[petsc-users] how to check if cell is local owned in DMPlex

Sun Mar 4 10:08:03 CST 2018

On Fri, Mar 2, 2018 at 3:22 PM, Danyang Su <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>

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> 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> 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>
>>> 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).
>>>
>>> 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/manualpage
>> s/DM/DMGetPointSF.html
>>
>> Then you can look at
>>
>>   https://bitbucket.org/petsc/petsc/src/1788fc36644e622df8cb
>> 1a0de85676ccc5af0239/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? 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/~mk51/>
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