
>>>> release (3.17.4 from
>>>> https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.17.4.tar.gz).
>>>> I see it in the current repository, though. Is the 3.17.4 tarball just
>>>> missing it, or will it be added in the next release?
>>>>
>>>
>>> Yes, it is in main (https://petsc.org/main/docs/changes/dev/) since it
>>> was an interface change. Our main branch is quite stable, and I would
>>> recommend
>>> it for development work.
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> Thanks
>>>> Nicholas
>>>>
>>>> On Wed, Aug 31, 2022 at 7:45 AM Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Tue, Aug 30, 2022 at 6:37 PM Nicholas Arnold-Medabalimi <
>>>>> narnoldm at umich.edu> wrote:
>>>>>
>>>>>> Hi
>>>>>>
>>>>>> Thanks for all the help. I'm looking to tag several cells based on
>>>>>> metrics occurring at run time. In addition to the metric-defined cells I
>>>>>> also want to label the surrounding cells. This is no problem as I can
>>>>>> traverse the DMPlex chart to get the neighboring cells. The issue only
>>>>>> arises if an identified cell is on a partition boundary. this leads to the
>>>>>> neighbor cell in the overlap halo being tagged. However, the root cell on
>>>>>> the adjacent partition is not tagged. Is there a built-in way to
>>>>>> synchronize the labels from the leafs to the roots?
>>>>>>
>>>>>> Right now, I iterate through the root and leaf cells of each
>>>>>> processor, but it is somewhat wasteful as I don't see a way for the root
>>>>>> cell partition to know if a corresponding leaf cell label value without
>>>>>> communicating it first.
>>>>>>
>>>>>
>>>>> What I think you want is this:
>>>>>
>>>>>
>>>>> https://petsc.org/main/docs/manualpages/DMLabel/DMLabelPropagateBegin/
>>>>>
>>>>> I use this to do the same kind of labeling I think. It is setup to
>>>>> allow multiple rounds,
>>>>> so that you can use the communicated labeling to continue on the new
>>>>> rank.
>>>>>
>>>>> Will this work?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> Thanks
>>>>>> Nicholas
>>>>>>
>>>>>> --
>>>>>> Nicholas Arnold-Medabalimi
>>>>>>
>>>>>> Ph.D. Candidate
>>>>>> Computational Aeroscience Lab
>>>>>> University of Michigan
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>> https://www.cse.buffalo.edu/~knepley/
>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>
>>>>
>>>>
>>>> --
>>>> Nicholas Arnold-Medabalimi
>>>>
>>>> Ph.D. Candidate
>>>> Computational Aeroscience Lab
>>>> University of Michigan
>>>>
>>>
>>>
>>> --
>>> 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
>>>
>>> https://www.cse.buffalo.edu/~knepley/
>>> <http://www.cse.buffalo.edu/~knepley/>
>>>
>>
>>
>> --
>> Nicholas Arnold-Medabalimi
>>
>> Ph.D. Candidate
>> Computational Aeroscience Lab
>> University of Michigan
>>
>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
--
Nicholas Arnold-Medabalimi
Ph.D. Candidate
Computational Aeroscience Lab
University of Michigan
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