[petsc-users] Usage of parallel FFT for doing batch 1d-FFTs over the columns of a dense 2d-matrix
Barry Smith
bsmith at petsc.dev
Fri Dec 4 18:59:34 CST 2020
Roland,
If you store your matrix as described in a parallel PETSc dense matrix then you should be able to call
fftw_plan_many_dft() directly on the value obtained with MatDenseGetArray(). You just need to pass the arguments regarding column major ordering appropriately. Probably identically to what you do with your previous code.
Barry
> On Dec 4, 2020, at 6:47 AM, Roland Richter <roland.richter at ntnu.no> wrote:
>
> Ideally those FFTs could be handled in parallel, after they are not depending on each other. Is that possible with MatFFT, or should I rather use FFTW for that?
>
> Thanks,
>
> Roland
>
> Am 04.12.20 um 13:19 schrieb Matthew Knepley:
>> On Fri, Dec 4, 2020 at 5:32 AM Roland Richter <roland.richter at ntnu.no <mailto:roland.richter at ntnu.no>> wrote:
>> Hei,
>>
>> I am currently working on a problem which requires a large amount of
>> transformations of a field E(r, t) from time space to Fourier space E(r,
>> w) and back. The field is described in a 2d-matrix, with the r-dimension
>> along the columns and the t-dimension along the rows.
>>
>> For the transformation from time to frequency space and back I therefore
>> have to apply a 1d-FFT operation over each row of my matrix. For my
>> earlier attempts I used armadillo as matrix library and FFTW for doing
>> the transformations. Here I could use fftw_plan_many_dft to do all FFTs
>> at the same time. Unfortunately, armadillo does not support MPI, and
>> therefore I had to switch to PETSc for larger matrices.
>>
>> Based on the examples (such as example 143) PETSc has a way of doing
>> FFTs internally by creating an FFT object (using MatCreateFFT).
>> Unfortunately, I can not see how I could use that object to conduct the
>> operation described above without having to iterate over each row in my
>> original matrix (i.e. doing it sequential, not in parallel).
>>
>> Ideally I could distribute the FFTs such over my nodes that each node
>> takes several rows of the original matrix and applies the FFT to each of
>> them. As example, for a matrix with a size of 4x4 and two nodes node 0
>> would take row 0 and 1, while node 1 takes row 2 and 3, to avoid
>> unnecessary memory transfer between the nodes while conducting the FFTs.
>> Is that something PETSc can do, too?
>>
>> The way I understand our setup (I did not write it), we use plan_many_dft to handle
>> multiple dof FFTs, but these would be interlaced. You want many FFTs for non-interlaced
>> storage, which is not something we do right now. You could definitely call FFTW directly
>> if you want.
>>
>> Second, above it seems like you just want serial FFTs. You can definitely create a MatFFT
>> with PETSC_COMM_SELF, and apply it to each row in the local rows, or create the plan
>> yourself for the stack of rows.
>>
>> Thanks,
>>
>> Matt
>>
>> Thanks!
>>
>> Regards,
>>
>> Roland
>>
>>
>>
>> --
>> 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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