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https://issues.apache.org/jira/browse/NUTCH-2756?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16992323#comment-16992323
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Lucas Pauchard edited comment on NUTCH-2756 at 12/10/19 8:52 AM:
-----------------------------------------------------------------
Hi [~snagel],
This time, the problem happened on the partition 1
(<segment>/parse_text/part-r-00001/data).
{panel:title=Log namenode}
/user/hadoop/crawloneokhttp/segment/20191210055117/parse_text/part-r-00001/data
is closed by DFSClient_attempt_1575911127307_0231_r_000001_0_1139952023_
{panel}
The task log writing this part gave me the following stderr:
{panel:title=errlog}
Dec 10, 2019 6:33:34 AM
com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory register
INFO: Registering
org.apache.hadoop.mapreduce.v2.app.webapp.JAXBContextResolver as a provider
class
Dec 10, 2019 6:33:34 AM
com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory register
INFO: Registering org.apache.hadoop.yarn.webapp.GenericExceptionHandler as a
provider class
Dec 10, 2019 6:33:34 AM
com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory register
INFO: Registering org.apache.hadoop.mapreduce.v2.app.webapp.AMWebServices as a
root resource class
Dec 10, 2019 6:33:34 AM
com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO: Initiating Jersey application, version 'Jersey: 1.19 02/11/2015 03:25 AM'
Dec 10, 2019 6:33:34 AM
com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory
getComponentProvider
INFO: Binding org.apache.hadoop.mapreduce.v2.app.webapp.JAXBContextResolver to
GuiceManagedComponentProvider with the scope "Singleton"
Dec 10, 2019 6:33:34 AM
com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory
getComponentProvider
INFO: Binding org.apache.hadoop.yarn.webapp.GenericExceptionHandler to
GuiceManagedComponentProvider with the scope "Singleton"
Dec 10, 2019 6:33:34 AM
com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory
getComponentProvider
INFO: Binding org.apache.hadoop.mapreduce.v2.app.webapp.AMWebServices to
GuiceManagedComponentProvider with the scope "PerRequest"
log4j:WARN No appenders could be found for logger
(org.apache.hadoop.mapreduce.v2.app.MRAppMaster).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See [http://logging.apache.org/log4j/1.2/faq.html#noconfig] for
more info.
{panel}
And the syslog of the task
{panel:title=syslog}
[^syslog]
{panel}
As you can see there is a "Container killed by the ApplicationMaster". So maybe
we still have some memory issues.
So I did what you said:
{quote}is the state reproducible by running the parser job on the same segment
again? Remove the subdirectories crawl_parse, parse_data and parse_text and run
the parser job again
{quote}
And this time I didn't have any issues.
I'll try to change the memory parameters as you said:
{quote}One point (although hardly related to the problem): the task memory
defined by mapreduce.\*.memory.mb should be higher than the Java -Xmx in
mapreduce.\*.java.opts
{quote}
and see if it happens again
was (Author: lucasp):
Hi [~snagel],
This time, the problem happened on the partition 1
(<segment>/parse_text/part-r-00001/data).
{panel:title=Log namenode}
/user/hadoop/crawloneokhttp/segment/20191210055117/parse_text/part-r-00001/data
is closed by DFSClient_attempt_1575911127307_0231_r_000001_0_1139952023_
{panel}
The task log writing this part gave me the following stderr:
{panel:title=errlog}
Dec 10, 2019 6:33:34 AM
com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory register
INFO: Registering
org.apache.hadoop.mapreduce.v2.app.webapp.JAXBContextResolver as a provider
class
Dec 10, 2019 6:33:34 AM
com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory register
INFO: Registering org.apache.hadoop.yarn.webapp.GenericExceptionHandler as a
provider class
Dec 10, 2019 6:33:34 AM
com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory register
INFO: Registering org.apache.hadoop.mapreduce.v2.app.webapp.AMWebServices as a
root resource class
Dec 10, 2019 6:33:34 AM
com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO: Initiating Jersey application, version 'Jersey: 1.19 02/11/2015 03:25 AM'
Dec 10, 2019 6:33:34 AM
com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory
getComponentProvider
INFO: Binding org.apache.hadoop.mapreduce.v2.app.webapp.JAXBContextResolver to
GuiceManagedComponentProvider with the scope "Singleton"
Dec 10, 2019 6:33:34 AM
com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory
getComponentProvider
INFO: Binding org.apache.hadoop.yarn.webapp.GenericExceptionHandler to
GuiceManagedComponentProvider with the scope "Singleton"
Dec 10, 2019 6:33:34 AM
com.sun.jersey.guice.spi.container.GuiceComponentProviderFactory
getComponentProvider
INFO: Binding org.apache.hadoop.mapreduce.v2.app.webapp.AMWebServices to
GuiceManagedComponentProvider with the scope "PerRequest"
log4j:WARN No appenders could be found for logger
(org.apache.hadoop.mapreduce.v2.app.MRAppMaster).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See [http://logging.apache.org/log4j/1.2/faq.html#noconfig] for
more info.
{panel}
And the syslog of the task
{panel:title=syslog}
[^syslog]
{panel}
As you can see there is a "Container killed by the ApplicationMaster". So maybe
we still have some memory issues.
So I did what you said:
{quote}is the state reproducible by running the parser job on the same segment
again? Remove the subdirectories crawl_parse, parse_data and parse_text and run
the parser job again
{quote}
And this time I didn't have any issues.
I'll try to change the memory parameters as you said:
{quote}One point (although hardly related to the problem): the task memory
defined by mapreduce.*.memory.mb should be higher than the Java -Xmx in
mapreduce.*.java.opts
{quote}
and see if it happens again
> Segment Part problem with HDFS on distibuted mode
> -------------------------------------------------
>
> Key: NUTCH-2756
> URL: https://issues.apache.org/jira/browse/NUTCH-2756
> Project: Nutch
> Issue Type: Bug
> Components: parser
> Affects Versions: 1.15
> Reporter: Lucas Pauchard
> Priority: Major
> Attachments: 0_byte_file_screenshot.PNG, hadoop-env.sh,
> hdfs-site.xml, mapred-site.xml, syslog, yarn-env.sh, yarn-site.xml
>
>
> During the parsing, it happens sometimes that parts of the data on the HDFS
> is missing after the parsing.
> When I take a look at our HDFS, I've got this file with 0 bytes (see
> attachments).
> After that the CrawlDB complains about this specific (corrupted?) part:
> {panel:title=log_crawl}
> 2019-12-04 22:25:57,454 INFO mapreduce.Job: Task Id :
> attempt_1575479127636_0047_m_000017_2, Status : FAILED
> Error: java.io.EOFException:
> hdfs://jobmaster:9000/user/hadoop/crawlmultiokhttp/segment/20191204221308/crawl_parse/part-r-00004
> not a SequenceFile
> at
> org.apache.hadoop.io.SequenceFile$Reader.init(SequenceFile.java:1964)
> at
> org.apache.hadoop.io.SequenceFile$Reader.initialize(SequenceFile.java:1923)
> at
> org.apache.hadoop.io.SequenceFile$Reader.<init>(SequenceFile.java:1872)
> at
> org.apache.hadoop.io.SequenceFile$Reader.<init>(SequenceFile.java:1886)
> at
> org.apache.hadoop.mapreduce.lib.input.SequenceFileRecordReader.initialize(SequenceFileRecordReader.java:54)
> at
> org.apache.hadoop.mapred.MapTask$NewTrackingRecordReader.initialize(MapTask.java:560)
> at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:798)
> at org.apache.hadoop.mapred.MapTask.run(MapTask.java:347)
> at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:174)
> at java.security.AccessController.doPrivileged(Native Method)
> at javax.security.auth.Subject.doAs(Subject.java:422)
> at
> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1729)
> at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:168)~
> {panel}
> When I check the namenode logs, I don't see any error during the writing of
> the segment part but one hour later, I've got the following log:
> {panel:title=log_namenode}
> 2019-12-04 23:23:13,750 INFO
> org.apache.hadoop.hdfs.server.namenode.FSNamesystem: Recovering [Lease.
> Holder: DFSClient_attempt_1575479127636_0046_r_000004_1_1307945884_1, pending
> creates: 2],
> src=/user/hadoop/crawlmultiokhttp/segment/20191204221308/parse_data/part-r-00004/index
> 2019-12-04 23:23:13,750 WARN org.apache.hadoop.hdfs.StateChange: BLOCK*
> internalReleaseLease: All existing blocks are COMPLETE, lease removed, file
> /user/hadoop/crawlmultiokhttp/segment/20191204221308/parse_data/part-r-00004/index
> closed.
> 2019-12-04 23:23:13,750 INFO
> org.apache.hadoop.hdfs.server.namenode.FSNamesystem: Recovering [Lease.
> Holder: DFSClient_attempt_1575479127636_0046_r_000004_1_1307945884_1, pending
> creates: 1],
> src=/user/hadoop/crawlmultiokhttp/segment/20191204221308/crawl_parse/part-r-00004
> 2019-12-04 23:23:13,750 WARN org.apache.hadoop.hdfs.StateChange: BLOCK*
> internalReleaseLease: All existing blocks are COMPLETE, lease removed, file
> /user/hadoop/crawlmultiokhttp/segment/20191204221308/crawl_parse/part-r-00004
> closed.
> {panel}
> This issue is hard to reproduce and I can't figure out what are the
> preconditions. It seems that it just happens randomly.
> Maybe the problem is coming from a bad management when we close the file.
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