[petsc-users] A question about DMPlexDistribute

[leejearl]

Hi, Matt:



 > Can you verify that you are running the master branch?
I am not sure, how can I verify this?
And I configure PETSc with this command
"./configure --prefix=$HOME/Install/petsc-openmpi 
--with-mpi=/home/leejearl/Install/openmpi/gnu/1.8.4 
--download-exodusii=yes --download-netcdf 
--with-hdf5-dir=/home/leejearl/Install/hdf5-1.8.14 --download-metis=yes".
Is there some problem? Can you show me your command for configuring PETSc?


Thanks

leejearl





On 2016年08月13日 01:10, Matthew Knepley wrote:
> On Thu, Aug 11, 2016 at 8:00 PM, leejearl <leejearl at 126.com 
> <mailto:leejearl at 126.com>> wrote:
>
>     Thank you for your reply. I have attached the code, grid and the
>     error message.
>
>     cavity.c is the code file, cavity.exo is the grid, and error.dat
>     is the error message.
>
>     The command is "mpirun -n 2 ./cavity
>
>
> Can you verify that you are running the master branch? I just ran this 
> and got
>
> DM Object: 2 MPI processes
>   type: plex
> DM_0x84000004_0 in 2 dimensions:
>   0-cells: 5253 5252
>   1-cells: 10352 10350
>   2-cells: 5298 (198) 5297 (198)
> Labels:
>   ghost: 2 strata of sizes (199, 400)
>   vtk: 1 strata of sizes (4901)
>   Cell Sets: 1 strata of sizes (5100)
>   Face Sets: 3 strata of sizes (53, 99, 50)
>   depth: 3 strata of sizes (5253, 10352, 5298)
>
>   Thanks,
>
>      Matt
>
>     On 2016年08月11日 23:29, Matthew Knepley wrote:
>>     On Thu, Aug 11, 2016 at 3:14 AM, leejearl <leejearl at 126.com
>>     <mailto:leejearl at 126.com>> wrote:
>>
>>         Hi,
>>             Thank you for your reply. It help me very much.
>>             But, for "/petsc-3.7.2/src/ts/examples/tutorials/ex11.c",
>>         when I set the overlap to 2 levels, the command is
>>         "mpirun -n 3 ./ex11 -f annulus-20.exo -ufv_mesh_overlap 2
>>         -physics sw", it suffers a error.
>>             It seems to me that setting overlap to 2 is very common.
>>         Are there issues that I have not take into consideration?
>>             Any help are appreciated.
>>
>>     I will check this out. I have not tested an overlap of 2 here
>>     since I generally use nearest neighbor FV methods for
>>     unstructured stuff. I have test examples that run fine for
>>     overlap > 1. Can you send the entire error message?
>>
>>     If the error is not in the distribution, but rather in the
>>     analytics, that is understandable because this example is only
>>     intended to be run using a nearest neighbor FV method, and thus
>>     might be confused if we give it two layers of ghost
>>     cells.
>>
>>        Matt
>>
>>
>>         leejearl
>>
>>
>>         On 2016年08月11日 14:57, Julian Andrej wrote:
>>>         Hi,
>>>
>>>         take a look at slide 10 of [1], there is visually explained
>>>         what the overlap between partitions is.
>>>
>>>         [1]
>>>         https://www.archer.ac.uk/training/virtual/files/2015/06-PETSc/slides.pdf
>>>         <https://www.archer.ac.uk/training/virtual/files/2015/06-PETSc/slides.pdf>
>>>
>>>         On Thu, Aug 11, 2016 at 8:48 AM, leejearl <leejearl at 126.com
>>>         <mailto:leejearl at 126.com>> wrote:
>>>
>>>             Hi, all:
>>>                 I want to use PETSc to build my FVM code. Now, I
>>>             have a question about
>>>             the function DMPlexDistribute(DM dm, PetscInt overlap,
>>>             PetscSF *sf, DM *dmOverlap) .
>>>
>>>                 In the example
>>>             "/petsc-3.7.2/src/ts/examples/tutorials/ex11.c". When I
>>>             set the overlap
>>>             as 0 or 1, it works well. But, if I set the overlap as
>>>             2, it suffers a problem.
>>>                 I am confused about the value of overlap. Can it be
>>>             set as 2? What is the meaning of
>>>             the parameter overlap?
>>>                 Any helps are appreciated!
>>>
>>>             leejearl
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>     -- 
>>     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
>
>
>
>
> -- 
> 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

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