While running HBase using HDFS as datanodes, we noticed excessive high GC pause spikes. For example with jdk8 update 40 and G1 collector, we saw datanode GC pauses spiked toward 160 milliseconds while they should be around 20 milliseconds.
We tracked down to GC logs and found those long GC pauses were devoted to process high number of final references.
For example, this Young GC:
2715.501: [GC pause (G1 Evacuation Pause) (young) 0.1529017 secs]
2715.572: [SoftReference, 0 refs, 0.0001034 secs]
2715.572: [WeakReference, 0 refs, 0.0000123 secs]
2715.572: [FinalReference, 8292 refs, 0.0748194 secs]
2715.647: [PhantomReference, 0 refs, 160 refs, 0.0001333 secs]
2715.647: [JNI Weak Reference, 0.0000140 secs]
[Ref Proc: 122.3 ms]
[Eden: 910.0M(910.0M)->0.0B(911.0M) Survivors: 11.0M->10.0M Heap: 951.1M(1536.0M)->40.2M(1536.0M)]
[Times: user=0.47 sys=0.01, real=0.15 secs]
This young GC took 152.9 milliseconds STW pause, while spent 122.3 milliseconds in Ref Proc, which processed 8292 FinalReference in 74.8 milliseconds plus some overhead.
We used JFR and JMAP with Memory Analyzer to track down and found those FinalReference were all from FileInputStream. We checked HDFS code and saw the use of the FileInputStream in datanode:
We looked up https://docs.oracle.com/javase/7/docs/api/java/io/FileInputStream.html and
http://hg.openjdk.java.net/jdk7/jdk7/jdk/file/23bdcede4e39/src/share/classes/java/io/FileInputStream.java and noticed FileInputStream relies on the Finalizer to release its resource.
When a class that has a finalizer created, an entry for that class instance is put on a queue in the JVM so the JVM knows it has a finalizer that needs to be executed.
The current issue is: even with programmers do call close() after using FileInputStream, its finalize() method will still be called. In other words, still get the side effect of the FinalReference being registered at FileInputStream allocation time, and also reference processing to reclaim the FinalReference during GC (any GC solution has to deal with this).
We can imagine When running industry deployment HDFS, millions of files could be opened and closed which resulted in a very large number of finalizers being registered and subsequently being executed. That could cause very long GC pause times.
We tried to use Files.newInputStream() to replace FileInputStream, but it was clear we could not replace FileInputStream in hdfs/server/datanode/fsdataset/impl/MappableBlock.java
We notified Oracle JVM team of this performance issue that impacting all Big Data applications using HDFS. We recommended the proper fix in Java SE FileInputStream. Because (1) it is really nothing wrong to use FileInputStream in above datanode code, (2) as the object with a finalizer is registered with finalizer list within the JVM at object allocation time, if someone makes an explicit call to close or free the resources that are to be done in the finalizer, then the finalizer should be pulled off the internal JVM’s finalizer list. That will release the JVM from having to treat the object as special because it has a finalizer, i.e. no need for GC to execute the finalizer as part of Reference Processing.
As the java fix involves both JVM code and Java SE code, it might take time for the full solution to be available in future JDK releases. We would like to file his JIRA to notify Big Data, HDFS community to aware this issue while using HDFS and while writing code using FileInputStream
One alternative is to use Files.newInputStream() to substitute FileInputStream if it is possible. File.newInputStream() will give an InputStream and do so in a manner that does not include a finalizer.
We welcome HDFS community to discuss this issue and see if there are additional ideas to solve this problem.