Merge pull request #14 from apache/master

latest apache spark

LICENSE

@@ -237,6 +237,7 @@ The text of each license is also included at licenses/LICENSE-[project].txt.
 
      (BSD 3 Clause) netlib core (com.github.fommil.netlib:core:1.1.2 - https://github.com/fommil/netlib-java/core)
      (BSD 3 Clause) JPMML-Model (org.jpmml:pmml-model:1.2.7 - https://github.com/jpmml/jpmml-model)
+     (BSD 3 Clause) jmock (org.jmock:jmock-junit4:2.8.4 - http://jmock.org/)
      (BSD License) AntLR Parser Generator (antlr:antlr:2.7.7 - http://www.antlr.org/)
      (BSD License) ANTLR 4.5.2-1 (org.antlr:antlr4:4.5.2-1 - http://wwww.antlr.org/)
      (BSD licence) ANTLR ST4 4.0.4 (org.antlr:ST4:4.0.4 - http://www.stringtemplate.org)

R/pkg/NAMESPACE

@@ -201,6 +201,7 @@ exportMethods("%<=>%",
               "approxCountDistinct",
               "approxQuantile",
               "array_contains",
+              "array_join",
               "array_max",
               "array_min",
               "array_position",

R/pkg/R/functions.R

@@ -221,7 +221,9 @@ NULL
 #' head(select(tmp3, element_at(tmp3$v3, "Valiant")))
 #' tmp4 <- mutate(df, v4 = create_array(df$mpg, df$cyl), v5 = create_array(df$cyl, df$hp))
 #' head(select(tmp4, concat(tmp4$v4, tmp4$v5), arrays_overlap(tmp4$v4, tmp4$v5)))
-#' head(select(tmp, concat(df$mpg, df$cyl, df$hp)))}
+#' head(select(tmp, concat(df$mpg, df$cyl, df$hp)))
+#' tmp5 <- mutate(df, v6 = create_array(df$model, df$model))
+#' head(select(tmp5, array_join(tmp5$v6, "#"), array_join(tmp5$v6, "#", "NULL")))}
 NULL
 
 #' Window functions for Column operations
@@ -3006,6 +3008,27 @@ setMethod("array_contains",
             column(jc)
           })
 
+#' @details
+#' \code{array_join}: Concatenates the elements of column using the delimiter.
+#' Null values are replaced with nullReplacement if set, otherwise they are ignored.
+#'
+#' @param delimiter a character string that is used to concatenate the elements of column.
+#' @param nullReplacement an optional character string that is used to replace the Null values.
+#' @rdname column_collection_functions
+#' @aliases array_join array_join,Column-method
+#' @note array_join since 2.4.0
+setMethod("array_join",
+         signature(x = "Column", delimiter = "character"),
+         function(x, delimiter, nullReplacement = NULL) {
+           jc <- if (is.null(nullReplacement)) {
+             callJStatic("org.apache.spark.sql.functions", "array_join", x@jc, delimiter)
+           } else {
+             callJStatic("org.apache.spark.sql.functions", "array_join", x@jc, delimiter,
+                         as.character(nullReplacement))
+           }
+           column(jc)
+         })
+
 #' @details
 #' \code{array_max}: Returns the maximum value of the array.
 #'
@@ -3197,8 +3220,8 @@ setMethod("size",
 #' (or starting from the end if start is negative) with the specified length.
 #'
 #' @rdname column_collection_functions
-#' @param start an index indicating the first element occuring in the result.
-#' @param length a number of consecutive elements choosen to the result.
+#' @param start an index indicating the first element occurring in the result.
+#' @param length a number of consecutive elements chosen to the result.
 #' @aliases slice slice,Column-method
 #' @note slice since 2.4.0
 setMethod("slice",

R/pkg/R/generics.R

@@ -757,6 +757,10 @@ setGeneric("approxCountDistinct", function(x, ...) { standardGeneric("approxCoun
 #' @name NULL
 setGeneric("array_contains", function(x, value) { standardGeneric("array_contains") })
 
+#' @rdname column_collection_functions
+#' @name NULL
+setGeneric("array_join", function(x, delimiter, ...) { standardGeneric("array_join") })
+
 #' @rdname column_collection_functions
 #' @name NULL
 setGeneric("array_max", function(x) { standardGeneric("array_max") })

R/pkg/tests/fulltests/test_sparkSQL.R

@@ -1518,6 +1518,21 @@ test_that("column functions", {
   result <- collect(select(df, arrays_overlap(df[[1]], df[[2]])))[[1]]
   expect_equal(result, c(TRUE, FALSE, NA))
 
+  # Test array_join()
+  df <- createDataFrame(list(list(list("Hello", "World!"))))
+  result <- collect(select(df, array_join(df[[1]], "#")))[[1]]
+  expect_equal(result, "Hello#World!")
+  df2 <- createDataFrame(list(list(list("Hello", NA, "World!"))))
+  result <- collect(select(df2, array_join(df2[[1]], "#", "Beautiful")))[[1]]
+  expect_equal(result, "Hello#Beautiful#World!")
+  result <- collect(select(df2, array_join(df2[[1]], "#")))[[1]]
+  expect_equal(result, "Hello#World!")
+  df3 <- createDataFrame(list(list(list("Hello", NULL, "World!"))))
+  result <- collect(select(df3, array_join(df3[[1]], "#", "Beautiful")))[[1]]
+  expect_equal(result, "Hello#Beautiful#World!")
+  result <- collect(select(df3, array_join(df3[[1]], "#")))[[1]]
+  expect_equal(result, "Hello#World!")
+
   # Test array_sort() and sort_array()
   df <- createDataFrame(list(list(list(2L, 1L, 3L, NA)), list(list(NA, 6L, 5L, NA, 4L))))
 

README.md

@@ -81,6 +81,8 @@ can be run using:
 Please see the guidance on how to
 [run tests for a module, or individual tests](http://spark.apache.org/developer-tools.html#individual-tests).
 
+There is also a Kubernetes integration test, see resource-managers/kubernetes/integration-tests/README.md
+
 ## A Note About Hadoop Versions
 
 Spark uses the Hadoop core library to talk to HDFS and other Hadoop-supported

bin/docker-image-tool.sh

@@ -63,16 +63,25 @@ function build {
   if [ ! -d "$IMG_PATH" ]; then
     error "Cannot find docker image. This script must be run from a runnable distribution of Apache Spark."
   fi
-
-  local DOCKERFILE=${DOCKERFILE:-"$IMG_PATH/spark/Dockerfile"}
-
-  docker build "${BUILD_ARGS[@]}" \
+  local BINDING_BUILD_ARGS=(
+    --build-arg
+    base_img=$(image_ref spark)
+  )
+  local BASEDOCKERFILE=${BASEDOCKERFILE:-"$IMG_PATH/spark/Dockerfile"}
+  local PYDOCKERFILE=${PYDOCKERFILE:-"$IMG_PATH/spark/bindings/python/Dockerfile"}
+
+  docker build $NOCACHEARG "${BUILD_ARGS[@]}" \
     -t $(image_ref spark) \
-    -f "$DOCKERFILE" .
+    -f "$BASEDOCKERFILE" .
+
+  docker build $NOCACHEARG "${BINDING_BUILD_ARGS[@]}" \
+    -t $(image_ref spark-py) \
+    -f "$PYDOCKERFILE" .
 }
 
 function push {
   docker push "$(image_ref spark)"
+  docker push "$(image_ref spark-py)"
 }
 
 function usage {
@@ -86,10 +95,12 @@ Commands:
   push        Push a pre-built image to a registry. Requires a repository address to be provided.
 
 Options:
-  -f file     Dockerfile to build. By default builds the Dockerfile shipped with Spark.
+  -f file     Dockerfile to build for JVM based Jobs. By default builds the Dockerfile shipped with Spark.
+  -p file     Dockerfile with Python baked in. By default builds the Dockerfile shipped with Spark.
   -r repo     Repository address.
   -t tag      Tag to apply to the built image, or to identify the image to be pushed.
   -m          Use minikube's Docker daemon.
+  -n          Build docker image with --no-cache
 
 Using minikube when building images will do so directly into minikube's Docker daemon.
 There is no need to push the images into minikube in that case, they'll be automatically
@@ -116,14 +127,18 @@ fi
 
 REPO=
 TAG=
-DOCKERFILE=
-while getopts f:mr:t: option
+BASEDOCKERFILE=
+PYDOCKERFILE=
+NOCACHEARG=
+while getopts f:mr:t:n option
 do
  case "${option}"
  in
- f) DOCKERFILE=${OPTARG};;
+ f) BASEDOCKERFILE=${OPTARG};;
+ p) PYDOCKERFILE=${OPTARG};;
  r) REPO=${OPTARG};;
  t) TAG=${OPTARG};;
+ n) NOCACHEARG="--no-cache";;
  m)
    if ! which minikube 1>/dev/null; then
      error "Cannot find minikube."

build/mvn

@@ -154,4 +154,4 @@ export MAVEN_OPTS=${MAVEN_OPTS:-"$_COMPILE_JVM_OPTS"}
 echo "Using \`mvn\` from path: $MVN_BIN" 1>&2
 
 # Last, call the `mvn` command as usual
-${MVN_BIN} -DzincPort=${ZINC_PORT} "$@"
+"${MVN_BIN}" -DzincPort=${ZINC_PORT} "$@"

common/network-common/src/main/java/org/apache/spark/network/protocol/MessageWithHeader.java

@@ -137,30 +137,15 @@ protected void deallocate() {
   }
 
   private int copyByteBuf(ByteBuf buf, WritableByteChannel target) throws IOException {
-    ByteBuffer buffer = buf.nioBuffer();
-    int written = (buffer.remaining() <= NIO_BUFFER_LIMIT) ?
-      target.write(buffer) : writeNioBuffer(target, buffer);
+    // SPARK-24578: cap the sub-region's size of returned nio buffer to improve the performance
+    // for the case that the passed-in buffer has too many components.
+    int length = Math.min(buf.readableBytes(), NIO_BUFFER_LIMIT);
+    ByteBuffer buffer = buf.nioBuffer(buf.readerIndex(), length);
+    int written = target.write(buffer);
     buf.skipBytes(written);
     return written;
   }
 
-  private int writeNioBuffer(
-      WritableByteChannel writeCh,
-      ByteBuffer buf) throws IOException {
-    int originalLimit = buf.limit();
-    int ret = 0;
-
-    try {
-      int ioSize = Math.min(buf.remaining(), NIO_BUFFER_LIMIT);
-      buf.limit(buf.position() + ioSize);
-      ret = writeCh.write(buf);
-    } finally {
-      buf.limit(originalLimit);
-    }
-
-    return ret;
-  }
-
   @Override
   public MessageWithHeader touch(Object o) {
     super.touch(o);

common/network-common/src/main/java/org/apache/spark/network/util/JavaUtils.java

@@ -17,10 +17,7 @@
 
 package org.apache.spark.network.util;
 
-import java.io.Closeable;
-import java.io.EOFException;
-import java.io.File;
-import java.io.IOException;
+import java.io.*;
 import java.nio.ByteBuffer;
 import java.nio.channels.ReadableByteChannel;
 import java.nio.charset.StandardCharsets;
@@ -91,11 +88,24 @@ public static String bytesToString(ByteBuffer b) {
    * @throws IOException if deletion is unsuccessful
    */
   public static void deleteRecursively(File file) throws IOException {
+    deleteRecursively(file, null);
+  }
+
+  /**
+   * Delete a file or directory and its contents recursively.
+   * Don't follow directories if they are symlinks.
+   *
+   * @param file Input file / dir to be deleted
+   * @param filter A filename filter that make sure only files / dirs with the satisfied filenames
+   *               are deleted.
+   * @throws IOException if deletion is unsuccessful
+   */
+  public static void deleteRecursively(File file, FilenameFilter filter) throws IOException {
     if (file == null) { return; }
 
     // On Unix systems, use operating system command to run faster
     // If that does not work out, fallback to the Java IO way
-    if (SystemUtils.IS_OS_UNIX) {
+    if (SystemUtils.IS_OS_UNIX && filter == null) {
       try {
         deleteRecursivelyUsingUnixNative(file);
         return;
@@ -105,15 +115,17 @@ public static void deleteRecursively(File file) throws IOException {
       }
     }
 
-    deleteRecursivelyUsingJavaIO(file);
+    deleteRecursivelyUsingJavaIO(file, filter);
   }
 
-  private static void deleteRecursivelyUsingJavaIO(File file) throws IOException {
+  private static void deleteRecursivelyUsingJavaIO(
+      File file,
+      FilenameFilter filter) throws IOException {
     if (file.isDirectory() && !isSymlink(file)) {
       IOException savedIOException = null;
-      for (File child : listFilesSafely(file)) {
+      for (File child : listFilesSafely(file, filter)) {
         try {
-          deleteRecursively(child);
+          deleteRecursively(child, filter);
         } catch (IOException e) {
           // In case of multiple exceptions, only last one will be thrown
           savedIOException = e;
@@ -124,10 +136,13 @@ private static void deleteRecursivelyUsingJavaIO(File file) throws IOException {
       }
     }
 
-    boolean deleted = file.delete();
-    // Delete can also fail if the file simply did not exist.
-    if (!deleted && file.exists()) {
-      throw new IOException("Failed to delete: " + file.getAbsolutePath());
+    // Delete file only when it's a normal file or an empty directory.
+    if (file.isFile() || (file.isDirectory() && listFilesSafely(file, null).length == 0)) {
+      boolean deleted = file.delete();
+      // Delete can also fail if the file simply did not exist.
+      if (!deleted && file.exists()) {
+        throw new IOException("Failed to delete: " + file.getAbsolutePath());
+      }
     }
   }
 
@@ -157,9 +172,9 @@ private static void deleteRecursivelyUsingUnixNative(File file) throws IOExcepti
     }
   }
 
-  private static File[] listFilesSafely(File file) throws IOException {
+  private static File[] listFilesSafely(File file, FilenameFilter filter) throws IOException {
     if (file.exists()) {
-      File[] files = file.listFiles();
+      File[] files = file.listFiles(filter);
       if (files == null) {
         throw new IOException("Failed to list files for dir: " + file);
       }

common/network-shuffle/src/main/java/org/apache/spark/network/shuffle/ExternalShuffleBlockHandler.java

@@ -138,6 +138,13 @@ public void applicationRemoved(String appId, boolean cleanupLocalDirs) {
     blockManager.applicationRemoved(appId, cleanupLocalDirs);
   }
 
+  /**
+   * Clean up any non-shuffle files in any local directories associated with an finished executor.
+   */
+  public void executorRemoved(String executorId, String appId) {
+    blockManager.executorRemoved(executorId, appId);
+  }
+
   /**
    * Register an (application, executor) with the given shuffle info.
    *