For my application, the memory used by the Java process is much more than the heap size.
The system where the containers are running starts to have memory problem because the container is taking much more memory than the heap size.
The heap size is set to 128 MB (-Xmx128m -Xms128m) while the container takes up to 1GB of memory. Under normal condition, it needs 500MB. If the docker container has a limit below (e.g. mem_limit=mem_limit=400MB) the process gets killed by the out of memory killer of the OS.
Could you explain why the Java process is using much more memory than the heap? How to size correctly the Docker memory limit? Is there a way to reduce the off-heap memory footprint of the Java process?
I gather some details about the issue using command from Native memory tracking in JVM.
From the host system, I get the memory used by the container.
$ docker stats --no-stream 9afcb62a26c8
CONTAINER ID NAME CPU % MEM USAGE / LIMIT MEM % NET I/O BLOCK I/O PIDS
9afcb62a26c8 xx-xxxxxxxxxxxxx-xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.0acbb46bb6fe3ae1b1c99aff3a6073bb7b7ecf85 0.93% 461MiB / 9.744GiB 4.62% 286MB / 7.92MB 157MB / 2.66GB 57
From inside the container, I get the memory used by the process.
$ ps -p 71 -o pcpu,rss,size,vsize
%CPU RSS SIZE VSZ
11.2 486040 580860 3814600
$ jcmd 71 VM.native_memory
71:
Native Memory Tracking:
Total: reserved=1631932KB, committed=367400KB
- Java Heap (reserved=131072KB, committed=131072KB)
(mmap: reserved=131072KB, committed=131072KB)
- Class (reserved=1120142KB, committed=79830KB)
(classes #15267)
( instance classes #14230, array classes #1037)
(malloc=1934KB #32977)
(mmap: reserved=1118208KB, committed=77896KB)
( Metadata: )
( reserved=69632KB, committed=68272KB)
( used=66725KB)
( free=1547KB)
( waste=0KB =0.00%)
( Class space:)
( reserved=1048576KB, committed=9624KB)
( used=8939KB)
( free=685KB)
( waste=0KB =0.00%)
- Thread (reserved=24786KB, committed=5294KB)
(thread #56)
(stack: reserved=24500KB, committed=5008KB)
(malloc=198KB #293)
(arena=88KB #110)
- Code (reserved=250635KB, committed=45907KB)
(malloc=2947KB #13459)
(mmap: reserved=247688KB, committed=42960KB)
- GC (reserved=48091KB, committed=48091KB)
(malloc=10439KB #18634)
(mmap: reserved=37652KB, committed=37652KB)
- Compiler (reserved=358KB, committed=358KB)
(malloc=249KB #1450)
(arena=109KB #5)
- Internal (reserved=1165KB, committed=1165KB)
(malloc=1125KB #3363)
(mmap: reserved=40KB, committed=40KB)
- Other (reserved=16696KB, committed=16696KB)
(malloc=16696KB #35)
- Symbol (reserved=15277KB, committed=15277KB)
(malloc=13543KB #180850)
(arena=1734KB #1)
- Native Memory Tracking (reserved=4436KB, committed=4436KB)
(malloc=378KB #5359)
(tracking overhead=4058KB)
- Shared class space (reserved=17144KB, committed=17144KB)
(mmap: reserved=17144KB, committed=17144KB)
- Arena Chunk (reserved=1850KB, committed=1850KB)
(malloc=1850KB)
- Logging (reserved=4KB, committed=4KB)
(malloc=4KB #179)
- Arguments (reserved=19KB, committed=19KB)
(malloc=19KB #512)
- Module (reserved=258KB, committed=258KB)
(malloc=258KB #2356)
$ cat /proc/71/smaps | grep Rss | cut -d: -f2 | tr -d " " | cut -f1 -dk | sort -n | awk '{ sum += $1 } END { print sum }'
491080
The application is a web server using Jetty/Jersey/CDI bundled inside a fat far of 36 MB.
The following version of OS and Java are used (inside the container). The Docker image is based on openjdk:11-jre-slim.
$ java -version
openjdk version "11" 2018-09-25
OpenJDK Runtime Environment (build 11+28-Debian-1)
OpenJDK 64-Bit Server VM (build 11+28-Debian-1, mixed mode, sharing)
$ uname -a
Linux service1 4.9.125-linuxkit #1 SMP Fri Sep 7 08:20:28 UTC 2018 x86_64 GNU/Linux
https://gist.github.com/prasanthj/48e7063cac88eb396bc9961fb3149b58
Virtual memory used by a Java process extends far beyond just Java Heap. You know, JVM includes many subsytems: Garbage Collector, Class Loading, JIT compilers etc., and all these subsystems require certain amount of RAM to function.
JVM is not the only consumer of RAM. Native libraries (including standard Java Class Library) may also allocate native memory. And this won't be even visible to Native Memory Tracking. Java application itself can also use off-heap memory by means of direct ByteBuffers.
So what takes memory in a Java process?
JVM parts (mostly shown by Native Memory Tracking)
1. Java Heap
The most obvious part. This is where Java objects live. Heap takes up to -Xmx amount of memory.
2. Garbage Collector
GC structures and algorithms require additional memory for heap management. These structures are Mark Bitmap, Mark Stack (for traversing object graph), Remembered Sets (for recording inter-region references) and others. Some of them are directly tunable, e.g. -XX:MarkStackSizeMax, others depend on heap layout, e.g. the larger are G1 regions (-XX:G1HeapRegionSize), the smaller are remembered sets.
GC memory overhead varies between GC algorithms. -XX:+UseSerialGC and -XX:+UseShenandoahGC have the smallest overhead. G1 or CMS may easily use around 10% of total heap size.
3. Code Cache
Contains dynamically generated code: JIT-compiled methods, interpreter and run-time stubs. Its size is limited by -XX:ReservedCodeCacheSize (240M by default). Turn off -XX:-TieredCompilation to reduce the amount of compiled code and thus the Code Cache usage.
4. Compiler
JIT compiler itself also requires memory to do its job. This can be reduced again by switching off Tiered Compilation or by reducing the number of compiler threads: -XX:CICompilerCount.
5. Class loading
Class metadata (method bytecodes, symbols, constant pools, annotations etc.) is stored in off-heap area called Metaspace. The more classes are loaded - the more metaspace is used. Total usage can be limited by -XX:MaxMetaspaceSize (unlimited by default) and -XX:CompressedClassSpaceSize (1G by default).
6. Symbol tables
Two main hashtables of the JVM: the Symbol table contains names, signatures, identifiers etc. and the String table contains references to interned strings. If Native Memory Tracking indicates significant memory usage by a String table, it probably means the application excessively calls String.intern.
7. Threads
Thread stacks are also responsible for taking RAM. The stack size is controlled by -Xss. The default is 1M per thread, but fortunately things are not so bad. The OS allocates memory pages lazily, i.e. on the first use, so the actual memory usage will be much lower (typically 80-200 KB per thread stack). I wrote a script to estimate how much of RSS belongs to Java thread stacks.
There are other JVM parts that allocate native memory, but they do not usually play a big role in total memory consumption.
Direct buffers
An application may explicitly request off-heap memory by calling ByteBuffer.allocateDirect. The default off-heap limit is equal to -Xmx, but it can be overridden with -XX:MaxDirectMemorySize. Direct ByteBuffers are included in Other section of NMT output (or Internal before JDK 11).
The amount of direct memory in use is visible through JMX, e.g. in JConsole or Java Mission Control:
Besides direct ByteBuffers there can be MappedByteBuffers - the files mapped to virtual memory of a process. NMT does not track them, however, MappedByteBuffers can also take physical memory. And there is no a simple way to limit how much they can take. You can just see the actual usage by looking at process memory map: pmap -x <pid>
Address Kbytes RSS Dirty Mode Mapping
...
00007f2b3e557000 39592 32956 0 r--s- some-file-17405-Index.db
00007f2b40c01000 39600 33092 0 r--s- some-file-17404-Index.db
^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^
Native libraries
JNI code loaded by System.loadLibrary can allocate as much off-heap memory as it wants with no control from JVM side. This also concerns standard Java Class Library. In particular, unclosed Java resources may become a source of native memory leak. Typical examples are ZipInputStream or DirectoryStream.
JVMTI agents, in particular, jdwp debugging agent - can also cause excessive memory consumption.
This answer describes how to profile native memory allocations with async-profiler.
Allocator issues
A process typically requests native memory either directly from OS (by mmap system call) or by using malloc - standard libc allocator. In turn, malloc requests big chunks of memory from OS using mmap, and then manages these chunks according to its own allocation algorithm. The problem is - this algorithm can lead to fragmentation and excessive virtual memory usage.
jemalloc, an alternative allocator, often appears smarter than regular libc malloc, so switching to jemalloc may result in a smaller footprint for free.
Conclusion
There is no guaranteed way to estimate full memory usage of a Java process, because there are too many factors to consider.
Total memory = Heap + Code Cache + Metaspace + Symbol tables +
Other JVM structures + Thread stacks +
Direct buffers + Mapped files +
Native Libraries + Malloc overhead + ...
It is possible to shrink or limit certain memory areas (like Code Cache) by JVM flags, but many others are out of JVM control at all.
One possible approach to setting Docker limits would be to watch the actual memory usage in a "normal" state of the process. There are tools and techniques for investigating issues with Java memory consumption: Native Memory Tracking, pmap, jemalloc, async-profiler.
Update
Here is a recording of my presentation Memory Footprint of a Java Process.
In this video, I discuss what may consume memory in a Java process, how to monitor and restrain the size of certain memory areas, and how to profile native memory leaks in a Java application.
https://developers.redhat.com/blog/2017/04/04/openjdk-and-containers/:
Why is it when I specify -Xmx=1g my JVM uses up more memory than 1gb
of memory?
Specifying -Xmx=1g is telling the JVM to allocate a 1gb heap. It’s not
telling the JVM to limit its entire memory usage to 1gb. There are
card tables, code caches, and all sorts of other off heap data
structures. The parameter you use to specify total memory usage is
-XX:MaxRAM. Be aware that with -XX:MaxRam=500m your heap will be approximately 250mb.
Java sees host memory size and it is not aware of any container memory limitations. It doesn't create memory pressure, so GC also doesn't need to release used memory. I hope XX:MaxRAM will help you to reduce memory footprint. Eventually, you can tweak GC configuration (-XX:MinHeapFreeRatio,-XX:MaxHeapFreeRatio, ...)
There is many types of memory metrics. Docker seems to be reporting RSS memory size, that can be different than "committed" memory reported by jcmd (older versions of Docker report RSS+cache as memory usage).
Good discussion and links: Difference between Resident Set Size (RSS) and Java total committed memory (NMT) for a JVM running in Docker container
(RSS) memory can be eaten also by some other utilities in the container - shell, process manager, ... We don't know what else is running in the container and how do you start processes in container.
TL;DR
The detail usage of the memory is provided by Native Memory Tracking (NMT) details (mainly code metadata and garbage collector). In addition to that, the Java compiler and optimizer C1/C2 consume the memory not reported in the summary.
The memory footprint can be reduced using JVM flags (but there is impacts).
The Docker container sizing must be done through testing with the expected load the application.
Detail for each components
The shared class space can be disabled inside a container since the classes won't be shared by another JVM process. The following flag can be used. It will remove the shared class space (17MB).
-Xshare:off
The garbage collector serial has a minimal memory footprint at the cost of longer pause time during garbage collect processing (see Aleksey Shipilëv comparison between GC in one picture). It can be enabled with the following flag. It can save up to the GC space used (48MB).
-XX:+UseSerialGC
The C2 compiler can be disabled with the following flag to reduce profiling data used to decide whether to optimize or not a method.
-XX:+TieredCompilation -XX:TieredStopAtLevel=1
The code space is reduced by 20MB. Moreover, the memory outside JVM is reduced by 80MB (difference between NMT space and RSS space). The optimizing compiler C2 needs 100MB.
The C1 and C2 compilers can be disabled with the following flag.
-Xint
The memory outside the JVM is now lower than the total committed space. The code space is reduced by 43MB. Beware, this has a major impact on the performance of the application. Disabling C1 and C2 compiler reduces the memory used by 170 MB.
Using Graal VM compiler (replacement of C2) leads to a bit smaller memory footprint. It increases of 20MB the code memory space and decreases of 60MB from outside JVM memory.
The article Java Memory Management for JVM provides some relevant information the different memory spaces.
Oracle provides some details in Native Memory Tracking documentation. More details about compilation level in advanced compilation policy and in disable C2 reduce code cache size by a factor 5. Some details on Why does a JVM report more committed memory than the Linux process resident set size? when both compilers are disabled.
Java needs a lot a memory. JVM itself needs a lot of memory to run. The heap is the memory which is available inside the virtual machine, available to your application. Because JVM is a big bundle packed with all goodies possible it takes a lot of memory just to load.
Starting with java 9 you have something called project Jigsaw, which might reduce the memory used when you start a java app(along with start time). Project jigsaw and a new module system were not necessarily created to reduce the necessary memory, but if it's important you can give a try.
You can take a look at this example: https://steveperkins.com/using-java-9-modularization-to-ship-zero-dependency-native-apps/. By using the module system it resulted in CLI application of 21MB(with JRE embeded). JRE takes more than 200mb. That should translate to less allocated memory when the application is up(a lot of unused JRE classes will no longer be loaded).
Here is another nice tutorial: https://www.baeldung.com/project-jigsaw-java-modularity
If you don't want to spend time with this you can simply get allocate more memory. Sometimes it's the best.
How to size correctly the Docker memory limit?
Check the application by monitoring it for some-time. To restrict container's memory try using -m, --memory bytes option for docker run command - or something equivalant if you are running it otherwise
like
docker run -d --name my-container --memory 500m <iamge-name>
can't answer other questions.
I am trying to debug an embedded application with Valgrind.
Unfortunately, this application behaves differently than when I run it without Valgrind. At one point a driver allocates a data block of about 4 MB. This allocation fails even though there is still about 90 MB of memory available. Could it be that Valgrind fragments the memory so much that no contiguous block of that size is available anymore?
Does anyone have an idea how to remedy this?
Is there a way to tell valgrind from inside my code when to start and when to stop checking for memory leaks?
I am using a legacy testing framework which must link with my testing program in order to run. The framework has memory leaks in it - valgrind shows about 50KB of memory that has not been released, but is reachable via heuristic. This is annoying, because I must keep this number in mind to see how much memory is leaked from my code. It would be a lot more convenient if I could tell valgrind to start collecting memory stats when my first test begins, and stop collecting when the last test is over. Is there an API for it?
valgrind memcheck allows to do a "differential" leak search. The differential leak search reports the delta between the previous leak search and the current situation.
You can do such a differential leak search using monitor commands with vgdb, either from the shell or from gdb. See https://www.valgrind.org/docs/manual/mc-manual.html#mc-manual.monitor-commands.
You can also use the client request VALGRIND_DO_CHANGED_LEAK_CHECK from your program, see https://www.valgrind.org/docs/manual/mc-manual.html#mc-manual.clientreqs.
I had run valgrind on a sample daemon program. The parent exits after allocating a chunk of 1000B, but the child that runs on the background keeps on allocating 200B of memory on the heap through malloc, after every two seconds.
My question is: does valgrind execute the program on the actual processor, or on a synthetic CPU?
Does it allocate the memory on the actual heap or on a synthetic RAm which doesn't exist?
Since I let the program run for a quite a long duration so much so that the child allocated some 2GB of memory on the heap. On implementing the program on massif, I got one output file for the parent, and on killing the daemon process, I got another massif.out. for the child which showed the allocation of the memory on the heap.
Valgrind run program in its own synthetic CPU, nothing from the program machine code reaches the host CPU.
Memory allocation is hooked with Memcheck, if you use it, otherwise Valgrind calls the libc memory allocation routines.
This facts may complicate Valgrind debugging of system services, indeed.
If you turn on the memcheck(which is the default), then Valgrind will manage the heap, i.e. all the memory related methods (malloc/free/memmove etc.) will be replaced by Valgrind's version of the corresponding methods.
As already told, your program is running on virtual CPU created and managed by valgrind.
There is no notion of synthetic RAM as far I know. In any case, all this is very transparent to the running process(your daemon) and shoudl not change the behavior of your program in any way.
So the answer is YES for synthetic CPU and no for synthetic RAM.
I am developing a GUI-heavy C++ application on a Freescale MX51-based board Linux 2.6.35. I would like to perform heap profiling.
Unfortunately, all heap profiling tools I have found have either been too intrusive or ostensibly non-working on ARM. Specific tools I've tried:
Valgrind Massif: unworkable on my platform due to the platform's feeble CPU. The 80% CPU time overhead introduced by Massif causes a range of problems in my application that cannot be compensated for.
gperftools (formerly Google Performance Tools) tcmalloc: All features of this rather un-intrusive, library-based libc malloc() replacement work on my target except for the heap profiler. To rephrase, the thread caching allocator works but the profiler does not. I'll explain the failure mode of the profiler below for anyone curious.
Can anyone suggest a set of replacement tools for performing C++ heap profiling on ARM platforms? Ideal output would ultimately be a directed allocation graph, similar to what gperftools' tcmalloc outputs. Low resource utilization is a must- my platform is highly resource constrained.
Failure mode of gperftools' tcmalloc explained:
I'm providing this information only for those that are curious; I do not expect a response. I'm seeing something similar to gperftools' issue #407 below, except on ARM rather than x86.
Specifically, I always get the message "Hooked allocator frame not found, returning empty trace." I spent some time debugging the issue and it appears that, when dynamically linking the tcmalloc library, frame pointers at the boundary between my application and the dynamic library are null- the stack cannot be walked "above" the call into the dynamic library.
gperftools issue #407: https://github.com/gperftools/gperftools/issues/410
stackoverflow user seeing similar problems on ARM: Missing frames on shared libraries on ARM
Heaps. Many ways to do them, but I've only run across 3 main types that matter in embedded land:
Linked list heaps. Each alloc is tracked in a "used" list. Once freed, they are dropped into a "free" list. On freeing, adjacent blocks of free memory are "joined" into larger pieces. Allocs can be any size. Each alloc and free is a O(N) op as it has to traverse the free list to give you a piece of memory plus break the free block into a size close to what you asked for while leaving the remaining block in the free list. Because of the increasing overhead per alloc, this system cannot be used by itself on smaller systems. This also tends to cause memory fragmentation over time if steps aren't taken to minimize it.
Fixed size (unit) heaps. You break your heap into equal size (smaller) parts. This wastes memory a bit, depending on how big the chunks are (and how many different sized, fixed allocator heaps you create), but alloc and free are both O(1) time operations. No searching, no joining. This style is often combined with the first one for "small object allocations" as the engines I've worked with have 95% of their allocations below a set size (say 256 bytes). This way, you use the unit heap for small allocs for huge speed and only minimal memory loss, while using the list heap for larger allocs. No external fragmentation of memory either.
Relocatable memory heaps. You don't give out pointers to memory, but handles. That way, behind the scenes, you can change memory pointers when needed to remove fragmentation or whatever. High overhead. High pain the the #$$ quotient as it's easy to abuse and get dangling pointer all over. Also added overhead for each memory dereference. But wanted to mention it.
There's some basic patterns. You can find all sorts of libs out in the wild that use them and also have built in statistics for number of allocs, fragmentation, and other useful stats. It's also not the hard to roll your own really, though I'd not recommend it for anything outside of satisfying curiosity as debugging without a working malloc is painful indeed. Adding thread support is pretty straightforward as well, but again, downloading a ready made solution is the better choice.
The above info applies to all platforms, ARM or otherwise, though most of my experience has been on low level ARM stuff so the above info is battle tested for your platform. Hope this helps!