[
https://issues.apache.org/jira/browse/FLINK-19111?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Tobias Kaymak updated FLINK-19111:
----------------------------------
Description:
After upgrading my cluster using the official Docker image for Flink from 1.9
to 1.10.1 I noticed that all checkpoints failed for my existing pipelines.
Checkpoints are saved in a local (NFS backed) directory, so full UNIX
permissions apply.
I went onto the jobmanager pod and saw that it created the checkpoint folder
with root:root as the owner. Even after fixing this or giving the top-folder it
super relaxed permissions (chmod 777) I couldn't make it work.
I checked the changes in the Flink Docker repository on GitHub, but couldn't
spot any \{{gosu }}or similar related changes. I tried 1.10.2 too, but the
issue remained. Downgrading to the 1.9.1 docker image made the issue disappear.
The web interface just gives me
*Failure Message:* The job has failed.
The logs show that there is in fact a permission problem:
{{2020-09-01 10:44:02,226 INFO
org.apache.flink.runtime.checkpoint.CheckpointCoordinator - Discarding
checkpoint 29 of job 5be99250cdea84d1ce400a4d0939bafa. }}
{{java.lang.Exception: Could not materialize checkpoint 29 for operator Source:
BigQueryIO.Write/BatchLoads/CreateEmptyFailedInserts/Read(CreateSource) ->
BigQueryIO.Write/BatchLoads/View.AsSingleton/Combine.GloballyAsSingletonView/DropInputs/ParMultiDo(NoOp)
(1/1). }}
{{ at
org.apache.flink.streaming.runtime.tasks.StreamTask$AsyncCheckpointRunnable.handleExecutionException(StreamTask.java:1221)
}}
{{ at
org.apache.flink.streaming.runtime.tasks.StreamTask$AsyncCheckpointRunnable.run(StreamTask.java:1163)
}}
{{ at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
}}
{{ at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
}}
{{ at java.lang.Thread.run(Thread.java:748) }}
{{Caused by: java.util.concurrent.ExecutionException: java.io.IOException:
Could not flush and close the file system output stream to null in order to
obtain the stream state handle }}
{{ at java.util.concurrent.FutureTask.report(FutureTask.java:122) }}
{{ at java.util.concurrent.FutureTask.get(FutureTask.java:192) }}
{{ at
org.apache.flink.runtime.concurrent.FutureUtils.runIfNotDoneAndGet(FutureUtils.java:461)
}}
{{ at
org.apache.flink.streaming.api.operators.OperatorSnapshotFinalizer.<init>(OperatorSnapshotFinalizer.java:53)
}}
{{ at
org.apache.flink.streaming.runtime.tasks.StreamTask$AsyncCheckpointRunnable.run(StreamTask.java:1126)
}}
{{ ... 3 more }}
{{Caused by: java.io.IOException: Could not flush and close the file system
output stream to null in order to obtain the stream state handle }}
{{ at
org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.closeAndGetHandle(FsCheckpointStreamFactory.java:334)
}}
{{ at
org.apache.flink.runtime.state.DefaultOperatorStateBackendSnapshotStrategy$1.callInternal(DefaultOperatorStateBackendSnapshotStrategy.java:179)
}}
{{ at
org.apache.flink.runtime.state.DefaultOperatorStateBackendSnapshotStrategy$1.callInternal(DefaultOperatorStateBackendSnapshotStrategy.java:108)
}}
{{ at
org.apache.flink.runtime.state.AsyncSnapshotCallable.call(AsyncSnapshotCallable.java:75)
}}
{{ at java.util.concurrent.FutureTask.run(FutureTask.java:266) }}
{{ at
org.apache.flink.runtime.concurrent.FutureUtils.runIfNotDoneAndGet(FutureUtils.java:458)
}}
{{ ... 5 more }}
{{Caused by: java.io.IOException: Could not open output stream for state
backend }}
{{ at
org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.createStream(FsCheckpointStreamFactory.java:367)
}}
{{ at
org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.flush(FsCheckpointStreamFactory.java:234)}}
{{ at
org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.closeAndGetHandle(FsCheckpointStreamFactory.java:309)
}}
{{ ... 10 more }}
{{Caused by: java.io.FileNotFoundException:
/mnt/checkpoints/5be99250cdea84d1ce400a4d0939bafa/chk-29/218d235b-bcd0-497b-8925-12d6d4bbc4f5
(Permission denied)}}
{{ at java.io.FileOutputStream.open0(Native Method) }}
{{ at java.io.FileOutputStream.open(FileOutputStream.java:270) }}
{{ at java.io.FileOutputStream.<init>(FileOutputStream.java:213) }}
{{ at java.io.FileOutputStream.<init>(FileOutputStream.java:162) }}
{{ at
org.apache.flink.core.fs.local.LocalDataOutputStream.<init>(LocalDataOutputStream.java:47)}}
{{ at
org.apache.flink.core.fs.local.LocalFileSystem.create(LocalFileSystem.java:273)
}}
{{ at
org.apache.flink.core.fs.SafetyNetWrapperFileSystem.create(SafetyNetWrapperFileSystem.java:126)}}
{{ at
org.apache.flink.core.fs.EntropyInjector.createEntropyAware(EntropyInjector.java:61)
}}
{{ at
org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.createStream(FsCheckpointStreamFactory.java:356)}}
{{ ... 12 more}}
was:
After upgrading my cluster using the official Docker image for Flink from 1.9
to 1.10.1 I noticed that all checkpoints failed for my existing pipelines.
Checkpoints are saved in a local (NFS backed) directory, so full UNIX
permissions apply.
I went onto the jobmanager pod and saw that it created the checkpoint folder
with root:root as the owner. Even after fixing this or giving the top-folder it
super relaxed permissions (chmod 777) I couldn't make it work.
I checked the changes in the Flink Docker repository on GitHub, but couldn't
spot any \{{gosu }}or similar related changes. I tried 1.10.2 too, but the
issue remained. Downgrading to the 1.9.1 docker image made the issue disappear.
The web interface just gives me
*Failure Message:* The job has failed.
The logs show that there is in fact a permission problem:
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager 2020-09-01 10:44:02,226 INFO
org.apache.flink.runtime.checkpoint.CheckpointCoordinator - Discarding
checkpoint 29 of job 5be99250cdea84d1ce400a4d0939bafa.
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager java.lang.Exception: Could not
materialize checkpoint 29 for operator Source:
BigQueryIO.Write/BatchLoads/CreateEmptyFailedInserts/Read(CreateSource) ->
BigQueryIO.Write/BatchLoads/View.AsSingleton/Combine.GloballyAsSingletonView/DropInputs/ParMultiDo(NoOp)
(1/1). }}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.streaming.runtime.tasks.StreamTask$AsyncCheckpointRunnable.handleExecutionException(StreamTask.java:1221)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.streaming.runtime.tasks.StreamTask$AsyncCheckpointRunnable.run(StreamTask.java:1163)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
java.lang.Thread.run(Thread.java:748)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager Caused by:
java.util.concurrent.ExecutionException: java.io.IOException: Could not flush
and close the file system output stream to null in order to obtain the stream
state handle
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
java.util.concurrent.FutureTask.report(FutureTask.java:122)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
java.util.concurrent.FutureTask.get(FutureTask.java:192)
flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.runtime.concurrent.FutureUtils.runIfNotDoneAndGet(FutureUtils.java:461)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.streaming.api.operators.OperatorSnapshotFinalizer.<init>(OperatorSnapshotFinalizer.java:53)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.streaming.runtime.tasks.StreamTask$AsyncCheckpointRunnable.run(StreamTask.java:1126)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager ... 3 more
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager Caused by: java.io.IOException:
Could not flush and close the file system output stream to null in order to
obtain the stream state handle
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.closeAndGetHandle(FsCheckpointStreamFactory.java:334)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.runtime.state.DefaultOperatorStateBackendSnapshotStrategy$1.callInternal(DefaultOperatorStateBackendSnapshotStrategy.java:179)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.runtime.state.DefaultOperatorStateBackendSnapshotStrategy$1.callInternal(DefaultOperatorStateBackendSnapshotStrategy.java:108)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.runtime.state.AsyncSnapshotCallable.call(AsyncSnapshotCallable.java:75)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
java.util.concurrent.FutureTask.run(FutureTask.java:266)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.runtime.concurrent.FutureUtils.runIfNotDoneAndGet(FutureUtils.java:458)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager ... 5 more
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager Caused by: java.io.IOException:
Could not open output stream for state backend
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.createStream(FsCheckpointStreamFactory.java:367)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.flush(FsCheckpointStreamFactory.java:234)}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.closeAndGetHandle(FsCheckpointStreamFactory.java:309)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager ... 10 more
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager Caused by:
java.io.FileNotFoundException:
/mnt/checkpoints/5be99250cdea84d1ce400a4d0939bafa/chk-29/218d235b-bcd0-497b-8925-12d6d4bbc4f5
(Permission denied)}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
java.io.FileOutputStream.open0(Native Method)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
java.io.FileOutputStream.open(FileOutputStream.java:270)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
java.io.FileOutputStream.<init>(FileOutputStream.java:213)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
java.io.FileOutputStream.<init>(FileOutputStream.java:162)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.core.fs.local.LocalDataOutputStream.<init>(LocalDataOutputStream.java:47)}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.core.fs.local.LocalFileSystem.create(LocalFileSystem.java:273)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.core.fs.SafetyNetWrapperFileSystem.create(SafetyNetWrapperFileSystem.java:126)}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.core.fs.EntropyInjector.createEntropyAware(EntropyInjector.java:61)
}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager at
org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.createStream(FsCheckpointStreamFactory.java:356)}}
{{flink-jobmanager-5ff5bf9b5d-4fkcw jobmanager ... 12 more}}
> Flink Docker image creates checkpoints as root user and hits permission
> denied afterwards
> ------------------------------------------------------------------------------------------
>
> Key: FLINK-19111
> URL: https://issues.apache.org/jira/browse/FLINK-19111
> Project: Flink
> Issue Type: Bug
> Components: flink-docker
> Affects Versions: 1.10.0, 1.10.1
> Reporter: Tobias Kaymak
> Priority: Major
>
> After upgrading my cluster using the official Docker image for Flink from 1.9
> to 1.10.1 I noticed that all checkpoints failed for my existing pipelines.
> Checkpoints are saved in a local (NFS backed) directory, so full UNIX
> permissions apply.
> I went onto the jobmanager pod and saw that it created the checkpoint folder
> with root:root as the owner. Even after fixing this or giving the top-folder
> it super relaxed permissions (chmod 777) I couldn't make it work.
> I checked the changes in the Flink Docker repository on GitHub, but couldn't
> spot any \{{gosu }}or similar related changes. I tried 1.10.2 too, but the
> issue remained. Downgrading to the 1.9.1 docker image made the issue
> disappear.
> The web interface just gives me
> *Failure Message:* The job has failed.
> The logs show that there is in fact a permission problem:
> {{2020-09-01 10:44:02,226 INFO
> org.apache.flink.runtime.checkpoint.CheckpointCoordinator - Discarding
> checkpoint 29 of job 5be99250cdea84d1ce400a4d0939bafa. }}
> {{java.lang.Exception: Could not materialize checkpoint 29 for operator
> Source:
> BigQueryIO.Write/BatchLoads/CreateEmptyFailedInserts/Read(CreateSource) ->
> BigQueryIO.Write/BatchLoads/View.AsSingleton/Combine.GloballyAsSingletonView/DropInputs/ParMultiDo(NoOp)
> (1/1). }}
> {{ at
> org.apache.flink.streaming.runtime.tasks.StreamTask$AsyncCheckpointRunnable.handleExecutionException(StreamTask.java:1221)
> }}
> {{ at
> org.apache.flink.streaming.runtime.tasks.StreamTask$AsyncCheckpointRunnable.run(StreamTask.java:1163)
> }}
> {{ at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
> }}
> {{ at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
> }}
> {{ at java.lang.Thread.run(Thread.java:748) }}
> {{Caused by: java.util.concurrent.ExecutionException: java.io.IOException:
> Could not flush and close the file system output stream to null in order to
> obtain the stream state handle }}
> {{ 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$AsyncCheckpointRunnable.run(StreamTask.java:1126)
> }}
> {{ ... 3 more }}
> {{Caused by: java.io.IOException: Could not flush and close the file system
> output stream to null in order to obtain the stream state handle }}
> {{ at
> org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.closeAndGetHandle(FsCheckpointStreamFactory.java:334)
> }}
> {{ at
> org.apache.flink.runtime.state.DefaultOperatorStateBackendSnapshotStrategy$1.callInternal(DefaultOperatorStateBackendSnapshotStrategy.java:179)
> }}
> {{ at
> org.apache.flink.runtime.state.DefaultOperatorStateBackendSnapshotStrategy$1.callInternal(DefaultOperatorStateBackendSnapshotStrategy.java:108)
> }}
> {{ at
> org.apache.flink.runtime.state.AsyncSnapshotCallable.call(AsyncSnapshotCallable.java:75)
> }}
> {{ at java.util.concurrent.FutureTask.run(FutureTask.java:266) }}
> {{ at
> org.apache.flink.runtime.concurrent.FutureUtils.runIfNotDoneAndGet(FutureUtils.java:458)
> }}
> {{ ... 5 more }}
> {{Caused by: java.io.IOException: Could not open output stream for state
> backend }}
> {{ at
> org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.createStream(FsCheckpointStreamFactory.java:367)
> }}
> {{ at
> org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.flush(FsCheckpointStreamFactory.java:234)}}
> {{ at
> org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.closeAndGetHandle(FsCheckpointStreamFactory.java:309)
> }}
> {{ ... 10 more }}
> {{Caused by: java.io.FileNotFoundException:
> /mnt/checkpoints/5be99250cdea84d1ce400a4d0939bafa/chk-29/218d235b-bcd0-497b-8925-12d6d4bbc4f5
> (Permission denied)}}
> {{ at java.io.FileOutputStream.open0(Native Method) }}
> {{ at java.io.FileOutputStream.open(FileOutputStream.java:270) }}
> {{ at java.io.FileOutputStream.<init>(FileOutputStream.java:213) }}
> {{ at java.io.FileOutputStream.<init>(FileOutputStream.java:162) }}
> {{ at
> org.apache.flink.core.fs.local.LocalDataOutputStream.<init>(LocalDataOutputStream.java:47)}}
> {{ at
> org.apache.flink.core.fs.local.LocalFileSystem.create(LocalFileSystem.java:273)
> }}
> {{ at
> org.apache.flink.core.fs.SafetyNetWrapperFileSystem.create(SafetyNetWrapperFileSystem.java:126)}}
> {{ at
> org.apache.flink.core.fs.EntropyInjector.createEntropyAware(EntropyInjector.java:61)
> }}
> {{ at
> org.apache.flink.runtime.state.filesystem.FsCheckpointStreamFactory$FsCheckpointStateOutputStream.createStream(FsCheckpointStreamFactory.java:356)}}
> {{ ... 12 more}}
>
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