Merge pull request #907 from tqchen/master

[DIST] Enable multiple thread  make rabit and xgboost threadsafe

.gitignore

@@ -78,5 +78,4 @@ tags
 *.iml
 *.class
 target
-
 *.swp

NEWS.md

@@ -22,6 +22,11 @@ This file records the changes in xgboost library in reverse chronological order.
   - The windows version is still blocked due to Rtools do not support ```std::thread```.
 * rabit and dmlc-core are maintained through git submodule
   - Anyone can open PR to update these dependencies now.
+* Improvements
+  - Rabit and xgboost libs are not thread-safe and use thread local PRNGs
+  - This could fix some of the previous problem which runs xgboost on multiple threads.
+* JVM Package
+  - Enable xgboost4j for java and scala
 
 ## v0.47 (2016.01.14)
 

jvm-packages/.gitignore

@@ -0,0 +1,2 @@
+tracker.py
+build.sh

jvm-packages/create_jni.sh

@@ -27,6 +27,8 @@ fi
 
 rm -f xgboost4j/src/main/resources/lib/libxgboost4j.${dl}
 mv lib/libxgboost4j.so xgboost4j/src/main/resources/lib/libxgboost4j.${dl}
+# copy python to native resources
+cp ../dmlc-core/tracker/dmlc_tracker/tracker.py xgboost4j/src/main/resources/tracker.py
 
 popd > /dev/null
 echo "complete"

jvm-packages/test_distributed.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
 # Simple script to test distributed version, to be deleted later.
 cd xgboost4j-demo
-../../dmlc-core/tracker/dmlc-submit --cluster=local --num-workers=3 java -cp target/xgboost4j-demo-0.1-jar-with-dependencies.jar ml.dmlc.xgboost4j.demo.DistTrain
+java  -XX:OnError="gdb - %p" -cp target/xgboost4j-demo-0.1-jar-with-dependencies.jar ml.dmlc.xgboost4j.demo.DistTrain 4
 cd ..

jvm-packages/xgboost4j-demo/src/main/java/ml/dmlc/xgboost4j/demo/DistTrain.java

@@ -2,19 +2,37 @@ package ml.dmlc.xgboost4j.demo;
 
 import java.io.IOException;
 import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 
 import ml.dmlc.xgboost4j.*;
 
+
 /**
  * Distributed training example, used to quick test distributed training.
  *
  * @author tqchen
  */
 public class DistTrain {
+  private static final Log logger = LogFactory.getLog(DistTrain.class);
+  private Map<String, String> envs = null;
 
-  public static void main(String[] args) throws IOException, XGBoostError {
+  private class Worker implements Runnable {
+    private final int workerId;
+
+    Worker(int workerId) {
+      this.workerId = workerId;
+    }
+
+    public void run() {
+      try {
+        Map<String, String> worker_env = new HashMap<String, String>(envs);
+
+        worker_env.put("DMLC_TASK_ID", String.valueOf(workerId));
         // always initialize rabit module before training.
-    Rabit.init(new HashMap<String, String>());
+        Rabit.init(worker_env);
 
         // load file from text file, also binary buffer generated by xgboost4j
         DMatrix trainMat = new DMatrix("../../demo/data/agaricus.txt.train");
@@ -24,9 +42,9 @@ public class DistTrain {
         params.put("eta", 1.0);
         params.put("max_depth", 2);
         params.put("silent", 1);
+        params.put("nthread", 2);
         params.put("objective", "binary:logistic");
 
-
         HashMap<String, DMatrix> watches = new HashMap<String, DMatrix>();
         watches.put("train", trainMat);
         watches.put("test", testMat);
@@ -39,5 +57,24 @@ public class DistTrain {
 
         // always shutdown rabit module after training.
         Rabit.shutdown();
+      } catch (Exception ex){
+        logger.error(ex);
+      }
+    }
+  }
+
+  void start(int nWorkers) throws IOException, XGBoostError, InterruptedException {
+    RabitTracker tracker = new RabitTracker(nWorkers);
+    if (tracker.start()) {
+      envs = tracker.getWorkerEnvs();
+      for (int i = 0; i < nWorkers; ++i) {
+        new Thread(new Worker(i)).start();
+      }
+      tracker.waitFor();
+    }
+  }
+
+  public static void main(String[] args) throws IOException, XGBoostError, InterruptedException {
+    new DistTrain().start(Integer.parseInt(args[0]));
   }
 }

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

@@ -1,9 +1,10 @@
 package ml.dmlc.xgboost4j;
 
 import java.io.IOException;
+import java.io.Serializable;
 import java.util.Map;
 
-public interface Booster {
+public interface Booster extends Serializable {
 
   /**
    * set parameter
@@ -109,12 +110,25 @@ public interface Booster {
   float[][] predict(DMatrix data, int treeLimit, boolean predLeaf) throws XGBoostError;
 
   /**
-   * save model to modelPath
+   * save model to modelPath, the model path support depends on the path support
-   *
+   * in libxgboost. For example, if we want to save to hdfs, libxgboost need to be
+   * compiled with HDFS support.
+   * See also toByteArray
    * @param modelPath model path
    */
   void saveModel(String modelPath) throws XGBoostError;
 
+  /**
+   * Save the model as byte array representation.
+   * Write these bytes to a file will give compatible format with other xgboost bindings.
+   *
+   * If java natively support HDFS file API, use toByteArray and write the ByteArray,
+   *
+   * @return the saved byte array.
+   * @throws XGBoostError
+   */
+  byte[] toByteArray() throws XGBoostError;
+
   /**
    * Dump model into a text file.
    *

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

@@ -57,7 +57,6 @@ class JavaBoosterImpl implements Booster {
     setParams(params);
   }
 
-
   /**
    * load model from modelPath
    *
@@ -440,6 +439,22 @@ class JavaBoosterImpl implements Booster {
     return featureScore;
   }
 
+  /**
+   * Save the model as byte array representation.
+   * Write these bytes to a file will give compatible format with other xgboost bindings.
+   *
+   * If java natively support HDFS file API, use toByteArray and write the ByteArray,
+   *
+   * @return the saved byte array.
+   * @throws XGBoostError
+   */
+  public byte[] toByteArray() throws XGBoostError {
+    byte[][] bytes = new byte[1][];
+    JNIErrorHandle.checkCall(XgboostJNI.XGBoosterGetModelRaw(this.handle, bytes));
+    return bytes[0];
+  }
+
+
   /**
    * Load the booster model from thread-local rabit checkpoint.
    * This is only used in distributed training.
@@ -475,6 +490,27 @@ class JavaBoosterImpl implements Booster {
     return handles;
   }
 
+  // making Booster serializable
+  private void writeObject(java.io.ObjectOutputStream out)
+          throws IOException {
+    try {
+      out.writeObject(this.toByteArray());
+    } catch (XGBoostError ex) {
+      throw new IOException(ex.toString());
+    }
+  }
+
+  private void readObject(java.io.ObjectInputStream in)
+          throws IOException, ClassNotFoundException {
+    try {
+      this.init(null);
+      byte[] bytes = (byte[])in.readObject();
+      JNIErrorHandle.checkCall(XgboostJNI.XGBoosterLoadModelFromBuffer(this.handle, bytes));
+    } catch (XGBoostError ex) {
+      throw new IOException(ex.toString());
+    }
+  }
+
   @Override
   protected void finalize() throws Throwable {
     super.finalize();

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

@@ -21,6 +21,7 @@ import java.lang.reflect.Field;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+
 /**
  * class to load native library
  *
@@ -61,12 +62,32 @@ class NativeLibLoader {
    * three characters
    */
   private static void loadLibraryFromJar(String path) throws IOException, IllegalArgumentException{
+    String temp = createTempFileFromResource(path);
+    // Finally, load the library
+    System.load(temp);
+  }
 
+  /**
+   * Create a temp file that copies the resource from current JAR archive
+   * <p/>
+   * The file from JAR is copied into system temp file.
+   * The temporary file is deleted after exiting.
+   * Method uses String as filename because the pathname is "abstract", not system-dependent.
+   * <p/>
+   * The restrictions of {@link File#createTempFile(java.lang.String, java.lang.String)} apply to
+   * {@code path}.
+   * @param path Path to the resources in the jar
+   * @return The created temp file.
+   * @throws IOException
+   * @throws IllegalArgumentException
+   */
+  static String createTempFileFromResource(String path) throws
+          IOException, IllegalArgumentException {
+    // Obtain filename from path
     if (!path.startsWith("/")) {
       throw new IllegalArgumentException("The path has to be absolute (start with '/').");
     }
 
-    // Obtain filename from path
     String[] parts = path.split("/");
     String filename = (parts.length > 1) ? parts[parts.length - 1] : null;
 
@@ -83,7 +104,6 @@ class NativeLibLoader {
     if (filename == null || prefix.length() < 3) {
       throw new IllegalArgumentException("The filename has to be at least 3 characters long.");
     }
-
     // Prepare temporary file
     File temp = File.createTempFile(prefix, suffix);
     temp.deleteOnExit();
@@ -113,9 +133,7 @@ class NativeLibLoader {
       os.close();
       is.close();
     }
-
+    return temp.getAbsolutePath();
-    // Finally, load the library
-    System.load(temp.getAbsolutePath());
   }
 
   /**
@@ -133,8 +151,9 @@ class NativeLibLoader {
       try {
         String libraryFromJar = nativeResourcePath + System.mapLibraryName(libName);
         loadLibraryFromJar(libraryFromJar);
-      } catch (IOException e1) {
+      } catch (IOException ioe) {
-        throw e1;
+        logger.error("failed to load library from both native path and jar");
+        throw ioe;
       }
     }
   }

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

@@ -0,0 +1,144 @@
+package ml.dmlc.xgboost4j;
+
+
+
+import java.io.*;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.concurrent.atomic.AtomicReference;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+/**
+ * Distributed RabitTracker, need to be started on driver code before running distributed jobs.
+ */
+public class RabitTracker {
+  // Maybe per tracker logger?
+  private static final Log logger = LogFactory.getLog(RabitTracker.class);
+  // tracker python file.
+  private static String tracker_py = null;
+  // environment variable to be pased.
+  private Map<String, String> envs = new HashMap<String, String>();
+  // number of workers to be submitted.
+  private int num_workers;
+  private AtomicReference<Process> trackerProcess = new AtomicReference<Process>();
+
+  static {
+    try {
+      initTrackerPy();
+    } catch (IOException ex) {
+      logger.error("load tracker library failed.");
+      logger.error(ex);
+    }
+  }
+
+  /**
+   * Tracker logger that logs output from tracker.
+   */
+  private class TrackerProcessLogger implements Runnable {
+    public void run() {
+
+      Log trackerProcessLogger = LogFactory.getLog(TrackerProcessLogger.class);
+      BufferedReader reader = new BufferedReader(new InputStreamReader(
+              trackerProcess.get().getErrorStream()));
+      String line;
+      try {
+        while ((line = reader.readLine()) != null) {
+          trackerProcessLogger.info(line);
+        }
+      } catch (IOException ex) {
+        trackerProcessLogger.error(ex.toString());
+      }
+    }
+  }
+
+  private static void initTrackerPy() throws IOException {
+    try {
+      tracker_py = NativeLibLoader.createTempFileFromResource("/tracker.py");
+    } catch (IOException ioe) {
+      logger.trace("cannot access tracker python script");
+      throw ioe;
+    }
+  }
+
+
+  public RabitTracker(int num_workers) {
+    this.num_workers = num_workers;
+  }
+
+  /**
+   * Get environments that can be used to pass to worker.
+   * @return The environment settings.
+   */
+  public Map<String, String> getWorkerEnvs() {
+    return envs;
+  }
+
+  private void loadEnvs(InputStream ins) throws IOException {
+    try {
+      BufferedReader reader = new BufferedReader(new InputStreamReader(ins));
+      assert reader.readLine().trim().equals("DMLC_TRACKER_ENV_START");
+      String line;
+      while ((line = reader.readLine()) != null) {
+        if (line.trim().equals("DMLC_TRACKER_ENV_END")) {
+          break;
+        }
+        String[] sep = line.split("=");
+        if (sep.length == 2) {
+          envs.put(sep[0], sep[1]);
+        }
+      }
+      reader.close();
+    } catch (IOException ioe){
+      logger.error("cannot get runtime configuration from tracker process");
+      ioe.printStackTrace();
+      throw ioe;
+    }
+  }
+
+  private boolean startTrackerProcess() {
+    try {
+      trackerProcess.set(Runtime.getRuntime().exec("python " + tracker_py +
+              " --num-workers=" + String.valueOf(num_workers)));
+      loadEnvs(trackerProcess.get().getInputStream());
+      return true;
+    } catch (IOException ioe) {
+      ioe.printStackTrace();
+      return false;
+    }
+  }
+
+  private void stop() {
+    if (trackerProcess.get() != null) {
+      trackerProcess.get().destroy();
+    }
+  }
+
+  public boolean start() {
+    if (startTrackerProcess()) {
+      logger.debug("Tracker started, with env=" + envs.toString());
+      // also start a tracker logger
+      Thread logger_thread = new Thread(new TrackerProcessLogger());
+      logger_thread.setDaemon(true);
+      logger_thread.start();
+      return true;
+    } else {
+      logger.error("FAULT: failed to start tracker process");
+      stop();
+      return false;
+    }
+  }
+
+  public void waitFor() {
+    try {
+      trackerProcess.get().waitFor();
+      logger.info("Tracker Process ends with exit code " + trackerProcess.get().exitValue());
+      stop();
+    } catch (InterruptedException e) {
+      // we should not get here as RabitTracker is accessed in the main thread
+      e.printStackTrace();
+      logger.error("the RabitTracker thread is terminated unexpectedly");
+    }
+  }
+}

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

@@ -74,9 +74,9 @@ class XgboostJNI {
 
   public final static native int XGBoosterSaveModel(long handle, String fname);
 
-  public final static native int XGBoosterLoadModelFromBuffer(long handle, long buf, long len);
+  public final static native int XGBoosterLoadModelFromBuffer(long handle, byte[] bytes);
 
-  public final static native int XGBoosterGetModelRaw(long handle, String[] out_string);
+  public final static native int XGBoosterGetModelRaw(long handle, byte[][] out_bytes);
 
   public final static native int XGBoosterDumpModel(long handle, String fmap, int with_stats,
                                                     String[][] out_strings);

jvm-packages/xgboost4j/src/main/scala/ml/dmlc/xgboost4j/scala/Booster.scala

@@ -23,7 +23,7 @@ import scala.collection.mutable
 import ml.dmlc.xgboost4j.XGBoostError
 
 
-trait Booster {
+trait Booster extends Serializable {
 
 
   /**

jvm-packages/xgboost4j/src/native/xgboost4j.cpp

@@ -13,6 +13,8 @@
 */
 
 #include <xgboost/c_api.h>
+#include <xgboost/base.h>
+#include <xgboost/logging.h>
 #include "./xgboost4j.h"
 #include <cstring>
 #include <vector>
@@ -276,27 +278,17 @@ JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_XgboostJNI_XGDMatrixNumRow
  */
 JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_XgboostJNI_XGBoosterCreate
   (JNIEnv *jenv, jclass jcls, jlongArray jhandles, jlongArray jout) {
-  DMatrixHandle* handles = NULL;
+  std::vector<DMatrixHandle> handles;
-  bst_ulong len = 0;
+  if (jhandles != nullptr) {
-  jlong* cjhandles = 0;
+    size_t len = jenv->GetArrayLength(jhandles);
-  BoosterHandle result;
+    jlong *cjhandles = jenv->GetLongArrayElements(jhandles, 0);
-
+    for (size_t i = 0; i < len; ++i) {
-  if (jhandles) {
+      handles.push_back((DMatrixHandle) cjhandles[i]);
-    len = (bst_ulong)jenv->GetArrayLength(jhandles);
-    handles = new DMatrixHandle[len];
-    //put handle from jhandles to chandles
-    cjhandles = jenv->GetLongArrayElements(jhandles, 0);
-    for(bst_ulong i=0; i<len; i++) {
-      handles[i] = (DMatrixHandle) cjhandles[i];
     }
-  }
-
-  int ret = XGBoosterCreate(handles, len, &result);
-  //release
-  if (jhandles) {
-    delete[] handles;
     jenv->ReleaseLongArrayElements(jhandles, cjhandles, 0);
   }
+  BoosterHandle result;
+  int ret = XGBoosterCreate(dmlc::BeginPtr(handles), handles.size(), &result);
   setHandle(jenv, jout, result);
   return ret;
 }
@@ -369,43 +361,34 @@ JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_XgboostJNI_XGBoosterBoostOneIter
 JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_XgboostJNI_XGBoosterEvalOneIter
   (JNIEnv *jenv, jclass jcls, jlong jhandle, jint jiter, jlongArray jdmats, jobjectArray jevnames, jobjectArray jout) {
   BoosterHandle handle = (BoosterHandle) jhandle;
-  DMatrixHandle* dmats = 0;
+  std::vector<DMatrixHandle> dmats;
-  char **evnames = 0;
+  std::vector<std::string> evnames;
-  char *result = 0;
+  std::vector<const char*> evchars;
-  bst_ulong len = (bst_ulong)jenv->GetArrayLength(jdmats);
+
-  if(len > 0) {
+  size_t len =  static_cast<size_t>(jenv->GetArrayLength(jdmats));
-    dmats = new DMatrixHandle[len];
-    evnames = new char*[len];
-  }
   // put handle from jhandles to chandles
   jlong* cjdmats = jenv->GetLongArrayElements(jdmats, 0);
-  for(bst_ulong i=0; i<len; i++) {
+  for (size_t i = 0; i < len; ++i) {
-    dmats[i] = (DMatrixHandle) cjdmats[i];
+    dmats.push_back((DMatrixHandle) cjdmats[i]);
-  }
-  //transfer jObjectArray to char**, user strcpy and release JNI char* inplace
-  for(bst_ulong i=0; i<len; i++) {
     jstring jevname = (jstring)jenv->GetObjectArrayElement(jevnames, i);
-    const char* cevname = jenv->GetStringUTFChars(jevname, 0);
+    const char *s =jenv->GetStringUTFChars(jevname, 0);
-    evnames[i] = new char[jenv->GetStringLength(jevname)];
+    evnames.push_back(std::string(s, jenv->GetStringLength(jevname)));
-    strcpy(evnames[i], cevname);
+    if (s != nullptr) jenv->ReleaseStringUTFChars(jevname, s);
-    jenv->ReleaseStringUTFChars(jevname, cevname);
   }
-
-  int ret = XGBoosterEvalOneIter(handle, jiter, dmats, (char const *(*)) evnames, len, (const char **) &result);
-  if(len > 0) {
-    delete[] dmats;
-    //release string chars
-    for(bst_ulong i=0; i<len; i++) {
-      delete[] evnames[i];
-    }
-    delete[] evnames;
   jenv->ReleaseLongArrayElements(jdmats, cjdmats, 0);
+  for (size_t i = 0; i < len; ++i) {
+    evchars.push_back(evnames[i].c_str());
+  }
+  const char* result;
+  int ret = XGBoosterEvalOneIter(handle, jiter,
+                                 dmlc::BeginPtr(dmats),
+                                 dmlc::BeginPtr(evchars),
+                                 len, &result);
+  jstring jinfo = nullptr;
+  if (result != nullptr) {
+    jinfo = jenv->NewStringUTF(result);
   }
-
-  jstring jinfo = 0;
-  if (result) jinfo = jenv->NewStringUTF((const char *) result);
   jenv->SetObjectArrayElement(jout, 0, jinfo);
-
   return ret;
 }
 
@@ -456,37 +439,40 @@ JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_XgboostJNI_XGBoosterSaveModel
 
   int ret = XGBoosterSaveModel(handle, fname);
   if (fname) jenv->ReleaseStringUTFChars(jfname, fname);
-
   return ret;
 }
 
 /*
  * Class:     ml_dmlc_xgboost4j_XgboostJNI
  * Method:    XGBoosterLoadModelFromBuffer
- * Signature: (JJJ)V
+ * Signature: (J[B)I
  */
 JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_XgboostJNI_XGBoosterLoadModelFromBuffer
-  (JNIEnv *jenv, jclass jcls, jlong jhandle, jlong jbuf, jlong jlen) {
+    (JNIEnv *jenv, jclass jcls, jlong jhandle, jbyteArray jbytes) {
   BoosterHandle handle = (BoosterHandle) jhandle;
-  void *buf = (void*) jbuf;
+  jbyte* buffer = jenv->GetByteArrayElements(jbytes, 0);
-  return XGBoosterLoadModelFromBuffer(handle, (void const *)buf, (bst_ulong) jlen);
+  int ret = XGBoosterLoadModelFromBuffer(
+      handle, buffer, jenv->GetArrayLength(jbytes));
+  jenv->ReleaseByteArrayElements(jbytes, buffer, 0);
+  return ret;
 }
 
 /*
  * Class:     ml_dmlc_xgboost4j_XgboostJNI
  * Method:    XGBoosterGetModelRaw
- * Signature: (J)Ljava/lang/String;
+ * Signature: (J[[B)I
  */
 JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_XgboostJNI_XGBoosterGetModelRaw
   (JNIEnv * jenv, jclass jcls, jlong jhandle, jobjectArray jout) {
   BoosterHandle handle = (BoosterHandle) jhandle;
   bst_ulong len = 0;
-  char *result;
+  const char* result;
+  int ret = XGBoosterGetModelRaw(handle, &len, &result);
 
-  int ret = XGBoosterGetModelRaw(handle, &len, (const char **) &result);
   if (result) {
-    jstring jinfo = jenv->NewStringUTF((const char *) result);
+    jbyteArray jarray = jenv->NewByteArray(len);
-    jenv->SetObjectArrayElement(jout, 0, jinfo);
+    jenv->SetByteArrayRegion(jarray, 0, len, (jbyte*)result);
+    jenv->SetObjectArrayElement(jout, 0, jarray);
   }
   return ret;
 }
@@ -553,15 +539,17 @@ JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_XgboostJNI_RabitInit
   bst_ulong len = (bst_ulong)jenv->GetArrayLength(jargs);
   for (bst_ulong i = 0; i < len; ++i) {
     jstring arg = (jstring)jenv->GetObjectArrayElement(jargs, i);
-    std::string s(jenv->GetStringUTFChars(arg, 0),
+    const char *s = jenv->GetStringUTFChars(arg, 0);
-                  jenv->GetStringLength(arg));
+    args.push_back(std::string(s, jenv->GetStringLength(arg)));
-    if (s.length() != 0) args.push_back(s);
+    if (s != nullptr) jenv->ReleaseStringUTFChars(arg, s);
+    if (args.back().length() == 0) args.pop_back();
   }
 
   for (size_t i = 0; i < args.size(); ++i) {
     argv.push_back(&args[i][0]);
   }
-  RabitInit(args.size(), args.size() == 0 ? NULL : &argv[0]);
+
+  RabitInit(args.size(), dmlc::BeginPtr(argv));
   return 0;
 }
 

jvm-packages/xgboost4j/src/native/xgboost4j.h

@@ -194,15 +194,15 @@ JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_XgboostJNI_XGBoosterSaveModel
 /*
  * Class:     ml_dmlc_xgboost4j_XgboostJNI
  * Method:    XGBoosterLoadModelFromBuffer
- * Signature: (JJJ)I
+ * Signature: (J[B)I
  */
 JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_XgboostJNI_XGBoosterLoadModelFromBuffer
-  (JNIEnv *, jclass, jlong, jlong, jlong);
+  (JNIEnv *, jclass, jlong, jbyteArray);
 
 /*
  * Class:     ml_dmlc_xgboost4j_XgboostJNI
  * Method:    XGBoosterGetModelRaw
- * Signature: (J[Ljava/lang/String;)I
+ * Signature: (J[[B)I
  */
 JNIEXPORT jint JNICALL Java_ml_dmlc_xgboost4j_XgboostJNI_XGBoosterGetModelRaw
   (JNIEnv *, jclass, jlong, jobjectArray);

src/common/common.cc

@@ -4,12 +4,20 @@
  * \brief Enable all kinds of global variables in common.
  */
 #include "./random.h"
+#include "./thread_local.h"
 
 namespace xgboost {
 namespace common {
+/*! \brief thread local entry for random. */
+struct RandomThreadLocalEntry {
+  /*! \brief the random engine instance. */
+  GlobalRandomEngine engine;
+};
+
+typedef ThreadLocalStore<RandomThreadLocalEntry> RandomThreadLocalStore;
+
 GlobalRandomEngine& GlobalRandom() {
-  static GlobalRandomEngine inst;
+  return RandomThreadLocalStore::Get()->engine;
-  return inst;
-}
 }
+}  // namespace common
 }  // namespace xgboost

src/common/random.h

@@ -61,7 +61,8 @@ typedef RandomEngine GlobalRandomEngine;
 
 /*!
  * \brief global singleton of a random engine.
- *  Only use this engine when necessary, not thread-safe.
+ *  This random engine is thread-local and
+ *  only visible to current thread.
  */
 GlobalRandomEngine& GlobalRandom(); // NOLINT(*)
 

src/common/thread_local.h

@@ -6,6 +6,8 @@
 #ifndef XGBOOST_COMMON_THREAD_LOCAL_H_
 #define XGBOOST_COMMON_THREAD_LOCAL_H_
 
+#include <dmlc/base.h>
+
 #if DMLC_ENABLE_STD_THREAD
 #include <mutex>
 #endif

src/gbm/gbtree.cc

@@ -15,6 +15,7 @@
 #include <utility>
 #include <string>
 #include <limits>
+#include "../common/common.h"
 
 namespace xgboost {
 namespace gbm {
@@ -265,13 +266,11 @@ class GBTree : public GradientBooster {
   inline void InitUpdater() {
     if (updaters.size() != 0) return;
     std::string tval = tparam.updater_seq;
-    char *pstr;
+    std::vector<std::string> ups = common::Split(tval, ',');
-    pstr = std::strtok(&tval[0], ",");
+    for (const std::string& pstr : ups) {
-    while (pstr != nullptr) {
+      std::unique_ptr<TreeUpdater> up(TreeUpdater::Create(pstr.c_str()));
-      std::unique_ptr<TreeUpdater> up(TreeUpdater::Create(pstr));
       up->Init(this->cfg);
       updaters.push_back(std::move(up));
-      pstr = std::strtok(nullptr, ",");
     }
   }
   // do group specific group