<html>
<head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 18-03-04 08:08 AM, Matthew Knepley
wrote:<br>
</div>
<blockquote
cite="mid:CAMYG4G=V0QYNdByAPO6kR5UpYCjmj72e2zBqrJO_5myUK1DQew@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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">
</div>
</div>
</div>
</div>
</blockquote>
Hi Matt,<br>
<br>
After including <br>
#include <petsc/finclude/petscis.h><br>
use petscis<br>
<br>
I still get error saying undefined reference to `petscsfgetgraph_'<br>
<br>
Did I miss any other head file?<br>
<br>
Thanks,<br>
<br>
Danyang<br>
<blockquote
cite="mid:CAMYG4G=V0QYNdByAPO6kR5UpYCjmj72e2zBqrJO_5myUK1DQew@mail.gmail.com"
type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<div><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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="http://www.caam.rice.edu/%7Emk51/"
target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
</body>
</html>