<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<p>Hi Matt,</p>
<p>To test the Segmentation Violation problem in my code, I modified
the example ex1f90.F to reproduce the problem I have in my own
code. <br>
</p>
<p>If use DMPlexCreateBoxMesh to generate the mesh, the code works
fine. However, if I use DMPlexCreateGmshFromFile, using the same
mesh exported from "DMPlexCreateBoxMesh", it gives Segmentation
Violation error.</p>
<p>Did I miss something in the input mesh file? My first guess is
the label "marker" used in the code, but I couldn't find any place
to set this label.</p>
<p>Would you please let me know how to solve this problem. My code
is done in a similar way as ex1f90, it reads mesh from external
file or creates from cell list, distributes the mesh (these
already work), and then creates sections and sets ndof to the
nodes.</p>
<p>Thanks,</p>
<p>Danyang<br>
</p>
<br>
<div class="moz-cite-prefix">On 18-02-20 10:07 AM, Danyang Su wrote:<br>
</div>
<blockquote type="cite"
cite="mid:f7ad951f-4c94-b549-80d0-508f0cc9315d@gmail.com">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
On 18-02-20 09:52 AM, Matthew Knepley wrote:<br>
<blockquote type="cite"
cite="mid:CAMYG4GknBNzGcKs-SuUwp_CEVPXB7n65DZbOrLWFjjA9iMTx9g@mail.gmail.com">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Tue, Feb 20, 2018 at 12:30 PM,
Danyang Su <span dir="ltr"><<a
href="mailto:danyang.su@gmail.com" target="_blank"
moz-do-not-send="true">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>Hi All,</p>
<p>I tried to compile the DMPlexCreateSection code but
got error information as shown below.<br>
</p>
<p>Error: Symbol 'petsc_null_is' at (1) has no
IMPLICIT type</p>
<p>I tried to use PETSC_NULL_OBJECT instead of
PETSC_NULL_IS, then the code can be compiled but run
into Segmentation Violation error in
DMPlexCreateSection.<br>
</p>
</div>
</blockquote>
<div>From the webpage</div>
<div><br>
</div>
<div> <a
href="http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DMPLEX/DMPlexCreateSection.html"
moz-do-not-send="true">http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DMPLEX/DMPlexCreateSection.html</a> <br>
</div>
<div><br>
</div>
<div>The F90 version is DMPlexCreateSectionF90. Doing this
with F77 arrays would have been too painful.</div>
</div>
</div>
</div>
</blockquote>
Hi Matt,<br>
<br>
Sorry, I still cannot compile the code if use
DMPlexCreateSectionF90 instead of DMPlexCreateSection. Would you
please tell me in more details? <br>
<br>
undefined reference to `dmplexcreatesectionf90_'<br>
<br>
then I #include <petsc/finclude/petscdmplex.h90>, but this
throws more error during compilation.<br>
<br>
<br>
Included at
/home/dsu/Soft/PETSc/petsc-3.7.5/include/petsc/finclude/petscdmplex.h90:6:<br>
Included at ../../solver/solver_ddmethod.F90:62:<br>
<br>
PETSCSECTION_HIDE section<br>
1<br>
Error: Unclassifiable statement at (1)<br>
/home/dsu/Soft/PETSc/petsc-3.7.5/include/petsc/finclude/ftn-custom/petscdmplex.h90:167.10:<br>
Included at
/home/dsu/Soft/PETSc/petsc-3.7.5/include/petsc/finclude/petscdmplex.h90:6:<br>
Included at ../../solver/solver_ddmethod.F90:62:<br>
<br>
PETSCSECTION_HIDE section<br>
1<br>
Error: Unclassifiable statement at (1)<br>
/home/dsu/Soft/PETSc/petsc-3.7.5/include/petsc/finclude/ftn-custom/petscdmplex.h90:179.10:<br>
Included at
/home/dsu/Soft/PETSc/petsc-3.7.5/include/petsc/finclude/petscdmplex.h90:6:<br>
Included at ../../solver/solver_ddmethod.F90:62:<br>
<br>
<blockquote type="cite"
cite="mid:CAMYG4GknBNzGcKs-SuUwp_CEVPXB7n65DZbOrLWFjjA9iMTx9g@mail.gmail.com">
<div dir="ltr">
<div class="gmail_extra">
<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> </p>
<p>dmda_flow%da is distributed dm object that works
fine. </p>
<p>The fortran example I follow is <a
class="gmail-m_8962138310016109093moz-txt-link-freetext"
href="http://www.mcs.anl.gov/petsc/petsc-dev/src/dm/impls/plex/examples/tutorials/ex1f90.F90"
target="_blank" moz-do-not-send="true">http://www.mcs.anl.gov/petsc/<wbr>petsc-dev/src/dm/impls/plex/<wbr>examples/tutorials/ex1f90.F90</a>.
<br>
</p>
<p>What parameters should I use if passing null to
bcField, bcComps, bcPoints and perm.<br>
</p>
<pre style="color:rgb(0,0,0);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;word-spacing:0px;text-decoration-style:initial;text-decoration-color:initial"><a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscErrorCode.html#PetscErrorCode" target="_blank" moz-do-not-send="true">PetscErrorCode</a> <a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/DMPLEX/DMPlexCreateSection.html#DMPlexCreateSection" target="_blank" moz-do-not-send="true">DMPlexCreateSection</a>(<a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/DM/DM.html#DM" target="_blank" moz-do-not-send="true">DM</a> dm, <a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscInt.html#PetscInt" target="_blank" moz-do-not-send="true">PetscInt</a> dim, <a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscInt.html#PetscInt" target="_blank" moz-do-not-send="true">PetscInt</a> numFields,const <a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscInt.html#PetscInt" target="_blank" moz-do-not-send="true">PetscInt</a> numComp[],const <a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscInt.html#PetscInt" target="_blank" moz-do-not-send="true">PetscInt</a> numDof[], <a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscInt.html#PetscInt" target="_blank" moz-do-not-send="true">PetscInt</a> numBC,const <a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/Vec/PetscInt.html#PetscInt" target="_blank" moz-do-not-send="true">PetscInt</a> bcField[],
const <a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/IS/IS.html#IS" target="_blank" moz-do-not-send="true">IS</a> bcComps[], const <a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/IS/IS.html#IS" target="_blank" moz-do-not-send="true">IS</a> bcPoints[], <a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/IS/IS.html#IS" target="_blank" moz-do-not-send="true">IS</a> perm, <a href="https://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/IS/PetscSection.html#PetscSection" target="_blank" moz-do-not-send="true">PetscSection</a> *section)
</pre>
<p>#include <petsc/finclude/petscis.h><br>
#include <petsc/finclude/petscis.h90><br>
#include <petsc/finclude/petscdmplex.h></p>
<p>...<br>
</p>
<p>#ifdef USG<br>
numFields = 1<br>
numComp(1) = 1<br>
pNumComp => numComp<br>
<br>
do i = 1, numFields*(dmda_flow%dim+1)<br>
numDof(i) = 0<br>
end do<br>
numDof(0*(dmda_flow%dim+1)+1) =
dmda_flow%dof<br>
pNumDof => numDof<br>
<br>
numBC = 0<br>
<br>
call DMPlexCreateSection(dmda_flow%<wbr>da,dmda_flow%dim,
&<br>
<wbr>
numFields,pNumComp,pNumDof, <wbr>
&<br>
<wbr>
numBC,PETSC_NULL_INTEGER, <wbr>
&<br>
<wbr>
PETSC_NULL_IS,PETSC_NULL_IS, <wbr>
& !Error here<br>
<wbr>
PETSC_NULL_IS,section,ierr)<br>
CHKERRQ(ierr)<br>
<br>
call PetscSectionSetFieldName(<wbr>section,0,'flow',ierr)<br>
CHKERRQ(ierr)<br>
<br>
call DMSetDefaultSection(dmda_flow%<wbr>da,section,ierr)<br>
CHKERRQ(ierr)<br>
<br>
call PetscSectionDestroy(section,<wbr>ierr)<br>
CHKERRQ(ierr)<br>
#endif</p>
<p>Thanks,</p>
<p>Danyang<br>
</p>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="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/%7Emk51/"
target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
</blockquote>
<br>
</body>
</html>