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

Smith, Barry F. bsmith at mcs.anl.gov
Mon Mar 5 13:50:47 CST 2018 

> MatSolverPackage    

became MatSolverType



> On Mar 5, 2018, at 1:35 PM, Danyang Su <danyang.su at gmail.com> wrote:
> 
> 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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