[petsc-users] A question about DMPlexDistribute

Tue Aug 16 23:38:07 CDT 2016

The maint branch is a more or less "stable" branch. Features go into
"master" at first then get merged into "maint".

So

git clone -b master https://bitbucket.org/petsc/petsc petsc

will always be the most recent code you can possibly obtain.

On Wed, Aug 17, 2016 at 3:48 AM, leejearl <leejearl at 126.com> wrote:
> Thank you for your help. The problem has been overcome following your
> advices.
>
> Now, I give some notes for this problem which might be useful for others.
>
> 1. Up to now, we must use the code in the master branch. The source code can
> be downloaded using git with:
>
> git clone https://bitbucket.org/petsc/petsc petsc.
>
> 2. Just the other day, I download the code using git with: git clone -b
> maint https://bitbucket.org/petsc/petsc petsc.
>
>     But, this copy of code still has such a problem. I am not sure whether
> it is available now.
>
> 3. The code downloaded from website of PETSc(Version of 3.7.3) is not
> available for this problem, although it is in the branch master.
>
>
> Thanks for all helps again. Best wishes to you.
>
> leejearl
>
>
>
>
> On 2016年08月16日 19:34, Matthew Knepley wrote:
>
> 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
>
>