[petsc-users] Some Problems in Modifying Parallel Programs

[Matthew Knepley]

On Mon, Oct 15, 2018 at 11:13 AM Yingjie Wu <yjwu16 at gmail.com> wrote:

> Thank you very much, Matt.
>
> My problem is actually a two-dimensional problem, and the matrix in my
> binary file is actually a two-dimensional array, each point corresponding
> to a value on the two-dimensional grid.
>

These are still vectors. Vec store fields, which gives values to points on
your grid. Matrices map between states, so between vectors.


> Your suggestion is very useful to me. I can try to convert the matrix
> binary file into a vector binary file to give program an initial value. So
> what I should do is:
> 1. establish parallel vectors.
>  2. reads data from binary files to vectors. (VecLoad())
> 3. use VecGetArray() in FormInitialGuess() to use vector elements to give
> the initial values of the field variables.
> I know DM can support parallel computing (domain decomposition). How can I
> ensure that the part of the vector built on each processor corresponds to
> the index of DM object? (Cause my field variables are established by
> DMDACreate2d,  and I want to assign initial values to field variables using
> read vectors )
>

Yes. Many times you will want to VecLoad, then DMGlobalToLocal() to get
ghosted vectors, then DMVecGetArray() to get ghosted arrays.

   Matt


>
> Thanks,
> Yingjie
>
> Matthew Knepley <knepley at gmail.com> 于2018年10月15日周一 下午10:52写道：
>
>> On Mon, Oct 15, 2018 at 10:42 AM Yingjie Wu <yjwu16 at gmail.com> wrote:
>>
>>> Dear Petsc developer:
>>> Hi,
>>> Thank you very much for your previous reply.
>>> I recently wanted to modify my program to parallel version, and
>>> encountered some problems in modifying it.
>>> 1. There are functions (read matrix) in the program that reads
>>> files,will they affect my parallelism?
>>>
>>
>> No, MatLoad works in parallel. This will work unchanged if you want the
>> default layout. If you want a special partition,
>> you must call MatSetSizes() after MatCreate().
>>
>>
>>> The codes are as follows:
>>>
>>> ierr = PetscViewerBinaryOpen (PETSC_COMM_WORLD, file, FILE_MODE_READ,
>>> &viewer); CHKERRQ (ierr);
>>> ierr = MatCreate (PETSC_COMM_WORLD, &A1); CHKERRQ (ierr);
>>> ierr = MatSetFromOptions (A1); CHKERRQ (ierr);
>>> ierr = MatCreate (PETSC_COMM_WORLD, &A2); CHKERRQ (ierr);
>>> ierr = MatSetFromOptions (A2); CHKERRQ (ierr);
>>> ierr = MatLoad (A1, viewer); CHKERRQ (ierr);
>>> ierr = MatLoad (A2, viewer); CHKERRQ (ierr);
>>> ierr = PetscViewerDestroy (&viewer); CHKERRQ (ierr);
>>>
>>> I read two matrix information from a binary file and wanted to use it on
>>> each processor (in fact, my goal was to use these two matrices to give
>>> initial values to the two field variables). The program can run in serial
>>> time. Now I want to change it to parallel program. What do I need to
>>> modify?
>>> 2. Following the last question, I used the following code in giving
>>> initial value procedure FormInitialGuess():
>>>
>>> ierr = MatSeqAIJGetArray (A1, &initial_phi1); CHKERRQ (ierr);
>>> ierr = MatSeqAIJGetArray (A2, &initial_phi2); CHKERRQ (ierr);
>>>
>>>
>>> I found this function on manualpages, and I felt that it could fulfill
>>> my need to represent the elements of the matrix in arrays to give field
>>> variables an initial value in each grid. The matrix A1 and A2 above are
>>> actually the matrix information that was read from the file before. Now I
>>> want to modify it as a parallel program. How do I use matrix information to
>>> give initial values in parallel? (In program, field variables are
>>> implemented through DM because parallel computing and Ghost Value are
>>> supported)
>>>
>>
>> I do not understand the use of matrices to initialize field values.
>> Usually field values are stored on Vec objects, and this is
>> the philosophy of DM objects.
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Thanks,
>>> Yingjie
>>>
>>
>>
>> --
>> 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/
>> <http://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/ <http://www.cse.buffalo.edu/~knepley/>
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