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Posted to commits@systemml.apache.org by mb...@apache.org on 2017/09/21 18:55:31 UTC
[2/4] systemml git commit: [SYTEMML-1924] Fix flaky right indexing
tests (incorrect R output)
[SYTEMML-1924] Fix flaky right indexing tests (incorrect R output)
This patch fixes intermittent test failures of the right indexing test
suite. These tests generate random data X and random indexing ranges
X[a:b,c:d]. The failures occurred whenever a==b because because R
implicitly converts the output (row vector) to a column vector. We now
check for these cases and explicitly transpose the R result.
Project: http://git-wip-us.apache.org/repos/asf/systemml/repo
Commit: http://git-wip-us.apache.org/repos/asf/systemml/commit/0bebfd86
Tree: http://git-wip-us.apache.org/repos/asf/systemml/tree/0bebfd86
Diff: http://git-wip-us.apache.org/repos/asf/systemml/diff/0bebfd86
Branch: refs/heads/master
Commit: 0bebfd869b6c715dfd9937a0916040053079e482
Parents: a3407ae
Author: Matthias Boehm <mb...@gmail.com>
Authored: Wed Sep 20 21:14:48 2017 -0700
Committer: Matthias Boehm <mb...@gmail.com>
Committed: Thu Sep 21 11:44:28 2017 -0700
----------------------------------------------------------------------
.../indexing/RightIndexingMatrixTest.java | 130 +++++++++----------
.../indexing/RightIndexingMatrixTest.R | 2 +
2 files changed, 63 insertions(+), 69 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/systemml/blob/0bebfd86/src/test/java/org/apache/sysml/test/integration/functions/indexing/RightIndexingMatrixTest.java
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diff --git a/src/test/java/org/apache/sysml/test/integration/functions/indexing/RightIndexingMatrixTest.java b/src/test/java/org/apache/sysml/test/integration/functions/indexing/RightIndexingMatrixTest.java
index 82f4d10..625dd50 100644
--- a/src/test/java/org/apache/sysml/test/integration/functions/indexing/RightIndexingMatrixTest.java
+++ b/src/test/java/org/apache/sysml/test/integration/functions/indexing/RightIndexingMatrixTest.java
@@ -33,10 +33,8 @@ import org.apache.sysml.test.integration.TestConfiguration;
import org.apache.sysml.test.utils.TestUtils;
-
public class RightIndexingMatrixTest extends AutomatedTestBase
{
-
private final static String TEST_NAME = "RightIndexingMatrixTest";
private final static String TEST_DIR = "functions/indexing/";
private final static String TEST_CLASS_DIR = TEST_DIR + RightIndexingMatrixTest.class.getSimpleName() + "/";
@@ -50,123 +48,117 @@ public class RightIndexingMatrixTest extends AutomatedTestBase
private final static double sparsity1 = 0.5;
private final static double sparsity2 = 0.01;
-
@Override
public void setUp() {
addTestConfiguration(TEST_NAME, new TestConfiguration(TEST_CLASS_DIR, TEST_NAME,
- new String[] {"B", "C", "D"}));
+ new String[] {"B", "C", "D"}));
}
@Test
- public void testRightIndexingDenseCP()
- {
+ public void testRightIndexingDenseCP() {
runRightIndexingTest(ExecType.CP, false);
}
@Test
- public void testRightIndexingDenseSP()
- {
+ public void testRightIndexingDenseSP() {
runRightIndexingTest(ExecType.SPARK, false);
}
@Test
- public void testRightIndexingDenseMR()
- {
+ public void testRightIndexingDenseMR() {
runRightIndexingTest(ExecType.MR, false);
}
@Test
- public void testRightIndexingSparseCP()
- {
+ public void testRightIndexingSparseCP() {
runRightIndexingTest(ExecType.CP, true);
}
@Test
- public void testRightIndexingSparseSP()
- {
+ public void testRightIndexingSparseSP() {
runRightIndexingTest(ExecType.SPARK, true);
}
@Test
- public void testRightIndexingSparseMR()
- {
+ public void testRightIndexingSparseMR() {
runRightIndexingTest(ExecType.MR, true);
}
- /**
- *
- * @param et
- * @param sparse
- */
- public void runRightIndexingTest( ExecType et, boolean sparse )
+ //various regression tests that led to test failures before
+
+ @Test
+ public void testRightIndexingDenseCPFixed1() {
+ runRightIndexingTest(ExecType.CP, false, 2083, 2083, 437, 842);
+ }
+
+ @Test
+ public void testRightIndexingDenseCPFixed2() {
+ runRightIndexingTest(ExecType.CP, false, 1632, 1632, 282, 345);
+ }
+
+ public void runRightIndexingTest( ExecType et, boolean sparse ) {
+ Random rand = new Random(System.currentTimeMillis());
+ long rl = (long)(rand.nextDouble()*((double)rows))+1;
+ long ru = (long)(rand.nextDouble()*((double)(rows-rl+1)))+rl;
+ long cl = (long)(rand.nextDouble()*((double)cols))+1;
+ long cu = (long)(rand.nextDouble()*((double)(cols-cl+1)))+cl;
+
+ runRightIndexingTest(et, sparse, rl, ru, cl, cu);
+ }
+
+ public void runRightIndexingTest( ExecType et, boolean sparse, long rl, long ru, long cl, long cu )
{
- RUNTIME_PLATFORM oldRTP = rtplatform;
-
+ RUNTIME_PLATFORM platformOld = rtplatform;
+ switch( et ){
+ case MR: rtplatform = RUNTIME_PLATFORM.HADOOP; break;
+ case SPARK: rtplatform = RUNTIME_PLATFORM.SPARK; break;
+ default: rtplatform = RUNTIME_PLATFORM.HYBRID; break;
+ }
+
boolean sparkConfigOld = DMLScript.USE_LOCAL_SPARK_CONFIG;
+ if( rtplatform == RUNTIME_PLATFORM.SPARK )
+ DMLScript.USE_LOCAL_SPARK_CONFIG = true;
try
{
- TestConfiguration config = getTestConfiguration(TEST_NAME);
- if(et == ExecType.SPARK) {
- rtplatform = RUNTIME_PLATFORM.SPARK;
- }
- else {
- rtplatform = (et==ExecType.MR)? RUNTIME_PLATFORM.HADOOP : RUNTIME_PLATFORM.SINGLE_NODE;
- }
- if( rtplatform == RUNTIME_PLATFORM.SPARK )
- DMLScript.USE_LOCAL_SPARK_CONFIG = true;
-
-
- double sparsity = sparse ? sparsity2 : sparsity1;
-
- config.addVariable("rows", rows);
- config.addVariable("cols", cols);
-
- long rowstart=216, rowend=429, colstart=967, colend=1009;
- Random rand=new Random(System.currentTimeMillis());
- rowstart=(long)(rand.nextDouble()*((double)rows))+1;
- rowend=(long)(rand.nextDouble()*((double)(rows-rowstart+1)))+rowstart;
- colstart=(long)(rand.nextDouble()*((double)cols))+1;
- colend=(long)(rand.nextDouble()*((double)(cols-colstart+1)))+colstart;
- config.addVariable("rowstart", rowstart);
- config.addVariable("rowend", rowend);
- config.addVariable("colstart", colstart);
- config.addVariable("colend", colend);
+ TestConfiguration config = getTestConfiguration(TEST_NAME);
+ double sparsity = sparse ? sparsity2 : sparsity1;
+ config.addVariable("rows", rows);
+ config.addVariable("cols", cols);
+ config.addVariable("rowstart", rl);
+ config.addVariable("rowend", ru);
+ config.addVariable("colstart", cl);
+ config.addVariable("colend", cu);
loadTestConfiguration(config);
-
- /* This is for running the junit test the new way, i.e., construct the arguments directly */
+
String RI_HOME = SCRIPT_DIR + TEST_DIR;
fullDMLScriptName = RI_HOME + TEST_NAME + ".dml";
- programArgs = new String[]{"-args", input("A"),
+ programArgs = new String[]{"-explain","-args", input("A"),
Long.toString(rows), Long.toString(cols),
- Long.toString(rowstart), Long.toString(rowend),
- Long.toString(colstart), Long.toString(colend),
+ Long.toString(rl), Long.toString(ru),
+ Long.toString(cl), Long.toString(cu),
output("B"), output("C"), output("D") };
fullRScriptName = RI_HOME + TEST_NAME + ".R";
rCmd = "Rscript" + " " + fullRScriptName + " " +
- inputDir() + " " + rowstart + " " + rowend + " " + colstart + " " + colend + " " + expectedDir();
-
+ inputDir() + " " + rl + " " + ru + " " + cl + " " + cu + " " + expectedDir();
+
double[][] A = getRandomMatrix(rows, cols, min, max, sparsity, System.currentTimeMillis());
- writeInputMatrix("A", A, true);
-
- boolean exceptionExpected = false;
- int expectedNumberOfJobs = -1;
- runTest(true, exceptionExpected, null, expectedNumberOfJobs);
+ writeInputMatrix("A", A, true);
+ //run tests
+ runTest(true, false, null, -1);
runRScript(true);
- //disableOutAndExpectedDeletion();
-
- for(String file: config.getOutputFiles())
- {
+
+ //compare results
+ for(String file: config.getOutputFiles()) {
HashMap<CellIndex, Double> dmlfile = readDMLMatrixFromHDFS(file);
HashMap<CellIndex, Double> rfile = readRMatrixFromFS(file);
TestUtils.compareMatrices(dmlfile, rfile, epsilon, file+"-DML", file+"-R");
}
}
- finally
- {
- rtplatform = oldRTP;
+ finally {
+ rtplatform = platformOld;
DMLScript.USE_LOCAL_SPARK_CONFIG = sparkConfigOld;
}
}
http://git-wip-us.apache.org/repos/asf/systemml/blob/0bebfd86/src/test/scripts/functions/indexing/RightIndexingMatrixTest.R
----------------------------------------------------------------------
diff --git a/src/test/scripts/functions/indexing/RightIndexingMatrixTest.R b/src/test/scripts/functions/indexing/RightIndexingMatrixTest.R
index 62009d7..ed5b341 100644
--- a/src/test/scripts/functions/indexing/RightIndexingMatrixTest.R
+++ b/src/test/scripts/functions/indexing/RightIndexingMatrixTest.R
@@ -28,6 +28,8 @@ A1=readMM(paste(args[1], "A.mtx", sep=""))
A = as.matrix(A1);
B=A[args[2]:args[3],args[4]:args[5]]
+if( args[2]==args[3] )
+ B = t(B) #correct implicit row to column vector conversion
C=A[1:args[3],args[4]:ncol(A)]
D=A[,args[4]:args[5]]
writeMM(as(B,"CsparseMatrix"), paste(args[6], "B", sep=""), format="text")