[petsc-users] how to check if cell is local owned in DMPlex
Danyang Su
danyang.su at gmail.com
Fri Mar 2 14:22:46 CST 2018
Hi Matt,
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.
#ifdef PETSC_V3_8_X
#include <petsc/finclude/petscsys.h>
#include <petsc/finclude/petscdmplex.h>
#include <petsc/finclude/petscdmlabel.h>
#include <petscsf.h>
use petscsys
use petscdmplex
use petscsf
#endif
Thanks,
Danyang
On 18-03-02 12:08 PM, Matthew Knepley wrote:
> On Fri, Mar 2, 2018 at 3:00 PM, Danyang Su <danyang.su at gmail.com
> <mailto:danyang.su at gmail.com>> wrote:
>
> On 18-03-02 10:58 AM, Matthew Knepley wrote:
>
>> On Fri, Mar 2, 2018 at 1:41 PM, Danyang Su <danyang.su at gmail.com
>> <mailto:danyang.su at gmail.com>> wrote:
>>
>>
>> On 18-02-19 03:30 PM, Matthew Knepley wrote:
>>> On Mon, Feb 19, 2018 at 3:11 PM, Danyang Su
>>> <danyang.su at gmail.com <mailto:danyang.su at gmail.com>> wrote:
>>>
>>> Hi Matt,
>>>
>>> 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.
>>>
>>>
>>> If a cell is in the PetscSF, then it is not locally owned.
>>> The local nodes in the SF are sorted, so I use
>>> PetscFindInt
>>> (http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscFindInt.html
>>> <http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscFindInt.html>).
>> Hi Matt,
>>
>> 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).
>>
>>
>> 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
>> one returned by DMPlexDistribute(). This is mapping the serial
>> mesh to the parallel mesh. You want
>>
>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMGetPointSF.html
>> <http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMGetPointSF.html>
>>
>> Then you can look at
>>
>> https://bitbucket.org/petsc/petsc/src/1788fc36644e622df8cb1a0de85676ccc5af0239/src/dm/impls/plex/plexsubmesh.c?at=master&fileviewer=file-view-default#plexsubmesh.c-683
>> <https://bitbucket.org/petsc/petsc/src/1788fc36644e622df8cb1a0de85676ccc5af0239/src/dm/impls/plex/plexsubmesh.c?at=master&fileviewer=file-view-default#plexsubmesh.c-683>
>>
>> I get the pointSF, get out the list of leaves, and find points in
>> it using PetscFindInt()
> Hi Matt,
> 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.
>
>
> Also, make sure you are using the latest Fortran style for PETSc:
>
> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/UsingFortran.html
>
> [0] Number of roots=11449, leaves=825, remote ranks=1
> [0] 4944 <- (1,0)
> [0] 4945 <- (1,28)
> [0] 4946 <- (1,56)
> ...
> [1] Number of roots=11695, leaves=538, remote ranks=1
> [1] 5056 <- (0,21)
> [1] 5057 <- (0,43)
> [1] 5058 <- (0,65)
> [1] 5059 <- (0,87)
>
> In file included from /usr/include/features.h:375:0,
> from /usr/include/stdio.h:28,
> from
> /home/dsu/Soft/PETSc/petsc-3.8.3/include/petscsys.h:175,
> from
> /home/dsu/Soft/PETSc/petsc-3.8.3/include/petscsf.h:7,
> from ../../solver/solver_ddmethod.F90:4837:
> /usr/include/x86_64-linux-gnu/sys/cdefs.h:30:3: error: #error "You
> need a ISO C conforming compile\
> r to use the glibc headers"
> # error "You need a ISO C conforming compiler to use the glibc
> headers"
>
>
> Can you send this to petsc-maint at mcs.anl.gov
> <mailto:petsc-maint at mcs.anl.gov>? It looks like a build problem that
> can be fixed.
>
> Thanks,
>
> Matt
>
> Thanks,
>
> Danyang
>>
>> Thanks,
>>
>> Matt
>>
>> Thanks,
>>
>> Danyang
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>> Thanks,
>>>
>>> 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.caam.rice.edu/%7Emk51/>
>>
>>
>>
>>
>> --
>> 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.caam.rice.edu/%7Emk51/>
>
>
>
>
> --
> 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.caam.rice.edu/%7Emk51/>
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