I think native methods are not in a forked process. It is just a malloc() call that failed, probably an I/O buffer or so. This might mean that there really is no native memory available any more, meaning the process has hit its limit. In any case, a bit more JVM overhead should solve this.
On Fri, Apr 24, 2020 at 10:24 AM Xintong Song <tonysong...@gmail.com> wrote: > I might be wrong about how JNI works. Isn't a native method always > executed in another process? > > I was searching for the java error message "Cannot allocate memory", and > it seems this happens when JVM cannot allocate memory from the OS. Given > the exception is thrown from calling a native method, I think the problem > is that not enough native memory can be allocated for executing the native > method. > > Thank you~ > > Xintong Song > > > > On Fri, Apr 24, 2020 at 3:40 PM Stephan Ewen <se...@apache.org> wrote: > >> @Xintong - out of curiosity, where do you see that this tries to fork a >> process? I must be overlooking something, I could only see the native >> method call. >> >> On Fri, Apr 24, 2020 at 4:53 AM Xintong Song <tonysong...@gmail.com> >> wrote: >> >>> @Stephan, >>> I don't think so. If JVM hits the direct memory limit, you should see >>> the error message "OutOfMemoryError: Direct buffer memory". >>> >>> Thank you~ >>> >>> Xintong Song >>> >>> >>> >>> On Thu, Apr 23, 2020 at 6:11 PM Stephan Ewen <se...@apache.org> wrote: >>> >>>> @Xintong and @Lasse could it be that the JVM hits the "Direct Memory" >>>> limit here? >>>> Would increasing the "taskmanager.memory.framework.off-heap.size" help? >>>> >>>> On Mon, Apr 20, 2020 at 11:02 AM Zahid Rahman <zahidr1...@gmail.com> >>>> wrote: >>>> >>>>> As you can see from the task manager tab of flink web dashboard >>>>> >>>>> Physical Memory:3.80 GB >>>>> JVM Heap Size:1.78 GB >>>>> Flink Managed Memory:128 MB >>>>> >>>>> *Flink is only using 128M MB which can easily cause OOM* >>>>> *error.* >>>>> >>>>> *These are DEFAULT settings.* >>>>> >>>>> *I dusted off an old laptop so it only 3.8 GB RAM.* >>>>> >>>>> What does your job metrics say ? >>>>> >>>>> On Mon, 20 Apr 2020, 07:26 Xintong Song, <tonysong...@gmail.com> >>>>> wrote: >>>>> >>>>>> Hi Lasse, >>>>>> >>>>>> From what I understand, your problem is that JVM tries to fork some >>>>>> native process (if you look at the exception stack the root exception is >>>>>> thrown from a native method) but there's no enough memory for doing that. >>>>>> This could happen when either Mesos is using cgroup strict mode for >>>>>> memory >>>>>> control, or there's no more memory on the machine. Flink cannot prevent >>>>>> native processes from using more memory. It can only reserve certain >>>>>> amount >>>>>> of memory for such native usage when requesting worker memory from the >>>>>> deployment environment (in your case Mesos) and allocating Java heap / >>>>>> direct memory. >>>>>> >>>>>> My suggestion is to try increasing the JVM overhead configuration. >>>>>> You can leverage the configuration options >>>>>> 'taskmanager.memory.jvm-overhead.[min|max|fraction]'. See more details in >>>>>> the documentation[1]. >>>>>> >>>>>> Thank you~ >>>>>> >>>>>> Xintong Song >>>>>> >>>>>> >>>>>> [1] >>>>>> https://ci.apache.org/projects/flink/flink-docs-release-1.10/ops/config.html#taskmanager-memory-jvm-overhead-max >>>>>> >>>>>> On Sat, Apr 18, 2020 at 4:02 AM Zahid Rahman <zahidr1...@gmail.com> >>>>>> wrote: >>>>>> >>>>>>> >>>>>>> https://betsol.com/java-memory-management-for-java-virtual-machine-jvm/ >>>>>>> >>>>>>> Backbutton.co.uk >>>>>>> ¯\_(ツ)_/¯ >>>>>>> ♡۶Java♡۶RMI ♡۶ >>>>>>> Make Use Method {MUM} >>>>>>> makeuse.org >>>>>>> <http://www.backbutton.co.uk> >>>>>>> >>>>>>> >>>>>>> On Fri, 17 Apr 2020 at 14:07, Lasse Nedergaard < >>>>>>> lassenedergaardfl...@gmail.com> wrote: >>>>>>> >>>>>>>> Hi. >>>>>>>> >>>>>>>> We have migrated to Flink 1.10 and face out of memory exception and >>>>>>>> hopeful can someone point us in the right direction. >>>>>>>> >>>>>>>> We have a job that use broadcast state, and we sometimes get out >>>>>>>> memory when it creates a savepoint. See stacktrack below. >>>>>>>> We have assigned 2.2 GB/task manager and >>>>>>>> configured taskmanager.memory.process.size : 2200m >>>>>>>> In Flink 1.9 our container was terminated because OOM, so 1.10 do a >>>>>>>> better job, but it still not working and the task manager is leaking >>>>>>>> mem >>>>>>>> for each OOM and finial kill by Mesos >>>>>>>> >>>>>>>> >>>>>>>> Any idea what we can do to figure out what settings we need to >>>>>>>> change? >>>>>>>> >>>>>>>> Thanks in advance >>>>>>>> >>>>>>>> Lasse Nedergaard >>>>>>>> >>>>>>>> >>>>>>>> WARN o.a.flink.runtime.state.filesystem.FsCheckpointStreamFactory - >>>>>>>> Could not close the state stream for >>>>>>>> s3://flinkstate/dcos-prod/checkpoints/fc9318cc236d09f0bfd994f138896d6c/chk-3509/cf0714dc-ad7c-4946-b44c-96d4a131a4fa. >>>>>>>> java.io.IOException: Cannot allocate memory at >>>>>>>> java.io.FileOutputStream.writeBytes(Native Method) at >>>>>>>> java.io.FileOutputStream.write(FileOutputStream.java:326) at >>>>>>>> java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82) >>>>>>>> at >>>>>>>> java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140) at >>>>>>>> java.io.FilterOutputStream.flush(FilterOutputStream.java:140) at >>>>>>>> java.io.FilterOutputStream.close(FilterOutputStream.java:158) at >>>>>>>> com.facebook.presto.hive.s3.PrestoS3FileSystem$PrestoS3OutputStream.close(PrestoS3FileSystem.java:995) >>>>>>>> at >>>>>>>> org.apache.hadoop.fs.FSDataOutputStream$PositionCache.close(FSDataOutputStream.java:72) >>>>>>>> at >>>>>>>> org.apache.hadoop.fs.FSDataOutputStream.close(FSDataOutputStream.java:101) >>>>>>>> at >>>>>>>> org.apache.flink.fs.s3presto.common.HadoopDataOutputStream.close(HadoopDataOutputStream.java:52) >>>>>>>> at >>>>>>>> org.apache.flink.core.fs.ClosingFSDataOutputStream.close(ClosingFSDataOutputStream.java:64) >>>>>>>> at >>>>>>>> org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.close(FsCheckpointStreamFactory.java:277) >>>>>>>> at org.apache.flink.util.IOUtils.closeQuietly(IOUtils.java:263) at >>>>>>>> org.apache.flink.util.IOUtils.closeAllQuietly(IOUtils.java:250) at >>>>>>>> org.apache.flink.util.AbstractCloseableRegistry.close(AbstractCloseableRegistry.java:122) >>>>>>>> at >>>>>>>> org.apache.flink.runtime.state.AsyncSnapshotCallable.closeSnapshotIO(AsyncSnapshotCallable.java:167) >>>>>>>> at >>>>>>>> org.apache.flink.runtime.state.AsyncSnapshotCallable.call(AsyncSnapshotCallable.java:83) >>>>>>>> at java.util.concurrent.FutureTask.run(FutureTask.java:266) at >>>>>>>> org.apache.flink.runtime.concurrent.FutureUtils.runIfNotDoneAndGet(FutureUtils.java:458) >>>>>>>> at >>>>>>>> org.apache.flink.streaming.api.operators.OperatorSnapshotFinalizer.<init>(OperatorSnapshotFinalizer.java:53) >>>>>>>> at >>>>>>>> org.apache.flink.streaming.runtime.tasks.StreamTask$AsyncCheckpointRunnable.run(StreamTask.java:1143) >>>>>>>> at >>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) >>>>>>>> at >>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) >>>>>>>> at java.lang.Thread.run(Thread.java:748) >>>>>>>> >>>>>>>> INFO org.apache.flink.runtime.checkpoint.CheckpointCoordinator - >>>>>>>> Discarding checkpoint 3509 of job fc9318cc236d09f0bfd994f138896d6c. >>>>>>>> org.apache.flink.util.SerializedThrowable: Could not materialize >>>>>>>> checkpoint >>>>>>>> 3509 for operator Feature extraction (8/12). at >>>>>>>> org.apache.flink.streaming.runtime.tasks.StreamTask$AsyncCheckpointRunnable.handleExecutionException(StreamTask.java:1238) >>>>>>>> at >>>>>>>> org.apache.flink.streaming.runtime.tasks.StreamTask$AsyncCheckpointRunnable.run(StreamTask.java:1180) >>>>>>>> at >>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) >>>>>>>> at >>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) >>>>>>>> at java.lang.Thread.run(Thread.java:748) Caused by: >>>>>>>> org.apache.flink.util.SerializedThrowable: java.io.IOException: Cannot >>>>>>>> allocate memory at >>>>>>>> java.util.concurrent.FutureTask.report(FutureTask.java:122) at >>>>>>>> java.util.concurrent.FutureTask.get(FutureTask.java:192) at >>>>>>>> org.apache.flink.runtime.concurrent.FutureUtils.runIfNotDoneAndGet(FutureUtils.java:461) >>>>>>>> at >>>>>>>> org.apache.flink.streaming.api.operators.OperatorSnapshotFinalizer.<init>(OperatorSnapshotFinalizer.java:53) >>>>>>>> at >>>>>>>> org.apache.flink.streaming.runtime.tasks.StreamTask$AsyncCheckpointRunnable.run(StreamTask.java:1143) >>>>>>>> ... 3 common frames omitted Caused by: >>>>>>>> org.apache.flink.util.SerializedThrowable: Cannot allocate memory at >>>>>>>> java.io.FileOutputStream.writeBytes(Native Method) at >>>>>>>> java.io.FileOutputStream.write(FileOutputStream.java:326) at >>>>>>>> java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82) >>>>>>>> at >>>>>>>> java.io.BufferedOutputStream.write(BufferedOutputStream.java:95) at >>>>>>>> java.io.FilterOutputStream.write(FilterOutputStream.java:77) at >>>>>>>> java.io.FilterOutputStream.write(FilterOutputStream.java:125) at >>>>>>>> org.apache.hadoop.fs.FSDataOutputStream$PositionCache.write(FSDataOutputStream.java:57) >>>>>>>> at java.io.DataOutputStream.write(DataOutputStream.java:107) at >>>>>>>> org.apache.flink.fs.s3presto.common.HadoopDataOutputStream.write(HadoopDataOutputStream.java:47) >>>>>>>> at >>>>>>>> org.apache.flink.core.fs.FSDataOutputStreamWrapper.write(FSDataOutputStreamWrapper.java:66) >>>>>>>> at >>>>>>>> org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.write(FsCheckpointStreamFactory.java:220) >>>>>>>> at java.io.DataOutputStream.write(DataOutputStream.java:107) at >>>>>>>> org.apache.flink.formats.avro.utils.DataOutputEncoder.writeBytes(DataOutputEncoder.java:92) >>>>>>>> at >>>>>>>> org.apache.flink.formats.avro.utils.DataOutputEncoder.writeString(DataOutputEncoder.java:113) >>>>>>>> at org.apache.avro.io.Encoder.writeString(Encoder.java:130) at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.writeString(GenericDatumWriter.java:323) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.writeMap(GenericDatumWriter.java:281) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:139) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:82) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:144) >>>>>>>> at >>>>>>>> org.apache.avro.specific.SpecificDatumWriter.writeField(SpecificDatumWriter.java:98) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.writeRecord(GenericDatumWriter.java:195) >>>>>>>> at >>>>>>>> org.apache.avro.specific.SpecificDatumWriter.writeRecord(SpecificDatumWriter.java:83) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:130) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:82) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.writeArray(GenericDatumWriter.java:234) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:136) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:82) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:144) >>>>>>>> at >>>>>>>> org.apache.avro.specific.SpecificDatumWriter.writeField(SpecificDatumWriter.java:98) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.writeRecord(GenericDatumWriter.java:195) >>>>>>>> at >>>>>>>> org.apache.avro.specific.SpecificDatumWriter.writeRecord(SpecificDatumWriter.java:83) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:130) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:82) >>>>>>>> at >>>>>>>> org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:72) >>>>>>>> at >>>>>>>> org.apache.flink.formats.avro.typeutils.AvroSerializer.serialize(AvroSerializer.java:185) >>>>>>>> at >>>>>>>> org.apache.flink.runtime.state.HeapBroadcastState.write(HeapBroadcastState.java:109) >>>>>>>> at >>>>>>>> org.apache.flink.runtime.state.DefaultOperatorStateBackendSnapshotStrategy$1.callInternal(DefaultOperatorStateBackendSnapshotStrategy.java:167) >>>>>>>> at >>>>>>>> org.apache.flink.runtime.state.DefaultOperatorStateBackendSnapshotStrategy$1.callInternal(DefaultOperatorStateBackendSnapshotStrategy.java:108) >>>>>>>> at >>>>>>>> org.apache.flink.runtime.state.AsyncSnapshotCallable.call(AsyncSnapshotCallable.java:75) >>>>>>>> at java.util.concurrent.FutureTask.run(FutureTask.java:266) at >>>>>>>> org.apache.flink.runtime.concurrent.FutureUtils.runIfNotDoneAndGet(FutureUtils.java:458) >>>>>>>> >>>>>>>
