[petsc-users] A question about DMPlexDistribute

Matthew Knepley knepley at gmail.com
Tue Aug 16 06:34:03 CDT 2016 

On Mon, Aug 15, 2016 at 9:28 PM, leejearl <leejearl at 126.com> wrote:

> Thank you for all your helps. I have tried and reinstalled PETSc lots of
> times. The error are still existed.
>
> I can not find out the reasons. Now, I give the some messages in this
> letter.
>
> 1> The source code is downloaded from the website of PETSc, and the
> version is 3.7.2.
>
> You will need to run in the 'master' branch, not the release since we have
fixed some bugs. It is best to
use master for very new features like this. The instructions are here:
http://www.mcs.anl.gov/petsc/developers/index.html

   Thanks,

      Matt

> 2> Configure:
>
> >export PETSC_DIR=./
>
> >export PETSC_ARCH=arch
>
> >./configure --prefix=$HOME/Install/petsc --with-mpi-dir=/home/leejearl/Install/mpich_3.1.4/gnu
> --download-exodusii=../externalpackages/exodus-5.24.tar.bz2
> --download-netcdf=../externalpackages/netcdf-4.3.2.tar.gz
> --download-hdf5=../externalpackages/hdf5-1.8.12.tar.gz
> --download-metis=../externalpackages/git.metis.tar.gz
> --download-parmetis=yes
>
> 3> The process of installation has no error.
>
> 4> After the installation, I added the following statement into the file
> ~/.bashrc:
>
> export PETSC_ARCH=""
>
> export PETSC_DIR=$HOME/Install/pets/
>
> I wish to get some helps as follows:
>
> 1> Is there any problems in my installation?
>
> 2> Can any one help me a simple code in which the value of overlap used in
> DMPlexDistribute function is greater than 1.
>
> 3> I attach the code, makefile, grid and the error messages again, I hope
> some one can help me to figure out the problems.
>
>     3.1> code: cavity.c
>
>     3.2> makefile: makefile
>
>     3.3> grid: cavity.exo
>
>     3.4> error messages: error.dat
>
>     It is very strange that there is no error message when I run it using
> "mpirun -n 3 ./cavity", but when I run it using "mpirun -n 2 ./cavity", the
> errors happed.
>
> The error messages are shown in the file error.dat.
>
>
> Any helps are appreciated.
>
>
>
> On 2016年08月13日 09:04, leejearl wrote:
>
> 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> 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> 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> 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
>>>
>>> On Thu, Aug 11, 2016 at 8:48 AM, leejearl <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
>
>
>
>
>


-- 
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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