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<p>Hi Matthew,</p>
<p>we tried to use that. Now, we discovered that:</p>
<p>1- even if we "ask" for sfNatural creation with DMSetUseNatural,
it is not created because DMPlexCreateGlobalToNaturalSF looks for
a "section": this is not documented in DMSetUseNaturalso we are
asking ourselfs: "is this a permanent feature or a temporary
situation?"<br>
</p>
<p>2- We then tried to create a "section" in different manners: we
took the code into the example
petsc/src/dm/impls/plex/tests/ex15.c. However, we ended up with a
segfault:</p>
<p>corrupted size vs. prev_size<br>
[rohan:07297] *** Process received signal ***<br>
[rohan:07297] Signal: Aborted (6)<br>
[rohan:07297] Signal code: (-6)<br>
[rohan:07297] [ 0]
/lib64/libpthread.so.0(+0x13f80)[0x7f6f13be3f80]<br>
[rohan:07297] [ 1] /lib64/libc.so.6(gsignal+0x10b)[0x7f6f109b718b]<br>
[rohan:07297] [ 2] /lib64/libc.so.6(abort+0x175)[0x7f6f109b8585]<br>
[rohan:07297] [ 3] /lib64/libc.so.6(+0x7e2f7)[0x7f6f109fb2f7]<br>
[rohan:07297] [ 4] /lib64/libc.so.6(+0x857ea)[0x7f6f10a027ea]<br>
[rohan:07297] [ 5] /lib64/libc.so.6(+0x86036)[0x7f6f10a03036]<br>
[rohan:07297] [ 6] /lib64/libc.so.6(+0x861a3)[0x7f6f10a031a3]<br>
[rohan:07297] [ 7] /lib64/libc.so.6(+0x88740)[0x7f6f10a05740]<br>
[rohan:07297] [ 8]
/lib64/libc.so.6(__libc_malloc+0x1b8)[0x7f6f10a070c8]<br>
[rohan:07297] [ 9]
/lib64/libc.so.6(__backtrace_symbols+0x134)[0x7f6f10a8b064]<br>
[rohan:07297] [10]
/home/mefpp_ericc/GIREF/bin/MEF++.dev(_Z12reqBacktraceRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x4e)[0x4538ce]<br>
[rohan:07297] [11]
/home/mefpp_ericc/GIREF/bin/MEF++.dev(_Z15attacheDebuggerv+0x120)[0x4523c0]<br>
[rohan:07297] [12]
/home/mefpp_ericc/GIREF/lib/libgiref_dev_Util.so(traitementSignal+0x612)[0x7f6f28f503a2]<br>
[rohan:07297] [13] /lib64/libc.so.6(+0x3a210)[0x7f6f109b7210]</p>
<p>[rohan:07297] [14]
/opt/petsc-3.15.0_debug_openmpi-4.1.0_gcc7/lib/libpetsc.so.3.15(PetscTrMallocDefault+0x6fd)[0x7f6f22f1b8ed]<br>
[rohan:07297] [15]
/opt/petsc-3.15.0_debug_openmpi-4.1.0_gcc7/lib/libpetsc.so.3.15(PetscMallocA+0x5cd)[0x7f6f22f19c2d]<br>
[rohan:07297] [16]
/opt/petsc-3.15.0_debug_openmpi-4.1.0_gcc7/lib/libpetsc.so.3.15(PetscSFCreateSectionSF+0xb48)[0x7f6f23268e18]<br>
[rohan:07297] [17]
/opt/petsc-3.15.0_debug_openmpi-4.1.0_gcc7/lib/libpetsc.so.3.15(DMPlexCreateGlobalToNaturalSF+0x13b2)[0x7f6f241a5602]<br>
[rohan:07297] [18]
/opt/petsc-3.15.0_debug_openmpi-4.1.0_gcc7/lib/libpetsc.so.3.15(DMPlexDistribute+0x39b1)[0x7f6f23fdca21]<br>
</p>
<p>If we do not create a section, the call to DMPlexDistribute is
successful, but DMPlexGetGlobalToNaturalSF return a null SF
pointer...<br>
</p>
<p>Here are the operations we are calling ( this is almost the code
we are using, I just removed verifications and creation of the
connectivity which use our parallel structure and code):<br>
</p>
<p>===========</p>
<p> PetscInt* lCells = 0;<br>
PetscInt lNumCorners = 0;<br>
PetscInt lDimMail = 0;<br>
PetscInt lnumCells = 0;<br>
<br>
//At this point we create the cells for PETSc expected input for
DMPlexBuildFromCellListParallel and set lNumCorners, lDimMail and
lnumCells to correct values.<br>
...<br>
<br>
DM lDMBete = 0<br>
DMPlexCreate(lMPIComm,&lDMBete);<br>
<br>
DMSetDimension(lDMBete, lDimMail);<br>
<br>
DMPlexBuildFromCellListParallel(lDMBete,<br>
lnumCells,<br>
PETSC_DECIDE,<br>
pLectureElementsLocaux.reqNbTotalSommets(),<br>
lNumCorners,<br>
lCells,<br>
PETSC_NULL);<br>
<br>
DM lDMBeteInterp = 0;<br>
DMPlexInterpolate(lDMBete, &lDMBeteInterp);<br>
DMDestroy(&lDMBete);<br>
lDMBete = lDMBeteInterp;<br>
<br>
DMSetUseNatural(lDMBete,PETSC_TRUE);<br>
<br>
PetscSF lSFMigrationSansOvl = 0;<br>
PetscSF lSFMigrationOvl = 0;<br>
DM lDMDistribueSansOvl = 0;<br>
DM lDMAvecOverlap = 0;<br>
<br>
PetscPartitioner lPart;<br>
DMPlexGetPartitioner(lDMBete, &lPart);<br>
PetscPartitionerSetFromOptions(lPart);<br>
<br>
PetscSection section;<br>
PetscInt numFields = 1;<br>
PetscInt numBC = 0;<br>
PetscInt numComp[1] = {1};<br>
PetscInt numDof[4] = {1, 0, 0, 0};<br>
PetscInt bcFields[1] = {0};<br>
IS bcPoints[1] = {NULL};<br>
<br>
DMSetNumFields(lDMBete, numFields);<br>
<br>
DMPlexCreateSection(lDMBete, NULL, numComp, numDof, numBC,
bcFields, bcPoints, NULL, NULL, §ion);<br>
DMSetLocalSection(lDMBete, section);<br>
<br>
DMPlexDistribute(lDMBete, 0, &lSFMigrationSansOvl,
&lDMDistribueSansOvl); // segfault!<br>
</p>
<p>===========<br>
</p>
<p>So we have other question/remarks:</p>
<p>3- Maybe PETSc expect something specific that is missing/not
verified: for example, we didn't gave any coordinates since we
just want to partition and compute overlap for the mesh... and
then recover our element numbers in a "simple way"</p>
<p>4- We are telling ourselves it is somewhat a "big price to pay"
to have to build an unused section to have the global to natural
ordering set ? Could this requirement be avoided?</p>
<p>5- Are there any improvement towards our usages in 3.16 release?</p>
<p>Thanks,</p>
<p>Eric</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 2021-09-29 7:39 p.m., Matthew
Knepley wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAMYG4Gkb8qivU3xr1Bz0dxBBSYWJveE3RGScs93eVDjJRPGEOA@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">
<div dir="ltr">On Wed, Sep 29, 2021 at 5:18 PM Eric Chamberland
<<a href="mailto:Eric.Chamberland@giref.ulaval.ca"
moz-do-not-send="true">Eric.Chamberland@giref.ulaval.ca</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">Hi,<br>
<br>
I come back with _almost_ the original question:<br>
<br>
I would like to add an integer information (*our* original
element <br>
number, not petsc one) on each element of the DMPlex I
create with <br>
DMPlexBuildFromCellListParallel.<br>
<br>
I would like this interger to be distribruted by or the same
way <br>
DMPlexDistribute distribute the mesh.<br>
<br>
Is it possible to do this?<br>
</blockquote>
<div><br>
</div>
<div>I think we already have support for what you want. If you
call</div>
<div><br>
</div>
<div> <a
href="https://petsc.org/main/docs/manualpages/DM/DMSetUseNatural.html"
moz-do-not-send="true">https://petsc.org/main/docs/manualpages/DM/DMSetUseNatural.html</a></div>
<div><br>
</div>
<div>before DMPlexDistribute(), it will compute a PetscSF
encoding the global to natural map. You</div>
<div>can get it with</div>
<div><br>
</div>
<div> <a
href="https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexGetGlobalToNaturalSF.html"
moz-do-not-send="true">https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexGetGlobalToNaturalSF.html</a></div>
<div><br>
</div>
<div>and use it with</div>
<div><br>
</div>
<div> <a
href="https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexGlobalToNaturalBegin.html"
moz-do-not-send="true">https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexGlobalToNaturalBegin.html</a></div>
<div><br>
</div>
<div>Is this sufficient?</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">
Thanks,<br>
<br>
Eric<br>
<br>
On 2021-07-14 1:18 p.m., Eric Chamberland wrote:<br>
> Hi,<br>
><br>
> I want to use DMPlexDistribute from PETSc for computing
overlapping <br>
> and play with the different partitioners supported.<br>
><br>
> However, after calling DMPlexDistribute, I noticed the
elements are <br>
> renumbered and then the original number is lost.<br>
><br>
> What would be the best way to keep track of the element
renumbering?<br>
><br>
> a) Adding an optional parameter to let the user
retrieve a vector or <br>
> "IS" giving the old number?<br>
><br>
> b) Adding a DMLabel (seems a wrong good solution)<br>
><br>
> c) Other idea?<br>
><br>
> Of course, I don't want to loose performances with the
need of this <br>
> "mapping"...<br>
><br>
> Thanks,<br>
><br>
> Eric<br>
><br>
-- <br>
Eric Chamberland, ing., M. Ing<br>
Professionnel de recherche<br>
GIREF/Université Laval<br>
(418) 656-2131 poste 41 22 42<br>
<br>
</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" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<pre class="moz-signature" cols="72">--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42</pre>
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