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Posted to issues@flink.apache.org by "Niels Basjes (JIRA)" <ji...@apache.org> on 2016/08/25 14:04:21 UTC
[jira] [Commented] (FLINK-4485) Finished jobs in yarn session fill
/tmp filesystem
[ https://issues.apache.org/jira/browse/FLINK-4485?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15436917#comment-15436917 ]
Niels Basjes commented on FLINK-4485:
-------------------------------------
I just reproduced the effect on a non-secure Yarn cluster.
After having run a few jobs I see this on the node where the jobmanager runs:
{code}
[root@node1 ~]# lsof | fgrep '/tmp/blobStore'
java 15358 yarn mem REG 8,3 70243224 25936270 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/cache/blob_501262b25ff9158ff07ee1f4264b5e3afeaaf69f
java 15358 yarn DEL REG 8,3 25936269 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000027
java 15358 yarn DEL REG 8,3 25936268 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000026
java 15358 yarn DEL REG 8,3 25936267 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000025
java 15358 yarn DEL REG 8,3 25936266 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000024
java 15358 yarn DEL REG 8,3 25936265 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000023
java 15358 yarn DEL REG 8,3 25936264 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000022
java 15358 yarn DEL REG 8,3 25936263 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000021
java 15358 yarn DEL REG 8,3 25936258 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000020
java 15358 yarn DEL REG 8,3 25936257 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000019
java 15358 yarn DEL REG 8,3 25936260 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000018
java 15358 yarn DEL REG 8,3 25936259 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000017
java 15358 yarn DEL REG 8,3 25936256 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000016
java 15358 yarn DEL REG 8,3 25936255 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000015
java 15358 yarn DEL REG 8,3 25936254 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000014
java 15358 yarn DEL REG 8,3 25936253 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000013
java 15358 yarn DEL REG 8,3 25936252 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000012
java 15358 yarn DEL REG 8,3 25936251 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000011
java 15358 yarn DEL REG 8,3 25936250 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000010
java 15358 yarn DEL REG 8,3 25936249 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000009
java 15358 yarn DEL REG 8,3 25936248 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000008
java 15358 yarn DEL REG 8,3 25936247 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000007
java 15358 yarn DEL REG 8,3 25936246 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000006
java 15358 yarn DEL REG 8,3 25936244 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000005
java 15358 yarn DEL REG 8,3 25936222 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000004
java 15358 yarn DEL REG 8,3 25936221 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000003
java 15358 yarn DEL REG 8,3 25936220 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000002
java 15358 yarn DEL REG 8,3 25936215 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000001
java 15358 yarn 422r REG 8,3 70243224 25936222 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000004 (deleted)
java 15358 yarn 581u REG 8,3 70243224 25936265 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000023 (deleted)
java 15358 yarn 582u REG 8,3 70243224 25936267 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000025 (deleted)
java 15358 yarn 583r REG 8,3 70243224 25936246 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000006 (deleted)
java 15358 yarn 584r REG 8,3 70243224 25936215 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000001 (deleted)
java 15358 yarn 590u REG 8,3 70243224 25936266 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000024 (deleted)
java 15358 yarn 591r REG 8,3 70243224 25936220 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000002 (deleted)
java 15358 yarn 593r REG 8,3 70243224 25936221 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000003 (deleted)
java 15358 yarn 594u REG 8,3 70243224 25936268 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000026 (deleted)
java 15358 yarn 595u REG 8,3 70243224 25936270 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/cache/blob_501262b25ff9158ff07ee1f4264b5e3afeaaf69f
java 15358 yarn 597r REG 8,3 70243224 25936255 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000015 (deleted)
java 15358 yarn 598u REG 8,3 70243224 25936269 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000027 (deleted)
java 15358 yarn 599r REG 8,3 70243224 25936252 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000012 (deleted)
java 15358 yarn 600r REG 8,3 70243224 25936250 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000010 (deleted)
java 15358 yarn 601r REG 8,3 70243224 25936254 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000014 (deleted)
java 15358 yarn 602r REG 8,3 70243224 25936244 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000005 (deleted)
java 15358 yarn 603r REG 8,3 70243224 25936259 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000017 (deleted)
java 15358 yarn 604r REG 8,3 70243224 25936248 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000008 (deleted)
java 15358 yarn 605r REG 8,3 70243224 25936260 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000018 (deleted)
java 15358 yarn 607r REG 8,3 70243224 25936257 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000019 (deleted)
java 15358 yarn 608r REG 8,3 70243224 25936258 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000020 (deleted)
java 15358 yarn 609r REG 8,3 70243224 25936263 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000021 (deleted)
java 15358 yarn 610r REG 8,3 70243224 25936264 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000022 (deleted)
java 15358 yarn 613r REG 8,3 70243224 25936247 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000007 (deleted)
java 15358 yarn 617r REG 8,3 70243224 25936253 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000013 (deleted)
java 15358 yarn 618r REG 8,3 70243224 25936251 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000011 (deleted)
java 15358 yarn 619r REG 8,3 70243224 25936249 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000009 (deleted)
java 15358 yarn 631r REG 8,3 70243224 25936256 /tmp/blobStore-0864a537-f6fa-4b27-9b7f-8cb5a3722c3e/incoming/temp-00000016 (deleted)
java 15454 yarn mem REG 8,3 70243224 25936219 /tmp/blobStore-087a0b08-ee59-4d21-8523-c78a79984a4a/cache/blob_501262b25ff9158ff07ee1f4264b5e3afeaaf69f
java 15454 yarn 490r REG 8,3 70243224 25936219 /tmp/blobStore-087a0b08-ee59-4d21-8523-c78a79984a4a/cache/blob_501262b25ff9158ff07ee1f4264b5e3afeaaf69f
{code}
The two process ids you see here are:
{code}yarn 15358 4.9 0.3 1362160 431128 ? Sl 15:24 1:52 | \_ /usr/lib/jvm/jre/bin/java -Xmx424M -Dlog.file=/var/log/hadoop-yarn/containers/application_1464009968005_2639/container_1464009968005_2639_01_000001/jobmanager.log -Dlogback.configurationFile=file:logback.xml -Dlog4j.configuration=file:log4j.properties org.apache.flink.yarn.YarnApplicationMasterRunner{code}
{code}yarn 15454 10.1 0.6 1306404 801228 ? Sl 15:24 3:51 \_ /usr/lib/jvm/jre/bin/java -Xms424m -Xmx424m -XX:MaxDirectMemorySize=424m -Dlog.file=/var/log/hadoop-yarn/containers/application_1464009968005_2639/container_1464009968005_2639_01_000002/taskmanager.log -Dlogback.configurationFile=file:./logback.xml -Dlog4j.configuration=file:./log4j.properties org.apache.flink.yarn.YarnTaskManager --configDir .{code}
> 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
> 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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