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<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>
<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>
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