Added rfft! and irfft! functionality through PaddedRFFTArray type. #54

favba · 2018-01-05T06:12:24Z

This PR addresses #52. This is a rewrite of my code with fixes to address possible problems with usage of unsafe_wrap raised here. I don't fully understand those issues, so an expert review is needed to see if the changes I introduced indeed solved the problem.

The code is already functional. The test I wrote originally for my package are passing. The code still needs documentation of the new type and new functions.

favba · 2018-01-10T21:56:57Z

Due to the rapid changes on Julia now, I'll wait for the release of v0.7 to finish up this PR.

appleparan · 2018-03-28T19:56:58Z

Bump! Could you finish this up with v0.7-dev? It would be nice if this will release before v0.7 official release.

favba · 2018-03-28T23:55:45Z

I think all to major changes on Julia have been made. I'll work on it again.

into pull-request/2993370b

favba · 2018-03-29T20:56:07Z

I managed to avoid using unsafe views and this PR is ready for technical review now. If it is acceptable, it will only be missing docstrings.
FYI: Using the new reinterpret still provides really poor performance:

julia> versioninfo()
Julia Version 0.7.0-DEV.4702
Commit 524710f60d (2018-03-26 19:44 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin17.4.0)
  CPU: Intel(R) Core(TM) i5-5287U CPU @ 2.90GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-3.9.1 (ORCJIT, broadwell)
Environment:
  JULIA_NUM_THREADS = 2

julia> using FFTW

julia> a = PaddedRFFTArray(rand(8,8))
5×8 PaddedRFFTArray{Float64,2,false}:
 0.712979+0.28724im   0.509384+0.0177532im  …   0.958592+0.884517im   0.685513+0.401894im
 0.361746+0.369876im  0.968775+0.193823im      0.0521561+0.815999im   0.924453+0.528454im
 0.835827+0.403952im  0.775697+0.187061im       0.106656+0.0442893im  0.321887+0.859492im
 0.784735+0.141277im  0.436122+0.198054im       0.580609+0.22239im    0.266962+0.252452im
      0.0+0.0im            0.0+0.0im                 0.0+0.0im             0.0+0.0im

julia> rfft!(a)
5×8 PaddedRFFTArray{Float64,2,false}:
  32.2515+0.0im       -2.36603+0.797907im  …     2.8308-1.49447im     -2.36603-0.797907im
 0.521591+1.17158im  -0.190847-0.681372im     -0.334622+1.19408im     -2.46524-3.4627im
  1.14537-2.0369im    0.383983-0.265645im      -1.52369-1.83912im    0.0772888+2.13619im
  1.39388-1.77041im    1.46133+3.4213im        -1.50413+0.570226im  0.00780449-0.57811im
   2.6889+0.0im        3.28556-0.875104im       1.79742+1.84643im      3.28556+0.875104im

julia> b = Array(a)
5×8 Array{Complex{Float64},2}:
  32.2515+0.0im       -2.36603+0.797907im  …     2.8308-1.49447im     -2.36603-0.797907im
 0.521591+1.17158im  -0.190847-0.681372im     -0.334622+1.19408im     -2.46524-3.4627im
  1.14537-2.0369im    0.383983-0.265645im      -1.52369-1.83912im    0.0772888+2.13619im
  1.39388-1.77041im    1.46133+3.4213im        -1.50413+0.570226im  0.00780449-0.57811im
   2.6889+0.0im        3.28556-0.875104im       1.79742+1.84643im      3.28556+0.875104im

julia> using BenchmarkTools

julia> @benchmark @inbounds getindex($(b),1)
BenchmarkTools.Trial:
  memory estimate:  0 bytes
  allocs estimate:  0
  --------------
  minimum time:     1.542 ns (0.00% GC)
  median time:      1.549 ns (0.00% GC)
  mean time:        1.552 ns (0.00% GC)
  maximum time:     5.031 ns (0.00% GC)
  --------------
  samples:          10000
  evals/sample:     1000

julia> @benchmark @inbounds getindex($(a.c),1)
BenchmarkTools.Trial:
  memory estimate:  0 bytes
  allocs estimate:  0
  --------------
  minimum time:     15.493 ns (0.00% GC)
  median time:      15.699 ns (0.00% GC)
  mean time:        15.729 ns (0.00% GC)
  maximum time:     50.897 ns (0.00% GC)
  --------------
  samples:          10000
  evals/sample:     998

julia> @benchmark @inbounds getindex($(a),1)
BenchmarkTools.Trial:
  memory estimate:  0 bytes
  allocs estimate:  0
  --------------
  minimum time:     1.846 ns (0.00% GC)
  median time:      1.853 ns (0.00% GC)
  mean time:        1.856 ns (0.00% GC)
  maximum time:     9.709 ns (0.00% GC)
  --------------
  samples:          10000
  evals/sample:     1000

julia> @benchmark sum($b)
BenchmarkTools.Trial:
  memory estimate:  0 bytes
  allocs estimate:  0
  --------------
  minimum time:     34.567 ns (0.00% GC)
  median time:      34.638 ns (0.00% GC)
  mean time:        34.957 ns (0.00% GC)
  maximum time:     91.601 ns (0.00% GC)
  --------------
  samples:          10000
  evals/sample:     993

julia> @benchmark sum($(a.c))
BenchmarkTools.Trial:
  memory estimate:  208 bytes
  allocs estimate:  6
  --------------
  minimum time:     865.900 ns (0.00% GC)
  median time:      875.400 ns (0.00% GC)
  mean time:        1.011 μs (9.66% GC)
  maximum time:     705.103 μs (99.77% GC)
  --------------
  samples:          10000
  evals/sample:     60

julia> @benchmark sum($(a))
BenchmarkTools.Trial:
  memory estimate:  0 bytes
  allocs estimate:  0
  --------------
  minimum time:     35.123 ns (0.00% GC)
  median time:      35.186 ns (0.00% GC)
  mean time:        35.756 ns (0.00% GC)
  maximum time:     70.551 ns (0.00% GC)
  --------------
  samples:          10000
  evals/sample:     992

favba · 2018-03-31T13:55:19Z

Did I mess this pull request up with incorrect rebase/merges stuff? Or this is the way to go? Should I start a new clean PR with those final changes?

favba · 2018-07-17T20:42:55Z

I consider this finished now. Julia v0.7 probably won't have any other disruptive change.
If this PR is accepted I could (slowly) start working on documentation...

stevengj · 2018-07-18T15:16:49Z

src/rfft!.jl

+ d = data(A)
+ i = $ip
+ I = $t
+ @boundscheck checkbounds(d,i,I...)


Shouldn't it also check bounds with i-1?

Oh, I guess since ip=2*I2[1], if it is in-bounds then i-1 must also be in-bounds.

stevengj · 2018-07-18T15:22:50Z

src/rfft!.jl

+ (1 in region) || throw(ArgumentError("The first dimension must always be transformed"))
+ if flags&PRESERVE_INPUT != 0
+ a = similar(X)
+ return rFFTWPlan{Complex{T},BACKWARD,true,N}(complex_view(a), real(a), region, flags,timelimit)


What's going on here? IIRC, PRESERVE_INPUT only affects out-of-place plans.

Oh my... That is reminiscent from early stage development, when I didn't notice that inplace r2c and c2r were already exposed on Julia. I tried hacking out-of-place plans to work inplace, thus this PRESERVE_INPUT flag.
I'll change this.

stevengj · 2018-07-18T15:24:07Z

test/test_rfft!.jl

+@testset "Read binary file to PaddedRFFTArray" begin
+ for s in ((8,4,4),(9,4,4),(8,),(9,))
+ aa = rand(Float64,s)
+ f = Base.Filesystem.tempname()


you should be able to test i/o with an IOBuffer rather than a file.

stevengj · 2018-07-19T17:26:12Z

src/rfft!.jl

+ else
+ x = similar(X)
+ p = rFFTWPlan{T,FORWARD,true,N}(real(x), complex_view(x), region, flags, timelimit)
+ end


I guess you are trying to avoid overwriting X during planning, but I don't think it's a good idea:

plan_fft is documented to overwrite the input during non-ESTIMATE planning, so we should be consistent.

Creating the plan for x = similar(X) could result in the plan not being applicable to X in the unlikely event that the X array is not 16-byte aligned.

favba · 2018-07-19T19:32:29Z

Sorry for this late change. But I just observed that performance is slightly better if we use Colons instead of UnitRages for the array view:

julia> a = rand(128,128,128);

julia> b = view(a,1:126,:,:);

julia> c = view(a,1:126,1:128,1:128);

julia> using BenchmarkTools

julia> @benchmark sum($b)
BenchmarkTools.Trial:
  memory estimate:  0 bytes
  allocs estimate:  0
  --------------
  minimum time:     4.533 ms (0.00% GC)
  median time:      4.620 ms (0.00% GC)
  mean time:        4.689 ms (0.00% GC)
  maximum time:     6.707 ms (0.00% GC)
  --------------
  samples:          1064
  evals/sample:     1

julia> @benchmark sum($c)
BenchmarkTools.Trial:
  memory estimate:  0 bytes
  allocs estimate:  0
  --------------
  minimum time:     5.150 ms (0.00% GC)
  median time:      5.208 ms (0.00% GC)
  mean time:        5.267 ms (0.00% GC)
  maximum time:     7.113 ms (0.00% GC)
  --------------
  samples:          947
  evals/sample:     1

julia> @benchmark reduce($(*),$b)
BenchmarkTools.Trial:
  memory estimate:  560 bytes
  allocs estimate:  14
  --------------
  minimum time:     4.531 ms (0.00% GC)
  median time:      4.608 ms (0.00% GC)
  mean time:        4.678 ms (0.00% GC)
  maximum time:     6.404 ms (0.00% GC)
  --------------
  samples:          1067
  evals/sample:     1

julia> @benchmark reduce($(*),$c)
BenchmarkTools.Trial:
  memory estimate:  560 bytes
  allocs estimate:  14
  --------------
  minimum time:     5.161 ms (0.00% GC)
  median time:      5.227 ms (0.00% GC)
  mean time:        5.291 ms (0.00% GC)
  maximum time:     7.780 ms (0.00% GC)
  --------------
  samples:          943
  evals/sample:     1

julia> versioninfo()
Julia Version 0.7.0-beta2.0
Commit b145832402* (2018-07-13 19:54 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin17.6.0)
  CPU: Intel(R) Core(TM) i5-5287U CPU @ 2.90GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.0 (ORCJIT, broadwell)
Environment:
  JULIA_NUM_THREADS = 2

stevengj · 2018-07-19T21:00:25Z

src/rfft!.jl

- rsize = (nx,rrsize[2:end]...)
- r = view(rr,(1:l for l in rsize)...)
- return new{T, N, N === 1 ? true : false}(rr,r,c)
+ r = view(rr, 1:nx, ntuple(i->Colon(),Nm1)...)


You can pass Val{Nm1}() here to get a compiler-unrolled ntuple on 0.7. On 0.6 you need Val{Nm1}.

Because Val(n) is a pure function now I can just put Val(Nm1) instead of Val{Nm1}(), right?

stevengj · 2018-07-20T19:57:54Z

LGTM, now just needs docs.

stevengj · 2019-05-08T11:58:38Z

Would be good to get documentation so that we can merge this.

favba · 2019-06-25T13:59:35Z

Just to give some update. I' currently finishing my thesis, so I don't think I'll be able to work on this until a month from...

navidcy · 2020-02-02T03:26:27Z

@favba news on this PR? Seems neat and it would be very nice to have it merged in FFTW.jl

roflmaostc · 2021-03-30T11:09:15Z

I would also very appreciate that feature!

BioTurboNick · 2021-09-29T02:54:06Z

I took a stab at reviving this, but it has some issues. My motivation was to allow simply replacing irfft with irfft! in code like ImageFiltering.jl, where the new type can be used internally to manage the memory. rfft! is the trickier one, given that the output array needs to be bigger than the input array.

There's little difference in performance because most of the time is spent in the C routines, but there is less memory churn. My version can be found here: https://github.com/BioTurboNick/FFTW.jl/tree/in-place-rfft

I don't know the API that well, so I've hit a stumbling block in a couple places. Maybe someone else can pick up from here.

favba · 2021-10-09T00:30:17Z

The only missing piece for this PR is documentation, correct?
If someone could point me to any guidance on how to make the documentation correctly I could finally finish this PR.

@BioTurboNick, I didn't understand what is the missing functionality you are adding in your PR. Could you try clarifying that to me? Maybe it can be done here.

BioTurboNick · 2021-10-09T00:46:56Z

A few issues:

Not able to use irfft! directly on the output of rfft
real function should probably be renamed, as it is doing something quite different from the real function in Base.
An inconsistency: the irfft! and brfft! functions here allow the form irfft!(b, (1, 3)) but the existing functions require an integer to be provided e.g. irfft(b, 8, (1, 3))

BioTurboNick · 2021-10-09T00:52:11Z

Also, not sure if all the special indexing methods in this PR are necessary anymore, as those are noted as needed due to inefficiencies back in Julia v0.7.

favba · 2021-10-09T18:19:47Z

Both issues

* Not able to use `irfft!` directly on the output of `rfft`

and

* An inconsistency: the `irfft!` and `brfft!` functions here allow the form `irfft!(b, (1, 3))` but the existing functions require an integer to be provided e.g. `irfft(b, 8, (1, 3))`

are related to the fact that there is not a one-to-one mapping between the size of the complex array and the corresponding real array after the inverse transform.

The PaddedRFFTArray already has the size information of the real view of the array, so it is really not necessary to inform it the the irfft! function.
It does become inconsistent with irfft, but irfft is really the oddball here. The proposed function signature on this PR is consistent with all other in-place inverse transforms: ifft!, bfft!, FFTW.idct! (FFTW.r2r! is an exception that requires a kind parameter...)

Now, in order to be able to use irfft! directly on the output of rfft, it seems to me we'd have to change the output of rfft to return a PaddedRFFTAraay (remember: we have to save the size information of the original real array...).
That would be quite a disruptive change... But it could be discussed in a separate issue after/if this PR is merged.

And I agree that

* `real` function should probably be renamed, as it is doing something quite different from the `real` function in Base.

favba · 2021-10-09T18:29:14Z

Also, not sure if all the special indexing methods in this PR are necessary anymore, as those are noted as needed due to inefficiencies back in Julia v0.7.

Unfortunately, it seems those issues are still present on Julia 1.6.3
On my machine I have:

julia> versioninfo()
Julia Version 1.6.3
Commit ae8452a9e0 (2021-09-23 17:34 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin19.5.0)
  CPU: Intel(R) Core(TM) i5-8279U CPU @ 2.40GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, skylake)
Environment:
  JULIA_CUDA_SILENT = true
  JULIA_MPI_PATH = /usr/local/Cellar/open-mpi/4.0.3
  JULIA_NUM_THREADS = 4

julia> a = rand(256,256);

julia> b = reinterpret(Complex{Float64},a);

julia> c = Array(b);

julia> using BenchmarkTools

julia> @benchmark sum($c)
BenchmarkTools.Trial: 10000 samples with 1 evaluation.
 Range (min … max):   9.504 μs … 55.548 μs  ┊ GC (min … max): 0.00% … 0.00%
 Time  (median):      9.745 μs              ┊ GC (median):    0.00%
 Time  (mean ± σ):   10.203 μs ±  2.793 μs  ┊ GC (mean ± σ):  0.00% ± 0.00%

  █▇▅▁                                                        ▁
  ████▇▅▅▆▄▁▁▃▅▁▁▁▄▁▃▁▁▁▁▁▃▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▃▆▅▄▁▃▁▃█▇▇▅▄▃▃▃▆ █
  9.5 μs       Histogram: log(frequency) by time      28.5 μs <

 Memory estimate: 0 bytes, allocs estimate: 0.

julia> @benchmark sum($b)
BenchmarkTools.Trial: 10000 samples with 1 evaluation.
 Range (min … max):  20.482 μs … 130.839 μs  ┊ GC (min … max): 0.00% … 0.00%
 Time  (median):     21.765 μs               ┊ GC (median):    0.00%
 Time  (mean ± σ):   23.524 μs ±   5.070 μs  ┊ GC (mean ± σ):  0.00% ± 0.00%

   ▇██▅▃ ▁ ▃▃▄▄▄▄▄▄▂                        ▁▁     ▁           ▂
  ▆██████████████████▇▅▆▅▅▃▁▅▁▃▃▁▃▄▁▃▁▄▄▁▁▄▆██▇▅▅▄███▇▇▇▆▇▇▆▆▆ █
  20.5 μs       Histogram: log(frequency) by time      44.6 μs <

 Memory estimate: 0 bytes, allocs estimate: 0.

BioTurboNick · 2021-10-09T18:31:05Z

Does my PR fail in some way? Because it implements what I suggested with respect to being able to use irfft! on rfft output. That is, without changing the return type of rfft.

favba · 2021-10-09T19:21:54Z

Does my PR fail in some way? Because it implements what I suggested with respect to being able to use irfft! on rfft output. That is, without changing the return type of rfft.

Ok, I see it now... Since you kept the irfft signature, which requires explicitly the first dimension of the real array, you are able to provide that feature...

I think that can be easily incorporated into this PR, keeping different signatures for irfft! when it is applied to a PaddedRFFTArray or an Array{Complex{T}}.

And I think I know a way to make rfft! work at best effort at least with SubArrays such that the following would work:

a = rand(256,256)
b = rfft!(irfft!(rfft(a),size(a,1))) # same as rfft(a)

@BioTurboNick , do you mind If I incorporate those features you provided in your PR to this one? or would you rather keep working on that one?
The most important features, at least for me, already implemented on this PR are the efficient indexing and the capability of reading data directly to a PaddedRFFTArray, such that absolutely no copy of data is necessary. (I've been using it to perform FFTs of real data that hardly fits memory...)

BioTurboNick · 2021-10-09T19:26:15Z

Absolutely, go for it!

favba · 2021-10-09T22:43:22Z

Maintaining good index performance while adding those features is trickier than I thought it would be...
I think I'll work on that on a different PR, as it will involve finding a different solution for the slow reinterpret problem.

BioTurboNick · 2021-10-09T23:13:51Z

Ah, dang. Fair enough. Wonder what would be necessary to resolve the underlying slowness... I have a tendency to poke around on problems like that.

antoine-levitt · 2021-10-10T06:31:20Z

If it's a julia issue can you open an issue there? Maybe it can be fixed

BioTurboNick · 2021-10-13T04:58:06Z

If it's a julia issue can you open an issue there? Maybe it can be fixed

I took a look and it appears to be a fairly low-level issue. At the bottom is one or more memcpy calls that are interposed between the array and the produced value.

I was about to suggest unsafe_wrap but you already moved away from that... But looking at the concerns around it, maybe there's a way to create the PaddedRFFTArray type to address these issues?

It sounds like the main issue is you want to ensure consumers can't normally get a reference to the wrapped data. Thus, it could be have a real mode or complex mode as far as external code is concerned.

Something like:

data = rand(256, 256)
a = PaddedRFFTArray(data) # copies real data into expanded array, starts in Real mode. Getindex/setindex all access via internal real_view.
rfft!(a) # real_view and complex_view used internally, not exported
# a is now in Complex mode. Getindex/setindex all access via internal complex_view
irfft!(a)
# a is now in Real mode again.

timholy · 2021-10-13T08:18:25Z

as it will involve finding a different solution for the slow reinterpret problem.

Try reinterpret(reshape, T, A). I've seen this be 20x faster than reshape(reinterpret(T, A), sz). Requires Julia 1.6+

Also, in case it's helpful: https://github.com/HolyLab/RFFT.jl. Steal anything you like, keeping in mind that was originally written back in the Julia 0.2 days or so and only minimally updated since then. (Prior to docstrings, Documenter.jl, my current understanding of fast & inferrable tuple handling, keyword arguments, etc.)

favba · 2021-10-13T17:28:10Z

Try reinterpret(reshape, T, A). I've seen this be 20x faster than reshape(reinterpret(T, A), sz). Requires Julia 1.6+

I think the issue is at a lower level than that... see my benchmark here. It doesn't seem to involve any reshaping

I was about to suggest unsafe_wrap but you already moved away from that... But looking at the concerns around it, maybe there's a way to create the PaddedRFFTArray type to address these issues?

That is my plan... to fiddle with references and/or pointers again.
Basically, my idea is to change the data field from an Array{T,N} to something like WrappedArray{T,N,A} where WrappedArray wraps either a real-valued or a complex-valued array (A being the type of the array), depending on how you initialize it, but indexing it always return a real value.

I'd put the "unsafe" indexing routines inside this WrappedArray (in the case it is initialized with a complex array), so it is hidden in this extra layer, and maybe keep the current indexing strategy for the complex view of the array.
This WrappedArray would also be useful to initialize the PaddedRFFTArray directly with the complex data so

a = rand(256,256)
irff!(rfft(a),256)

should work.

timholy · 2021-10-13T18:39:14Z

It doesn't seem to involve any reshaping

And that's the problem.

julia> a = rand(256,256); ars = rand(2, 128, 256);

julia> b = reinterpret(Complex{Float64},a); brs = reinterpret(reshape, Complex{Float64}, ars);

julia> @btime sum($b);
  20.360 μs (0 allocations: 0 bytes)

julia> @btime sum($brs);
  11.583 μs (0 allocations: 0 bytes)

julia> @btime sum($c);
  11.362 μs (0 allocations: 0 bytes)

favba · 2021-10-20T22:10:16Z

The new implementation is here.

Added rfft! and irfft! functionality through PaddedRFFTArray type.

2993370

favba added 3 commits March 28, 2018 20:10

Added rfft! and irfft! functionality through PaddedRFFTArray type.

76e5bce

Removed unsafe complex view. Using custom getindex and setindex!

9c87761

Merge branch 'pull-request/2993370b' of https://github.com/favba/FFTW.jl

ad9a293

into pull-request/2993370b

favba added 3 commits July 17, 2018 16:05

merge master.

6c48ff5

Remove compatibility with v0.6.

87327dd

Using let block for tests.

e7e994a

favba changed the title ~~[W.I.P.] Added rfft! and irfft! functionality through PaddedRFFTArray type.~~ Added rfft! and irfft! functionality through PaddedRFFTArray type. Jul 17, 2018

Fix rand deprecation warning on tests.

6fe7cd7

stevengj reviewed Jul 18, 2018

View reviewed changes

favba added 2 commits July 19, 2018 12:19

fix plan_brfft! flags.

833d973

Use IOBuffer instead of tem_file for tests.

b7ec5bf

stevengj reviewed Jul 19, 2018

View reviewed changes

favba added 2 commits July 19, 2018 14:48

Let array be overridden by plan.

044fc26

Use Colon instead of UnitRange for real view.

de2657e

stevengj reviewed Jul 19, 2018

View reviewed changes

favba added 2 commits July 20, 2018 11:28

Val(Nm1) instead of Nm1 for tuple creation.

a88455b

micro-optimization: OneTo for first dimension of real view.

102af34

jipolanco mentioned this pull request Jan 9, 2020

PencilFFTs on GPUs? jipolanco/PencilFFTs.jl#3

Closed

BioTurboNick mentioned this pull request Sep 29, 2021

In-place irfft/brfft #219

Closed

favba mentioned this pull request Oct 20, 2021

Implemented rfft!, irfft! and brfft! #222

Open

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Added rfft! and irfft! functionality through PaddedRFFTArray type. #54

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Added rfft! and irfft! functionality through PaddedRFFTArray type. #54

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favba commented Jan 5, 2018

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