[petsc-users] Some Problems in Modifying Parallel Programs

[Matthew Knepley]

On Mon, Oct 15, 2018 at 12:03 PM Yingjie Wu <yjwu16 at gmail.com> wrote:

> Thanks,Matt
>
> I'm sorry I didn't describe the problem clearly.
> I'm still wondering how, although VecLoad supports parallel vector
> reading, how can I guarantee that the local vector on the processor
> corresponds to the DM's IS?
> For example, when in FormInitialGuess, I want to make sure that the array
> VecGetArray() obtained by the local vector(Vectors read from binary files)
> and the array  DMGlobalToLocal () DMVecGetArray () obtained by the DM
> belong to the same processor, so that some errors in the mpi can be avoided.
>

I think I understand your question. If you give in a Vec in natural
ordering, you can use VecLoad with a Vec you get from
DMCreateGlobalVector(), and it will automatically reorder it into the right
parallel ordering.

  Thanks,

    Matt


> Thanks,
> Yingjie
>
> Matthew Knepley <knepley at gmail.com> 于2018年10月15日周一 下午11:32写道：
>
>> 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/>
>>
>

-- 
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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