Slide deck from meetup 15 Dec 2016 at Moscow

1. What Dev and Ops
should know about
Java on Linux?
Alexey Ragozin
alexey.ragozin@gmail.com

2. Java Memory
Java Heap
Young Gen
Old Gen
Perm Gen
Non-Heap
JVM Memory
Thread Stacks
NIO Direct Buffers
Metaspace
Compressed Class Space
Code Cache
Native JVM Memory
Non-JVM Memory (native libraries)
Java 7
Java 8
Java 8
-Xms/-Xmx
-Xmn
-XX:PermSize
-XX:MaxDirectMemorySize
-XX:ReservedCodeCacheSize
-XX:MaxMetaspaceSize
-XX:CompressedClassSpaceSize
JavaProcessMemory
-XX:ThreadStackSize per thread

3. Linux memory
Memory is managed in pages (4k) onx86/AMD64
(Huge page support is mostly defunct in Linux)
Pages from process point of view
- Virtual address reservation
- Committed memory page
- File mapped memory page

4. Linux memory
Pages from OS point of view
PrivateShared
Anonymous File backed
Shared
memory
Private
process
memory
Executables / Libraries
Memory mapped files
Memory
mapped files
Cache / Buffers
https://techtalk.intersec.com/2013/07/memory-part-1-memory-types/

5. Understanding memory metrics

6. Understanding memory metrics
OS Memory
 Memory Used/Free – misleading metric
 Swap used – should be zero
 Buffers/Cached – essentially this is free memory*
Process
 VIRT – address space reservation - not a memory!
 RES – resident size - key memory footprint
 SHR – shared size

7. Understanding memory metrics
 Buffers – pages used for file system metadata
 Cached – pages mapped to file data
Non-dirty pages used for buffers/cache can
immediately to fulfill memory allocation request.
Dirty pages – writable file mapped pages which has
modifications not synchronized to disk.

8. Linux Process Memory Summary
Virtual
Commited
Resident
Zeroed pages
Swapped pages

9. Java Memory Facts
Swapping intolerance
 GC does heap wide scans
 SWT pauses prolonged by swapping
are affecting whole application threads
Java never give up memory to OS
 Strictly speaking serial GC and G1 does
 Practically you should assume it does not
JVM Process footprint > JVM Heap size

10. JVM Out of Memory
JVM heap is full and at –Xmx limit
 Full GC, then OOM error if not enough memory reclaimed
 OOM error is not recoverable, useful to shutdown gracefully
 -XX:OnOutOfMemoryError="kill -9 %p“
JVM heap is full but below –Xmx limit
 Heap is extended by requesting more memory from OS
 If OS rejects memory requests JVM would crash (no OOM error)
NIOdirectbufferscapacityiscappedbyJVM
 -XX:MaxDirectMemorySize=16g
 Cap is enfored by JVM
 OOM error in case is limit has been reached - recoverable
If request for memory from JVM rejected by OS
 JVM would crash

11. Low memory conditions
Low memory condition on server
 Swapping / Paging
 Dramatic application performance degradation
 Application freezes
 JVM crashes
Always plan server memory capacity
You should always have physical memory reserve.

12. Linux paravirtualization
In Docker container
 Guest resources are capped via Linux cgroups
https://en.wikipedia.org/wiki/Cgroups
 Kernel memory pools can be limited
resident / swap / memory mapped
 Limits are global for container
 Resources restrictions violations remediated by kill -9
Plan your container size carefully

13. ulimits
> ulimit -a
core file size (blocks, -c) 1
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 4134823
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) 449880520
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 4134823
virtual memory (kbytes, -v) 425094640
file locks (-x) unlimited
May prevent you
form starting
large JVM
Core dump disabled

14. Setting up JVM
 -Xms = -Xmx – reserve memory on start
 GC logging options (-XX:+PrintGCDetails, etc)
http://blog.ragozin.info/2016/10/hotspot-jvm-garbage-collection-options.html
GC logging is synchronous avoid network / slow mounts
 Do JVM sizing exercise
 Choose right GC parallel threads (-XX:ParallelGCThredas)
Sometimes less is better
 Getting dump on crash
-XX:+HeapDumpOnOutOfMemoryError – may “crash” Linux
Java heap dump can be produced from Linux core dump
https://docs.oracle.com/javase/8/docs/technotes/guides/
troubleshoot/bugreports004.html#CHDHDCJD

15. Network tuning
Cross region data transfers (client or server)
 Tune options at socket level
 Tune Linux network caps (sysctl)
net.ipv4.tcp_rmem
net.ipv4.tcp_wmem
UDP based communications
net.core.wmem_max
net.core.rmem_max

16. Other OS related tuning
NUMA
 numactl --cpunodebind=xxx
 ignore JVM Numa* options
 KVM hypervisor does not support NUMA for guests
Assigning threads to cores
 taskset
Exploiting CPU isolation
 Kernel level configuration
 Threads should be taskset explicitly

17. Troubleshooting
Diagnostics

18. Troubleshooting / Diagnostics
 Native Linux tools
ps / top / vmstat / pmap / etc
 JDK tools
PID based
 JVM Attach based tools
 Perf counter based tools
JMX based tools (JVisualVM / JConsole)
JVM Flight Recorder – post analysis
 GC / JVM logs

19. Troubleshooting / Diagnostics
 Native Linux tools
ps / top / vmstat / pmap / etc
 JDK tools
PID based
 JVM Attach based tools
 Perf counter based tools
JMX based tools (JVisualVM / JConsole)
JVM Flight Recorder – post analysis
 GC / JVM logs
Affected by
JVM freezes

20. Thread CPU usage
ragoale@axcord02:~> ps -T -p 6857 -o pid,tid,%cpu,time,comm
PID TID %CPU TIME COMMAND
6857 6857 0.0 00:00:00 java
6857 6858 0.0 00:00:00 java
6857 6859 0.0 00:00:16 java
6857 6860 0.0 00:00:16 java
6857 6861 0.0 00:00:18 java
6857 6862 0.1 00:13:05 java
6857 6863 0.0 00:00:00 java
6857 6864 0.0 00:00:00 java
6857 6877 0.0 00:00:00 java
6857 6878 0.0 00:00:00 java
6857 6880 0.0 00:00:20 java
6857 6881 0.0 00:00:04 java
6857 6886 0.0 00:00:00 java
6857 6887 0.0 00:03:07 java
...
This thread mapping is “typical” and not accurate,
use jstack to get Java thread information for thread ID
VM Thread
GC Threads
Other application
and JVM threads

21. Thread CPU usage
jstack (JDK tool)
Full thread dump Java HotSpot(TM) 64-Bit Server VM (25.60-b23 mixed mode):
"Attach Listener" #65 daemon prio=9 os_prio=0 tid=0x0000000000cbc800 nid=0x1f0 waiting on condition [0x0000000000000000]
java.lang.Thread.State: RUNNABLE
"pool-1-thread-20" #64 prio=5 os_prio=0 tid=0x00000000009d5000 nid=0x1c04 waiting on condition [0x00007fa109e55000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000000d3ab9e50> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1088)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1067)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
"pool-1-thread-19" #63 prio=5 os_prio=0 tid=0x0000000000a1e800 nid=0x1bff waiting on condition [0x00007fa109f56000]
java.lang.Thread.State: WAITING (parking)
at sun.misc.Unsafe.park(Native Method)
- parking to wait for <0x00000000d3ab9e50> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:1088)
at java.util.concurrent.ScheduledThreadPoolExecutor$DelayedWorkQueue.take(ScheduledThreadPoolExecutor.java:809)
...
Linux thread ID in hex
jstack forces STW pause in target JVM!

22. Thread CPU usage
sjk ttop command - https://github.com/aragozin/jvm-tools
2016-07-27T07:47:20.674-0400 Process summary
process cpu=8.11%
application cpu=2.17% (user=1.52% sys=0.65%)
other: cpu=5.95%
GC cpu=0.00% (young=0.00%, old=0.00%)
heap allocation rate 1842kb/s
safe point rate: 1.1 (events/s) avg. safe point pause: 0.43ms
safe point sync time: 0.01% processing time: 0.04% (wallclock time)
[003120] user= 1.12% sys= 0.24% alloc= 983kb/s - RMI TCP Connection(1)-172.17.168.11
[000039] user= 0.30% sys= 0.26% alloc= 701kb/s - DB feed - UserPermission.DBWatcher
[000053] user= 0.00% sys= 0.05% alloc= 50kb/s - Statistics
[000038] user= 0.00% sys= 0.05% alloc= 4584b/s – Reactor-0
[000049] user= 0.00% sys= 0.03% alloc= 38kb/s - DB feed - UserInfo.DBWatcher
[000036] user= 0.00% sys= 0.03% alloc= 0b/s - Abandoned connection cleanup thread
[003122] user= 0.00% sys= 0.03% alloc= 4915b/s - JMX server connection timeout 3122
[000040] user= 0.10% sys=-0.09% alloc= 8321b/s - DB feed - Report.DBWatcher
[000050] user= 0.00% sys= 0.01% alloc= 24kb/s - DB feed - Rule.DBWatcher
[000051] user= 0.00% sys= 0.01% alloc= 9034b/s - DB feed - EmailAccount.DBWatcher
[000044] user= 0.00% sys= 0.01% alloc= 4840b/s - DB feed - Analytics.DBWatcher
[000041] user= 0.00% sys= 0.01% alloc= 9999b/s - DB feed - Contact.DBWatcher
[000054] user= 0.00% sys= 0.01% alloc= 3481b/s – Statistics
[000001] user= 0.00% sys= 0.00% alloc= 0b/s - main
[000002] user= 0.00% sys= 0.00% alloc= 0b/s - Reference Handler
[000003] user= 0.00% sys= 0.00% alloc= 0b/s - Finalizer
[000005] user= 0.00% sys= 0.00% alloc= 0b/s - Signal Dispatcher
[000008] user= 0.00% sys= 0.00% alloc= 0b/s - JFR request timer
[000010] user= 0.00% sys= 0.00% alloc= 0b/s - VM JFR Buffer Thread
Does not infer STW pauses on target process

23. Leaking OS resources
Linux OS has number cap on file handles
if exceeded …
 Cannot open new files
 Cannot connect / accept socket connections
Garbage collector closes handles automatically
 Files and sockets
 Eventually …
 Always close your files and sockets
Resources which cannot be explicitly disposed
 File memory mappings
 NIO direct buffers
Unfinalized objects can be inspected in heap dump

24. Other useful JDK tools
jinfo
 query / update XX JVM options (e.g. enable/adjust GC logging)
 query system properties (including dynamically updated)
jstat
 can be used for monitoring heap dynamics
jcmd
 universal tool for JVM Attach interface
 jcmd PID PerfCounter.print – dumps all JVM perfcounters,
useful for monitoring

25. THANK YOU
Alexey Ragozin
alexey.ragozin@gmail.com
http://blog.ragozin.info