org.apache.mahout.h2obindings.H2OHelper Maven / Gradle / Ivy
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* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.apache.mahout.h2obindings;
import org.apache.mahout.math.Matrix;
import org.apache.mahout.math.Vector;
import org.apache.mahout.math.DenseMatrix;
import org.apache.mahout.math.SparseMatrix;
import org.apache.mahout.math.DenseVector;
import water.MRTask;
import water.Futures;
import water.fvec.Frame;
import water.fvec.Vec;
import water.fvec.Chunk;
import water.parser.ValueString;
import water.util.ArrayUtils;
import java.util.Map;
import java.util.HashMap;
import java.io.Serializable;
import org.apache.mahout.h2obindings.drm.H2ODrm;
import org.apache.mahout.h2obindings.drm.H2OBCast;
// for makeEmptyStrVec
import water.Key;
import water.DKV;
import water.fvec.CStrChunk;
import scala.Function1;
import scala.Function2;
/**
* Collection of helper methods for H2O backend.
*/
public class H2OHelper {
/**
* Predicate to check if data is sparse in Frame.
*
* If the number of missing elements is 32x times the number of present
* elements, consider it as sparse.
*
* @param frame Frame storing matrix data.
* @return True if data is sparse in Frame.
*/
public static boolean isSparse(Frame frame) {
long rows = frame.numRows();
long cols = frame.numCols();
/**
* MRTask to aggregate precalculated per-chunk sparse lengths
*/
class MRTaskNZ extends MRTask {
long sparselen;
@Override
public void map(Chunk chks[]) {
for (Chunk chk : chks) {
sparselen += chk.sparseLen();
}
}
@Override
public void reduce(MRTaskNZ other) {
sparselen += other.sparselen;
}
}
long sparselen = new MRTaskNZ().doAll(frame).sparselen;
return (((rows * cols) / (sparselen + 1)) > 32);
}
/**
* Create a Mahout Matrix from a DRM.
*
* Create either Sparse or Dense Matrix depending on number of missing
* elements in DRM.
*
* @param drm DRM object to create Matrix from.
* @return created Matrix.
*/
public static Matrix matrixFromDrm(H2ODrm drm) {
Frame frame = drm.frame;
Vec labels = drm.keys;
Matrix m;
if (isSparse(frame)) {
m = new SparseMatrix((int)frame.numRows(), frame.numCols());
} else {
m = new DenseMatrix((int)frame.numRows(), frame.numCols());
}
int c = 0;
// Fill matrix, column at a time.
for (Vec v : frame.vecs()) {
for (int r = 0; r < frame.numRows(); r++) {
double d;
if (!v.isNA(r) && ((d = v.at(r)) != 0.0)) {
m.setQuick(r, c, d);
}
}
c++;
}
// If string keyed, set the stings as rowlabels.
if (labels != null) {
Map map = new HashMap<>();
ValueString vstr = new ValueString();
for (long i = 0; i < labels.length(); i++) {
map.put(labels.atStr(vstr, i).toString(), (int)i);
}
m.setRowLabelBindings(map);
}
return m;
}
/**
* Calculate Means of elements in a column, and return as a Vector.
*
* H2O precalculates means in a Vec, and a Vec corresponds to a column.
*
* @param frame Frame backing the H2O DRM.
* @return Vector of pre-calculated means.
*/
public static Vector colMeans(Frame frame) {
double means[] = new double[frame.numCols()];
for (int i = 0; i < frame.numCols(); i++) {
means[i] = frame.vecs()[i].mean();
}
return new DenseVector(means);
}
/**
* Calculate Sums of elements in a column, and return as a Vector.
*
* Run an MRTask Job to add up sums.
* WARNING: Vulnerable to overflow. No way around it.
*
* @param frame Frame backing the H2O DRM.
* @return Vector of calculated sums.
*/
public static Vector colSums(Frame frame) {
/**
* MRTask to calculate sums of elements in all columns.
*/
class MRTaskSum extends MRTask {
public double sums[];
@Override
public void map(Chunk chks[]) {
sums = new double[chks.length];
for (int c = 0; c < chks.length; c++) {
for (int r = 0; r < chks[c].len(); r++) {
sums[c] += chks[c].atd(r);
}
}
}
@Override
public void reduce(MRTaskSum other) {
ArrayUtils.add(sums, other.sums);
}
}
return new DenseVector(new MRTaskSum().doAll(frame).sums);
}
/**
* Calculate Sum of squares of all elements in the DRM.
*
* Run an MRTask Job to add up sums of squares.
* WARNING: Vulnerable to overflow. No way around it.
*
* @param frame Frame backing the H2O DRM.
* @return Sum of squares of all elements in the DRM.
*/
public static double sumSqr(Frame frame) {
/**
* MRTask to calculate sums of squares of all elements.
*/
class MRTaskSumSqr extends MRTask {
public double sumSqr;
@Override
public void map(Chunk chks[]) {
for (Chunk chk : chks) {
for (int r = 0; r < chk.len(); r++) {
sumSqr += (chk.atd(r) * chk.atd(r));
}
}
}
@Override
public void reduce(MRTaskSumSqr other) {
sumSqr += other.sumSqr;
}
}
return new MRTaskSumSqr().doAll(frame).sumSqr;
}
/**
* Count non-zero elements in all columns, and return as a Vector.
*
* Run an MRTask Job to count non-zero elements per column.
*
* @param frame Frame backing the H2O DRM.
* @return Vector of counted non-zero elements.
*/
public static Vector nonZeroCnt(Frame frame) {
/**
* MRTask to count all non-zero elements.
*/
class MRTaskNonZero extends MRTask {
public double sums[];
@Override
public void map(Chunk chks[]) {
sums = new double[chks.length];
for (int c = 0; c < chks.length; c++) {
for (int r = 0; r < chks[c].len(); r++) {
if ((long)chks[c].atd(r) != 0) {
sums[c] ++;
}
}
}
}
@Override
public void reduce(MRTaskNonZero other) {
ArrayUtils.add(sums, other.sums);
}
}
return new DenseVector(new MRTaskNonZero().doAll(frame).sums);
}
/** Convert String->Integer map to Integer->String map */
private static Map reverseMap(Map map) {
if (map == null) {
return null;
}
Map rmap = new HashMap<>();
for(Map.Entry entry : map.entrySet()) {
rmap.put(entry.getValue(),entry.getKey());
}
return rmap;
}
/**
* Calculate optimum chunk size for given parameters.
*
* Chunk size is the number of elements stored per partition per column.
*
* @param nrow Number of rows in the DRM.
* @param minHint Minimum number of partitions to create, if passed value is not -1.
* @param exactHint Exact number of partitions to create, if passed value is not -1.
* @return Calculated optimum chunk size.
*/
private static int chunkSize(long nrow, int minHint, int exactHint) {
int chunkSz;
int partsHint = Math.max(minHint, exactHint);
if (partsHint < 1) {
/* XXX: calculate based on cloud size and # of cpu */
partsHint = 4;
}
chunkSz = (int)(((nrow - 1) / partsHint) + 1);
if (exactHint > 0) {
return chunkSz;
}
if (chunkSz > 1e6) {
chunkSz = (int)1e6;
}
if (minHint > 0) {
return chunkSz;
}
if (chunkSz < 1e3) {
chunkSz = (int)1e3;
}
return chunkSz;
}
/**
* Ingest a Mahout Matrix into an H2O DRM.
*
* Frame is the backing data structure behind CheckpointedDrm.
*
* @param m Mahout Matrix to ingest data from.
* @param minHint Hint for minimum number of partitions in created DRM.
* @param exactHint Hint for exact number of partitions in created DRM.
* @return Created H2O backed DRM.
*/
public static H2ODrm drmFromMatrix(Matrix m, int minHint, int exactHint) {
// First create an empty (0-filled) frame of the required dimensions
Frame frame = emptyFrame(m.rowSize(), m.columnSize(), minHint, exactHint);
Vec labels = null;
Vec.Writer writers[] = new Vec.Writer[m.columnSize()];
Futures closer = new Futures();
// "open" vectors for writing efficiently in bulk
for (int i = 0; i < writers.length; i++) {
writers[i] = frame.vecs()[i].open();
}
for (int r = 0; r < m.rowSize(); r++) {
for (int c = 0; c < m.columnSize(); c++) {
writers[c].set(r, m.getQuick(r, c));
}
}
for (int c = 0; c < m.columnSize(); c++) {
writers[c].close(closer);
}
// If string labeled matrix, create aux Vec
Map map = m.getRowLabelBindings();
if (map != null) {
// label vector must be similarly partitioned like the Frame
labels = makeEmptyStrVec(frame.anyVec());
Vec.Writer writer = labels.open();
Map rmap = reverseMap(map);
for (int r = 0; r < m.rowSize(); r++) {
writer.set(r, rmap.get(r));
}
writer.close(closer);
}
closer.blockForPending();
return new H2ODrm(frame, labels);
}
/**
* Create an empty (zero-filled) H2O Frame efficiently.
*
* Create a zero filled Frame with specified cardinality.
* Do not actually fill zeroes in each cell, create pre-compressed chunks.
* Time taken per column asymptotically at O(nChunks), not O(nrow).
*
* @param nrow Number of rows in the Frame.
* @param ncol Number of columns in the Frame.
* @param minHint Hint for minimum number of chunks per column in created Frame.
* @param exactHint Hint for exact number of chunks per column in created Frame.
* @return Created Frame.
*/
public static Frame emptyFrame(long nrow, int ncol, int minHint, int exactHint) {
Vec.VectorGroup vg = new Vec.VectorGroup();
return emptyFrame(nrow, ncol, minHint, exactHint, vg);
}
/**
* Create an empty (zero-filled) H2O Frame efficiently.
*
* Create a zero filled Frame with specified cardinality.
* Do not actually fill zeroes in each cell, create pre-compressed chunks.
* Time taken per column asymptotically at O(nChunks), not O(nrow).
*
* @param nrow Number of rows in the Frame.
* @param ncol Number of columns in the Frame.
* @param minHint Hint for minimum number of chunks per column in created Frame.
* @param exactHint Hint for exact number of chunks per column in created Frame.
* @param vg Shared VectorGroup so that all columns are similarly partitioned.
* @return Created Frame.
*/
public static Frame emptyFrame(long nrow, int ncol, int minHint, int exactHint, Vec.VectorGroup vg) {
int chunkSz = chunkSize(nrow, minHint, exactHint);
int nchunks = (int)((nrow - 1) / chunkSz) + 1; // Final number of Chunks per Vec
long espc[] = new long[nchunks + 1];
for (int i = 0; i < nchunks; i++) {
espc[i] = i * chunkSz;
}
espc[nchunks] = nrow;
// Create a vector template for new vectors
Vec vtemplate = new Vec(vg.addVec(), espc);
// Make ncol-numeric vectors
Vec[] vecs = vtemplate.makeCons(ncol, 0, null, null);
return new Frame(vecs);
}
/**
* The following two methods: vecChunkLen and makeEmptyStrVec
* are h2o-0.1.25 specific.
*/
public static Vec makeEmptyStrVec(final Vec template) {
final int nChunks = template.nChunks();
Key key = template.group().addVec();
final Vec emptystr = new Vec(key, template._espc, null, Vec.T_NUM);
new MRTask() {
@Override protected void setupLocal() {
for (int i = 0; i < nChunks; i++) {
Key k = emptystr.chunkKey(i);
int chklen = vecChunkLen(template, i);
int stridx[] = new int[chklen];
byte b[] = new byte[1]; b[0] = 0;
for (int j = 0; j < chklen; j++) stridx[j] = -1;
if (k.home()) DKV.put(k, new CStrChunk(1, b, chklen, stridx), _fs);
}
if (emptystr._key.home()) DKV.put(emptystr._key, emptystr, _fs);
}
}.doAllNodes();
return emptystr;
}
public static int vecChunkLen(Vec template, int chunk) {
return (int) (template._espc[chunk + 1] - template._espc[chunk]);
}
/**
* Create an empty (zero-filled) H2O DRM.
*
* Create a zero filled DRM with specified cardinality.
* Use the efficient emptyFrame() method internally.
*
* @param nrow Number of rows in the Frame.
* @param ncol Number of columns in the Frame.
* @param minHint Hint for minimum number of chunks per column in created Frame.
* @param exactHint Hint for exact number of chunks per column in created Frame.
* @return Created DRM.
*/
public static H2ODrm emptyDrm(long nrow, int ncol, int minHint, int exactHint) {
return new H2ODrm(emptyFrame(nrow, ncol, minHint, exactHint));
}
public static Matrix allreduceBlock(H2ODrm drmA, Object bmfn, Object rfn) {
class MRTaskMR extends MRTask {
H2OBCast bmf_out;
Serializable bmf;
Serializable rf;
public MRTaskMR(Object _bmf, Object _rf) {
bmf = (Serializable) _bmf;
rf = (Serializable) _rf;
}
@Override
public void map(Chunk chks[]) {
Function1 f = (Function1) bmf;
bmf_out = new H2OBCast((Matrix)f.apply(new scala.Tuple2(null, new H2OBlockMatrix(chks))));
}
@Override
public void reduce(MRTaskMR that) {
Function2 f = (Function2) rf;
bmf_out = new H2OBCast((Matrix)f.apply(this.bmf_out.value(), that.bmf_out.value()));
}
}
return new MRTaskMR(bmfn, rfn).doAll(drmA.frame).bmf_out.value();
}
}
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