<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Here is a screenshot of the partition I hard coded (top) and
vertices/element numbers (down):<br>
</p>
<p><img src="cid:part1.0FA9C37F.8D68AE7D@giref.ulaval.ca" alt=""></p>
<p>I have not yet modified the ex44.c example to properly assign the
coordinates... <br>
</p>
<p>(but I would not have done it like it is in the last version
because the sCoords array is the global array with global vertices
number)</p>
<p>I will have time to do this tomorrow...</p>
<p>Maybe I can first try to reproduce all this with a smaller mesh?<br>
</p>
<p>Eric<br>
</p>
<div class="moz-cite-prefix">On 2021-10-26 9:46 a.m., Matthew
Knepley wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAMYG4G=BwgH+Uxxzax+KRDXvawsyPNw6Ve8NF-Mu581d1PbvCQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Okay, I ran it. Something seems off with the mesh.
First, I cannot simply explain the partition. The number of
shared vertices and edges
<div>does not seem to come from a straight cut. Second, the mesh
look scrambled on output.</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 Sun, Oct 24, 2021 at 11:49
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>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi Matthew,</p>
<p>ok, I started back from your ex44.c example and added the
global array of coordinates. I just have to code the
creation of the local coordinates now.</p>
<p>Eric<br>
</p>
<div>On 2021-10-20 6:55 p.m., Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Wed, Oct 20, 2021 at 3:06 PM Eric
Chamberland <<a
href="mailto:Eric.Chamberland@giref.ulaval.ca"
target="_blank" 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">
<div>
<p>Hi Matthew,</p>
<p>we tried to reproduce the error in a simple
example.</p>
<p>The context is the following: We hard coded the
mesh and initial partition into the code (see
sConnectivity and sInitialPartition) for 2 ranks
and try to create a section in order to use the
DMPlexNaturalToGlobalBegin function to retreive
our initial element numbers.</p>
<p>Now the call to DMPlexDistribute give different
errors depending on what type of component we
ask the field to be created. For our objective,
we would like a global field to be created on
elements only (like a P0 interpolation).<br>
</p>
<p>We now have the following error generated:</p>
<p>[0]PETSC ERROR: --------------------- Error
Message
--------------------------------------------------------------<br>
[0]PETSC ERROR: Petsc has generated inconsistent
data<br>
[0]PETSC ERROR: Inconsistency in indices, 18
should be 17<br>
[0]PETSC ERROR: See <a
href="https://www.mcs.anl.gov/petsc/documentation/faq.html"
target="_blank" moz-do-not-send="true">https://www.mcs.anl.gov/petsc/documentation/faq.html</a>
for trouble shooting.<br>
[0]PETSC ERROR: Petsc Release Version 3.15.0,
Mar 30, 2021 <br>
[0]PETSC ERROR: ./bug on a named rohan by ericc
Wed Oct 20 14:52:36 2021<br>
[0]PETSC ERROR: Configure options
--prefix=/opt/petsc-3.15.0_debug_openmpi-4.1.0_gcc7
--with-mpi-compilers=1
--with-mpi-dir=/opt/openmpi-4.1.0_gcc7
--with-cxx-dialect=C++14 --with-make-np=12
--with-shared-libraries=1 --with-debugging=yes
--with-memalign=64 --with-visibility=0
--with-64-bit-indices=0 --download-ml=yes
--download-mumps=yes --download-superlu=yes
--download-hpddm=yes --download-slepc=yes
--download-superlu_dist=yes
--download-parmetis=yes --download-ptscotch=yes
--download-metis=yes --download-strumpack=yes
--download-suitesparse=yes --download-hypre=yes
--with-blaslapack-dir=/opt/intel/oneapi/mkl/2021.1.1/env/../lib/intel64
--with-mkl_pardiso-dir=/opt/intel/oneapi/mkl/2021.1.1/env/..
--with-mkl_cpardiso-dir=/opt/intel/oneapi/mkl/2021.1.1/env/..
--with-scalapack=1
--with-scalapack-include=/opt/intel/oneapi/mkl/2021.1.1/env/../include
--with-scalapack-lib="-L/opt/intel/oneapi/mkl/2021.1.1/env/../lib/intel64
-lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64"<br>
[0]PETSC ERROR: #1 PetscSFCreateSectionSF() at
/tmp/ompi-opt/petsc-3.15.0-debug/src/vec/is/sf/utils/sfutils.c:409<br>
[0]PETSC ERROR: #2
DMPlexCreateGlobalToNaturalSF() at
/tmp/ompi-opt/petsc-3.15.0-debug/src/dm/impls/plex/plexnatural.c:184<br>
[0]PETSC ERROR: #3 DMPlexDistribute() at
/tmp/ompi-opt/petsc-3.15.0-debug/src/dm/impls/plex/plexdistribute.c:1733<br>
[0]PETSC ERROR: #4 main() at bug_section.cc:159<br>
[0]PETSC ERROR: No PETSc Option Table entries<br>
[0]PETSC ERROR: ----------------End of Error
Message -------send entire error message to <a
href="mailto:petsc-maint@mcs.anl.gov"
target="_blank" moz-do-not-send="true">petsc-maint@mcs.anl.gov</a>----------<br>
<br>
</p>
<p>Hope the attached code is self-explaining, note
that to make it short, we have not included the
final part of it, just the buggy part we are
encountering right now...</p>
<p>Thanks for your insights,</p>
</div>
</blockquote>
<div>Thanks for making the example. I tweaked it
slightly. I put in a test case that just makes a
parallel 7 x 10 quad mesh. This works</div>
<div>fine. Thus I think it must be something connected
with the original mesh. It is hard to get a handle
on it without the coordinates.</div>
<div>Do you think you could put the coordinate array
in? I have added the code to load them (see attached
file).</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>Eric<br>
</p>
<div>On 2021-10-06 9:23 p.m., Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Wed, Oct 6, 2021 at 5:43 PM
Eric Chamberland <<a
href="mailto:Eric.Chamberland@giref.ulaval.ca"
target="_blank" 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">
<div>
<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>
</div>
</blockquote>
<div>I think explaining this will help clear
up a lot.</div>
<div><br>
</div>
<div>What the Natural2Global map does is
permute a solution vector into the
ordering that it would have had prior to
mesh distribution.</div>
<div>Now, in order to do this permutation, I
need to know the original (global) data
layout. If it is not specified _before_
distribution, we</div>
<div>cannot build the permutation. The
section describes the data layout, so I
need it before distribution.</div>
<div><br>
</div>
<div>I cannot think of another way that you
would implement this, but if you want
something else, let me know.</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>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>
</div>
</blockquote>
<div>I am not sure what happened here, but
if you could send a sample code, I will
figure it out. </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>If we do not create a section, the
call to DMPlexDistribute is
successful, but
DMPlexGetGlobalToNaturalSF return a
null SF pointer...<br>
</p>
</div>
</blockquote>
<div>Yes, it just ignores it in this case
because it does not have a global layout. </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> </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>
</div>
</blockquote>
<div>I don't think so. There would have to
be _some_ way of describing your data
layout in terms of mesh points, and I do
not see how you could use less memory
doing that. </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>5- Are there any improvement towards
our usages in 3.16 release?</p>
</div>
</blockquote>
<div>Let me try and run the code above.</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>Thanks,</p>
<p>Eric</p>
<p><br>
</p>
<div>On 2021-09-29 7:39 p.m., Matthew
Knepley wrote:<br>
</div>
<blockquote type="cite">
<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" target="_blank"
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"
target="_blank"
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"
target="_blank"
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"
target="_blank"
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">
<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 cols="72">--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42</pre>
</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"
moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<pre cols="72">--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42</pre>
</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" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<pre cols="72">--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42</pre>
</div>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
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<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>
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<div><a href="http://www.cse.buffalo.edu/~knepley/"
target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
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<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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