[petsc-users] how to check if cell is local owned in DMPlex
Danyang Su
danyang.su at gmail.com
Sun Mar 4 13:05:05 CST 2018
On 18-03-04 08:08 AM, Matthew Knepley wrote:
> On Fri, Mar 2, 2018 at 3:22 PM, Danyang Su <danyang.su at gmail.com
> <mailto:danyang.su at gmail.com>> wrote:
>
> 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.
>
>
> I apologize for taking so long. The PetscSF definitions are in
>
> #include <petsc/finclude/petscis.h>
Hi Matt,
After including
#include <petsc/finclude/petscis.h>
use petscis
I still get error saying undefined reference to `petscsfgetgraph_'
Did I miss any other head file?
Thanks,
Danyang
>
> You are correct that they should be moved out.
>
> Thanks,
>
> Matt
>
> #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
>> <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/>
>
>
>
>
> --
> 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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