<div dir="ltr"><div dir="ltr">On Thu, Oct 24, 2024 at 6:04 PM Matteo Semplice <<a href="mailto:matteo.semplice@uninsubria.it">matteo.semplice@uninsubria.it</a>> wrote:</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"><u></u>
<div>
<p>Hi. The HDF5 solution looks good to me, but I now get this error<br>
</p>
<p><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"></span></span></p></div></blockquote><div>Okay, I can make a workaround for this. Here is what is happening.</div><div><br></div><div>When you output solutions, you really want the essential boundary conditions included in the</div><div>output, and the only way I have to do that is for you to tell me about the discretization, so I</div><div>require the DS.</div><div><br></div><div>What I can do is ignore this step if there is no DS. Let me do that and mail you with the branch.</div><div><br></div><div> Thanks!</div><div><br></div><div> Matt </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><p><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">$
../src/saveDemo </span><br>
Creating mesh with (10,10) faces <br>
<span style="font-weight:bold;color:rgb(255,84,84);background-color:rgb(255,255,255)">[0]PETSC
ERROR: --------------------- Error Message
--------------------------------------------------------------</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">
</span><br>
[0]PETSC ERROR: Object is in wrong state
<br>
[0]PETSC ERROR: Need to call DMCreateDS() before calling
DMGetDS()
<br>
[0]PETSC ERROR: See <a href="https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!dLtO-GGeUrd81R06hiAmfndS-cgZrVE4t8Hipjb8bHTF-vqn1VNb3pjTj5fljYzb6ejXt1QTiLZq1kEPxNH0$" target="_blank">https://petsc.org/release/faq/</a> for trouble
shooting.
<br>
[0]PETSC ERROR: Petsc Release Version 3.21.5, unknown <br>
[0]PETSC ERROR: ../src/saveDemo on a named dentdherens by
matteo Fri Oct 25 00:00:44 2024
<br>
[0]PETSC ERROR: Configure options --COPTFLAGS="-O3 -march=native
-mtune=native -mavx2" --CXXOPTFLAGS="-O3 -march=native
-mtune=native -mavx2" --FOPTFLAGS="-O3 -march=native
-mtune=native -mavx2" --PETSC_ARCH=op<br>
t --with-strict-petscerrorcode --download-hdf5
--prefix=/home/matteo/software/petsc/3.21-opt/
--with-debugging=0 --with-gmsh --with-metis --with-parmetis
--with-triangle PETSC_DIR=/home/matteo/software/petsc --<br>
force
<br>
[0]PETSC ERROR: #1 DMGetDS() at
/home/matteo/software/petsc/src/dm/interface/dm.c:5525
<br>
[0]PETSC ERROR: #2 DMPlexInsertBoundaryValues_Plex() at
/home/matteo/software/petsc/src/dm/impls/plex/plexfem.c:1136
<br>
[0]PETSC ERROR: #3 DMPlexInsertBoundaryValues() at
/home/matteo/software/petsc/src/dm/impls/plex/plexfem.c:1274
<br>
[0]PETSC ERROR: #4 VecView_Plex_HDF5_Internal() at
/home/matteo/software/petsc/src/dm/impls/plex/plexhdf5.c:477
<br>
[0]PETSC ERROR: #5 VecView_Plex() at
/home/matteo/software/petsc/src/dm/impls/plex/plex.c:656
<br>
[0]PETSC ERROR: #6 VecView() at
/home/matteo/software/petsc/src/vec/vec/interface/vector.c:806
<br>
[0]PETSC ERROR: #7 main() at saveDemo.cpp:123
<br>
[0]PETSC ERROR: No PETSc Option Table entries
<br>
<span style="font-weight:bold;color:rgb(255,84,84);background-color:rgb(255,255,255)">[0]PETSC
ERROR: ----------------End of Error Message -------send entire
error message to <a href="mailto:petsc-maint@mcs.anl.gov" target="_blank">petsc-maint@mcs.anl.gov</a>----------</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">
</span><br>
--------------------------------------------------------------------------
<br>
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
<br>
with errorcode 73.
<br>
<br>
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
processes.
<br>
You may or may not see output from other processes, depending on
<br>
exactly when Open MPI kills them.
<br>
--------------------------------------------------------------------------<br>
</span></p>
<p>I attach the modified sample code that produced the above error.<br>
</p>
<p>Thanks</p>
<p> Matteo<br>
</p>
<div>Il 24/10/24 22:20, Matthew Knepley ha
scritto:<br>
</div>
<blockquote type="cite">
<div dir="ltr">I just looked at the code. The VTK code is very
old, and does not check for cell overlap.
<div><br>
</div>
<div>We have been recommending that people use either HDF5 or
CGNS, both of which work in this case</div>
<div>I believe. I can fix VTK if that is what you want, but it
might take me a little while as it is very busy at</div>
<div>work right now. However, if you output HDF5, then you can
run</div>
<div><br>
</div>
<div> ./lib/petsc/bin/petsc_gen_xdmf.py mesh.h5</div>
<div><br>
</div>
<div>and it will generate an XDMF file so you can load it into
ParaView. Or you can output CGNS which I think</div>
<div>ParaView understands.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Oct 24, 2024 at
4:02 PM Semplice Matteo <<a href="mailto:matteo.semplice@uninsubria.it" target="_blank">matteo.semplice@uninsubria.it</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>
<div dir="ltr">
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Hi,</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
I tried again today and have (re?)discovered this
example <a href="https://urldefense.us/v3/__https://petsc.org/release/src/dm/impls/plex/tutorials/ex14.c.html__;!!G_uCfscf7eWS!dLtO-GGeUrd81R06hiAmfndS-cgZrVE4t8Hipjb8bHTF-vqn1VNb3pjTj5fljYzb6ejXt1QTiLZq1oOKrq2I$" id="m_2093919128985184015m_5982902773776001898LPlnk382398" target="_blank">
https://petsc.org/release/src/dm/impls/plex/tutorials/ex14.c.html</a>,
but I cannot understand if in my case I should call
<a href="https://urldefense.us/v3/__https://petsc.org/release/manualpages/PetscSF/PetscSFCreateSectionSF/__;!!G_uCfscf7eWS!dLtO-GGeUrd81R06hiAmfndS-cgZrVE4t8Hipjb8bHTF-vqn1VNb3pjTj5fljYzb6ejXt1QTiLZq1jGPN022$" id="m_2093919128985184015m_5982902773776001898OWA7823b4db-9caf-edfa-8c7d-7a06e4a231c3" target="_blank">
PetscSFCreateSectionSF</a> and, if so, how should I
then activate the returned SF.</div>
<div style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Matteo</div>
<hr style="display:inline-block;width:98%">
<div id="m_2093919128985184015m_5982902773776001898divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>Da:</b> Semplice Matteo<br>
<b>Inviato:</b> martedì 22 ottobre 2024 00:24<br>
<b>A:</b> Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>><br>
<b>Cc:</b> PETSc <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br>
<b>Oggetto:</b> Re: [petsc-users] local/global DMPlex
Vec output</font>
<div> </div>
</div>
<div>
<p>Dear Matt,</p>
<p> I guess you're right: thresholding by rank==0 and
rank==1 in paraview reveals that it is indeed the
overlap cells that are appear twice in the output.<br>
</p>
<p>The attached file is not exactly minimal but
hopefully short enough. If I run it in serial, all is
ok, but with</p>
<p> mpirun -np 2 ./saveDemo</p>
<p>it creates a 10x10 grid, but I get "output.vtu" with
a total of 120 cells. However the pointSF of the
DMPlex seems correct.</p>
<p>Thanks</p>
<p> Matteo<br>
</p>
<div>Il 21/10/24 19:15, Matthew Knepley ha scritto:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Mon, Oct 21, 2024 at 12:22 PM
Matteo Semplice via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>>
wrote:<br>
</div>
<div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Dear petsc-users,<br>
</p>
<p> I am having issues with output of
parallel data attached to a DMPlex (or maybe
more fundamental ones about DMPlex...).</p>
<p>So I currently</p>
<ol>
<li>create a DMPlex
(DMPlexCreateGmshFromFile or
DMPlexCreateBoxMesh)</li>
<li>partition it</li>
<li>and create a section for my data layout
with DMPlexCreateSection(ctx.dmMesh, NULL,
numComp, numDof, numBC, NULL, NULL, NULL,
NULL, &sUavg)</li>
<li>DMSetLocalSection(ctx.dmMesh, sUavg)</li>
<li>create solLoc and solGlob vectors with
DMCreateGlobalVector and
DMCreateLocalVector</li>
<li>solve ....</li>
<li>VecView(ctx.solGlob, vtkViewer) on a
.vtu file<br>
</li>
</ol>
<p>but when I load data in ParaView I get more
cells than expected and it is as if the
cells in the halo are put twice in output.
(I could create a MWE if the above is not
clear)<br>
</p>
</div>
</blockquote>
<div>I think we need an MWE here, because from the
explanation above, it should work.</div>
<div><br>
</div>
<div>However, I can try to guess the problem. When
you partition the mesh, I am guessing that you
have cells in the overlap. These cells</div>
<div>must be in the point SF in order for the
global section to give them a unique owner.
Perhaps something has gone wrong here.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt </div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>I guess that the culprit is point (4), but
if I replace it with DMSetGlobalSection then
I cannot create the local vector at point
(5).<br>
</p>
<p>How should I handle this properly? In my
code I need to create both local and global
vectors, to perform at least GlobalToLocal
and to save the global data.<br>
</p>
<p>(On a side note, I tried also HDF5 but then
it complains about the DM not having a
DS...; really, any working solution that
allows data to be explored with Paraview is
fine)<br>
</p>
<p>Thanks for any advice!<br>
</p>
<p>Matteo Semplice</p>
</div>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
<span>-- </span><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="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dLtO-GGeUrd81R06hiAmfndS-cgZrVE4t8Hipjb8bHTF-vqn1VNb3pjTj5fljYzb6ejXt1QTiLZq1o97P_XX$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<pre cols="72">--
---
Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como</pre>
</div>
</div>
</div>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
<span class="gmail_signature_prefix">-- </span><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="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dLtO-GGeUrd81R06hiAmfndS-cgZrVE4t8Hipjb8bHTF-vqn1VNb3pjTj5fljYzb6ejXt1QTiLZq1o97P_XX$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<pre cols="72">--
---
Professore Associato in Analisi Numerica
Dipartimento di Scienza e Alta Tecnologia
Università degli Studi dell'Insubria
Via Valleggio, 11 - Como</pre>
</div>
</blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!dLtO-GGeUrd81R06hiAmfndS-cgZrVE4t8Hipjb8bHTF-vqn1VNb3pjTj5fljYzb6ejXt1QTiLZq1o97P_XX$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>