[petsc-users] Some Problems in Modifying Parallel Programs

[Dave May]

On Mon, 15 Oct 2018 at 16:54, Matthew Knepley <knepley at gmail.com> wrote:

> 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.
>

Maybe this is a "matlab style" idea / way of thinking, e.g. representing 2d
meshes and fields as matrices because they "look kinda the same....". If
that is the case - don't do it! Use vectors to represent fields



>   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/>
>
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