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[SPARK-12652][PYSPARK] Upgrade Py4J to 0.9.1

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- [x] Upgrade Py4J to 0.9.1
- [x] SPARK-12657: Revert SPARK-12617
- [x] SPARK-12658: Revert SPARK-12511
  - Still keep the change that only reading checkpoint once. This is a manual change and worth to take a look carefully. bfd4b5c040
- [x] Verify no leak any more after reverting our workarounds

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #10692 from zsxwing/py4j-0.9.1.
This commit is contained in:
Shixiong Zhu 2016-01-12 14:27:05 -08:00
parent 8ed5f12d2b
commit 4f60651cbe
18 changed files with 20 additions and 112 deletions
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2
LICENSE
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@ -264,7 +264,7 @@ The text of each license is also included at licenses/LICENSE-[project].txt.
(New BSD license) Protocol Buffer Java API (org.spark-project.protobuf:protobuf-java:2.4.1-shaded - http://code.google.com/p/protobuf)
(The BSD License) Fortran to Java ARPACK (net.sourceforge.f2j:arpack_combined_all:0.1 - http://f2j.sourceforge.net)
(The BSD License) xmlenc Library (xmlenc:xmlenc:0.52 - http://xmlenc.sourceforge.net)
(The New BSD License) Py4J (net.sf.py4j:py4j:0.9 - http://py4j.sourceforge.net/)
(The New BSD License) Py4J (net.sf.py4j:py4j:0.9.1 - http://py4j.sourceforge.net/)
(Two-clause BSD-style license) JUnit-Interface (com.novocode:junit-interface:0.10 - http://github.com/szeiger/junit-interface/)
(BSD licence) sbt and sbt-launch-lib.bash
(BSD 3 Clause) d3.min.js (https://github.com/mbostock/d3/blob/master/LICENSE)

2
bin/pyspark
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@ -67,7 +67,7 @@ export PYSPARK_PYTHON
# Add the PySpark classes to the Python path:
export PYTHONPATH="${SPARK_HOME}/python/:$PYTHONPATH"
export PYTHONPATH="${SPARK_HOME}/python/lib/py4j-0.9-src.zip:$PYTHONPATH"
export PYTHONPATH="${SPARK_HOME}/python/lib/py4j-0.9.1-src.zip:$PYTHONPATH"
# Load the PySpark shell.py script when ./pyspark is used interactively:
export OLD_PYTHONSTARTUP="$PYTHONSTARTUP"

2
bin/pyspark2.cmd
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@ -30,7 +30,7 @@ if "x%PYSPARK_DRIVER_PYTHON%"=="x" (
)
set PYTHONPATH=%SPARK_HOME%\python;%PYTHONPATH%
set PYTHONPATH=%SPARK_HOME%\python\lib\py4j-0.9-src.zip;%PYTHONPATH%
set PYTHONPATH=%SPARK_HOME%\python\lib\py4j-0.9.1-src.zip;%PYTHONPATH%
set OLD_PYTHONSTARTUP=%PYTHONSTARTUP%
set PYTHONSTARTUP=%SPARK_HOME%\python\pyspark\shell.py

2
core/pom.xml
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@ -350,7 +350,7 @@
<dependency>
<groupId>net.sf.py4j</groupId>
<artifactId>py4j</artifactId>
<version>0.9</version>
<version>0.9.1</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>

2
core/src/main/scala/org/apache/spark/api/python/PythonUtils.scala
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@ -32,7 +32,7 @@ private[spark] object PythonUtils {
val pythonPath = new ArrayBuffer[String]
for (sparkHome <- sys.env.get("SPARK_HOME")) {
pythonPath += Seq(sparkHome, "python", "lib", "pyspark.zip").mkString(File.separator)
pythonPath += Seq(sparkHome, "python", "lib", "py4j-0.9-src.zip").mkString(File.separator)
pythonPath += Seq(sparkHome, "python", "lib", "py4j-0.9.1-src.zip").mkString(File.separator)
}
pythonPath ++= SparkContext.jarOfObject(this)
pythonPath.mkString(File.pathSeparator)

2
dev/deps/spark-deps-hadoop-2.2
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@ -160,7 +160,7 @@ pmml-agent-1.2.7.jar
pmml-model-1.2.7.jar
pmml-schema-1.2.7.jar
protobuf-java-2.5.0.jar
py4j-0.9.jar
py4j-0.9.1.jar
pyrolite-4.9.jar
quasiquotes_2.10-2.0.0-M8.jar
reflectasm-1.07-shaded.jar

2
dev/deps/spark-deps-hadoop-2.3
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@ -151,7 +151,7 @@ pmml-agent-1.2.7.jar
pmml-model-1.2.7.jar
pmml-schema-1.2.7.jar
protobuf-java-2.5.0.jar
py4j-0.9.jar
py4j-0.9.1.jar
pyrolite-4.9.jar
quasiquotes_2.10-2.0.0-M8.jar
reflectasm-1.07-shaded.jar

2
dev/deps/spark-deps-hadoop-2.4
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@ -152,7 +152,7 @@ pmml-agent-1.2.7.jar
pmml-model-1.2.7.jar
pmml-schema-1.2.7.jar
protobuf-java-2.5.0.jar
py4j-0.9.jar
py4j-0.9.1.jar
pyrolite-4.9.jar
quasiquotes_2.10-2.0.0-M8.jar
reflectasm-1.07-shaded.jar

2
dev/deps/spark-deps-hadoop-2.6
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@ -158,7 +158,7 @@ pmml-agent-1.2.7.jar
pmml-model-1.2.7.jar
pmml-schema-1.2.7.jar
protobuf-java-2.5.0.jar
py4j-0.9.jar
py4j-0.9.1.jar
pyrolite-4.9.jar
quasiquotes_2.10-2.0.0-M8.jar
reflectasm-1.07-shaded.jar

2
python/docs/Makefile
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@ -7,7 +7,7 @@ SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = _build
export PYTHONPATH=$(realpath ..):$(realpath ../lib/py4j-0.9-src.zip)
export PYTHONPATH=$(realpath ..):$(realpath ../lib/py4j-0.9.1-src.zip)
# User-friendly check for sphinx-build
ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)

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python/lib/py4j-0.9.1-src.zip Normal file
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89
python/pyspark/streaming/context.py
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@ -19,7 +19,6 @@ from __future__ import print_function
import os
import sys
from threading import RLock, Timer
from py4j.java_gateway import java_import, JavaObject
@ -33,63 +32,6 @@ from pyspark.streaming.util import TransformFunction, TransformFunctionSerialize
__all__ = ["StreamingContext"]
class Py4jCallbackConnectionCleaner(object):
"""
A cleaner to clean up callback connections that are not closed by Py4j. See SPARK-12617.
It will scan all callback connections every 30 seconds and close the dead connections.
"""
def __init__(self, gateway):
self._gateway = gateway
self._stopped = False
self._timer = None
self._lock = RLock()
def start(self):
if self._stopped:
return
def clean_closed_connections():
from py4j.java_gateway import quiet_close, quiet_shutdown
callback_server = self._gateway._callback_server
if callback_server:
with callback_server.lock:
try:
closed_connections = []
for connection in callback_server.connections:
if not connection.isAlive():
quiet_close(connection.input)
quiet_shutdown(connection.socket)
quiet_close(connection.socket)
closed_connections.append(connection)
for closed_connection in closed_connections:
callback_server.connections.remove(closed_connection)
except Exception:
import traceback
traceback.print_exc()
self._start_timer(clean_closed_connections)
self._start_timer(clean_closed_connections)
def _start_timer(self, f):
with self._lock:
if not self._stopped:
self._timer = Timer(30.0, f)
self._timer.daemon = True
self._timer.start()
def stop(self):
with self._lock:
self._stopped = True
if self._timer:
self._timer.cancel()
self._timer = None
class StreamingContext(object):
"""
Main entry point for Spark Streaming functionality. A StreamingContext
@ -105,9 +47,6 @@ class StreamingContext(object):
# Reference to a currently active StreamingContext
_activeContext = None
# A cleaner to clean leak sockets of callback server every 30 seconds
_py4j_cleaner = None
def __init__(self, sparkContext, batchDuration=None, jssc=None):
"""
Create a new StreamingContext.
@ -155,34 +94,12 @@ class StreamingContext(object):
# get the GatewayServer object in JVM by ID
jgws = JavaObject("GATEWAY_SERVER", gw._gateway_client)
# update the port of CallbackClient with real port
gw.jvm.PythonDStream.updatePythonGatewayPort(jgws, gw._python_proxy_port)
_py4j_cleaner = Py4jCallbackConnectionCleaner(gw)
_py4j_cleaner.start()
jgws.resetCallbackClient(jgws.getCallbackClient().getAddress(), gw._python_proxy_port)
# register serializer for TransformFunction
# it happens before creating SparkContext when loading from checkpointing
if cls._transformerSerializer is None:
transformer_serializer = TransformFunctionSerializer()
transformer_serializer.init(
SparkContext._active_spark_context, CloudPickleSerializer(), gw)
# SPARK-12511 streaming driver with checkpointing unable to finalize leading to OOM
# There is an issue that Py4J's PythonProxyHandler.finalize blocks forever.
# (https://github.com/bartdag/py4j/pull/184)
#
# Py4j will create a PythonProxyHandler in Java for "transformer_serializer" when
# calling "registerSerializer". If we call "registerSerializer" twice, the second
# PythonProxyHandler will override the first one, then the first one will be GCed and
# trigger "PythonProxyHandler.finalize". To avoid that, we should not call
# "registerSerializer" more than once, so that "PythonProxyHandler" in Java side won't
# be GCed.
#
# TODO Once Py4J fixes this issue, we should upgrade Py4j to the latest version.
transformer_serializer.gateway.jvm.PythonDStream.registerSerializer(
transformer_serializer)
cls._transformerSerializer = transformer_serializer
else:
cls._transformerSerializer.init(
SparkContext._active_spark_context, CloudPickleSerializer(), gw)
cls._transformerSerializer = TransformFunctionSerializer(
SparkContext._active_spark_context, CloudPickleSerializer(), gw)
@classmethod
def getOrCreate(cls, checkpointPath, setupFunc):

3
python/pyspark/streaming/util.py
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@ -89,10 +89,11 @@ class TransformFunctionSerializer(object):
it uses this class to invoke Python, which returns the serialized function
as a byte array.
"""
def init(self, ctx, serializer, gateway=None):
def __init__(self, ctx, serializer, gateway=None):
self.ctx = ctx
self.serializer = serializer
self.gateway = gateway or self.ctx._gateway
self.gateway.jvm.PythonDStream.registerSerializer(self)
self.failure = None
def dumps(self, id):

2
sbin/spark-config.sh
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@ -27,4 +27,4 @@ fi
export SPARK_CONF_DIR="${SPARK_CONF_DIR:-"${SPARK_HOME}/conf"}"
# Add the PySpark classes to the PYTHONPATH:
export PYTHONPATH="${SPARK_HOME}/python:${PYTHONPATH}"
export PYTHONPATH="${SPARK_HOME}/python/lib/py4j-0.9-src.zip:${PYTHONPATH}"
export PYTHONPATH="${SPARK_HOME}/python/lib/py4j-0.9.1-src.zip:${PYTHONPATH}"

10
streaming/src/main/scala/org/apache/spark/streaming/api/python/PythonDStream.scala
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@ -169,16 +169,6 @@ private[python] object PythonDStream {
PythonTransformFunctionSerializer.register(ser)
}
/**
* Update the port of callback client to `port`
*/
def updatePythonGatewayPort(gws: GatewayServer, port: Int): Unit = {
val cl = gws.getCallbackClient
val f = cl.getClass.getDeclaredField("port")
f.setAccessible(true)
f.setInt(cl, port)
}
/**
* helper function for DStream.foreachRDD(),
* cannot be `foreachRDD`, it will confusing py4j

4
yarn/src/main/scala/org/apache/spark/deploy/yarn/Client.scala
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@ -1044,9 +1044,9 @@ private[spark] class Client(
val pyArchivesFile = new File(pyLibPath, "pyspark.zip")
require(pyArchivesFile.exists(),
"pyspark.zip not found; cannot run pyspark application in YARN mode.")
val py4jFile = new File(pyLibPath, "py4j-0.9-src.zip")
val py4jFile = new File(pyLibPath, "py4j-0.9.1-src.zip")
require(py4jFile.exists(),
"py4j-0.9-src.zip not found; cannot run pyspark application in YARN mode.")
"py4j-0.9.1-src.zip not found; cannot run pyspark application in YARN mode.")
Seq(pyArchivesFile.getAbsolutePath(), py4jFile.getAbsolutePath())
}
}

4
yarn/src/test/scala/org/apache/spark/deploy/yarn/YarnClusterSuite.scala
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@ -151,9 +151,9 @@ class YarnClusterSuite extends BaseYarnClusterSuite {
// When running tests, let's not assume the user has built the assembly module, which also
// creates the pyspark archive. Instead, let's use PYSPARK_ARCHIVES_PATH to point at the
// needed locations.
val sparkHome = sys.props("spark.test.home");
val sparkHome = sys.props("spark.test.home")
val pythonPath = Seq(
s"$sparkHome/python/lib/py4j-0.9-src.zip",
s"$sparkHome/python/lib/py4j-0.9.1-src.zip",
s"$sparkHome/python")
val extraEnv = Map(
"PYSPARK_ARCHIVES_PATH" -> pythonPath.map("local:" + _).mkString(File.pathSeparator),