Currently we have a IBM BigInsight cluster with 1 namenode + 1 JobTracker + 42
data/task nodes, which runs with BigInsight V3.0.0.2, corresponding with Hadoop
2.2.0 with MR1.
Since IBM BigInsight doesn't come with Spark, so we build Spark 1.2.2 with
Hadoop 2.2.0 + Hive 0.12 by ourselves, and deploy it on the same cluster.
The IBM Biginsight comes with IBM jdk 1.7, but during our experience on stage
environment, we found out Spark works better with Oracle JVM. So we run spark
under Oracle JDK 1.7.0_79.
Now on production, we are facing a issue we never faced, nor can reproduce on
our staging cluster.
We are using Spark Standalone cluster, and here is the basic configurations:
more spark-env.shexport JAVA_HOME=/opt/javaexport
PATH=$JAVA_HOME/bin:$PATHexport
HADOOP_CONF_DIR=/opt/ibm/biginsights/hadoop-conf/export
SPARK_CLASSPATH=/opt/ibm/biginsights/IHC/lib/ibm-compression.jar:/opt/ibm/biginsights/hive/lib/db2jcc4-10.6.jarexport
SPARK_LOCAL_DIRS=/data1/spark/local,/data2/spark/local,/data3/spark/localexport
SPARK_MASTER_WEBUI_PORT=8081export SPARK_MASTER_IP=host1export
SPARK_MASTER_OPTS="-Dspark.deploy.defaultCores=42"export
SPARK_WORKER_MEMORY=24gexport SPARK_WORKER_CORES=6export
SPARK_WORKER_DIR=/tmp/spark/workexport SPARK_DRIVER_MEMORY=2gexport
SPARK_EXECUTOR_MEMORY=2g
more spark-defaults.confspark.master
spark://host1:7077spark.eventLog.enabled truespark.eventLog.dir
hdfs://host1:9000/spark/eventLogspark.serializer
org.apache.spark.serializer.KryoSerializerspark.executor.extraJavaOptions
-verbose:gc -XX:+PrintGCDetails -XX:+PrintGCTimeStamps
We are using AVRO file format a lot, and we have these 2 datasets, one is about
96G, and the other one is a little over 1T. Since we are using AVRO, so we also
built spark-avro of commit "a788c9fce51b0ec1bb4ce88dc65c1d55aaa675b8", which is
the latest version supporting Spark 1.2.x.
Here is the problem we are facing on our production cluster, even the following
simple spark-shell commands will hang in our production cluster:
import org.apache.spark.sql.SQLContextval sqlContext = new
org.apache.spark.sql.hive.HiveContext(sc)import com.databricks.spark.avro._val
bigData =
sqlContext.avroFile("hdfs://namenode:9000/bigData/")bigData.registerTempTable("bigData")bigData.count()
>From the console, we saw following:[Stage 0:>
> (44 + 42) / 7800]
no update for more than 30 minutes and longer.
The big dataset with 1T should generate 7800 HDFS block, but Spark's HDFS
client looks like having problem to read them. Since we are running Spark on
the data nodes, all the Spark tasks are running as "NODE_LOCAL" on locality
level.
If I go to the data/task node which Spark tasks hang, and use the JStack to
dump the thread, I got the following on the top:
015-08-11 15:38:38Full thread dump Java HotSpot(TM) 64-Bit Server VM (24.79-b02
mixed mode):
"Attach Listener" daemon prio=10 tid=0x00007f0660589000 nid=0x1584d waiting on
condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE
"org.apache.hadoop.hdfs.PeerCache@4a88ec00" daemon prio=10
tid=0x00007f06508b7800 nid=0x13302 waiting on condition [0x00007f060be94000]
java.lang.Thread.State: TIMED_WAITING (sleeping) at
java.lang.Thread.sleep(Native Method) at
org.apache.hadoop.hdfs.PeerCache.run(PeerCache.java:252) at
org.apache.hadoop.hdfs.PeerCache.access$000(PeerCache.java:39) at
org.apache.hadoop.hdfs.PeerCache$1.run(PeerCache.java:135) at
java.lang.Thread.run(Thread.java:745)
"shuffle-client-1" daemon prio=10 tid=0x00007f0650687000 nid=0x132fc runnable
[0x00007f060d198000] java.lang.Thread.State: RUNNABLE at
sun.nio.ch.EPollArrayWrapper.epollWait(Native Method) at
sun.nio.ch.EPollArrayWrapper.poll(EPollArrayWrapper.java:269) at
sun.nio.ch.EPollSelectorImpl.doSelect(EPollSelectorImpl.java:79) at
sun.nio.ch.SelectorImpl.lockAndDoSelect(SelectorImpl.java:87) - locked
<0x000000067bf47710> (a io.netty.channel.nio.SelectedSelectionKeySet) -
locked <0x000000067bf374e8> (a java.util.Collections$UnmodifiableSet) -
locked <0x000000067bf373d0> (a sun.nio.ch.EPollSelectorImpl) at
sun.nio.ch.SelectorImpl.select(SelectorImpl.java:98) at
io.netty.channel.nio.NioEventLoop.select(NioEventLoop.java:622) at
io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:310) at
io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116)
at java.lang.Thread.run(Thread.java:745)
Meantime, I can confirm our Hadoop/HDFS cluster works fine, as the MapReduce
jobs also run without any problem, and "Hadoop fs" command works fine in the
BigInsight.
I attached the jstack output with this email, but I don't know what could be
the root reason.The same Spark shell command works fine, if I point to the
small dataset, instead of big dataset. The small dataset will have around 800
HDFS blocks, and Spark finishes without any problem.
Here are some facts I know:
1) Since the BigInsight is running on IBM JDK, so I make the Spark run under
the same JDK, same problem for BigData set.2) I even changed
"--total-executor-cores" to 42, which will make each executor runs with one
core (as we have 42 Spark workers), to avoid any multithreads, but still no
luck.3) This problem of scanning 1T data hanging is NOT 100% for sure
happening. Sometime I didn't see it, but more than 50% I will see it if I
try.4) We never met this issue on our stage cluster, but it has only (1
namenode + 1 jobtracker + 3 data/task nodes), and the same dataset is only 160G
on it.5) While the Spark java processing hanging, I didn't see any exception or
issue on the HDFS data node log.
Does anyone have any clue about this?
Thanks
Yong
78090.log.gz
Description: GNU Zip compressed data
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