With SparkR, I'm trying for a PoC to collect an RDD that I created from text files which contains around 4M lines.
My Spark cluster is running in Google Cloud, is bdutil deployed and is composed with 1 master and 2 workers with 15gb of RAM and 4 cores each. My HDFS repository is based on Google Storage with gcs-connector 1.4.0. SparkR is intalled on each machine, and basic tests are working on small files.
Here is the script I use :
Sys.setenv("SPARK_MEM" = "1g")
sc <- sparkR.init("spark://xxxx:7077", sparkEnvir=list(spark.executor.memory="1g"))
lines <- textFile(sc, "gs://xxxx/dir/")
test <- collect(lines)
First time I run this, it seems to be working fine, all the tasks are run successfully, spark's ui says that the job completed, but I never get the R prompt back :
15/06/04 13:36:59 WARN SparkConf: Setting 'spark.executor.extraClassPath' to ':/home/hadoop/hadoop-install/lib/gcs-connector-1.4.0-hadoop1.jar' as a work-around.
15/06/04 13:36:59 WARN SparkConf: Setting 'spark.driver.extraClassPath' to ':/home/hadoop/hadoop-install/lib/gcs-connector-1.4.0-hadoop1.jar' as a work-around.
15/06/04 13:36:59 INFO Slf4jLogger: Slf4jLogger started
15/06/04 13:37:00 INFO Server: jetty-8.y.z-SNAPSHOT
15/06/04 13:37:00 INFO AbstractConnector: Started [email protected]:52439
15/06/04 13:37:00 INFO Server: jetty-8.y.z-SNAPSHOT
15/06/04 13:37:00 INFO AbstractConnector: Started [email protected]:4040
15/06/04 13:37:54 INFO GoogleHadoopFileSystemBase: GHFS version: 1.4.0-hadoop1
15/06/04 13:37:55 WARN LoadSnappy: Snappy native library is available
15/06/04 13:37:55 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
15/06/04 13:37:55 WARN LoadSnappy: Snappy native library not loaded
15/06/04 13:37:55 INFO FileInputFormat: Total input paths to process : 68
[Stage 0:=======================================================> (27 + 10) / 68]
Then after a CTRL-C to get the R prompt back, I try to run the collect method again, here is the result :
[Stage 1:==========================================================> (28 + 9) / 68]15/06/04 13:42:08 ERROR ActorSystemImpl: Uncaught fatal error from thread [sparkDriver-akka.remote.default-remote-dispatcher-5] shutting down ActorSystem [sparkDriver]
java.lang.OutOfMemoryError: Java heap space
at org.spark_project.protobuf.ByteString.toByteArray(ByteString.java:515)
at akka.remote.serialization.MessageContainerSerializer.fromBinary(MessageContainerSerializer.scala:64)
at akka.serialization.Serialization$$anonfun$deserialize$1.apply(Serialization.scala:104)
at scala.util.Try$.apply(Try.scala:161)
at akka.serialization.Serialization.deserialize(Serialization.scala:98)
at akka.remote.MessageSerializer$.deserialize(MessageSerializer.scala:23)
at akka.remote.DefaultMessageDispatcher.payload$lzycompute$1(Endpoint.scala:58)
at akka.remote.DefaultMessageDispatcher.payload$1(Endpoint.scala:58)
at akka.remote.DefaultMessageDispatcher.dispatch(Endpoint.scala:76)
at akka.remote.EndpointReader$$anonfun$receive$2.applyOrElse(Endpoint.scala:937)
at akka.actor.Actor$class.aroundReceive(Actor.scala:465)
at akka.remote.EndpointActor.aroundReceive(Endpoint.scala:415)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516)
at akka.actor.ActorCell.invoke(ActorCell.scala:487)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:238)
at akka.dispatch.Mailbox.run(Mailbox.scala:220)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:393)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
I understand the exception message, but I don't understand why I am getting this the second time. Also, why the collect never returns after completing in Spark?
I Googled every piece of information I have, but I had no luck finding a solution. Any help or hint would be greatly appreciated!
Thanks
This does appear to be a simple combination of Java in-memory object representations being inefficient combined with some apparent long-lived object references which cause some collections to fail to be garbage-collected in time for the new collect() call to overwrite the old one in-place.
I experimented with some options, and for my sample 256MB file that contains ~4M lines, I indeed reproduce your behavior where collect is fine the first time, but OOMs the second time, when using SPARK_MEM=1g. I then set SPARK_MEM=4g instead, and then I'm able to ctrl+c and re-run test <- collect(lines) as many times as I want.
For one thing, even if references didn't leak, note that after the first time you ran test <- collect(lines), the variable test is holding that gigantic array of lines, and the second time you call it, the collect(lines) executes before finally being assigned to the test variable and thus in any straightforward instruction-ordering, there's no way to garbage-collect the old contents of test. This means the second run will make the SparkRBackend process hold two copies of the entire collection at the same time, leading to the OOM you saw.
To diagnose, on the master I started SparkR and first ran
dhuo@dhuo-sparkr-m:~$ jps | grep SparkRBackend
8709 SparkRBackend
I also checked top and it was using around 22MB of memory. I fetched a heap profile with jmap:
jmap -heap:format=b 8709
mv heap.bin heap0.bin
Then I ran the first round of test <- collect(lines) at which point running top showed it using ~1.7g of RES memory. I grabbed another heap dump. Finally, I also tried test <- {} to get rid of references to allow garbage-collection. After doing this, and printing out test and showing it to be empty, I grabbed another heap dump and noticed RES still showed 1.7g. I used jhat heap0.bin to analyze the original heap dump, and got:
Heap Histogram
All Classes (excluding platform)
Class Instance Count Total Size
class [B 25126 14174163
class [C 19183 1576884
class [<other> 11841 1067424
class [Lscala.concurrent.forkjoin.ForkJoinTask; 16 1048832
class [I 1524 769384
...
After running collect, I had:
Heap Histogram
All Classes (excluding platform)
Class Instance Count Total Size
class [C 2784858 579458804
class [B 27768 70519801
class java.lang.String 2782732 44523712
class [Ljava.lang.Object; 2567 22380840
class [I 1538 8460152
class [Lscala.concurrent.forkjoin.ForkJoinTask; 27 1769904
Even after I nulled out test, it remained about the same. This shows us 2784858 instances of char[], for a total size of 579MB, and also 2782732 instances of String, presumably holding those char[]'s above it. I followed the reference graph all the way up, and got something like
char[] -> String -> String[] -> ... -> class scala.collection.mutable.DefaultEntry -> class [Lscala.collection.mutable.HashEntry; -> class scala.collection.mutable.HashMap -> class edu.berkeley.cs.amplab.sparkr.JVMObjectTracker$ -> java.util.Vector@0x785b48cd8 (36 bytes) -> sun.misc.Launcher$AppClassLoader@0x7855c31a8 (138 bytes)
And then AppClassLoader had something like thousands of inbound references. So somewhere along that chain something should've been removing their reference but failing to do so, causing the entire collected array to sit in memory while we try to fetch a second copy of it.
Finally, to answer your question about hanging after the collect, it appears it has to do with the data not fitting in the R process's memory; here's a thread related to that issue: https://www.mail-archive.com/[email protected]/msg29155.html
I confirmed that using a smaller file with only a handful of lines, and then running collect indeed does not hang.