On Fri, Sep 2, 2022 at 12:53 AM Nicholas Arnold-Medabalimi < narno...@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 <knep...@gmail.com> wrote: > >> On Wed, Aug 31, 2022 at 9:30 PM Nicholas Arnold-Medabalimi < >> narno...@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 <knep...@gmail.com> >>> wrote: >>> >>>> On Tue, Aug 30, 2022 at 6:37 PM Nicholas Arnold-Medabalimi < >>>> narno...@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/>