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

Danyang Su danyang.su at gmail.com
Wed Mar 7 17:26:38 CST 2018 

Hi All,

Thanks again for all your help during my code development and it turns 
out the DMPlex for unstructured grid works pretty well. I have another 
question.

  Is there any alternative method to get number of leaves without using 
PetscSFGetGraph?

Based on my test, this function works fine using current PETSc-dev 
version, but I cannot get it compiled correctly using other versions for 
Fortran code, as mentioned in the previous emails. I asked this question 
because some of the clusters we use do not have the PETSc-dev version 
and it takes time get staff reinstall another version.

Thanks,

Danyang

On 18-03-05 11:50 AM, Smith, Barry F. wrote:
>> 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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