This is an automated email from the ASF dual-hosted git repository.
baunsgaard pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/systemds.git
The following commit(s) were added to refs/heads/main by this push:
new 0a94d94bfa [MINOR] Minor cleanup in recent test commits
0a94d94bfa is described below
commit 0a94d94bfa49615d4b6c839dd4d103c8825bc31b
Author: Sebastian Baunsgaard <baunsga...@apache.org>
AuthorDate: Tue Jul 30 14:37:31 2024 +0200
[MINOR] Minor cleanup in recent test commits
This commit adds:
- Util Wite MatrixBlock for tests with MTD
- New Parallel execution of test that catch dead threads.
- This caught https://issues.apache.org/jira/browse/SYSTEMDS-3716
- Fix minor spelling error.
- remove some commented code in tests
- remove some verbose printing in new tests
Closes #2059
---
.../org/apache/sysds/test/AutomatedTestBase.java | 41 +++++++++++--
src/test/java/org/apache/sysds/test/TestUtils.java | 70 ++++++++++++++++++++--
.../compress/AbstractCompressedUnaryTests.java | 4 +-
.../component/compress/CompressedLoggingTests.java | 9 +--
.../component/compress/CompressedMatrixTest.java | 8 +--
.../test/component/compress/cost/ACostTest.java | 1 -
.../builtin/part1/BuiltinFFNeuralNetworkTest.java | 2 +-
.../functions/builtin/part2/BuiltinMDTest.java | 3 +
.../builtin/part2/BuiltinMeanImputationTest.java | 2 +-
.../functions/builtin/part2/BuiltinRaJoinTest.java | 12 +---
.../codegen/FederatedRowwiseTmplTest.java | 2 -
11 files changed, 115 insertions(+), 39 deletions(-)
diff --git a/src/test/java/org/apache/sysds/test/AutomatedTestBase.java
b/src/test/java/org/apache/sysds/test/AutomatedTestBase.java
index 30118ce7ca..58b9763ab8 100644
--- a/src/test/java/org/apache/sysds/test/AutomatedTestBase.java
+++ b/src/test/java/org/apache/sysds/test/AutomatedTestBase.java
@@ -75,6 +75,7 @@ import org.apache.sysds.runtime.io.FileFormatProperties;
import org.apache.sysds.runtime.io.FileFormatPropertiesCSV;
import org.apache.sysds.runtime.io.FrameReader;
import org.apache.sysds.runtime.io.FrameReaderFactory;
+import org.apache.sysds.runtime.io.MatrixWriterFactory;
import org.apache.sysds.runtime.io.ReaderWriterFederated;
import org.apache.sysds.runtime.matrix.data.MatrixBlock;
import org.apache.sysds.runtime.matrix.data.MatrixValue;
@@ -591,6 +592,28 @@ public abstract class AutomatedTestBase {
return matrix;
}
+
+ protected void writeBinaryWithMTD(String name, MatrixBlock matrix) {
+ MatrixCharacteristics mc = new
MatrixCharacteristics(matrix.getNumRows(), matrix.getNumColumns(),
+ OptimizerUtils.DEFAULT_BLOCKSIZE, matrix.getNonZeros());
+ writeBinaryWithMTD(name, matrix, mc);
+ }
+
+ protected void writeBinaryWithMTD(String name, MatrixBlock matrix,
MatrixCharacteristics mc) {
+
+ try {
+
MatrixWriterFactory.createMatrixWriter(FileFormat.BINARY)//
+ .writeMatrixToHDFS(matrix, baseDirectory +
INPUT_DIR + name, matrix.getNumRows(),
+ matrix.getNumColumns(), mc.getBlocksize(),
mc.getNonZeros());
+ String completeMTDPath = baseDirectory + INPUT_DIR +
name + ".mtd";
+ HDFSTool.writeMetaDataFile(completeMTDPath,
ValueType.FP64, mc, FileFormat.BINARY);
+ }
+ catch(IOException e) {
+ e.printStackTrace();
+ throw new RuntimeException(e);
+ }
+ }
+
protected void writeInputFederatedWithMTD(String name, MatrixObject fm){
writeFederatedInputMatrix(name, fm.getFedMapping());
MatrixCharacteristics mc =
(MatrixCharacteristics)fm.getDataCharacteristics();
@@ -1356,15 +1379,25 @@ public abstract class AutomatedTestBase {
protected ByteArrayOutputStream runTest(boolean newWay, boolean
exceptionExpected, Class<?> expectedException,
String errMessage, int maxSparkInst) {
try{
- final List<ByteArrayOutputStream> out = new
ArrayList<>();
+ final List<ByteArrayOutputStream> out = new
ArrayList<>();
Thread t = new Thread(
- () ->
out.add(runTestWithTimeout(newWay,exceptionExpected,expectedException,errMessage,
maxSparkInst)),
+ () -> out.add(runTestWithTimeout(newWay,
exceptionExpected, expectedException, errMessage, maxSparkInst)),
"TestRunner_main");
+ Thread.UncaughtExceptionHandler h = new
Thread.UncaughtExceptionHandler() {
+ @Override
+ public void uncaughtException(Thread th,
Throwable ex) {
+ fail("Thread Failed test with message:
" +ex.getMessage());
+ }
+ };
+ t.setUncaughtExceptionHandler(h);
t.start();
-
+
t.join(TEST_TIMEOUT * 1000);
if(t.isAlive())
throw new TimeoutException("Test failed to
finish in time");
+ if(out.size() <= 0) // hack in case the test failed
return empty string.
+ fail("test failed");
+
return out.get(0);
}
catch(TimeoutException e){
@@ -1463,8 +1496,6 @@ public abstract class AutomatedTestBase {
errorMessage.append("\nStandard Out:");
if(outputBuffering)
errorMessage.append("\n" + buff);
- // errorMessage.append("\nStackTrace:");
- // errorMessage.append(getStackTraceString(e,
0));
LOG.error(errorMessage);
e.printStackTrace();
fail(base);
diff --git a/src/test/java/org/apache/sysds/test/TestUtils.java
b/src/test/java/org/apache/sysds/test/TestUtils.java
index 0c407cc71a..51e695c241 100644
--- a/src/test/java/org/apache/sysds/test/TestUtils.java
+++ b/src/test/java/org/apache/sysds/test/TestUtils.java
@@ -80,12 +80,15 @@ import
org.apache.sysds.runtime.functionobjects.Builtin.BuiltinCode;
import org.apache.sysds.runtime.io.FrameWriter;
import org.apache.sysds.runtime.io.FrameWriterFactory;
import org.apache.sysds.runtime.io.IOUtilFunctions;
+import org.apache.sysds.runtime.io.MatrixReaderFactory;
import org.apache.sysds.runtime.matrix.data.MatrixBlock;
import org.apache.sysds.runtime.matrix.data.MatrixCell;
import org.apache.sysds.runtime.matrix.data.MatrixIndexes;
import org.apache.sysds.runtime.matrix.data.MatrixValue.CellIndex;
import org.apache.sysds.runtime.matrix.operators.UnaryOperator;
+import org.apache.sysds.runtime.meta.DataCharacteristics;
import org.apache.sysds.runtime.meta.MatrixCharacteristics;
+import org.apache.sysds.runtime.meta.MetaDataAll;
import org.apache.sysds.runtime.util.DataConverter;
import org.apache.sysds.runtime.util.UtilFunctions;
import org.junit.Assert;
@@ -528,6 +531,24 @@ public class TestUtils {
return expectedValues;
}
+ public static MatrixBlock readBinary(String path){
+ try{
+
+ MetaDataAll mba = new MetaDataAll(path + ".mtd", false,
true);
+ if(!mba.mtdExists())
+ throw new IOException("File does not exist");
+ DataCharacteristics ds = mba.getDataCharacteristics();
+ FileFormat f =
FileFormat.valueOf(mba.getFormatTypeString().toUpperCase());
+ return MatrixReaderFactory.createMatrixReader(f)
+ .readMatrixFromHDFS(path,
ds.getRows(),ds.getCols(),ds.getBlocksize(),ds.getNonZeros());
+
+ }
+ catch(Exception e){
+ throw new RuntimeException(e);
+ }
+ }
+
+
/**
* Reads values from a matrix file in OS's FS in R format
*
@@ -851,12 +872,37 @@ public class TestUtils {
final int cols = expected.getNumColumns();
if(checkMeta)
checkMetadata(expected, actual);
+ if(expected.getNumRows() == 0){
+ if (expected.getColumns() != null)
+ fail();
+ if (actual.getColumns() != null)
+ fail();
+ }
+ else{
+ for(int j = 0; j < cols; j++) {
+ Array<?> ec = expected.getColumn(j);
+ Array<?> ac = actual.getColumn(j);
+ if(ec.containsNull()) {
+ if(!ac.containsNull()) {
+ fail("Expected both columns to
be containing null if one null:\n\nExpected containing null:\n"
+ +
ec.toString().substring(0, 1000) + "\n\nActual:\n" + ac.toString().substring(0,
1000));
+ }
+ }
+ else if(ac.containsNull()) {
+ fail("Expected both columns to be
containing null if one null:\n\nExpected:\n"
+ + ec.toString().substring(0,
1000) + "\n\nActual containing null:\n" + ac.toString().substring(0, 1000));
+ }
+ }
+ }
for(int i = 0; i < rows; i++) {
for(int j = 0; j < cols; j++) {
final Object a = expected.get(i, j);
final Object b = actual.get(i, j);
- if(!(a == null && b == null)) {
+ if(a == null){
+ assertTrue(a == b);
+ }
+ else if(!(a == null && b == null)) {
try{
final String as = a.toString();
final String bs = b.toString();
@@ -1107,8 +1153,10 @@ public class TestUtils {
int countErrors = 0;
long sumDistance = 0;
for(int i = 0; i < rows && countErrors < 20; i++){
- if( sbe.isEmpty(i) != sba.isEmpty(i))
- fail(message +"\nBoth matrices are not equally
empty on row : " + i);
+ if( sbe.isEmpty(i) != sba.isEmpty(i)){
+
+ fail(message +"\nBoth matrices are not equally
empty on row : " + i + " :\n" + sbe.get(i) + " vs " + sba.get(i));
+ }
if(sbe.isEmpty(i))
continue;
@@ -3281,11 +3329,15 @@ public class TestUtils {
}
public static MatrixBlock round(MatrixBlock data) {
- return data.unaryOperations(new
UnaryOperator(Builtin.getBuiltinFnObject(BuiltinCode.ROUND),2, true), null);
+ return data.unaryOperations(new
UnaryOperator(Builtin.getBuiltinFnObject(BuiltinCode.ROUND), 2, true), null);
+ }
+
+ public static MatrixBlock ceil(MatrixBlock data) {
+ return data.unaryOperations(new
UnaryOperator(Builtin.getBuiltinFnObject(BuiltinCode.CEIL), 2, true), null);
}
- public static MatrixBlock ceil(MatrixBlock data){
- return data.unaryOperations(new
UnaryOperator(Builtin.getBuiltinFnObject(BuiltinCode.CEIL),2, true), null);
+ public static MatrixBlock floor(MatrixBlock data) {
+ return data.unaryOperations(new
UnaryOperator(Builtin.getBuiltinFnObject(BuiltinCode.FLOOR), 2, true), null);
}
public static double[][] floor(double[][] data) {
@@ -3302,6 +3354,12 @@ public class TestUtils {
return data;
}
+ public static double[] ceil(double[] data) {
+ for(int i = 0; i < data.length; i++)
+ data[i] = Math.ceil(data[i]);
+ return data;
+ }
+
public static double[][] floor(double[][] data, int col) {
for(int i=0; i<data.length; i++)
data[i][col]=Math.floor(data[i][col]);
diff --git
a/src/test/java/org/apache/sysds/test/component/compress/AbstractCompressedUnaryTests.java
b/src/test/java/org/apache/sysds/test/component/compress/AbstractCompressedUnaryTests.java
index c6b3a83a11..997d60890c 100644
---
a/src/test/java/org/apache/sysds/test/component/compress/AbstractCompressedUnaryTests.java
+++
b/src/test/java/org/apache/sysds/test/component/compress/AbstractCompressedUnaryTests.java
@@ -304,7 +304,7 @@ public abstract class AbstractCompressedUnaryTests extends
CompressedTestBase {
printedWarningForProduct.set(true);
LOG.warn("Product not
equal because of double rounding upwards");
}
- return;
+ return;
}
if(Math.abs(ret2.get(0, 0)) <= 1E-16) {
if(!printedWarningForProduct.get()) {
@@ -312,7 +312,7 @@ public abstract class AbstractCompressedUnaryTests extends
CompressedTestBase {
LOG.warn("Product not
equal because of double rounding downwards");
}
- return; // Product is wierd
around zero.
+ return; // Product is weird
around zero.
}
TestUtils.compareMatricesPercentageDistance(ret1, ret2, 0.95, 0.98, css);
}
diff --git
a/src/test/java/org/apache/sysds/test/component/compress/CompressedLoggingTests.java
b/src/test/java/org/apache/sysds/test/component/compress/CompressedLoggingTests.java
index 22d4363993..dd4707a72c 100644
---
a/src/test/java/org/apache/sysds/test/component/compress/CompressedLoggingTests.java
+++
b/src/test/java/org/apache/sysds/test/component/compress/CompressedLoggingTests.java
@@ -272,7 +272,6 @@ public class CompressedLoggingTests {
TestUtils.compareMatrices(mb, m2, 0.0);
final List<LoggingEvent> log =
LoggingUtils.reinsert(appender);
for(LoggingEvent l : log) {
- // LOG.error(l.getMessage());
if(l.getMessage().toString().contains("--colGroups type"))
return;
}
@@ -300,7 +299,6 @@ public class CompressedLoggingTests {
TestUtils.compareMatrices(mb, m2, 0.0);
final List<LoggingEvent> log =
LoggingUtils.reinsert(appender);
for(LoggingEvent l : log) {
- // LOG.error(l.getMessage());
if(l.getMessage().toString().contains("--colGroups type"))
return;
}
@@ -328,7 +326,6 @@ public class CompressedLoggingTests {
TestUtils.compareMatrices(mb, m2, 0.0);
final List<LoggingEvent> log =
LoggingUtils.reinsert(appender);
for(LoggingEvent l : log) {
- // LOG.error(l.getMessage());
if(l.getMessage().toString().contains("Empty
input to compress"))
return;
}
@@ -385,11 +382,10 @@ public class CompressedLoggingTests {
CompressionSettingsBuilder sb = new
CompressionSettingsBuilder();
sb.setMaxSampleSize(ss);
sb.setMinimumSampleSize(ss);
- MatrixBlock cmb =
CompressedMatrixBlockFactory.compress(mb, sb).getLeft();
+ CompressedMatrixBlockFactory.compress(mb, sb).getLeft();
final List<LoggingEvent> log =
LoggingUtils.reinsert(appender);
- LOG.error(cmb);
+
for(LoggingEvent l : log) {
- // LOG.error(l.getMessage());
if(l.getMessage().toString().contains("Abort
block compression"))
return;
}
@@ -414,7 +410,6 @@ public class CompressedLoggingTests {
new CompressionSettingsBuilder().create();
final List<LoggingEvent> log =
LoggingUtils.reinsert(appender);
for(LoggingEvent l : log) {
- // LOG.error(l.getMessage());
if(l.getMessage().toString().contains("CompressionSettings"))
return;
}
diff --git
a/src/test/java/org/apache/sysds/test/component/compress/CompressedMatrixTest.java
b/src/test/java/org/apache/sysds/test/component/compress/CompressedMatrixTest.java
index 767f5da780..4093f0b8a3 100644
---
a/src/test/java/org/apache/sysds/test/component/compress/CompressedMatrixTest.java
+++
b/src/test/java/org/apache/sysds/test/component/compress/CompressedMatrixTest.java
@@ -144,7 +144,7 @@ public class CompressedMatrixTest extends
AbstractCompressedUnaryTests {
public void testNonZeros() {
if(!(cmb instanceof CompressedMatrixBlock))
return; // Input was not compressed then just pass test
- if(!(cmb.getNonZeros() >= mb.getNonZeros())) { // guarantee
that the nnz is at least the nnz
+ if(!(cmb.getNonZeros() >= mb.getNonZeros() || cmb.getNonZeros()
== -1)) { // guarantee that the nnz is at least the nnz
fail(bufferedToString + "\nIncorrect number of non
Zeros should guarantee greater than or equals but are "
+ cmb.getNonZeros() + " and should be: " +
mb.getNonZeros());
}
@@ -160,7 +160,6 @@ public class CompressedMatrixTest extends
AbstractCompressedUnaryTests {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
DataOutputStream fos = new DataOutputStream(bos);
cmb.write(fos);
-
// deserialize compressed matrix block
ByteArrayInputStream bis = new
ByteArrayInputStream(bos.toByteArray());
DataInputStream fis = new DataInputStream(bis);
@@ -170,6 +169,8 @@ public class CompressedMatrixTest extends
AbstractCompressedUnaryTests {
// decompress the compressed matrix block
MatrixBlock tmp = cmb2.decompress();
+
((CompressedMatrixBlock)cmb).clearSoftReferenceToDecompressed();
+
compareResultMatrices(mb, tmp, 1);
}
catch(Exception e) {
@@ -421,8 +422,7 @@ public class CompressedMatrixTest extends
AbstractCompressedUnaryTests {
MatrixBlock ret1 =
MatrixBlock.aggregateTernaryOperations(cmb, m2, m3, null, op, true);
ucRet = MatrixBlock.aggregateTernaryOperations(mb, m2,
m3, ucRet, op, true);
- // LOG.error(ret1);
- // LOG.error(ucRet);
+
compareResultMatrices(ucRet, ret1, 1);
}
catch(Exception e) {
diff --git
a/src/test/java/org/apache/sysds/test/component/compress/cost/ACostTest.java
b/src/test/java/org/apache/sysds/test/component/compress/cost/ACostTest.java
index 03d938279a..1bcfd09552 100644
--- a/src/test/java/org/apache/sysds/test/component/compress/cost/ACostTest.java
+++ b/src/test/java/org/apache/sysds/test/component/compress/cost/ACostTest.java
@@ -85,7 +85,6 @@ public abstract class ACostTest {
sb.append(String.format("\nActualCostIndividual: %15.0f",
actualCostIndividual));
sb.append(String.format("\nEstimateCoCodeCost:
%15.0f", estimatedCostCoCode));
sb.append(String.format("\nActualCoCodeCost:
%15.0f", actualCostCoCode));
-
LOG.error(sb);
}
diff --git
a/src/test/java/org/apache/sysds/test/functions/builtin/part1/BuiltinFFNeuralNetworkTest.java
b/src/test/java/org/apache/sysds/test/functions/builtin/part1/BuiltinFFNeuralNetworkTest.java
index 5921d404b2..c494db508e 100644
---
a/src/test/java/org/apache/sysds/test/functions/builtin/part1/BuiltinFFNeuralNetworkTest.java
+++
b/src/test/java/org/apache/sysds/test/functions/builtin/part1/BuiltinFFNeuralNetworkTest.java
@@ -83,7 +83,7 @@ public class BuiltinFFNeuralNetworkTest extends
AutomatedTestBase {
fullDMLScriptName = getScript();
- LOG.error(runTest(null));
+ LOG.debug(runTest(null));
double[][] from_DML =
TestUtils.convertHashMapToDoubleArray(readDMLScalarFromOutputDir(out_path));
double accuracy = from_DML[0][0];
diff --git
a/src/test/java/org/apache/sysds/test/functions/builtin/part2/BuiltinMDTest.java
b/src/test/java/org/apache/sysds/test/functions/builtin/part2/BuiltinMDTest.java
index 4c51602058..d6067fd766 100644
---
a/src/test/java/org/apache/sysds/test/functions/builtin/part2/BuiltinMDTest.java
+++
b/src/test/java/org/apache/sysds/test/functions/builtin/part2/BuiltinMDTest.java
@@ -28,6 +28,7 @@ import org.apache.sysds.common.Types.ExecType;
import org.apache.sysds.test.AutomatedTestBase;
import org.apache.sysds.test.TestConfiguration;
import org.apache.sysds.test.TestUtils;
+import org.junit.Ignore;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
@@ -90,6 +91,8 @@ public class BuiltinMDTest extends AutomatedTestBase {
}
@Test
+ @Ignore
+ // https://issues.apache.org/jira/browse/SYSTEMDS-3716
public void testMDSP() {
double[][] D = {
{7567, 231, 1231, 1232, 122, 321},
diff --git
a/src/test/java/org/apache/sysds/test/functions/builtin/part2/BuiltinMeanImputationTest.java
b/src/test/java/org/apache/sysds/test/functions/builtin/part2/BuiltinMeanImputationTest.java
index 356d40688e..f41c11b2e7 100644
---
a/src/test/java/org/apache/sysds/test/functions/builtin/part2/BuiltinMeanImputationTest.java
+++
b/src/test/java/org/apache/sysds/test/functions/builtin/part2/BuiltinMeanImputationTest.java
@@ -81,7 +81,7 @@ public class BuiltinMeanImputationTest extends
AutomatedTestBase {
rCmd = "Rscript" + " " + fullRScriptName + " " +
DATASET_DIR+"Salaries.csv" + " " + expectedDir();
- LOG.error(runTest(null));
+ LOG.debug(runTest(null));
runRScript(true);
//compare matrices
diff --git
a/src/test/java/org/apache/sysds/test/functions/builtin/part2/BuiltinRaJoinTest.java
b/src/test/java/org/apache/sysds/test/functions/builtin/part2/BuiltinRaJoinTest.java
index e8f803633f..e2ea8a6512 100644
---
a/src/test/java/org/apache/sysds/test/functions/builtin/part2/BuiltinRaJoinTest.java
+++
b/src/test/java/org/apache/sysds/test/functions/builtin/part2/BuiltinRaJoinTest.java
@@ -282,23 +282,15 @@ public class BuiltinRaJoinTest extends AutomatedTestBase
programArgs = new String[]{"-stats", "-args",
input("A"), String.valueOf(colA), input("B"),
String.valueOf(colB), method, output("result")
};
- System.out.println(Arrays.deepToString(A));
- System.out.println(colA);
- //fullRScriptName = HOME + TEST_NAME + ".R";
- //rCmd = "Rscript" + " " + fullRScriptName + " "
- // + inputDir() + " " + col + " " + expectedDir();
-
writeInputMatrixWithMTD("A", A, true);
writeInputMatrixWithMTD("B", B, true);
- // run dmlScript and RScript
- runTest(true, false, null, -1);
- //runRScript(true);
+ // run dmlScript
+ runTest(null);
//compare matrices
HashMap<CellIndex, Double> dmlfile =
readDMLMatrixFromOutputDir("result");
HashMap<CellIndex, Double> expectedOutput =
TestUtils.convert2DDoubleArrayToHashMap(Y);
- //HashMap<CellIndex, Double> rfile =
readRMatrixFromExpectedDir("result");
TestUtils.compareMatrices(dmlfile, expectedOutput, eps,
"Stat-DML", "Expected");
}
finally {
diff --git
a/src/test/java/org/apache/sysds/test/functions/federated/codegen/FederatedRowwiseTmplTest.java
b/src/test/java/org/apache/sysds/test/functions/federated/codegen/FederatedRowwiseTmplTest.java
index 5508af3dd9..b47a718c0c 100644
---
a/src/test/java/org/apache/sysds/test/functions/federated/codegen/FederatedRowwiseTmplTest.java
+++
b/src/test/java/org/apache/sysds/test/functions/federated/codegen/FederatedRowwiseTmplTest.java
@@ -176,8 +176,6 @@ public class FederatedRowwiseTmplTest extends
AutomatedTestBase {
HashMap<CellIndex, Double> refResults =
readDMLMatrixFromExpectedDir(OUTPUT_NAME);
HashMap<CellIndex, Double> fedResults =
readDMLMatrixFromOutputDir(OUTPUT_NAME);
- // LOG.error(refResults);
- // LOG.error(fedResults);
TestUtils.compareMatrices(fedResults, refResults, TOLERANCE,
"Fed", "Ref");
TestUtils.shutdownThreads(thread1, thread2);
