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

Sun Mar 4 13:15:37 CST 2018

  See src/vec/is/sf/examples/tutorials/ex1f.F90 in the master branch of the PETSc git repository

  BTW: 

   git grep -i petscsfgetgraph 

will show every use of the function in the source code. Very useful tool

   Barry

> On Mar 4, 2018, at 1:05 PM, Danyang Su <danyang.su at gmail.com> wrote:
> 
> 
> 
> 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> 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> 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/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
>>>> 
>>>> 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/
>>>> 
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> 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/
>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> 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/
>> 
>> 
>> 
>> 
>> -- 
>> 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/
> 