<div dir="ltr"><div dir="ltr">On Tue, Nov 2, 2021 at 10:27 PM Eric Chamberland <<a href="mailto:Eric.Chamberland@giref.ulaval.ca">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>yes, it all works now!</p>
<p>I modified the example to do a NaturalToGlobal then a
GlobalToNatural and test if we have the good result...</p>
<p>The test would just need that we "force" the computed partition
to a given result, then we could check the result of the
NaturalToGlobal independently of the partitioner...</p>
<p>Thanks a lot!</p>
<p></p></div></blockquote><div>No problem. Thanks for generating a great test. I will get this into the CI tonight.</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</p>
<p><br>
</p>
<div>On 2021-11-02 5:16 a.m., Matthew
Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Mon, Nov 1, 2021 at 5:24 PM Eric Chamberland
<<a href="mailto:Eric.Chamberland@giref.ulaval.ca" target="_blank">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>ok, good news then! :)<br>
</p>
<p>Meanwhile, I tested it the "other way" with
DMPlexGlobalToNaturalBegin/End and it does not give a
"sensed" result neither. <br>
</p>
<p>Probably it does something like "GlobalToSequential"
too?</p>
</div>
</blockquote>
<div>I am not sure how it worked before, but I think I have it
fixed. I get the output you expect for the test. I
force-pushed the branch<br>
</div>
<div>so you will have to check it out again.</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 2021-11-01 3:25 p.m., Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Sun, Oct 31, 2021 at 10:07 AM Eric
Chamberland <<a href="mailto:Eric.Chamberland@giref.ulaval.ca" target="_blank">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 do not know if
DMPlexNaturalToGlobalBegin/End is buggy or if
it is our comprehension of what it should do
that is wrong...<br>
</p>
<p>Would you just check if what we try to do
from line 313 to 356 is good or wrong?</p>
<p>The expected result is that the global vector
"lGlobalVec" contains the element numbers from
the initial partition that have been put into
"lNatVec".<br>
</p>
<p>Thanks a lot for any insights!!</p>
</div>
</blockquote>
<div>Okay, I have found the problem.I confess to not
actually looking very closely at the
implementation before. GlobalToNatural was
assuming that</div>
<div>the "natural" was also sequential, and looking
at it all the tests are eq-to-parallel
distribution. I need to fix it for a parallel
natural state. Hopefully</div>
<div>it will not take me long.</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>
<p><br>
</p>
<div>On 2021-10-27 2:32 p.m., Eric Chamberland
wrote:<br>
</div>
<blockquote type="cite">
<p>Hi Matthew,</p>
<p>we continued the example. Now it must be
our misuse of PETSc that produced the wrong
result.</p>
<p>As stated into the code:</p>
<p>// The call to
DMPlexNaturalToGlobalBegin/End does not
produce our expected result...<br>
// In lGlobalVec, we expect to have:<br>
/*<br>
* Process [0]<br>
* 2.<br>
* 4.<br>
* 8.<br>
* 3.<br>
* 9.<br>
* Process [1]<br>
* 1.<br>
* 5.<br>
* 7.<br>
* 0.<br>
* 6.<br>
*<br>
* but we obtained:<br>
*<br>
* Process [0]<br>
* 2.<br>
* 4.<br>
* 8.<br>
* 0.<br>
* 0.<br>
* Process [1]<br>
* 0.<br>
* 0.<br>
* 0.<br>
* 0.<br>
* 0.<br>
*/</p>
<p>(see attached ex44.c)</p>
<p>Thanks,</p>
<p>Eric<br>
</p>
<div>On 2021-10-27 1:25 p.m., Eric Chamberland
wrote:<br>
</div>
<blockquote type="cite">
<p>Great!</p>
<p>Thanks Matthew, it is working for me up
to that point!</p>
<p>We are continuing the ex44.c and forward
it to you at the next blocking point...</p>
<p>Eric<br>
</p>
<div>On 2021-10-27 11:14 a.m., Matthew
Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Wed, Oct 27, 2021 at
8:29 AM Eric Chamberland <<a href="mailto:Eric.Chamberland@giref.ulaval.ca" target="_blank">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>the smallest mesh which crashes
the code is a 2x5 mesh:</p>
<p><img src="cid:17ce59a2638931bce1a1" alt=""></p>
<p>See the modified ex44.c</p>
<p>With smaller meshes(2x2, 2x4,
etc), it passes... But it bugs
latter when I try to use
DMPlexNaturalToGlobalBegin but
let's keep that other problem
for later...</p>
<p>Thanks a lot for helping
digging into this! :)</p>
</div>
</blockquote>
<div>I have made a small fix in this
branch</div>
<div><br>
</div>
<div> <a href="https://gitlab.com/petsc/petsc/-/commits/knepley/fix-plex-g2n" target="_blank">https://gitlab.com/petsc/petsc/-/commits/knepley/fix-plex-g2n</a></div>
<div><br>
</div>
<div>It seems to run for me. Can you
check it?</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>
<p>Eric</p>
<p>(sorry if you received this for
a 2nd times, I have trouble
with my mail)<br>
</p>
<div>On 2021-10-26 4:35 p.m.,
Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Tue, Oct 26,
2021 at 1:35 PM Eric
Chamberland <<a href="mailto:Eric.Chamberland@giref.ulaval.ca" target="_blank">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>Here is a screenshot
of the partition I
hard coded (top) and
vertices/element
numbers (down):<br>
</p>
<p><img src="cid:17ce59a263aa83f4cb82" 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>
</div>
</blockquote>
<div><br>
</div>
<div>That might make it
easier to find a problem.</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>
<p> </p>
<p>Eric<br>
</p>
<div>On 2021-10-26 9:46
a.m., Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<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" target="_blank">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">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">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">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">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">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">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">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">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">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">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">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">https://www.cse.buffalo.edu/~knepley/</a><br>
</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">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">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>
</blockquote>
<pre cols="72">--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42</pre>
</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">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">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" 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>