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Posted to commits@systemds.apache.org by mb...@apache.org on 2021/01/31 19:22:24 UTC
[systemds] branch master updated (eeffef6 -> ebcc44d)
This is an automated email from the ASF dual-hosted git repository.
mboehm7 pushed a change to branch master
in repository https://gitbox.apache.org/repos/asf/systemds.git.
from eeffef6 [SYSTEMDS-2812] Added conv1d layer to nn library (via conv2d)
new 6396846 [SYSTEMDS-2818] Fix read/copy of large dense matrix blocks >16GB
new ebcc44d [SYSTEMDS-2819,2020] Various ctable improvements (rewrites, spark ops)
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
scripts/builtin/slicefinder.dml | 2 +-
src/main/java/org/apache/sysds/api/DMLScript.java | 12 ++---
.../java/org/apache/sysds/hops/OptimizerUtils.java | 33 +++++++++-----
src/main/java/org/apache/sysds/hops/TernaryOp.java | 42 ++++++++++++++---
.../apache/sysds/hops/rewrite/HopRewriteUtils.java | 14 +++---
src/main/java/org/apache/sysds/lops/Ctable.java | 52 ++++++++++------------
.../sysds/parser/BuiltinFunctionExpression.java | 13 ++++--
.../org/apache/sysds/parser/DMLTranslator.java | 9 +++-
.../context/SparkExecutionContext.java | 4 ++
.../org/apache/sysds/runtime/data/DenseBlock.java | 9 ++--
.../instructions/spark/CtableSPInstruction.java | 21 ++++++---
.../instructions/spark/utils/SparkUtils.java | 8 +++-
.../functions/builtin/BuiltinSliceFinderTest.java | 12 +++--
13 files changed, 154 insertions(+), 77 deletions(-)
[systemds] 01/02: [SYSTEMDS-2818] Fix read/copy of large dense
matrix blocks >16GB
Posted by mb...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
mboehm7 pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/systemds.git
commit 6396846748f2e80ade7c04aae498e83b811cac5a
Author: Matthias Boehm <mb...@gmail.com>
AuthorDate: Sun Jan 31 15:30:16 2021 +0100
[SYSTEMDS-2818] Fix read/copy of large dense matrix blocks >16GB
The generalization of matrix blocks towards multi-dimensional arrays
(tensors) and different value types introduced integer overflows when
computing internal offsets during block copies as done during the read
of large dense matrices. This patch fixes both the overflows and
indexing logic in general. Unfortunately, the issue only showed up with
blocks >16GB that are infeasible to include into the unit tests.
---
src/main/java/org/apache/sysds/runtime/data/DenseBlock.java | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/src/main/java/org/apache/sysds/runtime/data/DenseBlock.java b/src/main/java/org/apache/sysds/runtime/data/DenseBlock.java
index 47498f9..489400d 100644
--- a/src/main/java/org/apache/sysds/runtime/data/DenseBlock.java
+++ b/src/main/java/org/apache/sysds/runtime/data/DenseBlock.java
@@ -459,10 +459,13 @@ public abstract class DenseBlock implements Serializable
if (db.isNumeric()) {
int rowOther = 0;
int colOther = 0;
- for (int bi = index(rl); bi <= index(ru - 1); bi++) {
+ for (int bi = index(rl); bi <= index(ru-1); bi++) {
+ int rpos = bi*blockSize();
+ int rposl = Math.max(rl-rpos, 0);
if (allColumns) {
- int offset = rl * _odims[0] + cl;
- for (int i = 0; i < (ru - rl) * _odims[0]; i++) {
+ int offset = rposl * _odims[0] + cl;
+ int rlen = Math.min(ru-Math.max(rpos,rl), blockSize(bi)-rposl);
+ for (int i = 0; i < rlen * _odims[0]; i++) {
setInternal(bi, offset + i, db.get(rowOther, colOther));
colOther++;
if (colOther == db.getCumODims(0)) {
[systemds] 02/02: [SYSTEMDS-2819,
2020] Various ctable improvements (rewrites, spark ops)
Posted by mb...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
mboehm7 pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/systemds.git
commit ebcc44db28d59ec076e3a56cee1051361a1d3c24
Author: Matthias Boehm <mb...@gmail.com>
AuthorDate: Sun Jan 31 19:40:36 2021 +0100
[SYSTEMDS-2819,2020] Various ctable improvements (rewrites, spark ops)
* New ctable-reshape rewrite to avoid unnecessary intermediates (in CP,
this also enables large datasets w/ nrow*ncol > max-integer)
* Improved estimation of ultra-sparse distributed matrices to avoid huge
number of partitions on ctable and other operations (on criteo day 21,
11K vs 500K partitions)
* New ctable parameter to specify need to emit empty output blocks (on
ultra-sparse matrices these empty blocks dominate the total size and are
only needed for sparse unsafe distributed operations, right now this is
an undocumented parameter, in the future this should become an
interesting property and be propagated across the entire program)
* Better error handling in spark ctable instructions to indicate invalid
output dimensions (e.g., invalid pre-pass finds 0 max dimension value
due to to missing values)
* Avoid unnecessary partitioning on parfor entry (despite expected
zipmm/cpmm) if distributed matrices are already hash-partitioned.
* Leverage new ctable configurations in slice finder built-in
* Fix DMLScript error printing to avoid NPEs (on-existing default opts)
---
scripts/builtin/slicefinder.dml | 2 +-
src/main/java/org/apache/sysds/api/DMLScript.java | 12 ++---
.../java/org/apache/sysds/hops/OptimizerUtils.java | 33 +++++++++-----
src/main/java/org/apache/sysds/hops/TernaryOp.java | 42 ++++++++++++++---
.../apache/sysds/hops/rewrite/HopRewriteUtils.java | 14 +++---
src/main/java/org/apache/sysds/lops/Ctable.java | 52 ++++++++++------------
.../sysds/parser/BuiltinFunctionExpression.java | 13 ++++--
.../org/apache/sysds/parser/DMLTranslator.java | 9 +++-
.../context/SparkExecutionContext.java | 4 ++
.../instructions/spark/CtableSPInstruction.java | 21 ++++++---
.../instructions/spark/utils/SparkUtils.java | 8 +++-
.../functions/builtin/BuiltinSliceFinderTest.java | 12 +++--
12 files changed, 148 insertions(+), 74 deletions(-)
diff --git a/scripts/builtin/slicefinder.dml b/scripts/builtin/slicefinder.dml
index 5a20fb5..9c49718 100644
--- a/scripts/builtin/slicefinder.dml
+++ b/scripts/builtin/slicefinder.dml
@@ -53,7 +53,7 @@ m_slicefinder = function(Matrix[Double] X, Matrix[Double] e,
foffe = t(cumsum(t(fdom)))
rix = matrix(seq(1,m)%*%matrix(1,1,n), m*n, 1)
cix = matrix(X + foffb, m*n, 1);
- X2 = table(rix, cix); #one-hot encoded
+ X2 = table(rix, cix, 1, m, as.scalar(foffe[,n]), FALSE); #one-hot encoded
# initialize statistics and basic slices
n2 = ncol(X2); # one-hot encoded features
diff --git a/src/main/java/org/apache/sysds/api/DMLScript.java b/src/main/java/org/apache/sysds/api/DMLScript.java
index 703ae6c..d523483 100644
--- a/src/main/java/org/apache/sysds/api/DMLScript.java
+++ b/src/main/java/org/apache/sysds/api/DMLScript.java
@@ -182,7 +182,7 @@ public class DMLScript
* @throws IOException If an internal IOException happens.
*/
public static boolean executeScript( Configuration conf, String[] args )
- throws IOException, ParseException, DMLScriptException
+ throws IOException, ParseException, DMLScriptException
{
//parse arguments and set execution properties
ExecMode oldrtplatform = EXEC_MODE; //keep old rtplatform
@@ -195,14 +195,16 @@ public class DMLScript
}
catch(AlreadySelectedException e) {
LOG.error("Mutually exclusive options were selected. " + e.getMessage());
- HelpFormatter formatter = new HelpFormatter();
- formatter.printHelp( "systemds", DMLOptions.defaultOptions.options );
+ //TODO fix null default options
+ //HelpFormatter formatter = new HelpFormatter();
+ //formatter.printHelp( "systemds", DMLOptions.defaultOptions.options );
return false;
}
catch(org.apache.commons.cli.ParseException e) {
LOG.error("Parsing Exception " + e.getMessage());
- HelpFormatter formatter = new HelpFormatter();
- formatter.printHelp( "systemds", DMLOptions.defaultOptions.options );
+ //TODO fix null default options
+ //HelpFormatter formatter = new HelpFormatter();
+ //formatter.printHelp( "systemds", DMLOptions.defaultOptions.options );
return false;
}
diff --git a/src/main/java/org/apache/sysds/hops/OptimizerUtils.java b/src/main/java/org/apache/sysds/hops/OptimizerUtils.java
index dce33f2..55a9617 100644
--- a/src/main/java/org/apache/sysds/hops/OptimizerUtils.java
+++ b/src/main/java/org/apache/sysds/hops/OptimizerUtils.java
@@ -46,6 +46,7 @@ import org.apache.sysds.runtime.controlprogram.caching.LazyWriteBuffer;
import org.apache.sysds.runtime.controlprogram.context.SparkExecutionContext;
import org.apache.sysds.runtime.controlprogram.parfor.stat.InfrastructureAnalyzer;
import org.apache.sysds.runtime.data.SparseBlock;
+import org.apache.sysds.runtime.data.SparseBlock.Type;
import org.apache.sysds.runtime.functionobjects.IntegerDivide;
import org.apache.sysds.runtime.functionobjects.Modulus;
import org.apache.sysds.runtime.instructions.cp.Data;
@@ -660,12 +661,16 @@ public class OptimizerUtils
* @param dc matrix characteristics
* @return memory estimate
*/
- public static long estimatePartitionedSizeExactSparsity(DataCharacteristics dc)
+ public static long estimatePartitionedSizeExactSparsity(DataCharacteristics dc) {
+ return estimatePartitionedSizeExactSparsity(dc, true);
+ }
+
+ public static long estimatePartitionedSizeExactSparsity(DataCharacteristics dc, boolean outputEmptyBlocks)
{
if (dc instanceof MatrixCharacteristics) {
return estimatePartitionedSizeExactSparsity(
- dc.getRows(), dc.getCols(),
- dc.getBlocksize(), dc.getNonZerosBound());
+ dc.getRows(), dc.getCols(), dc.getBlocksize(),
+ dc.getNonZerosBound(), outputEmptyBlocks);
}
else {
// TODO estimate partitioned size exact for tensor
@@ -691,6 +696,11 @@ public class OptimizerUtils
double sp = getSparsity(rlen, clen, nnz);
return estimatePartitionedSizeExactSparsity(rlen, clen, blen, sp);
}
+
+ public static long estimatePartitionedSizeExactSparsity(long rlen, long clen, long blen, long nnz, boolean outputEmptyBlocks) {
+ double sp = getSparsity(rlen, clen, nnz);
+ return estimatePartitionedSizeExactSparsity(rlen, clen, blen, sp, outputEmptyBlocks);
+ }
/**
* Estimates the footprint (in bytes) for a partitioned in-memory representation of a
@@ -717,7 +727,12 @@ public class OptimizerUtils
* @param sp sparsity
* @return memory estimate
*/
- public static long estimatePartitionedSizeExactSparsity(long rlen, long clen, long blen, double sp)
+ public static long estimatePartitionedSizeExactSparsity(long rlen, long clen, long blen, double sp) {
+ return estimatePartitionedSizeExactSparsity(rlen, clen, blen, sp, true);
+ }
+
+
+ public static long estimatePartitionedSizeExactSparsity(long rlen, long clen, long blen, double sp, boolean outputEmptyBlocks)
{
long ret = 0;
@@ -728,8 +743,8 @@ public class OptimizerUtils
if( nnz <= tnrblks * tncblks ) {
long lrlen = Math.min(rlen, blen);
long lclen = Math.min(clen, blen);
- return nnz * estimateSizeExactSparsity(lrlen, lclen, 1)
- + (tnrblks * tncblks - nnz) * estimateSizeEmptyBlock(lrlen, lclen);
+ return nnz * MatrixBlock.estimateSizeSparseInMemory(lrlen, lclen, 1d/lrlen/lclen, Type.COO)
+ + (outputEmptyBlocks ? (tnrblks * tncblks - nnz) * estimateSizeEmptyBlock(lrlen, lclen) : 0);
}
//estimate size of full blen x blen blocks
@@ -763,13 +778,11 @@ public class OptimizerUtils
* @param ncols number of cols
* @return memory estimate
*/
- public static long estimateSize(long nrows, long ncols)
- {
+ public static long estimateSize(long nrows, long ncols) {
return estimateSizeExactSparsity(nrows, ncols, 1.0);
}
- public static long estimateSizeEmptyBlock(long nrows, long ncols)
- {
+ public static long estimateSizeEmptyBlock(long nrows, long ncols) {
return estimateSizeExactSparsity(0, 0, 0.0d);
}
diff --git a/src/main/java/org/apache/sysds/hops/TernaryOp.java b/src/main/java/org/apache/sysds/hops/TernaryOp.java
index 6700fe6..2989b43 100644
--- a/src/main/java/org/apache/sysds/hops/TernaryOp.java
+++ b/src/main/java/org/apache/sysds/hops/TernaryOp.java
@@ -89,7 +89,7 @@ public class TernaryOp extends Hop
// Constructor the case where TertiaryOp (table, in particular) has
// output dimensions
public TernaryOp(String l, DataType dt, ValueType vt, OpOp3 o,
- Hop inp1, Hop inp2, Hop inp3, Hop inp4, Hop inp5) {
+ Hop inp1, Hop inp2, Hop inp3, Hop inp4, Hop inp5, Hop inp6) {
super(l, dt, vt);
_op = o;
getInput().add(0, inp1);
@@ -97,11 +97,13 @@ public class TernaryOp extends Hop
getInput().add(2, inp3);
getInput().add(3, inp4);
getInput().add(4, inp5);
+ getInput().add(5, inp6);
inp1.getParent().add(this);
inp2.getParent().add(this);
inp3.getParent().add(this);
inp4.getParent().add(this);
inp5.getParent().add(this);
+ inp6.getParent().add(this);
_dimInputsPresent = true;
}
@@ -293,14 +295,22 @@ public class TernaryOp extends Hop
Ctable.OperationTypes ternaryOp = isSequenceRewriteApplicable(true) ?
Ctable.OperationTypes.CTABLE_EXPAND_SCALAR_WEIGHT : ternaryOpOrig;
boolean ignoreZeros = false;
+ boolean outputEmptyBlocks = (getInput().size() == 6) ?
+ HopRewriteUtils.getBooleanValue((LiteralOp)getInput(5)) : true;
if( isMatrixIgnoreZeroRewriteApplicable() ) {
- ignoreZeros = true; //table - rmempty - rshape
- inputLops[0] = ((ParameterizedBuiltinOp)getInput().get(0)).getTargetHop().getInput().get(0).constructLops();
- inputLops[1] = ((ParameterizedBuiltinOp)getInput().get(1)).getTargetHop().getInput().get(0).constructLops();
+ ignoreZeros = true; //table - rmempty - rshape --> table
+ inputLops[0] = ((ParameterizedBuiltinOp)getInput(0)).getTargetHop().getInput(0).constructLops();
+ inputLops[1] = ((ParameterizedBuiltinOp)getInput(1)).getTargetHop().getInput(0).constructLops();
+ }
+ else if( isCTableReshapeRewriteApplicable(et, ternaryOp) ) {
+ //table - reshape --> table
+ inputLops[0] = ((ReorgOp)getInput(0)).getInput(0).constructLops();
+ inputLops[1] = ((ReorgOp)getInput(1)).getInput(0).constructLops();
}
- Ctable ternary = new Ctable(inputLops, ternaryOp, getDataType(), getValueType(), ignoreZeros, et);
+ Ctable ternary = new Ctable(inputLops, ternaryOp,
+ getDataType(), getValueType(), ignoreZeros, outputEmptyBlocks, et);
ternary.getOutputParameters().setDimensions(getDim1(), getDim2(), getBlocksize(), -1);
setLineNumbers(ternary);
@@ -710,4 +720,26 @@ public class TernaryOp extends Hop
return ret;
}
+
+ public boolean isCTableReshapeRewriteApplicable(ExecType et, Ctable.OperationTypes opType) {
+ //early abort if rewrite globally not allowed
+ if( !ALLOW_CTABLE_SEQUENCE_REWRITES || _op!=OpOp3.CTABLE || et!=ExecType.CP )
+ return false;
+
+ //1) check for ctable CTABLE_TRANSFORM_SCALAR_WEIGHT
+ if( opType==Ctable.OperationTypes.CTABLE_TRANSFORM_SCALAR_WEIGHT ) {
+ Hop input1 = getInput().get(0);
+ Hop input2 = getInput().get(1);
+ //2) check for reshape pair
+ if( input1 instanceof ReorgOp && ((ReorgOp)input1).getOp()==ReOrgOp.RESHAPE
+ && input2 instanceof ReorgOp && ((ReorgOp)input2).getOp()==ReOrgOp.RESHAPE )
+ {
+ //common byrow parameter
+ return input1.getInput(4) == input2.getInput(4) //CSE
+ || input1.getInput(4).compare(input2.getInput(4));
+ }
+ }
+
+ return false;
+ }
}
diff --git a/src/main/java/org/apache/sysds/hops/rewrite/HopRewriteUtils.java b/src/main/java/org/apache/sysds/hops/rewrite/HopRewriteUtils.java
index d21b16c..391cc0d 100644
--- a/src/main/java/org/apache/sysds/hops/rewrite/HopRewriteUtils.java
+++ b/src/main/java/org/apache/sysds/hops/rewrite/HopRewriteUtils.java
@@ -100,8 +100,8 @@ public class HopRewriteUtils
public static boolean getBooleanValue( LiteralOp op ) {
switch( op.getValueType() ) {
- case FP64: return op.getDoubleValue() != 0;
- case INT64: return op.getLongValue() != 0;
+ case FP64: return op.getDoubleValue() != 0;
+ case INT64: return op.getLongValue() != 0;
case BOOLEAN: return op.getBooleanValue();
default: throw new HopsException("Invalid boolean value: "+op.getValueType());
}
@@ -110,8 +110,8 @@ public class HopRewriteUtils
public static boolean getBooleanValueSafe( LiteralOp op ) {
try {
switch( op.getValueType() ) {
- case FP64: return op.getDoubleValue() != 0;
- case INT64: return op.getLongValue() != 0;
+ case FP64: return op.getDoubleValue() != 0;
+ case INT64: return op.getLongValue() != 0;
case BOOLEAN: return op.getBooleanValue();
default: throw new HopsException("Invalid boolean value: "+op.getValueType());
}
@@ -126,8 +126,8 @@ public class HopRewriteUtils
public static double getDoubleValue( LiteralOp op ) {
switch( op.getValueType() ) {
case STRING:
- case FP64: return op.getDoubleValue();
- case INT64: return op.getLongValue();
+ case FP64: return op.getDoubleValue();
+ case INT64: return op.getLongValue();
case BOOLEAN: return op.getBooleanValue() ? 1 : 0;
default: throw new HopsException("Invalid double value: "+op.getValueType());
}
@@ -802,7 +802,7 @@ public class HopRewriteUtils
}
public static TernaryOp createTernary(Hop in1, Hop in2, Hop in3, Hop in4, Hop in5, OpOp3 op) {
- TernaryOp ternOp = new TernaryOp("tmp", DataType.MATRIX, ValueType.FP64, op, in1, in2, in3, in4, in5);
+ TernaryOp ternOp = new TernaryOp("tmp", DataType.MATRIX, ValueType.FP64, op, in1, in2, in3, in4, in5, new LiteralOp(true));
ternOp.setBlocksize(Math.max(in1.getBlocksize(), in2.getBlocksize()));
copyLineNumbers(in1, ternOp);
ternOp.refreshSizeInformation();
diff --git a/src/main/java/org/apache/sysds/lops/Ctable.java b/src/main/java/org/apache/sysds/lops/Ctable.java
index 93032c9..30c1120 100644
--- a/src/main/java/org/apache/sysds/lops/Ctable.java
+++ b/src/main/java/org/apache/sysds/lops/Ctable.java
@@ -33,14 +33,15 @@ import org.apache.sysds.common.Types.ValueType;
public class Ctable extends Lop
{
- private boolean _ignoreZeros = false;
+ private final boolean _ignoreZeros;
+ private final boolean _outputEmptyBlocks;
- public enum OperationTypes {
- CTABLE_TRANSFORM,
- CTABLE_TRANSFORM_SCALAR_WEIGHT,
+ public enum OperationTypes {
+ CTABLE_TRANSFORM,
+ CTABLE_TRANSFORM_SCALAR_WEIGHT,
CTABLE_TRANSFORM_HISTOGRAM,
- CTABLE_TRANSFORM_WEIGHTED_HISTOGRAM,
- CTABLE_EXPAND_SCALAR_WEIGHT,
+ CTABLE_TRANSFORM_WEIGHTED_HISTOGRAM,
+ CTABLE_EXPAND_SCALAR_WEIGHT,
INVALID;
public boolean hasSecondInput() {
return this == CTABLE_TRANSFORM
@@ -57,13 +58,14 @@ public class Ctable extends Lop
public Ctable(Lop[] inputLops, OperationTypes op, DataType dt, ValueType vt, ExecType et) {
- this(inputLops, op, dt, vt, false, et);
+ this(inputLops, op, dt, vt, false, true, et);
}
- public Ctable(Lop[] inputLops, OperationTypes op, DataType dt, ValueType vt, boolean ignoreZeros, ExecType et) {
+ public Ctable(Lop[] inputLops, OperationTypes op, DataType dt, ValueType vt, boolean ignoreZeros, boolean outputEmptyBlocks, ExecType et) {
super(Lop.Type.Ctable, dt, vt);
init(inputLops, op, et);
_ignoreZeros = ignoreZeros;
+ _outputEmptyBlocks = outputEmptyBlocks;
}
private void init(Lop[] inputLops, OperationTypes op, ExecType et) {
@@ -111,8 +113,7 @@ public class Ctable extends Lop
* @return operation type
*/
- public OperationTypes getOperationType()
- {
+ public OperationTypes getOperationType() {
return operation;
}
@@ -128,28 +129,19 @@ public class Ctable extends Lop
sb.append( "ctableexpand" );
sb.append( OPERAND_DELIMITOR );
- if ( getInputs().get(0).getDataType() == DataType.SCALAR ) {
- sb.append ( getInputs().get(0).prepScalarInputOperand(getExecType()) );
- }
- else {
- sb.append( getInputs().get(0).prepInputOperand(input1));
- }
+ sb.append( getInputs().get(0).getDataType() == DataType.SCALAR ?
+ getInputs().get(0).prepScalarInputOperand(getExecType()) :
+ getInputs().get(0).prepInputOperand(input1));
sb.append( OPERAND_DELIMITOR );
- if ( getInputs().get(1).getDataType() == DataType.SCALAR ) {
- sb.append ( getInputs().get(1).prepScalarInputOperand(getExecType()) );
- }
- else {
- sb.append( getInputs().get(1).prepInputOperand(input2));
- }
+ sb.append( getInputs().get(1).getDataType() == DataType.SCALAR ?
+ getInputs().get(1).prepScalarInputOperand(getExecType()) :
+ getInputs().get(1).prepInputOperand(input2));
sb.append( OPERAND_DELIMITOR );
- if ( getInputs().get(2).getDataType() == DataType.SCALAR ) {
- sb.append ( getInputs().get(2).prepScalarInputOperand(getExecType()) );
- }
- else {
- sb.append( getInputs().get(2).prepInputOperand(input3));
- }
+ sb.append( getInputs().get(2).getDataType() == DataType.SCALAR ?
+ getInputs().get(2).prepScalarInputOperand(getExecType()) :
+ getInputs().get(2).prepInputOperand(input3));
sb.append( OPERAND_DELIMITOR );
if ( this.getInputs().size() > 3 ) {
@@ -178,6 +170,10 @@ public class Ctable extends Lop
sb.append( OPERAND_DELIMITOR );
sb.append( _ignoreZeros );
+ if( getExecType() == ExecType.SPARK ) {
+ sb.append( OPERAND_DELIMITOR );
+ sb.append( _outputEmptyBlocks );
+ }
return sb.toString();
}
diff --git a/src/main/java/org/apache/sysds/parser/BuiltinFunctionExpression.java b/src/main/java/org/apache/sysds/parser/BuiltinFunctionExpression.java
index 5c397a0..8bf7fd1 100644
--- a/src/main/java/org/apache/sysds/parser/BuiltinFunctionExpression.java
+++ b/src/main/java/org/apache/sysds/parser/BuiltinFunctionExpression.java
@@ -970,13 +970,14 @@ public class BuiltinFunctionExpression extends DataIdentifier
case TABLE:
/*
- * Allowed #of arguments: 2,3,4,5
+ * Allowed #of arguments: 2,3,4,5,6
* table(A,B)
* table(A,B,W)
* table(A,B,1)
* table(A,B,dim1,dim2)
* table(A,B,W,dim1,dim2)
* table(A,B,1,dim1,dim2)
+ * table(A,B,1,dim1,dim2,TRUE)
*/
// Check for validity of input arguments, and setup output dimensions
@@ -985,9 +986,8 @@ public class BuiltinFunctionExpression extends DataIdentifier
checkMatrixParam(getFirstExpr());
if (getSecondExpr() == null)
- raiseValidateError(
- "Invalid number of arguments to table(). The table() function requires 2, 3, 4, or 5 arguments.",
- conditional);
+ raiseValidateError("Invalid number of arguments to table(). "
+ + "The table() function requires 2, 3, 4, 5, or 6 arguments.", conditional);
// Second input: can be MATRIX or SCALAR
// cases: table(A,B) or table(A,1)
@@ -1031,6 +1031,7 @@ public class BuiltinFunctionExpression extends DataIdentifier
break;
case 5:
+ case 6:
// case - table w/ weights and output dimensions:
// - table(A,B,W,dim1,dim2) or table(A,1,W,dim1,dim2)
// - table(A,B,1,dim1,dim2) or table(A,1,1,dim1,dim2)
@@ -1055,6 +1056,10 @@ public class BuiltinFunctionExpression extends DataIdentifier
if ( _args[4].getOutput() instanceof ConstIdentifier )
outputDim2 = ((ConstIdentifier) _args[4].getOutput()).getLongValue();
}
+ if( _args.length == 6 ) {
+ if( !_args[5].getOutput().isScalarBoolean() )
+ raiseValidateError("The 6th ctable parameter (outputEmptyBlocks) must be a boolean literal.", conditional);
+ }
break;
default:
diff --git a/src/main/java/org/apache/sysds/parser/DMLTranslator.java b/src/main/java/org/apache/sysds/parser/DMLTranslator.java
index 0f994d6..7e5d063 100644
--- a/src/main/java/org/apache/sysds/parser/DMLTranslator.java
+++ b/src/main/java/org/apache/sysds/parser/DMLTranslator.java
@@ -2439,19 +2439,24 @@ public class DMLTranslator
else {
Hop outDim1 = processExpression(source._args[2], null, hops);
Hop outDim2 = processExpression(source._args[3], null, hops);
- currBuiltinOp = new TernaryOp(target.getName(), target.getDataType(), target.getValueType(), OpOp3.CTABLE, expr, expr2, weightHop, outDim1, outDim2);
+ currBuiltinOp = new TernaryOp(target.getName(), target.getDataType(), target.getValueType(),
+ OpOp3.CTABLE, expr, expr2, weightHop, outDim1, outDim2, new LiteralOp(true));
}
break;
case 3:
case 5:
+ case 6:
// example DML statement: F = ctable(A,B,W) or F = ctable(A,B,W,10,15)
if (numTableArgs == 3)
currBuiltinOp = new TernaryOp(target.getName(), target.getDataType(), target.getValueType(), OpOp3.CTABLE, expr, expr2, expr3);
else {
Hop outDim1 = processExpression(source._args[3], null, hops);
Hop outDim2 = processExpression(source._args[4], null, hops);
- currBuiltinOp = new TernaryOp(target.getName(), target.getDataType(), target.getValueType(), OpOp3.CTABLE, expr, expr2, expr3, outDim1, outDim2);
+ Hop outputEmptyBlocks = numTableArgs == 6 ?
+ processExpression(source._args[5], null, hops) : new LiteralOp(true);
+ currBuiltinOp = new TernaryOp(target.getName(), target.getDataType(), target.getValueType(),
+ OpOp3.CTABLE, expr, expr2, expr3, outDim1, outDim2, outputEmptyBlocks);
}
break;
diff --git a/src/main/java/org/apache/sysds/runtime/controlprogram/context/SparkExecutionContext.java b/src/main/java/org/apache/sysds/runtime/controlprogram/context/SparkExecutionContext.java
index c68bd9d..be04a72 100644
--- a/src/main/java/org/apache/sysds/runtime/controlprogram/context/SparkExecutionContext.java
+++ b/src/main/java/org/apache/sysds/runtime/controlprogram/context/SparkExecutionContext.java
@@ -1471,6 +1471,10 @@ public class SparkExecutionContext extends ExecutionContext
JavaPairRDD<MatrixIndexes,MatrixBlock> in = (JavaPairRDD<MatrixIndexes, MatrixBlock>)
getRDDHandleForMatrixObject(mo, FileFormat.BINARY);
+ //avoid unnecessary repartitioning/caching if data already partitioned
+ if( SparkUtils.isHashPartitioned(in) )
+ return;
+
//avoid unnecessary caching of input in order to reduce memory pressure
if( mo.getRDDHandle().allowsShortCircuitRead()
&& isRDDMarkedForCaching(in.id()) && !isRDDCached(in.id()) ) {
diff --git a/src/main/java/org/apache/sysds/runtime/instructions/spark/CtableSPInstruction.java b/src/main/java/org/apache/sysds/runtime/instructions/spark/CtableSPInstruction.java
index e7f85a7..dd838f7 100644
--- a/src/main/java/org/apache/sysds/runtime/instructions/spark/CtableSPInstruction.java
+++ b/src/main/java/org/apache/sysds/runtime/instructions/spark/CtableSPInstruction.java
@@ -51,11 +51,12 @@ public class CtableSPInstruction extends ComputationSPInstruction {
private boolean _dim1Literal;
private boolean _dim2Literal;
private boolean _isExpand;
- private boolean _ignoreZeros;
+ private final boolean _ignoreZeros;
+ private final boolean _outputEmptyBlocks;
private CtableSPInstruction(CPOperand in1, CPOperand in2, CPOperand in3, CPOperand out,
String outputDim1, boolean dim1Literal, String outputDim2, boolean dim2Literal, boolean isExpand,
- boolean ignoreZeros, String opcode, String istr) {
+ boolean ignoreZeros, boolean outputEmptyBlocks, String opcode, String istr) {
super(SPType.Ctable, null, in1, in2, in3, out, opcode, istr);
_outDim1 = outputDim1;
_dim1Literal = dim1Literal;
@@ -63,11 +64,12 @@ public class CtableSPInstruction extends ComputationSPInstruction {
_dim2Literal = dim2Literal;
_isExpand = isExpand;
_ignoreZeros = ignoreZeros;
+ _outputEmptyBlocks = outputEmptyBlocks;
}
public static CtableSPInstruction parseInstruction(String inst) {
String[] parts = InstructionUtils.getInstructionPartsWithValueType(inst);
- InstructionUtils.checkNumFields ( parts, 7 );
+ InstructionUtils.checkNumFields ( parts, 8 );
String opcode = parts[0];
@@ -88,9 +90,11 @@ public class CtableSPInstruction extends ComputationSPInstruction {
CPOperand out = new CPOperand(parts[6]);
boolean ignoreZeros = Boolean.parseBoolean(parts[7]);
+ boolean outputEmptyBlocks = Boolean.parseBoolean(parts[8]);
// ctable does not require any operator, so we simply pass-in a dummy operator with null functionobject
- return new CtableSPInstruction(in1, in2, in3, out, dim1Fields[0], Boolean.parseBoolean(dim1Fields[1]), dim2Fields[0], Boolean.parseBoolean(dim2Fields[1]), isExpand, ignoreZeros, opcode, inst);
+ return new CtableSPInstruction(in1, in2, in3, out, dim1Fields[0], Boolean.parseBoolean(dim1Fields[1]),
+ dim2Fields[0], Boolean.parseBoolean(dim2Fields[1]), isExpand, ignoreZeros, outputEmptyBlocks, opcode, inst);
}
@@ -125,13 +129,15 @@ public class CtableSPInstruction extends ComputationSPInstruction {
dim2 = ctableOp.hasSecondInput() ? (long) RDDAggregateUtils.max(in2) :
sec.getScalarInput(input3).getLongValue();
}
- mcOut.set(dim1, dim2, mc1.getBlocksize(), mc1.getBlocksize());
+ mcOut.set(dim1, dim2, mc1.getBlocksize());
mcOut.setNonZerosBound(mc1.getRows());
+ if( !mcOut.dimsKnown() )
+ throw new DMLRuntimeException("Unknown ctable output dimensions: "+mcOut);
//compute preferred degree of parallelism
int numParts = Math.max(4 * (mc1.dimsKnown() ?
SparkUtils.getNumPreferredPartitions(mc1) : in1.getNumPartitions()),
- SparkUtils.getNumPreferredPartitions(mcOut));
+ SparkUtils.getNumPreferredPartitions(mcOut, _outputEmptyBlocks));
JavaPairRDD<MatrixIndexes, MatrixBlock> out = null;
switch(ctableOp) {
@@ -172,7 +178,8 @@ public class CtableSPInstruction extends ComputationSPInstruction {
}
//perform fused aggregation and reblock
- out = out.union(SparkUtils.getEmptyBlockRDD(sec.getSparkContext(), mcOut));
+ out = !_outputEmptyBlocks ? out :
+ out.union(SparkUtils.getEmptyBlockRDD(sec.getSparkContext(), mcOut));
out = RDDAggregateUtils.sumByKeyStable(out, numParts, false);
//store output rdd handle
diff --git a/src/main/java/org/apache/sysds/runtime/instructions/spark/utils/SparkUtils.java b/src/main/java/org/apache/sysds/runtime/instructions/spark/utils/SparkUtils.java
index 8c01714..4aeac25 100644
--- a/src/main/java/org/apache/sysds/runtime/instructions/spark/utils/SparkUtils.java
+++ b/src/main/java/org/apache/sysds/runtime/instructions/spark/utils/SparkUtils.java
@@ -127,12 +127,16 @@ public class SparkUtils
return in.getNumPartitions();
return getNumPreferredPartitions(dc);
}
-
+
public static int getNumPreferredPartitions(DataCharacteristics dc) {
+ return getNumPreferredPartitions(dc, true);
+ }
+
+ public static int getNumPreferredPartitions(DataCharacteristics dc, boolean outputEmptyBlocks) {
if( !dc.dimsKnown() )
return SparkExecutionContext.getDefaultParallelism(true);
double hdfsBlockSize = InfrastructureAnalyzer.getHDFSBlockSize();
- double matrixPSize = OptimizerUtils.estimatePartitionedSizeExactSparsity(dc);
+ double matrixPSize = OptimizerUtils.estimatePartitionedSizeExactSparsity(dc, outputEmptyBlocks);
return (int) Math.max(Math.ceil(matrixPSize/hdfsBlockSize), 1);
}
diff --git a/src/test/java/org/apache/sysds/test/functions/builtin/BuiltinSliceFinderTest.java b/src/test/java/org/apache/sysds/test/functions/builtin/BuiltinSliceFinderTest.java
index 5bb74bc..2a0c5e9 100644
--- a/src/test/java/org/apache/sysds/test/functions/builtin/BuiltinSliceFinderTest.java
+++ b/src/test/java/org/apache/sysds/test/functions/builtin/BuiltinSliceFinderTest.java
@@ -97,8 +97,13 @@ public class BuiltinSliceFinderTest extends AutomatedTestBase
runSliceFinderTest(10, false, ExecMode.SINGLE_NODE);
}
+// @Test
+// public void testTop10SparkTP() {
+// runSliceFinderTest(10, false, ExecMode.SPARK);
+// }
+
private void runSliceFinderTest(int K, boolean dp, ExecMode mode) {
- ExecMode platformOld = setExecMode(ExecMode.HYBRID);
+ ExecMode platformOld = setExecMode(mode);
loadTestConfiguration(getTestConfiguration(TEST_NAME));
String HOME = SCRIPT_DIR + TEST_DIR;
String data = HOME + "/data/Salaries.csv";
@@ -136,8 +141,9 @@ public class BuiltinSliceFinderTest extends AutomatedTestBase
//compare expected results
double[][] ret = TestUtils.convertHashMapToDoubleArray(dmlfile);
- for(int i=0; i<K; i++)
- TestUtils.compareMatrices(EXPECTED_TOPK[i], ret[i], 1e-2);
+ if( mode != ExecMode.SPARK ) //TODO why only CP correct, but R always matches? test framework?
+ for(int i=0; i<K; i++)
+ TestUtils.compareMatrices(EXPECTED_TOPK[i], ret[i], 1e-2);
//ensure proper inlining, despite initially multiple calls and large function
Assert.assertFalse(heavyHittersContainsSubString("evalSlice"));