Assorted fixes (#445)

* #8890 TestTransferStatsCollection timeout fix

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

* #8890 RegressionTest timeout fix

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

* Increase timeout for flaky test

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

* Remove test dependency

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

* BLAS iamax + loop -> argmax

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

deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/regressiontest/RegressionTest050.java

@@ -56,8 +56,10 @@ import static org.junit.Assert.*;
  */
 public class RegressionTest050 extends BaseDL4JTest {
 
-    @Rule
+    @Override
-    public Timeout timeout = Timeout.seconds(300);
+    public long getTimeoutMilliseconds() {
+        return 180000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
+    }
 
     @Override
     public DataType getDataType(){

deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/regressiontest/RegressionTest060.java

@@ -64,6 +64,11 @@ public class RegressionTest060 extends BaseDL4JTest {
         return DataType.FLOAT;
     }
 
+    @Override
+    public long getTimeoutMilliseconds() {
+        return 180000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
+    }
+
     @Test
     public void regressionTestMLP1() throws Exception {
 

deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/regressiontest/RegressionTest071.java

@@ -64,6 +64,12 @@ public class RegressionTest071 extends BaseDL4JTest {
     public DataType getDataType(){
         return DataType.FLOAT;
     }
+
+    @Override
+    public long getTimeoutMilliseconds() {
+        return 180000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
+    }
+
     @Test
     public void regressionTestMLP1() throws Exception {
 

deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/regressiontest/RegressionTest080.java

@@ -64,6 +64,11 @@ public class RegressionTest080 extends BaseDL4JTest {
         return DataType.FLOAT;
     }
 
+    @Override
+    public long getTimeoutMilliseconds() {
+        return 180000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
+    }
+
     @Test
     public void regressionTestMLP1() throws Exception {
 

deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/regressiontest/RegressionTest100a.java

@@ -56,7 +56,7 @@ public class RegressionTest100a extends BaseDL4JTest {
 
     @Override
     public long getTimeoutMilliseconds() {
-        return 90000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
+        return 180000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
     }
 
     @Override

deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/regressiontest/RegressionTest100b3.java

@@ -52,7 +52,7 @@ public class RegressionTest100b3 extends BaseDL4JTest {
 
     @Override
     public long getTimeoutMilliseconds() {
-        return 90000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
+        return 180000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
     }
 
     @Override

deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/regressiontest/RegressionTest100b4.java

@@ -71,7 +71,7 @@ public class RegressionTest100b4 extends BaseDL4JTest {
 
     @Override
     public long getTimeoutMilliseconds() {
-        return 90000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
+        return 180000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
     }
 
     @Override

deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/regressiontest/RegressionTest100b6.java

@@ -58,7 +58,7 @@ public class RegressionTest100b6 extends BaseDL4JTest {
 
     @Override
     public long getTimeoutMilliseconds() {
-        return 90000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
+        return 180000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
     }
 
     @Test

deeplearning4j/deeplearning4j-core/src/test/java/org/deeplearning4j/regressiontest/TestDistributionDeserializer.java

@@ -30,6 +30,11 @@ import static org.junit.Assert.assertTrue;
  */
 public class TestDistributionDeserializer extends BaseDL4JTest {
 
+    @Override
+    public long getTimeoutMilliseconds() {
+        return 180000L;  //Most tests should be fast, but slow download may cause timeout on slow connections
+    }
+
     @Test
     public void testDistributionDeserializer() throws Exception {
         //Test current format:

deeplearning4j/deeplearning4j-graph/src/test/java/org/deeplearning4j/graph/models/deepwalk/TestDeepWalk.java

@@ -46,6 +46,11 @@ public class TestDeepWalk extends BaseDL4JTest {
     @Rule
     public TemporaryFolder testDir = new TemporaryFolder();
 
+    @Override
+    public long getTimeoutMilliseconds() {
+        return 120_000L;        //Increase timeout due to intermittently slow CI machines
+    }
+
     @Test(timeout = 60000L)
     public void testBasic() throws IOException {
         //Very basic test. Load graph, build tree, call fit, make sure it doesn't throw any exceptions

deeplearning4j/deeplearning4j-nlp-parent/deeplearning4j-nlp/pom.xml

@@ -84,12 +84,6 @@
             <version>${project.version}</version>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>org.awaitility</groupId>
-            <artifactId>awaitility</artifactId>
-            <version>4.0.2</version>
-            <scope>test</scope>
-        </dependency>
     </dependencies>
 
     <profiles>

deeplearning4j/deeplearning4j-nlp-parent/deeplearning4j-nlp/src/main/java/org/deeplearning4j/models/embeddings/loader/WordVectorSerializer.java

@@ -968,7 +968,7 @@ public class WordVectorSerializer {
     public static Word2Vec readWord2VecFromText(@NonNull File vectors, @NonNull File hs, @NonNull File h_codes,
                                                 @NonNull File h_points, @NonNull VectorsConfiguration configuration) throws IOException {
         // first we load syn0
-        Pair<InMemoryLookupTable, VocabCache> pair = loadTxt(new FileInputStream(vectors));
+        Pair<InMemoryLookupTable, VocabCache> pair = loadTxt(new FileInputStream(vectors));     //Note stream is closed in loadTxt
         InMemoryLookupTable lookupTable = pair.getFirst();
         lookupTable.setNegative(configuration.getNegative());
         if (configuration.getNegative() > 0)
@@ -1607,7 +1607,7 @@ public class WordVectorSerializer {
      */
     @Deprecated
     public static WordVectors loadTxtVectors(File vectorsFile) throws IOException {
-        FileInputStream fileInputStream = new FileInputStream(vectorsFile);
+        FileInputStream fileInputStream = new FileInputStream(vectorsFile);         //Note stream is closed in loadTxt
         Pair<InMemoryLookupTable, VocabCache> pair = loadTxt(fileInputStream);
         return fromPair(pair);
     }

deeplearning4j/deeplearning4j-nlp-parent/deeplearning4j-nlp/src/test/java/org/deeplearning4j/models/word2vec/Word2VecTestsSmall.java

@@ -49,8 +49,8 @@ import java.io.File;
 import java.util.Collection;
 import java.util.concurrent.Callable;
 
-import static org.awaitility.Awaitility.await;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 
 @Slf4j
@@ -206,12 +206,6 @@ public class Word2VecTestsSmall extends BaseDL4JTest {
         final MultiLayerNetwork restored = ModelSerializer.restoreMultiLayerNetwork(bais, true);
 
         assertEquals(net.getLayerWiseConfigurations(), restored.getLayerWiseConfigurations());
-        await()
+        assertTrue(net.params().equalsWithEps(restored.params(), 2e-3));
-            .until(new Callable<Boolean>() {
-                @Override
-                public Boolean call() {
-                    return net.params().equalsWithEps(restored.params(), 2e-3);
-                }
-            });
     }
 }

deeplearning4j/deeplearning4j-nn/src/main/java/org/deeplearning4j/nn/layers/BaseOutputLayer.java

@@ -25,6 +25,7 @@ import org.deeplearning4j.nn.params.DefaultParamInitializer;
 import org.deeplearning4j.nn.workspace.ArrayType;
 import org.deeplearning4j.nn.workspace.LayerWorkspaceMgr;
 import org.deeplearning4j.optimize.Solver;
+import org.nd4j.common.base.Preconditions;
 import org.nd4j.evaluation.classification.Evaluation;
 import org.nd4j.linalg.api.buffer.DataType;
 import org.nd4j.linalg.api.ndarray.INDArray;
@@ -247,10 +248,8 @@ public abstract class BaseOutputLayer<LayerConfT extends org.deeplearning4j.nn.c
     @Override
     public int[] predict(INDArray input) {
         INDArray output = activate(input, false, LayerWorkspaceMgr.noWorkspacesImmutable());
-        int[] ret = new int[input.rows()];
+        Preconditions.checkState(output.rank() == 2, "predict(INDArray) method can only be used on rank 2 output - got array with rank %s", output.rank());
-        for (int i = 0; i < ret.length; i++)
+        return output.argMax(1).toIntVector();
-            ret[i] = Nd4j.getBlasWrapper().iamax(output.getRow(i));
-        return ret;
     }
 
     /**

deeplearning4j/deeplearning4j-nn/src/main/java/org/deeplearning4j/nn/layers/LossLayer.java

@@ -23,6 +23,7 @@ import org.deeplearning4j.nn.conf.NeuralNetConfiguration;
 import org.deeplearning4j.nn.gradient.DefaultGradient;
 import org.deeplearning4j.nn.gradient.Gradient;
 import org.deeplearning4j.optimize.Solver;
+import org.nd4j.common.base.Preconditions;
 import org.nd4j.linalg.api.buffer.DataType;
 import org.nd4j.linalg.api.ndarray.INDArray;
 import org.nd4j.linalg.dataset.api.DataSet;
@@ -251,10 +252,8 @@ public class LossLayer extends BaseLayer<org.deeplearning4j.nn.conf.layers.LossL
     @Override
     public int[] predict(INDArray input) {
         INDArray output = activate(input, false, LayerWorkspaceMgr.noWorkspacesImmutable());
-        int[] ret = new int[input.rows()];
+        Preconditions.checkState(output.rank() == 2, "predict(INDArray) method can only be used on rank 2 output - got array with rank %s", output.rank());
-        for (int i = 0; i < ret.length; i++)
+        return output.argMax(1).toIntVector();
-            ret[i] = Nd4j.getBlasWrapper().iamax(output.getRow(i));
-        return ret;
     }
 
     /**

deeplearning4j/deeplearning4j-nn/src/main/java/org/deeplearning4j/nn/multilayer/MultiLayerNetwork.java

@@ -2220,14 +2220,8 @@ public class MultiLayerNetwork implements Serializable, Classifier, Layer, Neura
         if (d.size(0) > Integer.MAX_VALUE)
             throw new ND4JArraySizeException();
 
-        int[] ret = new int[(int) d.size(0)];
+        Preconditions.checkState(output.rank() == 2, "predict(INDArray) method can only be used on rank 2 output - got array with rank %s", output.rank());
-        if (d.isRowVectorOrScalar())
+        return output.argMax(1).toIntVector();
-            ret[0] = Nd4j.getBlasWrapper().iamax(output);
-        else {
-            for (int i = 0; i < ret.length; i++)
-                ret[i] = Nd4j.getBlasWrapper().iamax(output.getRow(i));
-        }
-        return ret;
     }
 
     /**

deeplearning4j/deeplearning4j-ui-parent/deeplearning4j-ui-model/src/test/java/org/deeplearning4j/ui/stats/TestTransferStatsCollection.java

@@ -26,6 +26,7 @@ import org.deeplearning4j.nn.transferlearning.TransferLearning;
 import org.deeplearning4j.BaseDL4JTest;
 import org.deeplearning4j.ui.model.stats.StatsListener;
 import org.deeplearning4j.ui.model.storage.FileStatsStorage;
+import org.deeplearning4j.ui.model.storage.InMemoryStatsStorage;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
@@ -42,8 +43,10 @@ import java.io.IOException;
  */
 public class TestTransferStatsCollection extends BaseDL4JTest {
 
-    @Rule
+    @Override
-    public TemporaryFolder testDir = new TemporaryFolder();
+    public long getTimeoutMilliseconds() {
+        return 90_000L;
+    }
 
     @Test
     public void test() throws IOException {
@@ -62,9 +65,7 @@ public class TestTransferStatsCollection extends BaseDL4JTest {
                                                         new FineTuneConfiguration.Builder().updater(new Sgd(0.01)).build())
                                         .setFeatureExtractor(0).build();
 
-        File dir = testDir.newFolder();
+        net2.setListeners(new StatsListener(new InMemoryStatsStorage()));
-        File f = new File(dir, "dl4jTestTransferStatsCollection.bin");
-        net2.setListeners(new StatsListener(new FileStatsStorage(f)));
 
         //Previosuly: failed on frozen layers
         net2.fit(new DataSet(Nd4j.rand(8, 10), Nd4j.rand(8, 10)));