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

Danyang Su danyang.su at gmail.com
Mon Mar 5 13:35:23 CST 2018 

Hi Barry and Matt,

The compiling problem should be caused by the PETSc version installed on 
my computer. When updated to PETSc-Dev version, the ex1f example works 
fine. However, I cannot compile this example under PETSc-3.8.3 version.

After updating to PETSc-Dev verison, I encounter another compiling 
problem in my code.

         MatSolverPackage :: solver_pkg_flow
         1
Error: Unclassifiable statement at (1)

Including petscmat.h or petscpc.h does not help to solve this problem. I 
can rewrite this part to get rid of this. But I would rather to keep 
this if there is alternative way to go. What is the head file should I 
include in order to use MatSolverPackage?

Thanks,

Danyang


On 18-03-04 11:15 AM, Smith, Barry F. wrote:
>    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/

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