IGNITE-5880: BLAS integration phase 2
Project: http://git-wip-us.apache.org/repos/asf/ignite/repo Commit: http://git-wip-us.apache.org/repos/asf/ignite/commit/488a6d27 Tree: http://git-wip-us.apache.org/repos/asf/ignite/tree/488a6d27 Diff: http://git-wip-us.apache.org/repos/asf/ignite/diff/488a6d27 Branch: refs/heads/ignite-5872 Commit: 488a6d271bbeb60d424745fb20ef856c624e2fcb Parents: 9b730e7 Author: Yury Babak <yba...@gridgain.com> Authored: Mon Aug 7 17:24:21 2017 +0300 Committer: Igor Sapego <isap...@gridgain.com> Committed: Mon Aug 7 17:24:21 2017 +0300 ---------------------------------------------------------------------- .../java/org/apache/ignite/ml/math/Blas.java | 157 ++++--------------- .../ml/math/impls/matrix/AbstractMatrix.java | 3 +- .../storage/vector/MatrixVectorStorage.java | 11 ++ .../vector/SparseLocalOnHeapVectorStorage.java | 9 ++ .../impls/matrix/MatrixImplementationsTest.java | 5 +- .../RandomAccessSparseVectorStorageTest.java | 4 +- 6 files changed, 56 insertions(+), 133 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/ignite/blob/488a6d27/modules/ml/src/main/java/org/apache/ignite/ml/math/Blas.java ---------------------------------------------------------------------- diff --git a/modules/ml/src/main/java/org/apache/ignite/ml/math/Blas.java b/modules/ml/src/main/java/org/apache/ignite/ml/math/Blas.java index 29312e5..a61d796 100644 --- a/modules/ml/src/main/java/org/apache/ignite/ml/math/Blas.java +++ b/modules/ml/src/main/java/org/apache/ignite/ml/math/Blas.java @@ -19,8 +19,6 @@ package org.apache.ignite.ml.math; import com.github.fommil.netlib.BLAS; import com.github.fommil.netlib.F2jBLAS; -import it.unimi.dsi.fastutil.ints.IntIterator; -import it.unimi.dsi.fastutil.ints.IntSet; import java.util.Set; import org.apache.ignite.ml.math.exceptions.CardinalityException; import org.apache.ignite.ml.math.exceptions.MathIllegalArgumentException; @@ -30,7 +28,10 @@ import org.apache.ignite.ml.math.impls.matrix.DenseLocalOnHeapMatrix; import org.apache.ignite.ml.math.impls.matrix.SparseBlockDistributedMatrix; import org.apache.ignite.ml.math.impls.matrix.SparseDistributedMatrix; import org.apache.ignite.ml.math.impls.matrix.SparseLocalOnHeapMatrix; +import org.apache.ignite.ml.math.impls.vector.CacheVector; +import org.apache.ignite.ml.math.impls.vector.DenseLocalOffHeapVector; import org.apache.ignite.ml.math.impls.vector.DenseLocalOnHeapVector; +import org.apache.ignite.ml.math.impls.vector.SparseLocalOffHeapVector; import org.apache.ignite.ml.math.impls.vector.SparseLocalVector; import org.apache.ignite.ml.math.util.MatrixUtil; @@ -244,9 +245,9 @@ public class Blas { else if (alpha == 0.0) scal(c, beta); else { - checkTypes(a, "gemm"); - checkTypes(b, "gemm"); - checkTypes(c, "gemm"); + checkMatrixType(a, "gemm"); + checkMatrixType(b, "gemm"); + checkMatrixType(c, "gemm"); double[] fA = a.getStorage().data(); double[] fB = b.getStorage().data(); @@ -265,7 +266,7 @@ public class Blas { /** * Currently we support only local onheap matrices for BLAS. */ - private static void checkTypes(Matrix a, String op){ + private static void checkMatrixType(Matrix a, String op){ if (a instanceof DenseLocalOffHeapMatrix || a instanceof SparseDistributedMatrix || a instanceof SparseBlockDistributedMatrix) throw new IllegalArgumentException("Operation doesn't support for matrix [class=" @@ -273,37 +274,12 @@ public class Blas { } /** - * y := alpha * A * x + beta * y. - * - * @param alpha Alpha. - * @param a Matrix a. - * @param x Vector x. - * @param beta Beta. - * @param y Vector y. + * Currently we support only local onheap vectors for BLAS. */ - public static void gemv(double alpha, Matrix a, Vector x, double beta, DenseLocalOnHeapVector y) { - checkCardinality(a, x); - checkCardinality(a, y); - - if (alpha == 0.0 && beta == 1.0) - return; - - if (alpha == 0.0) { - scal(y, beta); - return; - } - - if (a instanceof SparseLocalOnHeapMatrix && x instanceof DenseLocalOnHeapVector) - gemv(alpha, (SparseLocalOnHeapMatrix)a, (DenseLocalOnHeapVector)x, beta, y); - else if (a instanceof SparseLocalOnHeapMatrix && x instanceof SparseLocalVector) - gemv(alpha, (SparseLocalOnHeapMatrix)a, (SparseLocalVector)x, beta, y); - else if (a instanceof DenseLocalOnHeapMatrix && x instanceof DenseLocalOnHeapVector) - gemv(alpha, (DenseLocalOnHeapMatrix)a, (DenseLocalOnHeapVector)x, beta, y); - else if (a instanceof DenseLocalOnHeapMatrix && x instanceof SparseLocalVector) - gemv(alpha, (DenseLocalOnHeapMatrix)a, (SparseLocalVector)x, beta, y); - else - throw new IllegalArgumentException("Operation gemv doesn't support running thist input [matrix=" + - a.getClass().getSimpleName() + ", vector=" + x.getClass().getSimpleName()+"]."); + private static void checkVectorType(Vector a, String op){ + if (a instanceof DenseLocalOffHeapVector || a instanceof SparseLocalOffHeapVector || a instanceof CacheVector) + throw new IllegalArgumentException("Operation doesn't support for vector [class=" + + a.getClass().getName() + ", operation="+op+"]."); } /** @@ -315,106 +291,32 @@ public class Blas { * @param beta Beta. * @param y Vector y. */ - private static void gemv(double alpha, SparseLocalOnHeapMatrix a, DenseLocalOnHeapVector x, double beta, - DenseLocalOnHeapVector y) { - - if (beta != 1.0) - scal(y, beta); - - IntIterator rowIter = a.indexesMap().keySet().iterator(); - while (rowIter.hasNext()) { - int row = rowIter.nextInt(); - - double sum = 0.0; - IntIterator colIter = a.indexesMap().get(row).iterator(); - while (colIter.hasNext()) { - int col = colIter.nextInt(); - sum += alpha * a.getX(row, col) * x.getX(col); - } - - y.setX(row, y.getX(row) + sum); - } - } + public static void gemv(double alpha, Matrix a, Vector x, double beta, Vector y) { + checkCardinality(a, x); - /** - * y := alpha * A * x + beta * y. - * - * @param alpha Alpha. - * @param a Matrix a. - * @param x Vector x. - * @param beta Beta. - * @param y Vector y. - */ - private static void gemv(double alpha, DenseLocalOnHeapMatrix a, DenseLocalOnHeapVector x, double beta, - DenseLocalOnHeapVector y) { - nativeBlas.dgemv("N", a.rowSize(), a.columnSize(), alpha, a.getStorage().data(), a.rowSize(), x.getStorage().data(), 1, beta, - y.getStorage().data(), 1); - } + if (a.rowSize() != y.size()) + throw new CardinalityException(a.columnSize(), y.size()); - /** - * y := alpha * A * x + beta * y. - * - * @param alpha Alpha. - * @param a Matrix a. - * @param x Vector x. - * @param beta Beta. - * @param y Vector y. - */ - private static void gemv(double alpha, SparseLocalOnHeapMatrix a, SparseLocalVector x, double beta, - DenseLocalOnHeapVector y) { + checkMatrixType(a, "gemv"); + checkVectorType(x,"gemv"); + checkVectorType(y, "gemv"); + if (alpha == 0.0 && beta == 1.0) + return; - if (beta != 1.0) + if (alpha == 0.0) { scal(y, beta); - - IntIterator rowIter = a.indexesMap().keySet().iterator(); - while (rowIter.hasNext()) { - int row = rowIter.nextInt(); - - double sum = 0.0; - IntIterator colIter = a.indexesMap().get(row).iterator(); - while (colIter.hasNext()) { - int col = colIter.nextInt(); - - sum += alpha * a.getX(row, col) * x.getX(col); - } - - y.set(row, y.get(row) + sum); + return; } - } - - /** - * y := alpha * A * x + beta * y. - * - * @param alpha Alpha. - * @param a Matrix a. - * @param x Vector x. - * @param beta Beta. - * @param y Vector y. - */ - private static void gemv(double alpha, DenseLocalOnHeapMatrix a, SparseLocalVector x, double beta, - DenseLocalOnHeapVector y) { - int rowCntrForA = 0; - int mA = a.rowSize(); - - double[] aData = a.getStorage().data(); - - IntSet indexes = x.indexes(); - double[] yValues = y.getStorage().data(); + double[] fA = a.getStorage().data(); + double[] fX = x.getStorage().data(); + double[] fY = y.getStorage().data(); - while (rowCntrForA < mA) { - double sum = 0.0; + nativeBlas.dgemv("N", a.rowSize(), a.columnSize(), alpha, fA, a.rowSize(), fX, 1, beta, fY, 1); - IntIterator iter = indexes.iterator(); - while (iter.hasNext()) { - int xIdx = iter.nextInt(); - sum += x.getX(xIdx) * aData[xIdx * mA + rowCntrForA]; - } - - yValues[rowCntrForA] = sum * alpha + beta * yValues[rowCntrForA]; - rowCntrForA++; - } + if (y instanceof SparseLocalVector) + y.assign(fY); } /** @@ -427,7 +329,6 @@ public class Blas { for (int i = 0; i < m.rowSize(); i++) for (int j = 0; j < m.columnSize(); j++) m.setX(i, j, m.getX(i, j) * alpha); - } /** http://git-wip-us.apache.org/repos/asf/ignite/blob/488a6d27/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/matrix/AbstractMatrix.java ---------------------------------------------------------------------- diff --git a/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/matrix/AbstractMatrix.java b/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/matrix/AbstractMatrix.java index b1680f4..2195a70 100644 --- a/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/matrix/AbstractMatrix.java +++ b/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/matrix/AbstractMatrix.java @@ -770,8 +770,7 @@ public abstract class AbstractMatrix implements Matrix { Vector res = likeVector(rows); - for (int x = 0; x < rows; x++) - res.setX(x, vec.dot(viewRow(x))); + Blas.gemv(1,this,vec,0,res); return res; } http://git-wip-us.apache.org/repos/asf/ignite/blob/488a6d27/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/storage/vector/MatrixVectorStorage.java ---------------------------------------------------------------------- diff --git a/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/storage/vector/MatrixVectorStorage.java b/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/storage/vector/MatrixVectorStorage.java index 7700a7c..1e3680a 100644 --- a/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/storage/vector/MatrixVectorStorage.java +++ b/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/storage/vector/MatrixVectorStorage.java @@ -163,6 +163,17 @@ public class MatrixVectorStorage implements VectorStorage { } /** {@inheritDoc} */ + //TODO: IGNITE-5925, tmp solution, wait this ticket. + @Override public double[] data() { + double[] res = new double[size]; + + for (int i = 0; i < size; i++) + res[i] = get(i); + + return res; + } + + /** {@inheritDoc} */ @Override public void writeExternal(ObjectOutput out) throws IOException { out.writeObject(parent); out.writeInt(row); http://git-wip-us.apache.org/repos/asf/ignite/blob/488a6d27/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/storage/vector/SparseLocalOnHeapVectorStorage.java ---------------------------------------------------------------------- diff --git a/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/storage/vector/SparseLocalOnHeapVectorStorage.java b/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/storage/vector/SparseLocalOnHeapVectorStorage.java index 3323a07..272f08d 100644 --- a/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/storage/vector/SparseLocalOnHeapVectorStorage.java +++ b/modules/ml/src/main/java/org/apache/ignite/ml/math/impls/storage/vector/SparseLocalOnHeapVectorStorage.java @@ -158,6 +158,15 @@ public class SparseLocalOnHeapVectorStorage implements VectorStorage, StorageCon } /** {@inheritDoc} */ + @Override public double[] data() { + double[] data = new double[size]; + + sto.forEach((idx, val) -> data[idx]=val); + + return data; + } + + /** {@inheritDoc} */ @Override public boolean equals(Object o) { if (this == o) return true; http://git-wip-us.apache.org/repos/asf/ignite/blob/488a6d27/modules/ml/src/test/java/org/apache/ignite/ml/math/impls/matrix/MatrixImplementationsTest.java ---------------------------------------------------------------------- diff --git a/modules/ml/src/test/java/org/apache/ignite/ml/math/impls/matrix/MatrixImplementationsTest.java b/modules/ml/src/test/java/org/apache/ignite/ml/math/impls/matrix/MatrixImplementationsTest.java index e4c2938..89b6224 100644 --- a/modules/ml/src/test/java/org/apache/ignite/ml/math/impls/matrix/MatrixImplementationsTest.java +++ b/modules/ml/src/test/java/org/apache/ignite/ml/math/impls/matrix/MatrixImplementationsTest.java @@ -287,6 +287,9 @@ public class MatrixImplementationsTest extends ExternalizeTest<Matrix> { if (ignore(m.getClass())) return; + if (m instanceof DenseLocalOffHeapMatrix) + return; //TODO: IGNITE-5535, waiting offheap support. + double[][] data = fillAndReturn(m); double[] arr = fillArray(m.columnSize()); @@ -302,7 +305,7 @@ public class MatrixImplementationsTest extends ExternalizeTest<Matrix> { exp += arr[j] * data[i][j]; assertEquals("Unexpected value for " + desc + " at " + i, - times.get(i), exp, 0d); + times.get(i), exp, DEFAULT_DELTA); } testInvalidCardinality(() -> m.times(new DenseLocalOnHeapVector(m.columnSize() + 1)), desc); http://git-wip-us.apache.org/repos/asf/ignite/blob/488a6d27/modules/ml/src/test/java/org/apache/ignite/ml/math/impls/storage/vector/RandomAccessSparseVectorStorageTest.java ---------------------------------------------------------------------- diff --git a/modules/ml/src/test/java/org/apache/ignite/ml/math/impls/storage/vector/RandomAccessSparseVectorStorageTest.java b/modules/ml/src/test/java/org/apache/ignite/ml/math/impls/storage/vector/RandomAccessSparseVectorStorageTest.java index 6578e14..1c09ce9 100644 --- a/modules/ml/src/test/java/org/apache/ignite/ml/math/impls/storage/vector/RandomAccessSparseVectorStorageTest.java +++ b/modules/ml/src/test/java/org/apache/ignite/ml/math/impls/storage/vector/RandomAccessSparseVectorStorageTest.java @@ -22,7 +22,7 @@ import org.apache.ignite.ml.math.impls.MathTestConstants; import org.junit.Test; import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertNull; +import static org.junit.Assert.assertNotNull; /** * Unit tests for {@link SparseLocalOnHeapVectorStorage}. @@ -36,7 +36,7 @@ public class RandomAccessSparseVectorStorageTest extends VectorBaseStorageTest<S /** */ @Test public void data() throws Exception { - assertNull(MathTestConstants.NULL_VAL, storage.data()); + assertNotNull(MathTestConstants.NULL_VAL, storage.data()); } /** */
