<div dir="ltr"><div dir="ltr">On Fri, Sep 2, 2022 at 12:53 AM Nicholas Arnold-Medabalimi <<a href="mailto:narnoldm@umich.edu">narnoldm@umich.edu</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">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. <br><br>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.<br></div></blockquote><div><br></div><div>You are missing "PetscFunctionBeginUser;" at the start of your function. This must be paired with all PetscFunctionReturn() calls since we keep</div><div>track of the stack. We added this check in the new version.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><br><div style="color:rgb(255,255,255);background-color:rgb(0,36,81);font-family:Consolas,"Courier New",monospace;font-size:14px;line-height:19px;white-space:pre-wrap"><div><span style="color:rgb(255,238,173)">PetscErrorCode</span> <span style="color:rgb(187,218,255)">FileFastForward</span>(<span style="color:rgb(255,238,173)">PetscViewer</span> <span style="color:rgb(255,197,143)">viewer</span>, <span style="color:rgb(235,187,255)">char</span> <span style="color:rgb(255,197,143)">delim</span>, <span style="color:rgb(235,187,255)">bool</span> <span style="color:rgb(235,187,255)">&</span><span style="color:rgb(255,197,143)">eof</span>)</div><div>{</div><div> <span style="color:rgb(235,187,255)">int</span> <span style="color:rgb(255,157,164)">i</span> <span style="color:rgb(153,255,255)">=</span> <span style="color:rgb(255,197,143)">0</span>, <span style="color:rgb(255,157,164)">ret</span> <span style="color:rgb(153,255,255)">=</span> <span style="color:rgb(255,197,143)">0</span>;</div><div> <span style="color:rgb(235,187,255)">char</span> <span style="color:rgb(255,157,164)">buffer</span>;</div><div> <span style="color:rgb(235,187,255)">do</span></div><div> <span style="color:rgb(187,218,255)">PetscViewerRead</span>(<span style="color:rgb(255,197,143)">viewer</span>, <span style="color:rgb(153,255,255)">&</span>(<span style="color:rgb(255,157,164)">buffer</span>), <span style="color:rgb(255,197,143)">1</span>, <span style="color:rgb(153,255,255)">&</span><span style="color:rgb(255,157,164)">ret</span>, <span style="color:rgb(255,157,164)">PETSC_CHAR</span>);</div><div> <span style="color:rgb(235,187,255)">while</span> (<span style="color:rgb(255,157,164)">ret</span> <span style="color:rgb(153,255,255)">></span> <span style="color:rgb(255,197,143)">0</span> <span style="color:rgb(153,255,255)">&&</span> <span style="color:rgb(255,157,164)">buffer</span> <span style="color:rgb(153,255,255)">!=</span> <span style="color:rgb(255,197,143)">delim</span>);</div><div> <span style="color:rgb(235,187,255)">if</span> (<span style="color:rgb(255,157,164)">ret</span> <span style="color:rgb(153,255,255)">==</span> <span style="color:rgb(255,197,143)">0</span>)</div><div> {</div><div> <span style="color:rgb(187,218,255)">printf</span>(<span style="color:rgb(209,241,169)">"End of file reached before delimiter found</span><span style="color:rgb(255,197,143)">\n</span><span style="color:rgb(209,241,169)">"</span>);</div><div> <span style="color:rgb(255,197,143)">eof</span> <span style="color:rgb(153,255,255)">=</span> <span style="color:rgb(255,197,143)">false</span>;</div><div> }</div><div> <span style="color:rgb(235,187,255)">else</span></div><div> <span style="color:rgb(255,197,143)">eof</span> <span style="color:rgb(153,255,255)">=</span> <span style="color:rgb(255,197,143)">true</span>;</div><div> <span style="color:rgb(187,218,255)">PetscFunctionReturn</span>(<span style="color:rgb(255,197,143)">0</span>);</div><div>}</div></div>The viewer is opened using <br><div style="color:rgb(255,255,255);background-color:rgb(0,36,81);font-family:Consolas,"Courier New",monospace;font-size:14px;line-height:19px;white-space:pre-wrap"><div> <span style="color:rgb(187,218,255)">PetscViewerCreate</span>(<span style="color:rgb(255,157,164)">PETSC_COMM_WORLD</span>, <span style="color:rgb(153,255,255)">&</span><span style="color:rgb(255,157,164)">viewer</span>);</div><div> <span style="color:rgb(187,218,255)">PetscViewerSetType</span>(<span style="color:rgb(255,157,164)">viewer</span>, <span style="color:rgb(187,218,255)">PETSCVIEWERASCII</span>);</div><div> <span style="color:rgb(187,218,255)">PetscViewerFileSetMode</span>(<span style="color:rgb(255,157,164)">viewer</span>, <span style="color:rgb(255,157,164)">FILE_MODE_READ</span>);</div><div> <span style="color:rgb(187,218,255)">PetscViewerFileSetName</span>(<span style="color:rgb(255,157,164)">viewer</span>, <span style="color:rgb(255,157,164)">meshfile</span>);</div></div>The error that is thrown is <br><br>[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<br>[0]PETSC ERROR: Petsc has generated inconsistent data<br>[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)<br><br>[0]PETSC ERROR: See <a href="https://petsc.org/release/faq/" target="_blank">https://petsc.org/release/faq/</a> for trouble shooting.<br>[0]PETSC ERROR: Petsc Development GIT revision: unknown GIT Date: unknown<br>[0]PETSC ERROR: /home/narnoldm/code/solver-playground/build/bin/version on a named Dragoon by narnoldm Fri Sep 2 00:34:02 2022<br>[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<br>[0]PETSC ERROR: #1 FileFastForward() at /home/narnoldm/code/solver-playground/version_upgrade/version_debug.cpp:35<br>application called MPI_Abort(MPI_COMM_SELF, 77) - process 0<br>[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=77<br>:<br>system msg for write_line failure : Bad file descriptor<br><br><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Sep 1, 2022 at 5:32 AM Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">On Wed, Aug 31, 2022 at 9:30 PM Nicholas Arnold-Medabalimi <<a href="mailto:narnoldm@umich.edu" target="_blank">narnoldm@umich.edu</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi <br><br>Thanks, this looks like what I need, but I don't seem to have it in my release (3.17.4 from <a href="https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.17.4.tar.gz" target="_blank">https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.17.4.tar.gz</a>). 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? <br></div></blockquote><div><br></div><div>Yes, it is in main (<a href="https://petsc.org/main/docs/changes/dev/" target="_blank">https://petsc.org/main/docs/changes/dev/</a>) since it was an interface change. Our main branch is quite stable, and I would recommend</div><div>it for development work.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Thanks<br>Nicholas</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Aug 31, 2022 at 7:45 AM Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr">On Tue, Aug 30, 2022 at 6:37 PM Nicholas Arnold-Medabalimi <<a href="mailto:narnoldm@umich.edu" target="_blank">narnoldm@umich.edu</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi<br><br>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? <br><br>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. <br></div></blockquote><div><br></div><div>What I think you want is this:</div><div><br></div><div> <a href="https://petsc.org/main/docs/manualpages/DMLabel/DMLabelPropagateBegin/" target="_blank">https://petsc.org/main/docs/manualpages/DMLabel/DMLabelPropagateBegin/</a></div><div><br></div><div>I use this to do the same kind of labeling I think. It is setup to allow multiple rounds,</div><div>so that you can use the communicated labeling to continue on the new rank.</div><div><br></div><div>Will this work?</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Thanks<br>Nicholas<br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div style="font-family:arial;font-size:small"><font color="#000000">Nicholas Arnold-Medabalimi<br><br></font><span style="font-family:sans-serif;font-size:14px">Ph.D. Candidate</span><font color="#000000"><br>Computational Aeroscience Lab<br>University of Michigan</font></div></div></div></div></div></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div style="font-family:arial;font-size:small"><font color="#000000">Nicholas Arnold-Medabalimi<br><br></font><span style="font-family:sans-serif;font-size:14px">Ph.D. Candidate</span><font color="#000000"><br>Computational Aeroscience Lab<br>University of Michigan</font></div></div></div></div></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div style="font-family:arial;font-size:small"><font color="#000000">Nicholas Arnold-Medabalimi<br><br></font><span style="font-family:sans-serif;font-size:14px">Ph.D. Candidate</span><font color="#000000"><br>Computational Aeroscience Lab<br>University of Michigan</font></div></div></div></div></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>