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On 2018-12-04 12:37 p.m., Danyang Su wrote:<br>
<blockquote type="cite"
cite="mid:f6185468-b551-61f6-d533-670ae45c2cce@gmail.com">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<div class="moz-cite-prefix">On 2018-12-04 11:06 a.m., Matthew
Knepley wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAMYG4GkGUBE6P0pnd6LOF28zzuPtDFcRKYZ-xm_Ec_x3g+AdUQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html;
charset=UTF-8">
<div dir="ltr">
<div class="gmail_quote">
<div dir="ltr">On Mon, Dec 3, 2018 at 8:32 PM Danyang Su
<<a href="mailto:danyang.su@gmail.com"
moz-do-not-send="true">danyang.su@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0

.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p>Hi Matt,</p>
<p>Attached is the test example with source code,
makefile, data and screen output I wrote this
afternoon. This example reads 2D mesh from vtk file
and then distribute over all processors. I can get
correct global order of local nodes after
distribution, but the natural order of local nodes is
always zero after using
DMPlexGlobalToNaturalBegin/End(). Sounds like it does
not take effect. <br>
</p>
<p>Would you mind helping me to check/test this code at
you most convenience?</p>
</div>
</blockquote>
<div>On 2 procs, I get an SEGV</div>
<div><br>
</div>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">rank<span
class="gmail-Apple-converted-space"> </span>1 local
nodes with ghost <span
class="gmail-Apple-converted-space"> </span>47 local
cells with ghost <span
class="gmail-Apple-converted-space"> </span>75</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">rank<span
class="gmail-Apple-converted-space"> </span>0 local
nodes with ghost <span
class="gmail-Apple-converted-space"> </span>52 local
cells with ghost <span
class="gmail-Apple-converted-space"> </span>78</p>
</div>
</div>
</blockquote>
<p>Interesting. The output on your side is different. On my
computer, run the code with 2 processors, I get <br>
</p>
<p>rank 0 local nodes with ghost 47 local cells with ghost
76<br>
rank 1 local nodes with ghost 49 local cells with ghost
74</p>
<p>and there is no error. I can run this example using 1 to 5
processors without error. With 6 or more processors, it returns
some error as shown below. <br>
</p>
<p>Error in `./natural': corrupted size vs. prev_size:
0x0000000001b9a600<br>
</p>
<p>This seems reasonable if the mesh is too small with overlap =
1.<br>
</p>
<p>The version I use is</p>
<p>Petsc Development GIT revision: v3.10.2-832-ge28ad50 GIT Date:
2018-12-02 07:18:52 +0100</p>
<p>Configure options --with-cc=gcc --with-cxx=g++
--with-fc=gfortran --download-mpich --download-scalapack
--download-parmetis --download-metis --download-ptscotch
--download-fblaslapack --download-hypre --download-superlu_dist
--download-hdf5=yes --download-ctetgen --download-zlib
--download-netcdf --download-pnetcdf --download-exodusii
--download-netcdf --with-debugging=1</p>
</blockquote>
Hi Matt,
<p>Attached is a modified one without using
DMPlexGetVertexNumbering. This one set the global vector to one
instead and test the returned global vector with natural order. It
is supposed to return one after DMPlexGlobalToNaturalBegin/End().
However, the returned vector is zero. The example has been tested
using both 3.10.2 and develop version with up to 20 processors
without error.</p>
<p>Thanks,</p>
<p>Danyang</p>
<blockquote type="cite"
cite="mid:f6185468-b551-61f6-d533-670ae45c2cce@gmail.com">
<p>Thanks,</p>
<p>Danyang<br>
</p>
<blockquote type="cite"
cite="mid:CAMYG4GkGUBE6P0pnd6LOF28zzuPtDFcRKYZ-xm_Ec_x3g+AdUQ@mail.gmail.com">
<div dir="ltr">
<div class="gmail_quote">
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR:
------------------------------------------------------------------------</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: Caught signal number 11 SEGV: Segmentation
Violation, probably memory access out of range</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: Try option -start_in_debugger or
-on_error_attach_debugger</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: or see <a
href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind"
moz-do-not-send="true">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a></p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: or try <a href="http://valgrind.org"
moz-do-not-send="true">http://valgrind.org</a> on
GNU/linux and Apple Mac OS X to find memory corruption
errors</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: likely location of problem given in stack below</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: ---------------------<span
class="gmail-Apple-converted-space"> </span>Stack
Frames ------------------------------------</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: Note: The EXACT line numbers in the stack are not
available,</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: <span class="gmail-Apple-converted-space"> </span>INSTEAD
the line number of the start of the function</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: <span class="gmail-Apple-converted-space"> </span>is
given.</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: --------------------- Error Message
--------------------------------------------------------------</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: Signal received</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: See <a
href="http://www.mcs.anl.gov/petsc/documentation/faq.html"
moz-do-not-send="true">http://www.mcs.anl.gov/petsc/documentation/faq.html</a>
for trouble shooting.</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: Petsc Development GIT revision:
v3.9.3-1021-g8625415<span
class="gmail-Apple-converted-space"> </span>GIT Date:
2018-08-02 12:57:14 -0500</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: Unknown Name on a arch-master-debug named
MATTHEW-KNEPLEYs-MacBook-Air-2.local by knepley Tue Dec<span
class="gmail-Apple-converted-space"> </span>4 14:00:46
2018</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: Configure options --PETSC_ARCH=arch-master-debug
--download-chaco
--download-cmake=/Users/knepley/Downloads/cmake-3.7.2.tar.gz
--download-ctetgen --download-eigen --download-fftw
--download-hdf5 --download-med --download-metis
--download-mpich --download-netcdf --download-p4est
--download-parmetis --download-pnetcdf
--download-superlu_dist --download-triangle
--with-cc="/Users/knepley/MacSoftware/bin/ccache gcc
-Qunused-arguments"
--with-cxx="/Users/knepley/MacSoftware/bin/ccache g++
-Qunused-arguments"
--with-fc="/Users/knepley/MacSoftware/bin/ccache gfortran"
--with-shared-libraries</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[1]PETSC
ERROR: #1 User provided function() line 0 in<span
class="gmail-Apple-converted-space"> </span>unknown
file</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: application called MPI_Abort(MPI_COMM_WORLD, 59) -
process 1</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">------------------------------------------------------------------------</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: Caught signal number 11 SEGV: Segmentation
Violation, probably memory access out of range</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: Try option -start_in_debugger or
-on_error_attach_debugger</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: or see <a
href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind"
moz-do-not-send="true">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a></p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: or try <a href="http://valgrind.org"
moz-do-not-send="true">http://valgrind.org</a> on
GNU/linux and Apple Mac OS X to find memory corruption
errors</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: likely location of problem given in stack below</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: ---------------------<span
class="gmail-Apple-converted-space"> </span>Stack
Frames ------------------------------------</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: Note: The EXACT line numbers in the stack are not
available,</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: <span class="gmail-Apple-converted-space"> </span>INSTEAD
the line number of the start of the function</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: <span class="gmail-Apple-converted-space"> </span>is
given.</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: --------------------- Error Message
--------------------------------------------------------------</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: Signal received</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: See <a
href="http://www.mcs.anl.gov/petsc/documentation/faq.html"
moz-do-not-send="true">http://www.mcs.anl.gov/petsc/documentation/faq.html</a>
for trouble shooting.</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: Petsc Development GIT revision:
v3.9.3-1021-g8625415<span
class="gmail-Apple-converted-space"> </span>GIT Date:
2018-08-02 12:57:14 -0500</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: Unknown Name on a arch-master-debug named
MATTHEW-KNEPLEYs-MacBook-Air-2.local by knepley Tue Dec<span
class="gmail-Apple-converted-space"> </span>4 14:00:46
2018</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: Configure options --PETSC_ARCH=arch-master-debug
--download-chaco
--download-cmake=/Users/knepley/Downloads/cmake-3.7.2.tar.gz
--download-ctetgen --download-eigen --download-fftw
--download-hdf5 --download-med --download-metis
--download-mpich --download-netcdf --download-p4est
--download-parmetis --download-pnetcdf
--download-superlu_dist --download-triangle
--with-cc="/Users/knepley/MacSoftware/bin/ccache gcc
-Qunused-arguments"
--with-cxx="/Users/knepley/MacSoftware/bin/ccache g++
-Qunused-arguments"
--with-fc="/Users/knepley/MacSoftware/bin/ccache gfortran"
--with-shared-libraries</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">[0]PETSC
ERROR: #1 User provided function() line 0 in<span
class="gmail-Apple-converted-space"> </span>unknown
file</p>
<div><span style="font-family:Menlo;font-size:11px">application
called MPI_Abort(MPI_COMM_WORLD, 59) - process 0</span></div>
<div><br>
</div>
<div>which valgrind says comes from DMPlexCreateSection()</div>
<div><br>
</div>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">rank<span
class="gmail-Apple-converted-space"> </span>0 local
nodes with ghost <span
class="gmail-Apple-converted-space"> </span>52 local
cells with ghost <span
class="gmail-Apple-converted-space"> </span>78</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">rank<span
class="gmail-Apple-converted-space"> </span>1 local
nodes with ghost <span
class="gmail-Apple-converted-space"> </span>47 local
cells with ghost <span
class="gmail-Apple-converted-space"> </span>75</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">==14766==
Invalid write of size 4</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">==14766==<span
class="gmail-Apple-converted-space"> </span>at
0x1151A3B: dmplexcreatesection_ (zplexsectionf90.c:20)</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">==14766==<span
class="gmail-Apple-converted-space"> </span>by
0x1000042FA: MAIN__ (in ./natural)</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">==14766==<span
class="gmail-Apple-converted-space"> </span>by
0x10000497D: main (in ./natural)</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">==14766==<span
class="gmail-Apple-converted-space"> </span>Address
0x600001000 is not stack'd, malloc'd or (recently) free'd</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">==14766==<span
class="gmail-Apple-converted-space"> </span></p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">==14767==
Invalid write of size 4</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">==14767==<span
class="gmail-Apple-converted-space"> </span>at
0x1151A3B: dmplexcreatesection_ (zplexsectionf90.c:20)</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">==14767==<span
class="gmail-Apple-converted-space"> </span>by
0x1000042FA: MAIN__ (in ./natural)</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">==14767==<span
class="gmail-Apple-converted-space"> </span>by
0x10000497D: main (in ./natural)</p>
<p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">==14767==<span
class="gmail-Apple-converted-space"> </span>Address
0x600001000 is not stack'd, malloc'd or (recently) free'd</p>
<div><span style="font-family:Menlo;font-size:11px">==14767==</span><span
class="gmail-Apple-converted-space"
style="font-family:Menlo;font-size:11px"> </span></div>
<div><br>
</div>
<div>I cannot run the debugger on it because command line
arguments are not working with</div>
<div>my Fortran compiler (Ugh). Do you see this error?</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt </div>
<blockquote class="gmail_quote" style="margin:0 0 0

.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p>Thanks,</p>
<p>Danyang<br>
</p>
<div class="m_8975814135343234898moz-cite-prefix">On
2018-12-03 1:12 p.m., Danyang Su wrote:<br>
</div>
<blockquote type="cite">
<p><br>
</p>
<div class="m_8975814135343234898moz-cite-prefix">On
2018-12-03 12:56 p.m., Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">
<div class="gmail_quote">
<div dir="ltr">On Mon, Dec 3, 2018 at 3:40 PM
Danyang Su <<a
href="mailto:danyang.su@gmail.com"
target="_blank" moz-do-not-send="true">danyang.su@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 bgcolor="#FFFFFF">
<p><br>
</p>
<div
class="m_8975814135343234898gmail-m_397419241377719570moz-cite-prefix">On
2018-12-03 12:03 p.m., Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_quote">
<div dir="ltr">On Mon, Dec 3, 2018
at 2:27 PM Danyang Su <<a
href="mailto:danyang.su@gmail.com"
target="_blank"
moz-do-not-send="true">danyang.su@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 bgcolor="#FFFFFF">
<p>Hi Matt,</p>
<p>Thanks. <br>
</p>
<p>BTW: DmPlexGetVertexNumbering
now can work using the latest
develop version. But the index
is not in natural ordering
when DMSetUseNatural is
called. That's why I want to
use PetscSFDistributeSection
to check if I miss anything in
the code.</p>
</div>
</blockquote>
<div>Can you explain that a little
more? Maybe you can just push
forward what you want using the
migrationSF.</div>
</div>
</div>
</blockquote>
<p>Hi Matt,</p>
<p>Since I cannot figure what is wrong or
missing in my code, I followed an old
ex26.c example in
src/dm/impls/plex/examples/tests to
create similar code as shown below to
test global to natural ordering. The
code may be ugly with unnecessary
functions in it. Using
DmPlexGetVertexNumbering, I can get the
value but it is not in natural order,
instead, it is still in default PETSc
order without calling
DMSetUseNatural(dm,PETSC_TRUE,ierr).</p>
</div>
</blockquote>
<div>I do not understand what you are doing
below. You just need to call</div>
<div><br>
</div>
<div>
<div> ierr =
DMSetUseNatural(dm,PETSC_TRUE);CHKERRQ(ierr);</div>
<div> ierr =
DMPlexDistribute(dm,0,&migrationSF,&pdm);CHKERRQ(ierr);<br>
</div>
<div> if (pdm) {</div>
<div> ierr =
DMPlexSetMigrationSF(pdm,migrationSF);CHKERRQ(ierr);</div>
</div>
<div> }</div>
<div> </div>
<div>and the DMGlobalToNaturalBegin/End()
should work.</div>
</div>
</div>
</div>
</blockquote>
<p>You mean to use DMPlexGlobalToNaturalBegin/End(),
right? That's what I tried at first, but without
success.</p>
<p>I will create a test example to make further check
if I can reproduce the problem. <br>
</p>
<p>Thanks,</p>
<p>Danyang<br>
</p>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">
<div class="gmail_quote">
<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 bgcolor="#FFFFFF">
<p> if (rank == 0) then</p>
call
DMPlexCreateFromCellList(Petsc_Comm_World,ndim,num_cells,
num_nodes,num_nodes_per_cell, &<br>
Petsc_False,dmplex_cells,ndim,
dmplex_verts,dm,ierr)<br>
CHKERRQ(ierr)<br>
else<br>
call
DMPlexCreateFromCellList(Petsc_Comm_World,ndim,0,
0,num_nodes_per_cell, &<br>
Petsc_False,dmplex_cells,ndim,dmplex_verts,dm,ierr)<br>
CHKERRQ(ierr)<br>
end if<br>
<br>
if (nprocs > 1) then<br>
call
DMSetUseNatural(dm,PETSC_TRUE,ierr)<br>
CHKERRQ(ierr)<br>
end if<br>
<br>
call
DMPlexDistribute(dm,stencil_width,
&<br>
migrationsf,distributedMesh,ierr)<br>
CHKERRQ(ierr)<br>
<br>
if (distributedMesh /=
PETSC_NULL_DM) then<br>
call
PetscSFCreateInverseSF(migrationsf,migrationsf_inv,ierr)<br>
CHKERRQ(ierr)<br>
<br>
call
DMCreateGlobalToNatural(distributedMesh,migrationsf,migrationsf_inv,ierr)<br>
CHKERRQ(ierr)<br>
<br>
call
DMGetSection(distributedMesh,section,ierr)<br>
CHKERRQ(ierr)<br>
<br>
call
PetscSectionCreate(Petsc_Comm_World,section_seq,ierr)<br>
CHKERRQ(ierr)<br>
<br>
call
PetscSFDistributeSection(migrationsf_inv,section,
&<br>
PETSC_NULL_INTEGER,section_seq,ierr)<br>
CHKERRQ(ierr)<br>
<br>
call
DMPlexCreateGlobalToNaturalSF(distributedMesh,
&<br>
section_seq,migrationsf,sf_natural,ierr)<br>
CHKERRQ(ierr)<br>
<br>
call
DMSetUseNatural(distributedMesh,PETSC_TRUE,ierr)<br>
CHKERRQ(ierr)<br>
<br>
call
PetscSFDestroy(migrationsf,ierr)<br>
CHKERRQ(ierr)<br>
<br>
call
PetscSFDestroy(migrationsf_inv,ierr)<br>
CHKERRQ(ierr)<br>
<p> end if</p>
<p>Thanks,</p>
<p>Danyang<br>
</p>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_quote">
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt <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 bgcolor="#FFFFFF">
<p>Regards,</p>
<p>Danyang<br>
</p>
<div
class="m_8975814135343234898gmail-m_397419241377719570m_-4663990655342689142moz-cite-prefix">On
2018-12-03 5:22 a.m., Matthew
Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">I need to write
a custom Fortran stub for
this one. I will get it done
as soon as possible.
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Sat, Dec
1, 2018 at 7:16 PM Danyang
Su via petsc-users <<a
href="mailto:petsc-users@mcs.anl.gov" target="_blank"
moz-do-not-send="true">petsc-users@mcs.anl.gov</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">Hi
All,<br>
<br>
I got a simple compilation
error when use
PetscSFDistributeSection
in <br>
Fortran. It looks like the
required head files are
included and the <br>
parameters are correctly
defined. However, when
compile the code, I got <br>
error undefined reference
to
`petscsfdistributesection_'.
The code is <br>
shown below. Did I miss
anything here?<br>
<br>
#include
<petsc/finclude/petscsys.h><br>
#include
<petsc/finclude/petscvec.h><br>
#include
<petsc/finclude/petscdm.h><br>
#include
<petsc/finclude/petscdmplex.h><br>
use petscsys<br>
use petscvec<br>
use petscdm<br>
use petscdmplex<br>
<br>
implicit none<br>
<br>
PetscSection ::
section, section_seq<br>
PetscSF ::
migrationsf_inv,
sf_natural<br>
Vec :: vec_global,
vec_natural<br>
PetscErrorCode ::
ierr<br>
<br>
...<br>
<br>
call
PetscSFDistributeSection(migrationsf_inv,section,
&<br>
PETSC_NULL_INTEGER,section_seq,ierr)<br>
CHKERRQ(ierr)<br>
<br>
<br>
call
PetscSFDistributeSection(migrationsf_inv,section,
&<br>
PETSC_NULL_INTEGER,section_seq,ierr)<br>
CHKERRQ(ierr)<br>
<br>
Thanks,<br>
<br>
Danyang<br>
<br>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr"
class="m_8975814135343234898gmail-m_397419241377719570m_-4663990655342689142gmail_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>
</blockquote>
</div>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr"
class="m_8975814135343234898gmail-m_397419241377719570gmail_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>
</div>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr"
class="m_8975814135343234898gmail_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>
</div>
</blockquote>
</blockquote>
</div>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr" class="gmail_signature"
data-smartmail="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>
</blockquote>
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