On 18-11-29 06:13 PM, Matthew Knepley wrote:
On Thu, Nov 29, 2018 at 7:40 PM Danyang Su via petsc-maint
<petsc-ma...@mcs.anl.gov <mailto:petsc-ma...@mcs.anl.gov>> wrote:
Dear PETSc developers & users,
Sorry to bother you again. I just encounter some difficulties in
DMPlex
global to natural order. This is not the very necessary function
in my
code. But it's best to have it in case someone wants to feed code
with
initial conditions or parameters from external file using natural
ordering.
First I tried to use DmPlexGetVertexNumbering which seems pretty
straightforward, but I always get error saying "You need a ISO C
conforming compiler to use the glibc headers". I use Gfortran on
Linux.
Then I switched to use Label to save global-natural order before
distributing the mesh, everything works fine. The only problem is
that
it takes a very long time during mesh distribution when the size
of mesh
is very big.
Finally I tried to use GlobalToNatural ordering. Set Natural order to
TRUE before calling DMPlexDistribute and then call
DMPlexSetMigrationSF.
However, the function DMPlexGlobalToNaturalEnd seems doing nothing as
the returned vector is always unchanged. I got some help from Josh
who
has done similar work before. But I still cannot figure out what is
wrong in the code.
Can you run the example that Blaise recommended? Sometimes its easiest
to start
with an example and change it into your code.
I cannot compile ex26 due to missing exodusII.h file. Error information is
make ex26
/home/dsu/Soft/PETSc/petsc-3.10.2/linux-gnu-dbg/bin/mpicc -o ex26.o -c
-Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
-fstack-protector -fvisibility=hidden -g3
-I/home/dsu/Soft/PETSc/petsc-3.10.2/include
-I/home/dsu/Soft/PETSc/petsc-3.10.2/linux-gnu-dbg/include `pwd`/ex26.c
/home/dsu/Soft/PETSc/petsc-3.10.2/src/dm/impls/plex/examples/tests/ex26.c:10:22:
fatal error: exodusII.h: No such file or directory
compilation terminated.
/home/dsu/Soft/PETSc/petsc-3.10.2/lib/petsc/conf/rules:359: recipe for
target 'ex26.o' failed
Anyway, I will look at this example to get familiar with GlobalToNatural
related functions.
Thanks,
Danyang
Thanks,
Matt
Attached is the code section with related functions included,
together
with a mesh and output of global vector and natural vector. If
something
is wrong in the code, it should be in these four functions. The
related
functions are called in the following order.
call solver_dd_create_dmplex
call solver_dd_mapping_set_dmplex
call solver_dd_DMDACreate_flow
!call solver_dd_DMDACreate_react Not used in current testing
call solver_dd_mapping_global_natural
I really appreciate your help.
Regards,
Danyang
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which
their experiments lead.
-- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/
<http://www.cse.buffalo.edu/%7Eknepley/>
