[jvm-packages] allow partial evaluation of dataframe before prediction (#4407)

* allow partial evaluation of dataframe before prediction

* resume spark test

* comments

* Run unit tests after building JVM packages

CMakeLists.txt

@@ -78,7 +78,7 @@ else ()
 endif (MINGW OR R_LIB)
 add_library(rabit STATIC ${RABIT_SOURCES})
 target_include_directories(rabit PRIVATE
-  $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/rabit/include>
+  $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/dmlc-core/include>
   $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/rabit/include/rabit>)
 set_target_properties(rabit
   PROPERTIES

dmlc-core

@@ -1 +1 @@
-Subproject commit ac983092ee3b339f76a2d7e7c3b846570218200d
+Subproject commit 13d5acb8ba7e79550bbf2f730f1a3944ff0fa68b

jvm-packages/xgboost4j-spark/src/test/scala/ml/dmlc/xgboost4j/scala/spark/RabitRobustnessSuite.scala

@@ -16,14 +16,73 @@
 
 package ml.dmlc.xgboost4j.scala.spark
 
+import java.util.concurrent.LinkedBlockingDeque
+
+import scala.util.Random
+
 import ml.dmlc.xgboost4j.java.{IRabitTracker, Rabit, RabitTracker => PyRabitTracker}
 import ml.dmlc.xgboost4j.scala.rabit.{RabitTracker => ScalaRabitTracker}
 import ml.dmlc.xgboost4j.java.IRabitTracker.TrackerStatus
+import ml.dmlc.xgboost4j.scala.DMatrix
+
 import org.apache.spark.{SparkConf, SparkContext}
 import org.scalatest.FunSuite
 
 
-class RabitTrackerRobustnessSuite extends FunSuite with PerTest {
+class RabitSuite extends FunSuite with PerTest {
+
+  test("training with Scala-implemented Rabit tracker") {
+    val eval = new EvalError()
+    val training = buildDataFrame(Classification.train)
+    val testDM = new DMatrix(Classification.test.iterator)
+    val paramMap = Map("eta" -> "1", "max_depth" -> "6",
+      "objective" -> "binary:logistic", "num_round" -> 5, "num_workers" -> numWorkers,
+      "tracker_conf" -> TrackerConf(60 * 60 * 1000, "scala"))
+    val model = new XGBoostClassifier(paramMap).fit(training)
+    assert(eval.eval(model._booster.predict(testDM, outPutMargin = true), testDM) < 0.1)
+  }
+
+  test("test Rabit allreduce to validate Scala-implemented Rabit tracker") {
+    val vectorLength = 100
+    val rdd = sc.parallelize(
+      (1 to numWorkers * vectorLength).toArray.map { _ => Random.nextFloat() }, numWorkers).cache()
+
+    val tracker = new ScalaRabitTracker(numWorkers)
+    tracker.start(0)
+    val trackerEnvs = tracker.getWorkerEnvs
+    val collectedAllReduceResults = new LinkedBlockingDeque[Array[Float]]()
+
+    val rawData = rdd.mapPartitions { iter =>
+      Iterator(iter.toArray)
+    }.collect()
+
+    val maxVec = (0 until vectorLength).toArray.map { j =>
+      (0 until numWorkers).toArray.map { i => rawData(i)(j) }.max
+    }
+
+    val allReduceResults = rdd.mapPartitions { iter =>
+      Rabit.init(trackerEnvs)
+      val arr = iter.toArray
+      val results = Rabit.allReduce(arr, Rabit.OpType.MAX)
+      Rabit.shutdown()
+      Iterator(results)
+    }.cache()
+
+    val sparkThread = new Thread() {
+      override def run(): Unit = {
+        allReduceResults.foreachPartition(() => _)
+        val byPartitionResults = allReduceResults.collect()
+        assert(byPartitionResults(0).length == vectorLength)
+        collectedAllReduceResults.put(byPartitionResults(0))
+      }
+    }
+    sparkThread.start()
+    assert(tracker.waitFor(0L) == 0)
+    sparkThread.join()
+
+    assert(collectedAllReduceResults.poll().sameElements(maxVec))
+  }
+
   test("test Java RabitTracker wrapper's exception handling: it should not hang forever.") {
     /*
       Deliberately create new instances of SparkContext in each unit test to avoid reusing the
@@ -148,4 +207,23 @@ class RabitTrackerRobustnessSuite extends FunSuite with PerTest {
     // should fail due to connection timeout
     assert(tracker.waitFor(0L) == TrackerStatus.FAILURE.getStatusCode)
   }
+
+  test("should allow the dataframe containing rabit calls to be partially evaluated for" +
+    " multiple times (ISSUE-4406)") {
+    val paramMap = Map(
+      "eta" -> "1",
+      "max_depth" -> "6",
+      "silent" -> "1",
+      "objective" -> "binary:logistic")
+    val trainingDF = buildDataFrame(Classification.train)
+    val model = new XGBoostClassifier(paramMap ++ Array("num_round" -> 10,
+      "num_workers" -> numWorkers)).fit(trainingDF)
+    val prediction = model.transform(trainingDF)
+    // a partial evaluation of dataframe will cause rabit initialized but not shutdown in some
+    // threads
+    prediction.show()
+    // a full evaluation here will re-run init and shutdown all rabit proxy
+    // expecting no error
+    prediction.collect()
+  }
 }

jvm-packages/xgboost4j-spark/src/test/scala/ml/dmlc/xgboost4j/scala/spark/XGBoostGeneralSuite.scala

@@ -17,67 +17,17 @@
 package ml.dmlc.xgboost4j.scala.spark
 
 import java.nio.file.Files
-import java.util.concurrent.LinkedBlockingDeque
 
 import ml.dmlc.xgboost4j.{LabeledPoint => XGBLabeledPoint}
 import ml.dmlc.xgboost4j.scala.DMatrix
-import ml.dmlc.xgboost4j.scala.rabit.RabitTracker
 import ml.dmlc.xgboost4j.scala.{XGBoost => SXGBoost, _}
 import org.apache.hadoop.fs.{FileSystem, Path}
 
 import org.apache.spark.TaskContext
-import org.apache.spark.ml.linalg.Vectors
-import org.apache.spark.sql._
 import org.scalatest.FunSuite
-import scala.util.Random
-
-import ml.dmlc.xgboost4j.java.Rabit
-
-import org.apache.spark.ml.feature.VectorAssembler
 
 class XGBoostGeneralSuite extends FunSuite with PerTest {
 
-  test("test Rabit allreduce to validate Scala-implemented Rabit tracker") {
-    val vectorLength = 100
-    val rdd = sc.parallelize(
-      (1 to numWorkers * vectorLength).toArray.map { _ => Random.nextFloat() }, numWorkers).cache()
-
-    val tracker = new RabitTracker(numWorkers)
-    tracker.start(0)
-    val trackerEnvs = tracker.getWorkerEnvs
-    val collectedAllReduceResults = new LinkedBlockingDeque[Array[Float]]()
-
-    val rawData = rdd.mapPartitions { iter =>
-      Iterator(iter.toArray)
-    }.collect()
-
-    val maxVec = (0 until vectorLength).toArray.map { j =>
-      (0 until numWorkers).toArray.map { i => rawData(i)(j) }.max
-    }
-
-    val allReduceResults = rdd.mapPartitions { iter =>
-      Rabit.init(trackerEnvs)
-      val arr = iter.toArray
-      val results = Rabit.allReduce(arr, Rabit.OpType.MAX)
-      Rabit.shutdown()
-      Iterator(results)
-    }.cache()
-
-    val sparkThread = new Thread() {
-      override def run(): Unit = {
-        allReduceResults.foreachPartition(() => _)
-        val byPartitionResults = allReduceResults.collect()
-        assert(byPartitionResults(0).length == vectorLength)
-        collectedAllReduceResults.put(byPartitionResults(0))
-      }
-    }
-    sparkThread.start()
-    assert(tracker.waitFor(0L) == 0)
-    sparkThread.join()
-
-    assert(collectedAllReduceResults.poll().sameElements(maxVec))
-  }
-
   test("distributed training with the specified worker number") {
     val trainingRDD = sc.parallelize(Classification.train)
     val (booster, metrics) = XGBoost.trainDistributed(
@@ -101,18 +51,6 @@ class XGBoostGeneralSuite extends FunSuite with PerTest {
     assert(eval.eval(model._booster.predict(testDM, outPutMargin = true), testDM) < 0.1)
   }
 
-
-  test("training with Scala-implemented Rabit tracker") {
-    val eval = new EvalError()
-    val training = buildDataFrame(Classification.train)
-    val testDM = new DMatrix(Classification.test.iterator)
-    val paramMap = Map("eta" -> "1", "max_depth" -> "6",
-      "objective" -> "binary:logistic", "num_round" -> 5, "num_workers" -> numWorkers,
-      "tracker_conf" -> TrackerConf(60 * 60 * 1000, "scala"))
-    val model = new XGBoostClassifier(paramMap).fit(training)
-    assert(eval.eval(model._booster.predict(testDM, outPutMargin = true), testDM) < 0.1)
-  }
-
   test("test with quantile hist with monotone_constraints (lossguide)") {
     val eval = new EvalError()
     val training = buildDataFrame(Classification.train)

jvm-packages/xgboost4j/src/main/java/ml/dmlc/xgboost4j/java/Rabit.java

@@ -9,6 +9,7 @@ import java.util.Map;
  * Rabit global class for synchronization.
  */
 public class Rabit {
+
   public enum OpType implements Serializable {
     MAX(0), MIN(1), SUM(2), BITWISE_OR(3);
 

rabit

@@ -1 +1 @@
-Subproject commit 1cc34f01db56d28e8e80847cf0fc5e3ecf8bb67b
+Subproject commit a429748e244f67f6f144a697f3aa1b1978705b11

tests/ci_build/build_jvm_packages.sh

@@ -9,7 +9,7 @@ set -x
 rm -rf build/
 cd jvm-packages
 
-mvn --no-transfer-progress package -DskipTests
+mvn --no-transfer-progress package
 
 set +x
 set +e

tests/ci_build/test_jvm_cross.sh

@@ -35,8 +35,7 @@ if [ ! -z "$RUN_INTEGRATION_TEST" ]
 then
   python3 get_iris.py
   spark-submit --class ml.dmlc.xgboost4j.scala.example.spark.SparkTraining --master 'local[8]' ./target/xgboost4j-tester-1.0-SNAPSHOT-jar-with-dependencies.jar ${PWD}/iris.csv
-  # Disabled due to https://github.com/dmlc/xgboost/issues/4406
+  spark-submit --class ml.dmlc.xgboost4j.scala.example.spark.SparkMLlibPipeline --master 'local[8]' ./target/xgboost4j-tester-1.0-SNAPSHOT-jar-with-dependencies.jar ${PWD}/iris.csv ${PWD}/native_model ${PWD}/pipeline_model
-  #spark-submit --class ml.dmlc.xgboost4j.scala.example.spark.SparkMLlibPipeline --master 'local[8]' ./target/xgboost4j-tester-1.0-SNAPSHOT-jar-with-dependencies.jar ${PWD}/iris.csv ${PWD}/native_model ${PWD}/pipeline_model
 fi
 
 set +x