Sparse vector/matrix: add fast implementation of find_next and find_prev (fixed) #23317

tkluck · 2017-08-18T09:22:25Z

(Opening a new pull request instead of re-opening #23312 because I force-pushed and pull requests don't seem to like that.)

Before this commit, find_next() will just use the default implementation of looping over each element. When find_next is called without a function filter as first argument, we know that semantics are to find elements x satisfying x != 0, so for sparse matrices/vectors, we may only loop over the stored elements.

Some care must be taken for stored zero values; that's the reason for the indirection of _sparse_find_next (which only finds the next stored element) and the actual find_next (which does actual non-zero checks).

Before this commit, find_next() will just use the default implementation of looping over each element. When find_next is called without a function filter as first argument, we *know* that semantics are to find elements x satisfying x != 0, so for sparse matrices/vectors, we may only loop over the stored elements. Some care must be taken for stored zero values; that's the reason for the indirection of _sparse_find_next (which only finds the next stored element) and the actual find_next (which does actual non-zero checks).

fredrikekre · 2017-08-18T09:28:06Z

(Opening a new pull request instead of re-opening #23312 because I force-pushed and pull requests don't seem to like that.)

For next time, it is fine to leave incomplete PR's open :)

fredrikekre · 2017-08-18T09:35:24Z

base/sparse/sparsematrix.jl

+   end
+   row, col = ind2sub(m, i)
+   lo, hi = m.colptr[col], m.colptr[col+1]
+   n = searchsortedfirst(@view(m.rowval[lo:hi-1]), row)


You can specify start and stop index to searchsortedfirst instead of using a view:

julia/base/sort.jl

Lines 160 to 172 in a945af3

function searchsortedfirst(v::AbstractVector, x, lo::Int, hi::Int, o::Ordering)

lo = lo-1

hi = hi+1

@inbounds while lo < hi-1

m = (lo+hi)>>>1

if lt(o, v[m], x)

lo = m

else

hi = m

end

end

return hi

end

Ooooh good find, thanks. Pushing an update.

…ted(...,lo=,hi=)

tkelman · 2017-08-19T05:34:05Z

base/sparse/sparsematrix.jl

@@ -1332,6 +1332,42 @@ function findnz(S::SparseMatrixCSC{Tv,Ti}) where {Tv,Ti}
    return (I, J, V)
 end

+function _sparse_findnext(m::SparseMatrixCSC, i::Int)
+   if i > length(m)


these are slightly under-indented, should be 4 spaces rather than 3

tkelman · 2017-08-19T05:35:32Z

test/sparse/sparse.jl

@@ -1899,3 +1899,26 @@ end
        @test isfinite.(cov_sparse) == isfinite.(cov_dense)
    end
 end
+
+@testset "sparse findprev/findnext operations" begin


would be good to include some sparse test arrays with stored zeros

(Use git blame -w for finding the non-whitespace edits to this code.)

tkluck · 2017-08-20T09:11:42Z

That AppVeyor failure doesn't seem to be related at all; the code that's failing is

    tfile = tempname()
    io = open(tfile, "w")
    ccall(:jl_dump_compiles, Void, (Ptr{Void},), io.handle)
    eval(expand(Main, :(for i in 1:10 end)))
    ccall(:jl_dump_compiles, Void, (Ptr{Void},), C_NULL)
    close(io)
    tstats = stat(tfile)
    tempty = tstats.size == 0
    rm(tfile)
    @test tempty == true

My guess would be that it's a race condition between close() and stat(). If so, we may be able to fix it by just calling stat(io) instead, which will call fstat (2) under the hood.

tkluck · 2017-08-20T09:37:34Z

Just opened #23365 for that.

tkluck · 2017-08-29T19:51:46Z

Given the resolution of #23365, this should be good to go!

KristofferC · 2017-08-29T20:09:56Z

Needs a rebase.

tkluck · 2017-08-29T20:30:55Z

@KristofferC you got it :) let's see what CI says.

KristofferC · 2017-08-29T20:31:57Z

Seems like there is still a conflict here.

tkluck · 2017-08-29T20:32:34Z

Oops, merged master instead of origin/master. Testing+pushing that now.

Sacha0 · 2017-10-01T03:43:28Z

Linking to #23812 and #23120 in case this pull request need be updated in accord. Best!

This fixes a few merge conflicts resulting from other additions to the sparse codebase.

…e explicit Since we now need explicit predicates [1], this optimization only works if we know that the predicate is a function that is false for zero values. As suggested in that pull request, we could find out by calling `f(zero(eltype(array)))` and hoping that `f` is pure, but I like being a bit more conservative and only applying this optimization only to the case where we *know* `f` is equal to `!iszero`. For clarity, this commit also renames the helper method _sparse_findnext() to _sparse_findnextnz(), because now that the predicate-less version doesn't exist anymore, the `nz` part isn't implicit anymore either. [1]: JuliaLang#23812

tkluck · 2017-11-03T17:02:10Z

Updated this branch to align with the new semantics for find and friends as merged to master from #23812. Very interested to hear your thoughts!

@fredrikekre I accidentally merged from current master without first pulling your prior merge from 30th of September. That merge commit got lost in the process. As far as I can tell, no work of yours got lost through that (it was a clean merge) but if I missed anything, let me know and I'll recover.

tkluck · 2017-11-05T11:14:00Z

CI failures are libgit related and almost surely unrelated to the work in this branch. Should be good to merge!

fredrikekre · 2017-11-05T11:27:27Z

@Sacha0 wanna take a look? :)

Sacha0 · 2017-11-05T18:44:06Z

@Sacha0 wanna take a look? :)

I have blocked some time this evening for reviews, and will try to work this pull request in then :). Best!

Sacha0 · 2017-11-06T04:13:05Z

base/sparse/abstractsparse.jl

+        end
+    end
+    return j
+end


Perhaps the following? :)

function findnext(f::typeof(!iszero), v::AbstractSparseArray, i::Int) j = _sparse_findnextnz(v, i) while j != 0 && iszero(v[j]) j = _sparse_findnextnz(v, j+1) end return j end

Looks good! In the interest of expediency, feel free to commit+merge that if you have time.

Sacha0 · 2017-11-06T04:14:46Z

base/sparse/abstractsparse.jl

+        end
+    end
+    return j
+end


Similarly? :)

function findprev(f::typeof(!iszero), v::AbstractSparseArray, i::Int) j = _sparse_findprevnz(v, i) while j != 0 && iszero(v[j]) j = _sparse_findprevnz(v, j-1) end return j end

Sacha0 · 2017-11-06T04:51:30Z

base/sparse/sparsevector.jl

+    else
+        return v.nzind[n]
+    end
+end


A compact alternative:

function _sparse_findnextnz(v::SparseVector, i::Int) n = searchsortedfirst(v.nzind, i) return n <= length(v.nzind) ? v.nzind[n] : 0 end

Sacha0

lgtm modulo the minor comments! :)

@Sacha0

Thanks to @Sacha0 for the suggestion!

tkluck · 2017-11-10T17:19:53Z

Just updated with your comments @Sacha0 . I hope you don't mind I skipped replacing if/else/end by ?: (which is arguably a matter of taste), but the code duplication removal is an obvious improvement in clarity. Thanks again!

Sacha0 · 2017-11-13T20:50:12Z

base/sparse/sparsevector.jl

+function _sparse_findnextnz(v::SparseVector, i::Int)
+    n = searchsortedfirst(v.nzind, i)
+    if n > length(v.nzind)
+        return 0


For type stability, return zero(indtype(v))? (Likewise below.)

Sacha0

Modulo the minor type stability comment above, lgtm! Thanks @tkluck! :)

…types This mostly means returning `zero(indtype(...))` instead of `0` in the not-found case. In addition, this commit replaces a few `== 0` checks by `iszero()` to avoid unnecessary promotions. We could similarly replace `+ 1` by `+ one(...)` but that becomes cumbersome very quickly.

tkluck · 2017-11-14T19:40:56Z

Thanks for the review @Sacha0 ! Pushed those updates just now.

tkluck · 2018-01-04T21:58:24Z

Just added a commit that should resolve the merge conflicts. Do you think we could merge this?

Sacha0 · 2018-01-04T22:22:07Z

Looks like! Perhaps @fredrikekre and I should make a brief sweep of the rebased version and then merge?

Sacha0

Test failures appear related?

tkluck · 2018-01-06T11:04:47Z

Looks like. Keeping a pull request open for half a year really makes master a bit of a moving target 😕 I'm happy to fix it, but what can we do to make sure it gets merged quickly after that?

This is needed in response to JuliaLang#24715.

fredrikekre · 2018-01-06T13:03:26Z

Sorry this has taken so much time, it looks good to me but @Sacha0 should probably take a look and then we should merge!

Sacha0 · 2018-01-06T18:39:48Z

If you do not see movement within a few days on a pull request that is approved, passing CI, and not otherwise blocked, please feel welcome to bump! :) Chances are it simply fell off the collective radar and a bump would be appreciated. (Tangentially, having a bot that bumps pull requests under those conditions could work well.)

Sacha0

Thanks for seeing this work through @tkluck! :)

…#31354)" This seems to duplicate work from JuliaLang#23317 and it causes performance degradation in the cases that one was designed for. See JuliaLang#31354 (comment) This reverts commit e0bef65.

@mbauman

…artesian coordinates (#32007) Revert "sparse findnext findprev hash performance improved (#31354)" This seems to duplicate work from #23317 and it causes performance degradation in the cases that one was designed for. See #31354 (comment) This reverts commit e0bef65. Thanks to @mbauman for spotting this issue in #32007 (comment).

@mbauman

…artesian coordinates (#32007) Revert "sparse findnext findprev hash performance improved (#31354)" This seems to duplicate work from #23317 and it causes performance degradation in the cases that one was designed for. See #31354 (comment) This reverts commit e0bef65. Thanks to @mbauman for spotting this issue in #32007 (comment). (cherry picked from commit ec797ef)

fredrikekre added the domain:arrays:sparse Sparse arrays label Aug 18, 2017

fredrikekre reviewed Aug 18, 2017

View reviewed changes

Sparse findprev/findnext: replace searchsorted(@view...) by searchsor…

14f443a

…ted(...,lo=,hi=)

fredrikekre requested a review from Sacha0 August 18, 2017 22:43

tkelman reviewed Aug 19, 2017

View reviewed changes

tkluck added 2 commits August 19, 2017 09:13

_sparse_findnext/prev: fix indentation

92558be

(Use git blame -w for finding the non-whitespace edits to this code.)

sparse findprev/findnext: add doctest with stored zeros

4b54020

Merge branch 'master' into sparse-find-next

5dde4af

Merge remote-tracking branch 'origin/master' into sparse-find-next

daee267

fredrikekre requested review from Sacha0 and removed request for Sacha0 September 30, 2017 21:42

tkluck added 2 commits November 3, 2017 09:26

Merge remote-tracking branch 'origin/master' into sparse-find-next

1ac4141

This fixes a few merge conflicts resulting from other additions to the sparse codebase.

tkluck force-pushed the sparse-find-next branch from 026e479 to fe4b76e Compare November 3, 2017 17:00

Sacha0 reviewed Nov 6, 2017

View reviewed changes

Sacha0 approved these changes Nov 6, 2017

View reviewed changes

sparse findnext()/findprev(): remove code duplication

132ff27

Thanks to @Sacha0 for the suggestion!

Sacha0 reviewed Nov 13, 2017

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Sacha0 approved these changes Nov 14, 2017

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fredrikekre approved these changes Nov 14, 2017

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Merge branch 'master' into sparse-find-next

a33abbe

Sacha0 reviewed Jan 6, 2018

View reviewed changes

Fix sparse findprev()/findnext() for sub2ind deprecation

db62ae4

This is needed in response to JuliaLang#24715.

Sacha0 approved these changes Jan 6, 2018

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Sacha0 merged commit 2cfa6a5 into JuliaLang:master Jan 6, 2018

tkluck mentioned this pull request Nov 14, 2018

Implement optimizations for sparse findnext/findprev #28313

Closed

tkluck mentioned this pull request May 11, 2019

sparse findnext findprev hash performance improved #31354

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tkluck mentioned this pull request May 12, 2019

Sparse matrix: fix fast implementation of findnext and findprev for cartesian coordinates #32007

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Sparse vector/matrix: add fast implementation of find_next and find_prev (fixed) #23317

Sparse vector/matrix: add fast implementation of find_next and find_prev (fixed) #23317

tkluck commented Aug 18, 2017

fredrikekre commented Aug 18, 2017

fredrikekre Aug 18, 2017

tkluck Aug 18, 2017

tkelman Aug 19, 2017

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	function searchsortedfirst(v::AbstractVector, x, lo::Int, hi::Int, o::Ordering)
	lo = lo-1
	hi = hi+1
	@inbounds while lo < hi-1
	m = (lo+hi)>>>1
	if lt(o, v[m], x)
	lo = m
	else
	hi = m
	end
	end
	return hi
	end

Sparse vector/matrix: add fast implementation of find_next and find_prev (fixed) #23317

Sparse vector/matrix: add fast implementation of find_next and find_prev (fixed) #23317

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