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From java8964 <java8...@hotmail.com>
Subject RE: Spark Job Hangs on our production cluster
Date Tue, 18 Aug 2015 19:23:33 GMT
Hi, Imran:
Thanks for your reply. I am not sure what do you mean "repl". Can you be more detail about
that?
This is only happened when the Spark 1.2.2 try to scan big data set, and cannot reproduce
if it scans smaller dataset.
FYI, I have to build and deploy Spark 1.3.1 on our production cluster. Right now, I cannot
reproduce this hang problem on the same cluster for the same big dataset. On this point, we
will continue trying Spark 1.3.1, hope we will have more positive experience with it.
But just for wondering, what class Spark needs to be loaded at this time? From my understanding,
the executor already scan the first block data from HDFS, and hanging while starting the 2nd
block. All the class should be already loaded in JVM in this case.
Thanks
Yong
From: irashid@cloudera.com
Date: Tue, 18 Aug 2015 12:17:56 -0500
Subject: Re: Spark Job Hangs on our production cluster
To: java8964@hotmail.com
CC: user@spark.apache.org

just looking at the thread dump from your original email, the 3 executor threads are all trying
to load classes.  (One thread is actually loading some class, and the others are blocked waiting
to load a class, most likely trying to load the same thing.)  That is really weird, definitely
not something which should keep things blocked for 30 min.  It suggest something wrong w/
the jvm, or classpath configuration, or a combination.  Looks like you are trying to run in
the repl, and for whatever reason the http server for the repl to serve classes is not responsive.
 I'd try running outside of the repl and see if that works.
sorry not a full diagnosis but maybe this'll help a bit.
On Tue, Aug 11, 2015 at 3:19 PM, java8964 <java8964@hotmail.com> wrote:



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

 		 	   		  



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