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https://issues.apache.org/jira/browse/FLINK-4485?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15495900#comment-15495900
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ASF GitHub Bot commented on FLINK-4485:
---------------------------------------
Github user mxm commented on the issue:
https://github.com/apache/flink/pull/2499
Thanks! Just a few words to @nielsbasjes who reported the issue. I've
tested the fix using the test instructions you provided. Even before this fix,
I could get rid of the temp files by forcing a manual garbage collection on the
JVM, using `jcmd <pid> GC.run`. However, that only worked once the job meta
data had been removed from the archive, i.e. it doesn't show up in the web
interface anymore. With this fix, the class loader is cleared upon job
completion and the files are immediately removed. `lsof | fgrep blob_` didn't
show any of these files anymore.
Note, that we don't perform any cleanup on the TaskManager side. There we
also wind up with some left over files but they don't seem to pile up. It must
be that the garbage collector can figure out when to clean much earlier. Plus,
we don't keep a reference to old Task instances like we do for the web
interface on the JobManager side.
@StephanEwen I'm thinking about adding a similar fix for the TaskManager
side. What do you think?
> Finished jobs in yarn session fill /tmp filesystem
> --------------------------------------------------
>
> Key: FLINK-4485
> URL: https://issues.apache.org/jira/browse/FLINK-4485
> Project: Flink
> Issue Type: Bug
> Components: JobManager
> Affects Versions: 1.1.0
> Reporter: Niels Basjes
> Assignee: Maximilian Michels
> Priority: Blocker
>
> On a Yarn cluster I start a yarn-session with a few containers and task slots.
> Then I fire a 'large' number of Flink batch jobs in sequence against this
> yarn session. It is the exact same job (java code) yet it gets different
> parameters.
> In this scenario it is exporting HBase tables to files in HDFS and the
> parameters are about which data from which tables and the name of the target
> directory.
> After running several dozen jobs the jobs submission started to fail and we
> investigated.
> We found that the cause was that on the Yarn node which was hosting the
> jobmanager the /tmp file system was full (4GB was 100% full).
> How ever the output of {{du -hcs /tmp}} showed only 200MB in use.
> We found that a very large file (we guess it is the jar of the job) was put
> in /tmp , used, deleted yet the file handle was not closed by the jobmanager.
> As soon as we killed the jobmanager the disk space was freed.
> The summary of the impact of this is that a yarn-session that receives enough
> jobs brings down the Yarn node for all users.
> See parts of the output we got from {{lsof}} below.
> {code}
> COMMAND PID USER FD TYPE DEVICE SIZE
> NODE NAME
> java 15034 nbasjes 550r REG 253,17 66219695
> 245
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000003
> (deleted)
> java 15034 nbasjes 551r REG 253,17 66219695
> 252
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000007
> (deleted)
> java 15034 nbasjes 552r REG 253,17 66219695
> 267
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000012
> (deleted)
> java 15034 nbasjes 553r REG 253,17 66219695
> 250
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000005
> (deleted)
> java 15034 nbasjes 554r REG 253,17 66219695
> 288
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000018
> (deleted)
> java 15034 nbasjes 555r REG 253,17 66219695
> 298
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000025
> (deleted)
> java 15034 nbasjes 557r REG 253,17 66219695
> 254
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000008
> (deleted)
> java 15034 nbasjes 558r REG 253,17 66219695
> 292
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000019
> (deleted)
> java 15034 nbasjes 559r REG 253,17 66219695
> 275
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000013
> (deleted)
> java 15034 nbasjes 560r REG 253,17 66219695
> 159
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000002
> (deleted)
> java 15034 nbasjes 562r REG 253,17 66219695
> 238
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000001
> (deleted)
> java 15034 nbasjes 568r REG 253,17 66219695
> 246
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000004
> (deleted)
> java 15034 nbasjes 569r REG 253,17 66219695
> 255
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000009
> (deleted)
> java 15034 nbasjes 571r REG 253,17 66219695
> 299
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000026
> (deleted)
> java 15034 nbasjes 572r REG 253,17 66219695
> 293
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000020
> (deleted)
> java 15034 nbasjes 574r REG 253,17 66219695
> 256
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000010
> (deleted)
> java 15034 nbasjes 575r REG 253,17 66219695
> 302
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000029
> (deleted)
> java 15034 nbasjes 576r REG 253,17 66219695
> 294
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000021
> (deleted)
> java 15034 nbasjes 577r REG 253,17 66219695
> 262
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000011
> (deleted)
> java 15034 nbasjes 578r REG 253,17 66219695
> 251
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000006
> (deleted)
> java 15034 nbasjes 580r REG 253,17 66219695
> 295
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000022
> (deleted)
> java 15034 nbasjes 581r REG 253,17 66219695
> 300
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000027
> (deleted)
> java 15034 nbasjes 582r REG 253,17 66219695
> 188
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/cache/blob_e318d1698aa6e7dc91e5f4a9f8ba29781aebd8c4
> (deleted)
> java 15034 nbasjes 585r REG 253,17 66219695
> 279
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000014
> (deleted)
> java 15034 nbasjes 586r REG 253,17 66219695
> 296
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000023
> (deleted)
> java 15034 nbasjes 588r REG 253,17 66219695
> 301
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000028
> (deleted)
> java 15034 nbasjes 589r REG 253,17 66219695
> 297
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000024
> (deleted)
> java 15034 nbasjes 598r REG 253,17 66219695
> 280
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000015
> (deleted)
> java 15034 nbasjes 601r REG 253,17 66219695
> 289
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000016
> (deleted)
> java 15034 nbasjes 604r REG 253,17 66219695
> 284
> /tmp/blobStore-fbe9c4cf-1f85-48cb-aad9-180e8d4ec7ce/incoming/temp-00000017
> (deleted)
> {code}
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