From 569a46f87d3aef2a6365eb9740f90aec3e80491d Mon Sep 17 00:00:00 2001
From: Alex Black <blacka101@gmail.com>
Date: Wed, 5 Feb 2020 17:07:36 +1100
Subject: [PATCH] Fixes (#213)

* Increase timeouts for 2 tests occasionally failing on CI

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* Explicitly set character encoding via argline for maven surefire tests

Signed-off-by: AlexDBlack <blacka101@gmail.com>

* CUDA gradient check timeout fix + simple rnn masking fix

Signed-off-by: AlexDBlack <blacka101@gmail.com>
---
 arbiter/pom.xml                               |  2 +-
 datavec/pom.xml                               |  2 +-
 .../GradientCheckTestsMasking.java            | 32 +++++++++++--------
 .../deeplearning4j-dataimport-solrj/pom.xml   |  2 +-
 .../deeplearning4j-modelexport-solr/pom.xml   |  2 +-
 .../pom.xml                                   |  2 +-
 .../clustering/kmeans/KMeansTest.java         |  5 +++
 .../nn/layers/recurrent/SimpleRnn.java        |  6 ++++
 deeplearning4j/pom.xml                        |  2 +-
 .../nd4j-backend-impls/nd4j-cuda/pom.xml      |  2 +-
 nd4j/nd4j-backends/nd4j-backend-impls/pom.xml |  2 +-
 .../nd4j-tests-tensorflow/pom.xml             |  4 +--
 nd4j/nd4j-backends/nd4j-tests/pom.xml         |  2 +-
 .../java/org/nd4j/autodiff/TestOpMapping.java |  5 +++
 nd4j/nd4j-serde/nd4j-aeron/pom.xml            |  2 +-
 nd4j/nd4j-serde/nd4j-arrow/pom.xml            |  2 +-
 nd4j/nd4j-serde/nd4j-gson/pom.xml             |  2 +-
 nd4j/nd4j-serde/nd4j-kryo/pom.xml             |  2 +-
 18 files changed, 49 insertions(+), 29 deletions(-)

diff --git a/arbiter/pom.xml b/arbiter/pom.xml
index 364c6d904..93f877968 100644
--- a/arbiter/pom.xml
+++ b/arbiter/pom.xml
@@ -192,7 +192,7 @@
                     <artifactId>maven-surefire-plugin</artifactId>
                     <version>${maven-surefire-plugin.version}</version>
                     <configuration>
-                        <argLine>-Ddtype=double -Xmx3024m -Xms3024m</argLine>
+                        <argLine>-Ddtype=double -Dfile.encoding=UTF-8 -Xmx3024m -Xms3024m</argLine>
                         <!--
                          By default: Surefire will set the classpath based on the manifest. Because tests are not included
                          in the JAR, any tests that rely on class path scanning for resources in the tests directory will not
diff --git a/datavec/pom.xml b/datavec/pom.xml
index c706469a9..1c49960d6 100644
--- a/datavec/pom.xml
+++ b/datavec/pom.xml
@@ -148,7 +148,7 @@
                     <artifactId>maven-surefire-plugin</artifactId>
                     <version>${maven-surefire-plugin.version}</version>
                     <configuration>
-                        <argLine>-Ddtype=float</argLine>
+                        <argLine>-Ddtype=float -Dfile.encoding=UTF-8</argLine>
                         <!--
                         By default: Surefire will set the classpath based on the manifest. Because tests are not included
                         in the JAR, any tests that rely on class path scanning for resources in the tests directory will not
diff --git a/deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/gradientcheck/GradientCheckTestsMasking.java b/deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/gradientcheck/GradientCheckTestsMasking.java
index c0f5a2573..e38bcf274 100644
--- a/deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/gradientcheck/GradientCheckTestsMasking.java
+++ b/deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/gradientcheck/GradientCheckTestsMasking.java
@@ -56,6 +56,11 @@ public class GradientCheckTestsMasking extends BaseDL4JTest {
         Nd4j.setDataType(DataType.DOUBLE);
     }
 
+    @Override
+    public long getTimeoutMilliseconds() {
+        return 90000L;
+    }
+
     private static class GradientCheckSimpleScenario {
         private final ILossFunction lf;
         private final Activation act;
@@ -159,9 +164,8 @@ public class GradientCheckTestsMasking extends BaseDL4JTest {
                             .updater(new NoOp())
                             .dataType(DataType.DOUBLE)
                             .dist(new NormalDistribution(0, 1.0)).seed(12345L).list()
-                            .layer(0, new GravesBidirectionalLSTM.Builder().nIn(nIn).nOut(layerSize)
-                                            .activation(Activation.TANH).build())
-                            .layer(1, new GravesBidirectionalLSTM.Builder().nIn(layerSize).nOut(layerSize)
+                            .layer(0, new SimpleRnn.Builder().nIn(nIn).nOut(2).activation(Activation.TANH).build())
+                            .layer(1, new GravesBidirectionalLSTM.Builder().nIn(2).nOut(layerSize)
                                             .activation(Activation.TANH).build())
                             .layer(2, new RnnOutputLayer.Builder(LossFunctions.LossFunction.MCXENT)
                                             .activation(Activation.SOFTMAX).nIn(layerSize).nOut(nOut).build())
@@ -390,24 +394,24 @@ public class GradientCheckTestsMasking extends BaseDL4JTest {
         Nd4j.getRandom().setSeed(12345);
         //Idea: RNN input, global pooling, OutputLayer - with "per example" mask arrays
 
-        int mb = 10;
+        int mb = 4;
         int tsLength = 5;
         MultiLayerConfiguration conf = new NeuralNetConfiguration.Builder()
                 .dataType(DataType.DOUBLE)
                 .weightInit(new NormalDistribution(0,2))
                 .updater(new NoOp())
                 .list()
-                .layer(new LSTM.Builder().nIn(10).nOut(10).build())
+                .layer(new LSTM.Builder().nIn(3).nOut(3).build())
                 .layer(new GlobalPoolingLayer.Builder().poolingType(PoolingType.AVG).build())
-                .layer(new OutputLayer.Builder().nIn(10).nOut(10).activation(Activation.SOFTMAX).build())
-                .setInputType(InputType.recurrent(10))
+                .layer(new OutputLayer.Builder().nIn(3).nOut(3).activation(Activation.SOFTMAX).build())
+                .setInputType(InputType.recurrent(3))
                 .build();
 
         MultiLayerNetwork net = new MultiLayerNetwork(conf);
         net.init();
 
-        INDArray f = Nd4j.rand(new int[]{mb, 10, tsLength});
-        INDArray l = TestUtils.randomOneHot(mb, 10);
+        INDArray f = Nd4j.rand(new int[]{mb, 3, tsLength});
+        INDArray l = TestUtils.randomOneHot(mb, 3);
         INDArray lm = TestUtils.randomBernoulli(mb, 1);
 
         assertTrue(lm.sumNumber().intValue() > 0);
@@ -449,18 +453,18 @@ public class GradientCheckTestsMasking extends BaseDL4JTest {
                 .updater(new NoOp())
                 .graphBuilder()
                 .addInputs("in")
-                .layer("0", new LSTM.Builder().nIn(10).nOut(10).build(), "in")
+                .layer("0", new LSTM.Builder().nIn(3).nOut(3).build(), "in")
                 .layer("1", new GlobalPoolingLayer.Builder().poolingType(PoolingType.AVG).build(), "0")
-                .layer("out", new OutputLayer.Builder().nIn(10).nOut(10).activation(Activation.SOFTMAX).build(), "1")
+                .layer("out", new OutputLayer.Builder().nIn(3).nOut(3).activation(Activation.SOFTMAX).build(), "1")
                 .setOutputs("out")
-                .setInputTypes(InputType.recurrent(10))
+                .setInputTypes(InputType.recurrent(3))
                 .build();
 
         ComputationGraph net = new ComputationGraph(conf);
         net.init();
 
-        INDArray f = Nd4j.rand(new int[]{mb, 10, tsLength});
-        INDArray l = TestUtils.randomOneHot(mb, 10);
+        INDArray f = Nd4j.rand(new int[]{mb, 3, tsLength});
+        INDArray l = TestUtils.randomOneHot(mb, 3);
         INDArray lm = TestUtils.randomBernoulli(mb, 1);
 
         assertTrue(lm.sumNumber().intValue() > 0);
diff --git a/deeplearning4j/deeplearning4j-dataimport-solrj/pom.xml b/deeplearning4j/deeplearning4j-dataimport-solrj/pom.xml
index ecc33b57e..ed0160ccb 100644
--- a/deeplearning4j/deeplearning4j-dataimport-solrj/pom.xml
+++ b/deeplearning4j/deeplearning4j-dataimport-solrj/pom.xml
@@ -37,7 +37,7 @@
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-surefire-plugin</artifactId>
                     <configuration>
-                        <argLine>-Ddtype=float -Xmx8g -Dtest.solr.allowed.securerandom=NativePRNG</argLine>
+                        <argLine>-Ddtype=float -Dfile.encoding=UTF-8 -Xmx8g -Dtest.solr.allowed.securerandom=NativePRNG</argLine>
                         <includes>
                             <!-- Default setting only runs tests that start/end with "Test" -->
                             <include>*.java</include>
diff --git a/deeplearning4j/deeplearning4j-modelexport-solr/pom.xml b/deeplearning4j/deeplearning4j-modelexport-solr/pom.xml
index 02ce30a40..383eb1c8c 100644
--- a/deeplearning4j/deeplearning4j-modelexport-solr/pom.xml
+++ b/deeplearning4j/deeplearning4j-modelexport-solr/pom.xml
@@ -33,7 +33,7 @@
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-surefire-plugin</artifactId>
                     <configuration>
-                        <argLine>-Ddtype=float -Xmx8g -Dtest.solr.allowed.securerandom=NativePRNG</argLine>
+                        <argLine>-Ddtype=float -Dfile.encoding=UTF-8 -Xmx8g -Dtest.solr.allowed.securerandom=NativePRNG</argLine>
                         <includes>
                             <!-- Default setting only runs tests that start/end with "Test" -->
                             <include>*.java</include>
diff --git a/deeplearning4j/deeplearning4j-nearestneighbors-parent/deeplearning4j-nearestneighbor-server/pom.xml b/deeplearning4j/deeplearning4j-nearestneighbors-parent/deeplearning4j-nearestneighbor-server/pom.xml
index 2d4a4da14..911432cf0 100644
--- a/deeplearning4j/deeplearning4j-nearestneighbors-parent/deeplearning4j-nearestneighbor-server/pom.xml
+++ b/deeplearning4j/deeplearning4j-nearestneighbors-parent/deeplearning4j-nearestneighbor-server/pom.xml
@@ -36,7 +36,7 @@
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-surefire-plugin</artifactId>
                     <configuration>
-                        <argLine>-Ddtype=float -Xmx8g</argLine>
+                        <argLine>-Ddtype=float -Dfile.encoding=UTF-8 -Xmx8g</argLine>
                         <includes>
                             <!-- Default setting only runs tests that start/end with "Test" -->
                             <include>*.java</include>
diff --git a/deeplearning4j/deeplearning4j-nearestneighbors-parent/nearestneighbor-core/src/test/java/org/deeplearning4j/clustering/kmeans/KMeansTest.java b/deeplearning4j/deeplearning4j-nearestneighbors-parent/nearestneighbor-core/src/test/java/org/deeplearning4j/clustering/kmeans/KMeansTest.java
index 2f2619e78..abbfa04bc 100644
--- a/deeplearning4j/deeplearning4j-nearestneighbors-parent/nearestneighbor-core/src/test/java/org/deeplearning4j/clustering/kmeans/KMeansTest.java
+++ b/deeplearning4j/deeplearning4j-nearestneighbors-parent/nearestneighbor-core/src/test/java/org/deeplearning4j/clustering/kmeans/KMeansTest.java
@@ -38,6 +38,11 @@ public class KMeansTest extends BaseDL4JTest {
 
     private boolean[] useKMeansPlusPlus = {true, false};
 
+    @Override
+    public long getTimeoutMilliseconds() {
+        return 60000L;
+    }
+
     @Test
     public void testKMeans() {
         Nd4j.getRandom().setSeed(7);
diff --git a/deeplearning4j/deeplearning4j-nn/src/main/java/org/deeplearning4j/nn/layers/recurrent/SimpleRnn.java b/deeplearning4j/deeplearning4j-nn/src/main/java/org/deeplearning4j/nn/layers/recurrent/SimpleRnn.java
index 044f444c0..87d88efcb 100644
--- a/deeplearning4j/deeplearning4j-nn/src/main/java/org/deeplearning4j/nn/layers/recurrent/SimpleRnn.java
+++ b/deeplearning4j/deeplearning4j-nn/src/main/java/org/deeplearning4j/nn/layers/recurrent/SimpleRnn.java
@@ -282,6 +282,12 @@ public class SimpleRnn extends BaseRecurrentLayer<org.deeplearning4j.nn.conf.lay
 
             a.getActivation(currOut, training);
 
+            if( maskArray != null){
+                //If mask array is present: Also need to zero out errors to avoid sending anything but 0s to layer below for masked steps
+                INDArray maskCol = maskArray.getColumn(i, true).castTo(dataType);
+                currOut.muliColumnVector(maskCol);
+            }
+
             prevStepOut = currOut;
         }
 
diff --git a/deeplearning4j/pom.xml b/deeplearning4j/pom.xml
index bcf633e3a..17c89f931 100644
--- a/deeplearning4j/pom.xml
+++ b/deeplearning4j/pom.xml
@@ -380,7 +380,7 @@
                          -->
                         <useSystemClassLoader>true</useSystemClassLoader>
                         <useManifestOnlyJar>false</useManifestOnlyJar>
-                        <argLine>-Ddtype=float -Xmx8g</argLine>
+                        <argLine>-Ddtype=float -Dfile.encoding=UTF-8 -Xmx8g</argLine>
                         <includes>
                             <!-- Default setting only runs tests that start/end with "Test" -->
                             <include>*.java</include>
diff --git a/nd4j/nd4j-backends/nd4j-backend-impls/nd4j-cuda/pom.xml b/nd4j/nd4j-backends/nd4j-backend-impls/nd4j-cuda/pom.xml
index d98c7a6d1..36f25d636 100644
--- a/nd4j/nd4j-backends/nd4j-backend-impls/nd4j-cuda/pom.xml
+++ b/nd4j/nd4j-backends/nd4j-backend-impls/nd4j-cuda/pom.xml
@@ -60,7 +60,7 @@
                         Maximum heap size was set to 6g, as a minimum required value for tests run.
                         Depending on a build machine, default value is not always enough.
                     -->
-                    <argLine>-Ddtype=float -Xmx8g</argLine>
+                    <argLine>-Ddtype=float -Dfile.encoding=UTF-8 -Xmx8g</argLine>
                 </configuration>
             </plugin>
             <plugin>
diff --git a/nd4j/nd4j-backends/nd4j-backend-impls/pom.xml b/nd4j/nd4j-backends/nd4j-backend-impls/pom.xml
index 86ce07ff7..c6da5e6f0 100644
--- a/nd4j/nd4j-backends/nd4j-backend-impls/pom.xml
+++ b/nd4j/nd4j-backends/nd4j-backend-impls/pom.xml
@@ -117,7 +117,7 @@
                             Maximum heap size was set to 8g, as a minimum required value for tests run.
                             Depending on a build machine, default value is not always enough.
                         -->
-                        <argLine>-Ddtype=float -Xmx8g</argLine>
+                        <argLine>-Ddtype=float -Dfile.encoding=UTF-8 -Xmx8g</argLine>
                     </configuration>
                 </plugin>
                 <plugin>
diff --git a/nd4j/nd4j-backends/nd4j-tests-tensorflow/pom.xml b/nd4j/nd4j-backends/nd4j-tests-tensorflow/pom.xml
index 5f5c5fa90..6a3cc6eda 100644
--- a/nd4j/nd4j-backends/nd4j-tests-tensorflow/pom.xml
+++ b/nd4j/nd4j-backends/nd4j-tests-tensorflow/pom.xml
@@ -224,7 +224,7 @@
                                 Depending on a build machine, default value is not always enough.
                             -->
                             <skip>false</skip>
-                            <argLine>-Xmx6g</argLine>
+                            <argLine>-Xmx6g -Dfile.encoding=UTF-8</argLine>
                         </configuration>
                     </plugin>
                 </plugins>
@@ -296,7 +296,7 @@
                                 Maximum heap size was set to 6g, as a minimum required value for tests run.
                                 Depending on a build machine, default value is not always enough.
                             -->
-                            <argLine>-Xmx6g</argLine>
+                            <argLine>-Xmx6g -Dfile.encoding=UTF-8</argLine>
                             <skipTests>false</skipTests>
                             <skip>false</skip>
                         </configuration>
diff --git a/nd4j/nd4j-backends/nd4j-tests/pom.xml b/nd4j/nd4j-backends/nd4j-tests/pom.xml
index 9d098189f..8d250629a 100644
--- a/nd4j/nd4j-backends/nd4j-tests/pom.xml
+++ b/nd4j/nd4j-backends/nd4j-tests/pom.xml
@@ -252,7 +252,7 @@
                                 Maximum heap size was set to 6g, as a minimum required value for tests run.
                                 Depending on a build machine, default value is not always enough.
                             -->
-                            <argLine>-Ddtype=float -Xmx6g</argLine>
+                            <argLine>-Ddtype=float -Dfile.encoding=UTF-8 -Xmx6g</argLine>
                         </configuration>
                     </plugin>
                 </plugins>
diff --git a/nd4j/nd4j-backends/nd4j-tests/src/test/java/org/nd4j/autodiff/TestOpMapping.java b/nd4j/nd4j-backends/nd4j-tests/src/test/java/org/nd4j/autodiff/TestOpMapping.java
index ab56ae281..e88f195c0 100644
--- a/nd4j/nd4j-backends/nd4j-tests/src/test/java/org/nd4j/autodiff/TestOpMapping.java
+++ b/nd4j/nd4j-backends/nd4j-tests/src/test/java/org/nd4j/autodiff/TestOpMapping.java
@@ -44,6 +44,11 @@ public class TestOpMapping extends BaseNd4jTest {
         return 'c';
     }
 
+    @Override
+    public long getTimeoutMilliseconds() {
+        return 60000L;
+    }
+
     @Test
     public void testOpMappingCoverage() throws Exception {
         Reflections reflections = new Reflections("org.nd4j");
diff --git a/nd4j/nd4j-serde/nd4j-aeron/pom.xml b/nd4j/nd4j-serde/nd4j-aeron/pom.xml
index 87e9347dd..827afb23a 100644
--- a/nd4j/nd4j-serde/nd4j-aeron/pom.xml
+++ b/nd4j/nd4j-serde/nd4j-aeron/pom.xml
@@ -91,7 +91,7 @@
 
                   For testing large zoo models, this may not be enough (so comment it out).
               -->
-              <argLine>-Ddtype=float -Xmx8g</argLine>
+              <argLine>-Ddtype=float -Dfile.encoding=UTF-8 -Xmx8g</argLine>
             </configuration>
           </plugin>
         </plugins>
diff --git a/nd4j/nd4j-serde/nd4j-arrow/pom.xml b/nd4j/nd4j-serde/nd4j-arrow/pom.xml
index ddadc2df1..3a768c1a5 100644
--- a/nd4j/nd4j-serde/nd4j-arrow/pom.xml
+++ b/nd4j/nd4j-serde/nd4j-arrow/pom.xml
@@ -109,7 +109,7 @@
 
                                 For testing large zoo models, this may not be enough (so comment it out).
                             -->
-                            <argLine>-Ddtype=float -Xmx8g</argLine>
+                            <argLine>-Ddtype=float -Dfile.encoding=UTF-8 -Xmx8g</argLine>
                         </configuration>
                     </plugin>
                 </plugins>
diff --git a/nd4j/nd4j-serde/nd4j-gson/pom.xml b/nd4j/nd4j-serde/nd4j-gson/pom.xml
index f7215436a..f488bfde5 100644
--- a/nd4j/nd4j-serde/nd4j-gson/pom.xml
+++ b/nd4j/nd4j-serde/nd4j-gson/pom.xml
@@ -100,7 +100,7 @@
 
                                 For testing large zoo models, this may not be enough (so comment it out).
                             -->
-                            <argLine>-Ddtype=float -Xmx8g</argLine>
+                            <argLine>-Ddtype=float -Dfile.encoding=UTF-8 -Xmx8g</argLine>
                         </configuration>
                     </plugin>
                 </plugins>
diff --git a/nd4j/nd4j-serde/nd4j-kryo/pom.xml b/nd4j/nd4j-serde/nd4j-kryo/pom.xml
index 25acac26f..02970d5e2 100644
--- a/nd4j/nd4j-serde/nd4j-kryo/pom.xml
+++ b/nd4j/nd4j-serde/nd4j-kryo/pom.xml
@@ -220,7 +220,7 @@
                                 Maximum heap size was set to 6g, as a minimum required value for tests run.
                                 Depending on a build machine, default value is not always enough.
                             -->
-                            <argLine>-Ddtype=float -Xmx6g</argLine>
+                            <argLine>-Ddtype=float -Dfile.encoding=UTF-8 -Xmx6g</argLine>
                         </configuration>
                     </plugin>
                 </plugins>