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<div class="moz-cite-prefix">On 19/03/14 02:14, Matthew Knepley
wrote:<br>
</div>
<blockquote
cite="mid:CAMYG4GmOFPrDZnha+bkXoRTj2Tye7ctu9ZrO0Abc=W+uMAm9zw@mail.gmail.com"
type="cite">
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charset=ISO-8859-1">
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<div class="gmail_extra">
<div class="gmail_quote"><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">hi, I'm
trying to use the DMPlexComputeCellGeometryFVM() function
from a fortran program, but when I compile and link it
complains:<br>
<br>
undefined reference to `dmplexcomputecellgeometryfvm_'<br>
<br>
I am running the 'next' branch of PETSc (having previously
tried the master branch) and configured with
--with-fortran-interfaces=1. At the top of my code I have
#include <finclude/petsc.h90>.<br>
<br>
I noticed the fortran interfaces to some other functions
(e.g. DMPlexCreateFromDAG) also seemed to be missing in
older versions (e.g. the 'maint' branch)- is this one
perhaps still to be added too?<br>
</blockquote>
<div><br>
</div>
<div>This is my fault. I will push it to 'next' today.</div>
</div>
</div>
</div>
</blockquote>
<br>
Thanks for doing that. I can access DMPlexComputeCellGeometryFVM()
from fortran now.<br>
<br>
However at runtime it is giving me a segfault- perhaps I am not
declaring the centroid and normal arrays properly? I also tried
declaring them as ordinary fortran arrays instead of pointers, but
that also segfaulted. It works OK when I call it from C. My fortran
code is below- any clues much appreciated. The error it gives is:<br>
<br>
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
Violation, probably memory access out of range<br>
[0]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger<br>
[0]PETSC ERROR: or see
<a class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a>[0]PETSC
ERROR: or try <a class="moz-txt-link-freetext" href="http://valgrind.org">http://valgrind.org</a> on G<br>
NU/linux and Apple Mac OS X to find memory corruption
errors
<br>
[0]PETSC ERROR: likely location of problem given in stack below<br>
[0]PETSC ERROR: --------------------- Stack Frames
------------------------------------<br>
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
available,<br>
[0]PETSC ERROR: INSTEAD the line number of the start of the
function<br>
[0]PETSC ERROR: is given.<br>
[0]PETSC ERROR: [0] F90Array1dAccess line 70
/home/acro018/software/PETSc/code/src/sys/f90-src/f90_cwrap.c<br>
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------<br>
[0]PETSC ERROR: Signal received<br>
[0]PETSC ERROR: See
<a class="moz-txt-link-freetext" href="http://http://www.mcs.anl.gov/petsc/documentation/faq.html">http://http://www.mcs.anl.gov/petsc/documentation/faq.html</a> for
trouble shooting.<br>
[0]PETSC ERROR: Petsc Development GIT revision:
v3.4.4-4938-g89a3bfc GIT Date: 2014-03-19 17:00:11 +0000<br>
[0]PETSC ERROR: testdag on a linux-gnu-c-opt named des108 by acro018
Thu Mar 20 13:22:15 2014<br>
[0]PETSC ERROR: Configure options --download-netcdf
--download-exodusii --with-hdf5-dir=/usr/lib --with-numpy-dir=<br>
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file<br>
<br>
- Adrian<br>
<br>
--<br>
program main<br>
<br>
! setting up 3-D DMPlex using DMPlexCreateFromDAG(),
DMPlexInterpolate() and<br>
! DMPlexComputeCellGeometryFVM()<br>
<br>
implicit none<br>
<br>
#include <finclude/petsc.h90><br>
<br>
DM :: dm, dmi<br>
PetscInt :: dim = 3<br>
PetscInt :: depth = 1<br>
PetscErrorCode :: ierr<br>
PetscInt, allocatable :: numPoints(:)<br>
PetscInt, allocatable :: coneSize(:)<br>
PetscInt, allocatable :: cones(:)<br>
PetscInt, allocatable :: coneOrientations(:)<br>
PetscScalar, allocatable :: vertexCoords(:)<br>
PetscReal :: vol<br>
PetscReal, pointer :: centroid(:), normal(:)<br>
PetscInt :: i<br>
<br>
numPoints = [12, 2]<br>
coneSize = [8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]<br>
cones = [2,5,4,3,6,7,8,9, 3,4,11,10,7,12,13,8]<br>
coneOrientations = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0]<br>
vertexCoords = [ &<br>
-0.5,0.0,0.0, 0.0,0.0,0.0, 0.0,1.0,0.0, -0.5,1.0,0.0, &<br>
-0.5,0.0,1.0, 0.0,0.0,1.0, 0.0,1.0,1.0, -0.5,1.0,1.0, &<br>
0.5,0.0,0.0, 0.5,1.0,0.0, 0.5,0.0,1.0, 0.5,1.0,1.0 ]<br>
<br>
call PetscInitialize(PETSC_NULL_CHARACTER,ierr); CHKERRQ(ierr)<br>
<br>
call DMPlexCreate(PETSC_COMM_WORLD, dm, ierr); CHKERRQ(ierr)<br>
call PetscObjectSetName(dm, "testplex", ierr); CHKERRQ(ierr)<br>
call DMPlexSetDimension(dm, dim, ierr); CHKERRQ(ierr)<br>
<br>
call DMPlexCreateFromDAG(dm, depth, numPoints, coneSize, cones,
&<br>
coneOrientations, vertexCoords, ierr); CHKERRQ(ierr)<br>
<br>
call DMPlexInterpolate(dm, dmi, ierr); CHKERRQ(ierr)<br>
call DMPlexCopyCoordinates(dm, dmi, ierr); CHKERRQ(ierr)<br>
call DMDestroy(dm, ierr); CHKERRQ(ierr)<br>
dm = dmi<br>
<br>
call DMView(dm, PETSC_VIEWER_STDOUT_WORLD, ierr); CHKERRQ(ierr)<br>
<br>
do i = 0, 1<br>
call DMPlexComputeCellGeometryFVM(dm, i, vol, centroid, normal,
ierr)<br>
CHKERRQ(ierr)<br>
write(*, '(a, i2, a, f8.4, a, 3(f8.4, 1x))'), &<br>
'cell:', i, 'volume:', vol, 'centroid:', centroid(1),
centroid(2), centroid(3)<br>
end do<br>
<br>
call DMDestroy(dm, ierr); CHKERRQ(ierr)<br>
call PetscFinalize(ierr); CHKERRQ(ierr)<br>
deallocate(numPoints, coneSize, cones, coneOrientations,
vertexCoords)<br>
<br>
end program main<br>
<br>
<pre class="moz-signature" cols="72">--
Dr Adrian Croucher
Department of Engineering Science
University of Auckland
New Zealand
tel 64-9-373-7599 ext 84611
</pre>
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