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Fix a row-indexing bug with sparse matrices that have non-Int indices #18022

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Aug 17, 2016
Merged

Fix a row-indexing bug with sparse matrices that have non-Int indices #18022

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03f37f2
Add cygpath_w call so `make -C test/perf` works in cygwin-cross
tkelman Aug 11, 2016
2359ef8
fix deprecated syntax "global rng_state::Float64"
tkelman Aug 11, 2016
b1d5321
Fix a row-indexing bug with sparse matrices
tkelman Aug 14, 2016
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4 changes: 2 additions & 2 deletions base/sparse/sparsevector.jl
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Expand Up @@ -426,8 +426,8 @@ function Base.getindex{Tv,Ti}(A::SparseMatrixCSC{Tv,Ti}, i::Integer, J::Abstract
@inbounds for j = 1:nJ
col = J[j]
rowI = i
ptrA = colptrA[col]
stopA = colptrA[col+1]-1
ptrA = Int(colptrA[col])
stopA = Int(colptrA[col+1]-1)
if ptrA <= stopA
if rowvalA[ptrA] <= rowI
ptrA = searchsortedfirst(rowvalA, rowI, ptrA, stopA, Base.Order.Forward)
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6 changes: 1 addition & 5 deletions test/perf/Makefile
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Expand Up @@ -9,11 +9,7 @@ all: micro kernel cat shootout blas lapack simd sort spell sparse

micro kernel cat shootout blas lapack simd sort spell sparse:
@$(MAKE) $(QUIET_MAKE) -C $(SRCDIR)/shootout
ifneq ($(OS),WINNT)
@$(call spawn,$(JULIA_EXECUTABLE)) $(SRCDIR)/$@/perf.jl | perl -nle '@_=split/,/; printf "%-18s %8.3f %8.3f %8.3f %8.3f\n", $$_[1], $$_[2], $$_[3], $$_[4], $$_[5]'
else
@$(call spawn,$(JULIA_EXECUTABLE)) $(SRCDIR)/$@/perf.jl 2> /dev/null
endif
@$(call spawn,$(JULIA_EXECUTABLE)) $(call cygpath_w,$(SRCDIR)/$@/perf.jl) | perl -nle '@_=split/,/; printf "%-18s %8.3f %8.3f %8.3f %8.3f\n", $$_[1], $$_[2], $$_[3], $$_[4], $$_[5]'

codespeed:
@$(MAKE) $(QUIET_MAKE) -C $(SRCDIR)/shootout
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8 changes: 4 additions & 4 deletions test/perf/shootout/fasta.jl
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Expand Up @@ -22,7 +22,7 @@ const IA = 3877.0
const IC = 29573.0

function gen_random()
global rng_state::Float64 = ((rng_state::Float64 * IA + IC) % IM) / IM
global rng_state = ((rng_state::Float64 * IA + IC) % IM) / IM
end
function repeat_fasta(src, n)
k = length(src)
Expand Down Expand Up @@ -55,7 +55,7 @@ end

rng_state = 42.0
function fasta(n=25000000)
repeat_fasta(alu, 2n)
random_fasta(iub1, iub2, 3n)
random_fasta(homosapiens1, homosapiens2, 5n)
repeat_fasta(alu, 2n)
random_fasta(iub1, iub2, 3n)
random_fasta(homosapiens1, homosapiens2, 5n)
end
5 changes: 5 additions & 0 deletions test/sparsedir/sparse.jl
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Expand Up @@ -1588,3 +1588,8 @@ end

# Test temporary fix for issue #16548 in PR #16979. Brittle. Expect to remove with `\` revisions.
@test which(\, (SparseMatrixCSC, AbstractVecOrMat)).module == Base.SparseArrays

# Row indexing a SparseMatrixCSC with non-Int integer type
let A = sparse(UInt32[1,2,3], UInt32[1,2,3], [1.0,2.0,3.0])
@test A[1,1:3] == A[1,:] == [1,0,0]
end