[petsc-users] DMLabel Synchronize

Thu Sep 1 23:53:31 CDT 2022

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.

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
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