[petsc-users] A question about DMPlexDistribute

[leejearl]

Thank you for your reply. The source code I have used is from the 
website of PETSc, not from the git repository.

I will have a test with the code from git repository.


leejearl


On 2016年08月13日 08:49, Oxberry, Geoffrey Malcolm wrote:
>
>> On Aug 12, 2016, at 5:41 PM, leejearl <leejearl at 126.com 
>> <mailto:leejearl at 126.com>> wrote:
>>
>> Hi, Matt:
>>
>>
>>
>> > Can you verify that you are running the master branch?
>
> cd ${PETSC_DIR}
> git branch
>
> The last command should return something like a list of branch names, 
> and the branch name with an asterisk to the left of it will be the 
> branch you are currently on.
>
> Geoff
>
>> I am not sure, how can I verify this?
>> And I configure PETSc with this command
>> "./configure --prefix=$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
>>
>

-- 
李季
西北工业大学航空学院流体力学系
Phone: 13324530085
QQ: 188524324

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20160813/172070ef/attachment.html>