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From: Abhishek Das <abhishek.besu@gmail.com>
Date: Thu, 2 Mar 2017 15:59:04 -0800
Message-ID: <CAMjkPtHcmtetJ5pdLV5C1Yn9DtcLdGz=8qWRHM91GBw9dWR3Bg@mail.gmail.com>
Subject: LevelDB corruption in YARN Application TimelineServer
To: yarn-dev@hadoop.apache.org
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archived-at: Thu, 02 Mar 2017 23:59:33 -0000

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Hi,

I am running a hadoop 2.6.0 cluster in ec2 instances with r3.2xlarge as
instance of the master node. YARN Application TimelineServer running in the
master node is throwing an exception because of leveldb corruption. This
issue seems to be happening when the cluster has been up for a long time
(more than 7 days). The stack trace is given below.

ERROR org.apache.hadoop.yarn.server.timeline.TimelineDataManager: Skip the
timeline entity: { id: <task_id>, type: TEZ_TASK_ID }
java.lang.RuntimeException:
org.fusesource.leveldbjni.internal.NativeDB$DBException: *IO error:
/media/ephemeral0/hadoop-root/yarn/timeline/leveldb-timeline-store.ldb/330951.sst:
No such file or directory*
        at
org.fusesource.leveldbjni.internal.JniDBIterator.seek(JniDBIterator.java:68)
        at
org.apache.hadoop.yarn.server.timeline.LeveldbTimelineStore.getEntity(LeveldbTimelineStore.java:444)
        at
org.apache.hadoop.yarn.server.timeline.TimelineDataManager.postEntities(TimelineDataManager.java:257)
        at
org.apache.hadoop.yarn.server.timeline.webapp.TimelineWebServices.postEntities(TimelineWebServices.java:259)
        at sun.reflect.GeneratedMethodAccessor35.invoke(Unknown Source)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at
com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60)
        at
com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185)
        at
com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
        at
com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288)
        at
com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
        at
com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
        at
com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
        at
com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1469)
        at
com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1400)
        at
com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1349)
        at
com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1339)
        at
com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416)
        at
com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537)
        at
com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletContainer.java:886)
        at
com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletContainer.java:834)
        at
com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletContainer.java:795)
        at
com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:163)
        at
com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:58)
        at
com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:118)
        at
com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:113)
        at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1212)
        at
org.apache.hadoop.http.lib.StaticUserWebFilter$StaticUserFilter.doFilter(StaticUserWebFilter.java:96)
        at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1212)
        at
org.apache.hadoop.yarn.server.timeline.webapp.CrossOriginFilter.doFilter(CrossOriginFilter.java:95)
        at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1212)
        at
org.apache.hadoop.security.authentication.server.AuthenticationFilter.doFilter(AuthenticationFilter.java:572)
        at
org.apache.hadoop.security.token.delegation.web.DelegationTokenAuthenticationFilter.doFilter(DelegationTokenAuthenticationFilter.java:269)
        at
org.apache.hadoop.security.authentication.server.AuthenticationFilter.doFilter(AuthenticationFilter.java:542)
        at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1212)
        at
org.apache.hadoop.http.HttpServer2$QuotingInputFilter.doFilter(HttpServer2.java:1242)
        at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1212)
        at
org.apache.hadoop.http.NoCacheFilter.doFilter(NoCacheFilter.java:45)
        at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1212)
        at
org.apache.hadoop.http.NoCacheFilter.doFilter(NoCacheFilter.java:45)

There are lot of  .sst files in the level db directory.
*sudo ls -lrt
/media/ephemeral0/hadoop-root/yarn/timeline/leveldb-timeline-store.ldb/ |
wc -l*
*3848*

After this error the ResourceManager and Tez ApplicationMaster are not able
to post entities in the YARN ATS. So not able to see the history of the
running jobs.

Does anyone have any idea what is the root cause of this leveldb corruption
and how to get rid off this issue.

Thanks in advance.

Regards,
Abhishek

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