Hello everybody,
I was writing this email when a similar thread on this mailing list appeared.. The difference is that the other problem seems to be related with Flink 1.10 on YARN and does not output anything helpful in debugging the cause of the problem. Indeed, in my use case I use Flink 1.11.0 and Flink on a standalone session cluster (the job is submitted to the cluster using the CLI client). The problem arises when I submit the same job for about 20 times (this number unfortunately is not deterministic and can change a little bit). The error reported by the Task Executor is related to the ever growing Metaspace..the error seems to be pretty detailed [1]. I found the same issue in some previous threads on this mailing list and I've tried to figure it out the cause of the problem. The issue is that looking at the objects allocated I don't really get an idea of the source of the problem because the type of objects that are consuming the memory are of general purpose (i.e. Bytes, Integers and Strings)...these are my "top" memory consumers if looking at the output of jmap -histo <PID>: At run 0: num #instances #bytes class name (module) ------------------------------------------------------- 1: 46238 13224056 [B ([hidden email]) 2: 3736 6536672 [I ([hidden email]) 3: 38081 913944 java.lang.String ([hidden email]) 4: 26 852384 [Lakka.dispatch.forkjoin.ForkJoinTask; 5: 7146 844984 java.lang.Class ([hidden email]) At run 1: 1: 77.608 25.317.496 [B ([hidden email]) 2: 7.004 9.088.360 [I ([hidden email]) 3: 15.814 1.887.256 java.lang.Class ([hidden email]) 4: 67.381 1.617.144 java.lang.String ([hidden email]) 5: 3.906 1.422.960 [Ljava.util.HashMap$Node; ([hidden email]) At run 6: 1: 81.408 25.375.400 [B ([hidden email]) 2: 12.479 7.249.392 [I ([hidden email]) 3: 29.090 3.496.168 java.lang.Class ([hidden email]) 4: 4.347 2.813.416 [Ljava.util.HashMap$Node; ([hidden email]) 5: 71.584 1.718.016 java.lang.String ([hidden email]) At run 8: 1: 985.979 127.193.256 [B ([hidden email]) 2: 35.400 13.702.112 [I ([hidden email]) 3: 260.387 6.249.288 java.lang.String ([hidden email]) 4: 148.836 5.953.440 java.util.HashMap$KeyIterator ([hidden email]) 5: 17.641 5.222.344 [Ljava.util.HashMap$Node; ([hidden email]) Thanks in advance for any help, Flavio [1] -------------------------------------------------------------------------------------------------- java.lang.OutOfMemoryError: Metaspace. The metaspace out-of-memory error has occurred. This can mean two things: either the job requires a larger size of JVM metaspace to load classes or there is a class loading leak. In the first case 'taskmanager.memory.jvm-metaspace.size' configuration option should be increased. If the error persists (usually in cluster after several job (re-)submissions) then there is probably a class loading leak in user code or some of its dependencies which has to be investigated and fixed. The task executor has to be shutdown... at java.lang.ClassLoader.defineClass1(Native Method) ~[?:?] at java.lang.ClassLoader.defineClass(ClassLoader.java:1017) ~[?:?] at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:174) ~[?:?] at java.net.URLClassLoader.defineClass(URLClassLoader.java:550) ~[?:?] at java.net.URLClassLoader$1.run(URLClassLoader.java:458) ~[?:?] at java.net.URLClassLoader$1.run(URLClassLoader.java:452) ~[?:?] at java.security.AccessController.doPrivileged(Native Method) ~[?:?] at java.net.URLClassLoader.findClass(URLClassLoader.java:451) ~[?:?] at org.apache.flink.util.ChildFirstClassLoader.loadClassWithoutExceptionHandling(ChildFirstClassLoader.java:71) ~[flink-dist_2.12-1.11.0.jar:1.11.0] at org.apache.flink.util.FlinkUserCodeClassLoader.loadClass(FlinkUserCodeClassLoader.java:48) [flink-dist_2.12-1.11.0.jar:1.11.0] at java.lang.ClassLoader.loadClass(ClassLoader.java:522) [?:?] |
Hi Flavio, when I encountered quite similar problem that you describe, it was related to a static storage located in class that was loaded "parent-first". In my case it was it was in java.lang.ClassValue, but it might (and probably will be) different in your case. The problem is that if user-code registers something in some (static) storage located in class loaded with parent (TaskTracker) classloader, then its associated classes will never be GC'd and Metaspace will grow. A good starting point would be not to focus on biggest consumers of heap (in general), but to look at where the 15k objects of type Class are referenced from. That might help you figure this out. I'm not sure if there is something that can be done in general to prevent this type of leaks. That would be probably question on dev@ mailing list. Best, Jan On 11/16/20 2:27 PM, Flavio Pompermaier
wrote:
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Thank you Jan for your valuable feedback. Could it be that I should not use import shaded-jackson classes in my user code? For example import org.apache.flink.shaded.jackson2.com.fasterxml.jackson.databind.ObjectMapper? Bets, Flavio On Mon, Nov 16, 2020 at 3:15 PM Jan Lukavský <[hidden email]> wrote:
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Yes, that could definitely cause this. You should probably avoid using these flink-internal shaded classes and ship your own versions (not shaded). Best, Jan On 11/16/20 3:22 PM, Flavio Pompermaier
wrote:
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I've tried to remove all possible imports of classes not contained in the fat jar but I still face the same problem. I've also tried to reduce as much as possible the exclude in the shade section of the maven plugin (I took the one at [1]) so now I exclude only few dependencies..could it be that I should include org.slf4j:* if I use static import of it? <artifactSet> <excludes> <exclude>com.google.code.findbugs:jsr305</exclude> <exclude>org.slf4j:*</exclude> <exclude>log4j:*</exclude> </excludes> </artifactSet> On Mon, Nov 16, 2020 at 3:29 PM Jan Lukavský <[hidden email]> wrote:
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The exclusions should not have any impact on that, because what defines which classloader will load which class is not the presence or particular class in a specific jar, but the configuration of parent-first-patterns [1]. If you don't use any flink internal imports, than it still might
be the case, that a class in any of the packages defined by the
parent-first-pattern to hold reference to your user-code classes,
which would cause the leak. I'd recommend to inspect the heap dump
after several restarts of the application and look for reference
to Class objects from the root set. Jan [1]
https://ci.apache.org/projects/flink/flink-docs-stable/ops/config.html#class-loading On 11/16/20 5:34 PM, Flavio Pompermaier
wrote:
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Hello! The JVM metaspace is where all the classes (not class instances or objects) get loaded. jmap -histo is going to show you the heap space usage info not the metaspace. You could inspect what is happening in the metaspace by using jcmd (e.g., jcmd JPID VM.native_memory summary) after restarting the cluster with "-XX:NativeMemoryTracking=summary" As the error message suggests, you may need to increase taskmanager.memory.jvm-metaspace.size, but you need to be slightly careful when specifying the memory parameters in flink-conf.yaml in Flink 1.10 (they have an issue with a confusing error message). Anothing thing to keep in mind is that you may want to avoid using dynamic classloading (https://ci.apache.org/projects/flink/flink-docs-release-1.10/monitoring/debugging_classloading.html#avoiding-dynamic-classloading-for-user-code): when the job continuously fails for some temporary issues, it will load the same class files into the metaspace multiple times and could exceed whatever the limit you set it. -K On Mon, Nov 16, 2020 at 12:39 PM Jan Lukavský <[hidden email]> wrote:
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Thank you Kye for your insights...in my mind, if the job runs without problems one or more times the heap size, and thus the medatadata-size, is big enough and I should not increase it (on the same data of course). So I'll try to understand who is leaking what..the advice to avoid the dynamic class loading is just a workaround to me..there's something wrong going on and tomorrow I'll try to understand the root cause of the problem using -XX:NativeMemoryTracking=summary as you suggested. I'll keep you up to date with my findings.. Best, Flavio On Mon, Nov 16, 2020 at 8:22 PM Kye Bae <[hidden email]> wrote:
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Another big potential candidate is the fact that JDBC libs I use in my job are put into the Flink lib folder instead of putting them into the fat jar..tomorrow I'll try to see if the metaspace is getting cleared correctly after that change. Unfortunately our jobs were written before the child-first / parent-first classloading refactoring and at that time that was the way to go..but now it can cause this kind of problems if using child-first policy. On Mon, Nov 16, 2020 at 8:44 PM Flavio Pompermaier <[hidden email]> wrote:
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It is possible, but I am not entirely sure about the load order affecting the metaspace usage. To find out why your taskmanager container is exceeding the metaspace, we would need to know what value the max metaspace size is set to and then find out how much of the metaspace is actually being used and what the classloading stats are (before Yarn kills the container). If possible, please share the current metaspace setting and the native memory stats from one of your taskmanager instances (Java process as a Yarn container). I think those run as the yarn user as opposed to the hadoop user (it depends on your environment). # enable the native memory tracking referenced earlier - this may need to be passed in as the taskmanager JVM option parameter not the jobmanager. # log onto one of the taskmanager HW instances sudo su - yarn # or log on as the user that runs Yarn jps -v # grab the PID for one of the processes named YarnTaskExecutorRunner - this would be a taskmanager
jcmd TM_PID VM.native_memory summary # size information for "Class" - metaspace jcmd TM_PID VM.classloader_stats # how many classes were loaded by which classloader, sizes, etc. There is a gentleman who posts blogs on Flink, and he goes into a bit more detail there. This was against Flink 1.9, but the foundational concepts still apply to 1.10. http://cloudsqale.com/2020/04/29/flink-1-9-off-heap-memory-on-yarn-troubleshooting-container-is-running-beyond-physical-memory-limits-errors/ -K On Tue, Nov 17, 2020 at 12:47 PM Flavio Pompermaier <[hidden email]> wrote:
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Hi Kye, thanks a lot for the support! See my answers inline below On Tue, Nov 17, 2020 at 7:22 PM Kye Bae <[hidden email]> wrote:
Actually I don't use YARN, I use standalone cluster and MaxMetspaceSize is automatically computed and it is set to 256 MB (-XX:MaxMetaspaceSize=268435456)
6976: Native Memory Tracking: Total: reserved=1473311KB, committed=954707KB - Java Heap (reserved=524288KB, committed=524288KB) (mmap: reserved=524288KB, committed=524288KB) - Class (reserved=379640KB, committed=142024KB) (classes #23605) ( instance classes #22058, array classes #1547) (malloc=2808KB #48655) (mmap: reserved=376832KB, committed=139216KB) ( Metadata: ) ( reserved=122880KB, committed=121168KB) ( used=117529KB) ( free=3639KB) ( waste=0KB =0.00%) ( Class space:) ( reserved=253952KB, committed=18048KB) ( used=16516KB) ( free=1532KB) ( waste=0KB =0.00%) - Thread (reserved=76359KB, committed=6867KB) (thread #74) (stack: reserved=76012KB, committed=6520KB) (malloc=262KB #446) (arena=85KB #146) - Code (reserved=250407KB, committed=38911KB) (malloc=2719KB #11989) (mmap: reserved=247688KB, committed=36192KB) - GC (reserved=71481KB, committed=71481KB) (malloc=19121KB #17323) (mmap: reserved=52360KB, committed=52360KB) - Compiler (reserved=561KB, committed=561KB) (malloc=429KB #846) (arena=133KB #5) - Internal (reserved=855KB, committed=855KB) (malloc=823KB #2442) (mmap: reserved=32KB, committed=32KB) - Other (reserved=131857KB, committed=131857KB) (malloc=131857KB #4128) - Symbol (reserved=15702KB, committed=15702KB) (malloc=14288KB #165850) (arena=1415KB #1) - Native Memory Tracking (reserved=4072KB, committed=4072KB) (malloc=27KB #353) (tracking overhead=4045KB) - Shared class space (reserved=17044KB, committed=17044KB) (mmap: reserved=17044KB, committed=17044KB) - Arena Chunk (reserved=199KB, committed=199KB) (malloc=199KB) - Logging (reserved=4KB, committed=4KB) (malloc=4KB #191) - Arguments (reserved=20KB, committed=20KB) (malloc=20KB #501) - Module (reserved=568KB, committed=568KB) (malloc=568KB #3919) - Synchronizer (reserved=244KB, committed=244KB) (malloc=244KB #2054) - Safepoint (reserved=8KB, committed=8KB) (mmap: reserved=8KB, committed=8KB)
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0x00007f1cc80e1ad0 1 6144 3872 jdk.internal.reflect.DelegatingClassLoader 0x000000080036ef80 0x0000000000000000 0x00007f1d582879b0 112 843776 783312 jdk.internal.loader.ClassLoaders$PlatformClassLoader 3 9216 5432 + unsafe anonymous classes 0x000000080039f8b0 0x000000080036f648 0x00007f1cc8080100 1 6144 3952 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x0000000000000000 0x00007f1cc80873d0 1 6144 3952 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x000000080036f648 0x00007f1ccc00b300 1 6144 3952 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x00000008405a5288 0x00007f1ccc2e7b90 1 6144 3952 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x00000008405a5288 0x00007f1cb813c350 1 6144 3952 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x00000008405a5288 0x00007f1c90021200 1 6144 3952 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x000000080036f648 0x00007f1c3c210130 1 6144 3952 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x0000000000000000 0x00007f1cc8044950 1 6144 3872 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x000000080036f648 0x00007f1ca4031cc0 1 6144 3952 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x000000080036f648 0x00007f1d58d74ec0 1 6144 3960 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x000000080036f648 0x00007f1cc8081b00 1 6144 3952 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x000000080036f648 0x00007f1cc80ba9e0 1 6144 3952 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x000000080036f648 0x00007f1ccc011840 1 6144 3872 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x00000008405a5288 0x00007f1bb00da8d0 1 6144 4048 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x00000008405a5288 0x00007f1c9000d5a0 1 6144 3952 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x00000008405a5288 0x00007f1bb00e57b0 1 6144 4048 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x00000008405a5288 0x00007f1cb812e180 1 6144 3952 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x0000000000000000 0x00007f1cc8047410 1 6144 4008 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x000000080036f648 0x00007f1c3807a130 1 6144 3872 jdk.internal.reflect.DelegatingClassLoader 0x000000080039f8b0 0x00000008405a5288 0x00007f1cb8146e70 1 6144 3928 jdk.internal.reflect.DelegatingClassLoader Total = 431 23605 140124160 137261400 ChunkSz: Total size of all allocated metaspace chunks BlockSz: Total size of all allocated metaspace blocks (each chunk has several blocks)
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I see: ( Metadata: ) ( reserved=122880KB, committed=121168KB) ( used=117529KB) ( free=3639KB) ( waste=0KB =0.00%) Internal (reserved=855KB, committed=855KB) (malloc=823KB #2442) (mmap: reserved=32KB, committed=32KB) and 0x00000008405a5288 0x000000080036f648 0x00007f1d14005160 2547 15675392 15603040 org.apache.flink.util.ChildFirstClassLoader 0x00000008405a5288 0x000000080036f648 0x00007f1ccc059790 2648 16330752 16287960 org.apache.flink.util.ChildFirstClassLoader 0x00000008405a5288 0x000000080036f648 0x00007f1c90004d90 2626 16461824 16391336 org.apache.flink.util.ChildFirstClassLoader 0x00000008405a5288 0x000000080036f648 0x00007f1c38685650 2648 16330752 16286608 org.apache.flink.util.ChildFirstClassLoader 0x00000008405a5288 0x000000080036f648 0x00007f1c3801e590 2651 16408576 16320192 org.apache.flink.util.ChildFirstClassLoader The "Metadata" looks like there is a little over 3.5MB left. Not sure if this is enough. Also, "Internal" memory reserved is less than 1 MB, but this is where the Java direct memory buffers get allocated (Java NIO). Don't know the details of your Flink job, but is this enough? Flink 1.10 memory architecture requires care, and there should be enough for both Flink and JVM internal operations. It shouldn't hurt to review your memory requirements and allocate extra to account for unexpected spikes. Please keep in mind Yarn will kill a container immediately if the physical memory limit is breached. Also, it looks like ChildFirstClassLoader (user-code loader - dynamic) was used 5 times to load classes onto this taskmanager. Were there 5 job submissions to your standalone cluster or 4 job restarts for the same job? Additional (dynamic) loadings will likely result in exceeding the max metaspace limit. If your Flink cluster is meant to host a single job, I would avoid using the dynamic classloading altogether and then recapture the stats to see if there are still multiple loading of the user (your application) classes. If it doesn't, you might want to make that change to not use the dynamic classloading. -K On Tue, Nov 17, 2020 at 2:00 PM Flavio Pompermaier <[hidden email]> wrote:
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Hi Kye, thank you a lot for your help. There are a couple of things that are not clear to me: in an ideal world, ChildFirstClassLoader instances should all be garbage collected right? In my case they are not because they have some pointers to some parent class loader for some class..am I right? Debugging a little bit the internals of the ChildFirstClass.loadClassWithoutExceptionHandling I saw that there are a couple of classes that are demanded to the parent class loader (i.e. the super.loadClassWithoutExceptionHandling() is called because a class is not found in the user classloader in the snippet at [1]):
While the latter could be moved into the fat jar because it is the dependency of the JDBC connector, the other classes are correctly loaded from the system class loader.. Is this stopping the user classloader to be correctly garbage collected? And a final question about the possible workaround to put the user jar into the Flink lib: in this case I don't have a jar to pass as argument to the CLI java client..is this a problem of the CLI client or not..? Should the run action be callable without specifying a user JAR but just the main class (in the case that it is in the lib dir)? [1] try { // check the URLs c = findClass(name); } catch (ClassNotFoundException e) { // let URLClassLoader do it, which will eventually call the parent c = super.loadClassWithoutExceptionHandling(name, resolve); } On Tue, Nov 17, 2020 at 8:51 PM Kye Bae <[hidden email]> wrote:
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Could this problem be related to https://issues.apache.org/jira/browse/FLINK-20333, where the instances of java.io.ObjectStreamClass$Caches need to be cleaned up as a fix of https://bugs.openjdk.java.net/browse/JDK-8199589? On Wed, Nov 18, 2020 at 3:04 PM Flavio Pompermaier <[hidden email]> wrote:
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