[petsc-users] Usage of parallel FFT for doing batch 1d-FFTs over the columns of a dense 2d-matrix

Roland Richter roland.richter at ntnu.no
Fri Dec 4 06:47:22 CST 2020

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?



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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