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

Danyang Su Sun, 04 Mar 2018 11:06:06 -0800


On 18-03-04 08:08 AM, Matthew Knepley wrote:

On Fri, Mar 2, 2018 at 3:22 PM, Danyang Su <danyang...@gmail.com<mailto:danyang...@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...@gmail.com
    <mailto:danyang...@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...@gmail.com <mailto:danyang...@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...@gmail.com <mailto:danyang...@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
            
<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
        
<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
        
<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
    
<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-ma...@mcs.anl.gov
    <mailto:petsc-ma...@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 theirexperiments is infinitely more interesting than any results to whichtheir experiments lead.

-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/%7Emk51/>

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

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