[petsc-users] [petsc-maint] Fwd: DMPlex global to natural problem using DmPlexGetVertexNumbering or DMPlexGlobalToNatural

[Danyang Su]

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-maint at mcs.anl.gov <mailto:petsc-maint at 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/>

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