<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Fri, Mar 2, 2018 at 3:22 PM, Danyang Su <span dir="ltr"><<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>></span> wrote:<br><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,<br>
</p>
I use the latest Fortran style in PETSc 3.8. Enclosed are the PETSc
configuration, code compiling log and the function that causes
compiling error. The compiling error happens after I include
petscsf.h in the following section. I didn't find petscsf.h in
petsc/finclude/ folder so I use the head file in the 'include'
folder and this seems not allowed.<br></div></blockquote><div><br></div><div>I apologize for taking so long. The PetscSF definitions are in</div><div><br></div><div><span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline">#include <petsc/finclude/petscis.h></span><br style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><br></div><div>You are correct that they should be moved out.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div><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">
#ifdef PETSC_V3_8_X<br>
<br>
#include <petsc/finclude/petscsys.h><br>
#include <petsc/finclude/petscdmplex.h><br>
#include <petsc/finclude/petscdmlabel.<wbr>h><br>
#include <petscsf.h><br>
use petscsys<br>
use petscdmplex<br>
use petscsf<br>
<br>
#endif<br>
<br>
Thanks,<br>
<br>
Danyang<br>
<br>
<br>
<div class="m_3637613153403909148moz-cite-prefix">On 18-03-02 12:08 PM, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Fri, Mar 2, 2018 at 3:00 PM,
Danyang Su <span dir="ltr"><<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>></span>
wrote:<br>
<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>On 18-03-02 10:58 AM, Matthew Knepley wrote:<br>
</p>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Fri, Mar 2, 2018 at
1:41 PM, Danyang Su <span dir="ltr"><<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>></span>
wrote:<br>
<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"> <br>
<div class="m_3637613153403909148gmail-m_-2214224469709245128gmail-m_-4654060630000521438moz-cite-prefix">On
18-02-19 03:30 PM, Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Mon, Feb
19, 2018 at 3:11 PM, Danyang Su <span dir="ltr"><<a href="mailto:danyang.su@gmail.com" target="_blank">danyang.su@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi
Matt,<br>
<br>
Would you please let me know how
to check if a cell is local owned?
When overlap is 0 in
DMPlexDistribute, all the cells
are local owned. How about overlap
> 0? It sounds like impossible
to check by node because a cell
can be local owned even if none of
the nodes in this cell is local
owned.<br>
</blockquote>
<div><br>
</div>
<div>If a cell is in the PetscSF,
then it is not locally owned. The
local nodes in the SF are sorted,
so I use</div>
<div>PetscFindInt (<a href="http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscFindInt.html" target="_blank">http://www.mcs.anl.gov/petsc/<wbr>petsc-current/docs/manualpages<wbr>/Sys/PetscFindInt.html</a>).</div>
</div>
</div>
</div>
</blockquote>
Hi Matt,<br>
<br>
Would you please give me a little more about
how to mark the ghost cells when overlap
> 0? What do you mean a cell is in the
PetscSF? I use PetscSFView to export the
graph (original mesh file pile.vtk) and it
exports all the cells, including the ghost
cells (PETScSFView.txt).<br>
</div>
</blockquote>
<div><br>
</div>
<div>Yes, I will send you some sample code when
I get time. The first problem is that you are
looking at a different PetscSF. This looks
like the</div>
<div>one returned by DMPlexDistribute(). This is
mapping the serial mesh to the parallel mesh.
You want</div>
<div><br>
</div>
<div> <a href="http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMGetPointSF.html" target="_blank">http://www.mcs.anl.gov/petsc<wbr>/petsc-current/docs/manualpage<wbr>s/DM/DMGetPointSF.html</a></div>
<div><br>
</div>
<div>Then you can look at</div>
<div><br>
</div>
<div> <a href="https://bitbucket.org/petsc/petsc/src/1788fc36644e622df8cb1a0de85676ccc5af0239/src/dm/impls/plex/plexsubmesh.c?at=master&fileviewer=file-view-default#plexsubmesh.c-683" target="_blank">https://bitbucket.org/petsc/<wbr>petsc/src/1788fc36644e622df8cb<wbr>1a0de85676ccc5af0239/src/dm/<wbr>impls/plex/plexsubmesh.c?at=<wbr>master&fileviewer=file-view-<wbr>default#plexsubmesh.c-683</a></div>
<div><br>
</div>
<div>I get the pointSF, get out the list of
leaves, and find points in it using
PetscFindInt()</div>
</div>
</div>
</div>
</blockquote>
Hi Matt,<br>
By using the local dm, I can get the PetscSF I want, as
shown below. Now I need to get the number of ghost cells
or local cells (here 4944) or number of leaves (here
825) for each processor. I try to use PetscSFGetGraph to
get number of leaves in Fortran. After including
"petscsf.h", I got compilation error saying "You need a
ISO C conforming compiler to use the glibc headers". Is
there any alternative way to do this? I do not need the
ghost-neighbor mapping, but just the number of local
owned cells.<br>
</div>
</blockquote>
<div><br>
</div>
<div>Also, make sure you are using the latest Fortran style
for PETSc:</div>
<div><br>
</div>
<div> <a href="http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/UsingFortran.html" target="_blank">http://www.mcs.anl.gov/<wbr>petsc/petsc-current/docs/<wbr>manualpages/Sys/UsingFortran.<wbr>html</a></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 bgcolor="#FFFFFF"> [0] Number of roots=11449,
leaves=825, remote ranks=1<br>
[0] 4944 <- (1,0)<br>
[0] 4945 <- (1,28)<br>
[0] 4946 <- (1,56)<br>
...<br>
[1] Number of roots=11695, leaves=538, remote ranks=1<br>
[1] 5056 <- (0,21)<br>
[1] 5057 <- (0,43)<br>
[1] 5058 <- (0,65)<br>
[1] 5059 <- (0,87)<br>
<br>
In file included from /usr/include/features.h:375:0,<br>
from /usr/include/stdio.h:28,<br>
from /home/dsu/Soft/PETSc/petsc-3.8<wbr>.3/include/petscsys.h:175,<br>
from /home/dsu/Soft/PETSc/petsc-3.8<wbr>.3/include/petscsf.h:7,<br>
from ../../solver/solver_ddmethod.F<wbr>90:4837:<br>
/usr/include/x86_64-linux-gnu/<wbr>sys/cdefs.h:30:3:
error: #error "You need a ISO C conforming compile\<br>
r to use the glibc headers"<br>
# error "You need a ISO C conforming compiler to use
the glibc headers"<br>
</div>
</blockquote>
<div><br>
</div>
<div>Can you send this to <a href="mailto:petsc-maint@mcs.anl.gov" target="_blank">petsc-maint@mcs.anl.gov</a>? It
looks like a build problem that can be fixed.</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 bgcolor="#FFFFFF"> Thanks,<br>
<br>
Danyang<br>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<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 bgcolor="#FFFFFF"> Thanks,<br>
<br>
Danyang <br>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<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>
Danyang<span class="m_3637613153403909148gmail-HOEnZb"><font color="#888888"><span class="m_3637613153403909148gmail-m_-2214224469709245128gmail-HOEnZb"><font color="#888888"><br>
</font></span></font></span></blockquote>
<span class="m_3637613153403909148gmail-HOEnZb"><font color="#888888"> <span class="m_3637613153403909148gmail-m_-2214224469709245128gmail-HOEnZb"><font color="#888888"> </font></span></font></span></div>
<span class="m_3637613153403909148gmail-HOEnZb"><font color="#888888"> <span class="m_3637613153403909148gmail-m_-2214224469709245128gmail-HOEnZb"><font color="#888888"> -- <br>
<div class="m_3637613153403909148gmail-m_-2214224469709245128gmail-m_-4654060630000521438gmail-m_-8557986044721592658gmail_signature">
<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.caam.rice.edu/%7Emk51/" target="_blank">https://www.cse.buffalo.edu/~k<wbr>nepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</font></span></font></span></div>
<span class="m_3637613153403909148gmail-HOEnZb"><font color="#888888"> </font></span></div>
<span class="m_3637613153403909148gmail-HOEnZb"><font color="#888888"> </font></span></blockquote>
<span class="m_3637613153403909148gmail-HOEnZb"><font color="#888888"> <br>
</font></span></div>
<span class="m_3637613153403909148gmail-HOEnZb"><font color="#888888"> </font></span></blockquote>
<span class="m_3637613153403909148gmail-HOEnZb"><font color="#888888">
</font></span></div>
<span class="m_3637613153403909148gmail-HOEnZb"><font color="#888888">
<br>
<br clear="all"><span class="HOEnZb"><font color="#888888">
<div><br>
</div>
-- <br>
<div class="m_3637613153403909148gmail-m_-2214224469709245128gmail_signature">
<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.caam.rice.edu/%7Emk51/" target="_blank">https://www.cse.buffalo.edu/~k<wbr>nepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</font></span></font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
<br>
</font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="m_3637613153403909148gmail_signature">
<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.caam.rice.edu/%7Emk51/" target="_blank">https://www.cse.buffalo.edu/~<wbr>knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</font></span></div>
</div>
</blockquote>
<br>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><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.caam.rice.edu/~mk51/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div>
</div></div>