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[SPARK-20687][MLLIB] mllib.Matrices.fromBreeze may crash when converting from Breeze sparse matrix #17940

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[SPARK-20687][MLLIB] mllib.Matrices.fromBreeze may crash when converting from Breeze sparse matrix #17940

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62d78a2
Reproducing SPARK-20687
ghoto May 10, 2017
dbbd391
[SPARK-20687] mllib.Matrices.fromBreeze may cause crash when converti…
ghoto May 10, 2017
df84eb9
Line too long in test
ghoto May 11, 2017
b40a706
Addressing suggestions of @hhbyyh
ghoto May 12, 2017
bc8e14c
Shortening description+cosmetic
May 19, 2017
18ce388
Comment typo
May 20, 2017
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15 changes: 14 additions & 1 deletion mllib/src/main/scala/org/apache/spark/mllib/linalg/Matrices.scala
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Expand Up @@ -992,7 +992,20 @@ object Matrices {
new DenseMatrix(dm.rows, dm.cols, dm.data, dm.isTranspose)
case sm: BSM[Double] =>
// There is no isTranspose flag for sparse matrices in Breeze
new SparseMatrix(sm.rows, sm.cols, sm.colPtrs, sm.rowIndices, sm.data)

// Some Breeze CSCMatrices may have extra trailing zeros in
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@hhbyyh hhbyyh May 13, 2017 •
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minor: make this comment more compact in fewer lines.

// .rowIndices and .data, which are added after some matrix
// operations for efficiency.
//
// Therefore the last element of sm.colPtrs would no longer be
// coherent with the size of sm.rowIndices and sm.data
// despite sm being a valid CSCMatrix.
// We need to truncate both arrays (rowIndices, data)
// to the real size of the vector sm.activeSize to allow valid conversion

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@hhbyyh hhbyyh May 12, 2017 •
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Maybe we can add if (sm.activeSize != sm.rowIndices.length) here, since this is only needed when necessary.
Please refer to https://github.com/scalanlp/breeze/blob/master/math/src/main/scala/breeze/linalg/CSCMatrix.scala#L130

val truncRowIndices = sm.rowIndices.slice(0, sm.activeSize)
val truncData = sm.data.slice(0, sm.activeSize)
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@hhbyyh hhbyyh May 12, 2017 •
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This is the same as calling compact(). To make it less sensitive to the breeze internal implementation, how about:

val matCopy = sm.copy
matCopy.compact()

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@ghoto ghoto May 12, 2017

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I'm implementing both suggestions, however, wouldn't be the sm.copy more expensive than just doing those 2 slices?

new SparseMatrix(sm.rows, sm.cols, sm.colPtrs, truncRowIndices, truncData)
case _ =>
throw new UnsupportedOperationException(
s"Do not support conversion from type ${breeze.getClass.getName}.")
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20 changes: 20 additions & 0 deletions mllib/src/test/scala/org/apache/spark/mllib/linalg/MatricesSuite.scala
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Expand Up @@ -46,6 +46,26 @@ class MatricesSuite extends SparkFunSuite {
}
}

test("Test Breeze Conversion Bug - SPARK-20687") {
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@hhbyyh hhbyyh May 12, 2017

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specific name: Test FromBreeze when Breeze.CSCMatrix.rowIndices has trailing zeros.

And move the test after another unit test "fromBreeze with sparse matrix"

// (2, 0, 0)
// (2, 0, 0)
val mat1Brz = Matrices.sparse(2, 3, Array(0, 2, 2, 2), Array(0, 1), Array(2, 2)).asBreeze
// (2, 1E-15, 1E-15)
// (2, 1E-15, 1E-15)
val mat2Brz = Matrices.sparse(2, 3,
Array(0, 2, 4, 6),
Array(0, 0, 0, 1, 1, 1),
Array(2, 1E-15, 1E-15, 2, 1E-15, 1E-15)).asBreeze
val t1Brz = mat1Brz - mat2Brz
val t2Brz = mat2Brz - mat1Brz
// The following operations raise exceptions on un-patch Matrices.fromBreeze
val t1 = Matrices.fromBreeze(t1Brz)
val t2 = Matrices.fromBreeze(t2Brz)
// t1 == t1Brz && t2 == t2Brz
assert((t1.asBreeze - t1Brz).iterator.map((x) => math.abs(x._2)).sum < 1E-15)
assert((t2.asBreeze - t2Brz).iterator.map((x) => math.abs(x._2)).sum < 1E-15)
}

test("sparse matrix construction") {
val m = 3
val n = 4
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