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

Danyang Su Mon, 05 Mar 2018 11:35:56 -0800

Hi Barry and Matt,

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

After updating to PETSc-Dev verison, I encounter another compilingproblem 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. Ican rewrite this part to get rid of this. But I would rather to keepthis if there is alternative way to go. What is the head file should Iinclude 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 <[email protected]> wrote:



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

On Fri, Mar 2, 2018 at 3:22 PM, Danyang Su <[email protected]> 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 <[email protected]> wrote:
On 18-03-02 10:58 AM, Matthew Knepley wrote:

On Fri, Mar 2, 2018 at 1:41 PM, Danyang Su <[email protected]> wrote:

On 18-02-19 03:30 PM, Matthew Knepley wrote:

On Mon, Feb 19, 2018 at 3:11 PM, Danyang Su <[email protected]> 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 [email protected]? 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/

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

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