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From Sebastian Stipkovic <sebastian.stipko...@gmail.com>
Subject Re: out of core option
Date Thu, 05 Dec 2013 23:00:06 GMT
Hi Rob,

embarrassing. You are right. But now I get with the correct option the
following exception:


2013-12-05 23:10:18,568 INFO org.apache.hadoop.mapred.JobTracker: Adding
task (MAP) 'attempt_201312052304_0001_m_000001_0' to tip
task_201312052304_0001_m_000001, for tracker 'tracker_hduser:localhost/
127.0.0.1:39793' 2013-12-05 23:10:27,645 INFO
org.apache.hadoop.mapred.TaskInProgress: Error from
attempt_201312052304_0001_m_000001_0: java.lang.IllegalStateException: run:
Caught an unrecoverable exception waitFor: ExecutionException occurred
while waiting for
org.apache.giraph.utils.ProgressableUtils$FutureWaitable@62bf5822 at
org.apache.giraph.graph.GraphMapper.run(GraphMapper.java:101) at
org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:763) at
org.apache.hadoop.mapred.MapTask.run(MapTask.java:369) at
org.apache.hadoop.mapred.Child$4.run(Child.java:259) at
java.security.AccessController.doPrivileged(Native Method) at
javax.security.auth.Subject.doAs(Subject.java:415) at
org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1059)
at org.apache.hadoop.mapred.Child.main(Child.java:253) Caused by:
java.lang.IllegalStateException: waitFor: ExecutionException occurred while
waiting for
org.apache.giraph.utils.ProgressableUtils$FutureWaitable@62bf5822 at
org.apache.giraph.utils.ProgressableUtils.waitFor(ProgressableUtils.java:181)
at
org.apache.giraph.utils.ProgressableUtils.waitForever(ProgressableUtils.java:139)
at
org.apache.giraph.utils.ProgressableUtils.waitForever(ProgressableUtils.java:124)
at
org.apache.giraph.utils.ProgressableUtils.getFutureResult(ProgressableUtils.java:87)
at
org.apache.giraph.utils.ProgressableUtils.getResultsWithNCallables(ProgressableUtils.java:221)
at
org.apache.giraph.worker.BspServiceWorker.loadInputSplits(BspServiceWorker.java:281)
at
org.apache.giraph.worker.BspServiceWorker.loadVertices(BspServiceWorker.java:325)
at
org.apache.giraph.worker.BspServiceWorker.setup(BspServiceWorker.java:506)
at
org.apache.giraph.graph.GraphTaskManager.execute(GraphTaskManager.java:244)
at org.apache.giraph.graph.GraphMapper.run(GraphMapper.java:91) ... 7 more
Caused by: java.util.concurrent.ExecutionException:
java.lang.IllegalStateException: getOrCreatePartition: cannot retrieve
partition 0 at
java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:262) at
java.util.concurrent.FutureTask.get(FutureTask.java:119) at
org.apache.giraph.utils.ProgressableUtils$FutureWaitable.waitFor(ProgressableUtils.java:300)
at
org.apache.giraph.utils.ProgressableUtils.waitFor(ProgressableUtils.java:173)
... 16 more Caused by: java.lang.IllegalStateException:
getOrCreatePartition: cannot retrieve partition 0 at
org.apache.giraph.partition.DiskBackedPartitionStore.getOrCreatePartition(DiskBackedPartitionStore.java:243)
at
org.apache.giraph.comm.requests.SendWorkerVerticesRequest.doRequest(SendWorkerVerticesRequest.java:110)
at
org.apache.giraph.comm.netty.NettyWorkerClientRequestProcessor.doRequest(NettyWorkerClientRequestProcessor.java:482)
at
org.apache.giraph.comm.netty.NettyWorkerClientRequestProcessor.sendVertexRequest(NettyWorkerClientRequestProcessor.java:276)
at
org.apache.giraph.worker.VertexInputSplitsCallable.readInputSplit(VertexInputSplitsCallable.java:172)
at
org.apache.giraph.worker.InputSplitsCallable.loadInputSplit(InputSplitsCallable.java:267)
at
org.apache.giraph.worker.InputSplitsCallable.call(InputSplitsCallable.java:211)
at
org.apache.giraph.worker.InputSplitsCallable.call(InputSplitsCallable.java:60)
at
org.apache.giraph.utils.LogStacktraceCallable.call(LogStacktraceCallable.java:51)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at
java.util.concurrent.FutureTask.run(FutureTask.java:166) at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:724) Caused by:
java.util.concurrent.ExecutionException: java.lang.NullPointerException at
java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:252) at
java.util.concurrent.FutureTask.get(FutureTask.java:111) at
org.apache.giraph.partition.DiskBackedPartitionStore.getOrCreatePartition(DiskBackedPartitionStore.java:228)
... 13 more Caused by: java.lang.NullPointerException at
org.apache.giraph.partition.DiskBackedPartitionStore$GetPartition.call(DiskBackedPartitionStore.java:692)
at
org.apache.giraph.partition.DiskBackedPartitionStore$GetPartition.call(DiskBackedPartitionStore.java:658)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at
java.util.concurrent.FutureTask.run(FutureTask.java:166) at
org.apache.giraph.partition.DiskBackedPartitionStore$DirectExecutorService.execute(DiskBackedPartitionStore.java:972)
at
java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:132)
... 14 more


Thanks,
Sebastian


2013/12/5 Rob Vesse <rvesse@dotnetrdf.org>

> Sebastian
>
> You've made a minor typo in the configuration setting which means you
> haven't actually enabled out of core graph mode.
>
> You have *giraph.useOutOfCoreGiraph *when it should be *giraph.useOutOfCoreGraph
> *– note that the last word is Graph not Giraph
>
> Rob
>
> From: Sebastian Stipkovic <sebastian.stipkovic@gmail.com>
> Reply-To: <user@giraph.apache.org>
> Date: Thursday, 5 December 2013 20:39
> To: <user@giraph.apache.org>
> Subject: out of core option
>
> Hello,
>
> I had setup giraph 1.1.0 with hadoop-0.20.203.0rc1  on a single
> node cluster. It computes a tiny graph successful. But if the
> input graph is huge (5 GB), I get an OutOfMemory(Garbage Collector)
> exception, although I had turned on the out-of-memory-option. The job with
> out-of-memory-option works only well with a tiny graph (0.9 GB).  What is
> Wrong? Does I have to do furthermore configurations?
>
> My Configurations are as follows:
>
>
> namevalue*fs.s3n.impl*org.apache.hadoop.fs.s3native.NativeS3FileSystem
> *mapred.task.cache.levels*2*giraph.vertexOutputFormatClass*
> org.apache.giraph.examples.MyShortestPaths$MyOutputFormat*hadoop.tmp.dir*
> /app/hadoop/tmp*hadoop.native.lib*true*map.sort.class*
> org.apache.hadoop.util.QuickSort
> *dfs.namenode.decommission.nodes.per.interval*5
> *dfs.https.need.client.auth*false*ipc.client.idlethreshold*4000
> *dfs.datanode.data.dir.perm*755*mapred.system.dir*
> ${hadoop.tmp.dir}/mapred/system
> *mapred.job.tracker.persist.jobstatus.hours*0*dfs.datanode.address*
> 0.0.0.0:50010*dfs.namenode.logging.level*info
> *dfs.block.access.token.enable*false*io.skip.checksum.errors*false*fs.default.name
> <http://fs.default.name>*hdfs://localhost:54310
> *mapred.cluster.reduce.memory.mb*-1*mapred.child.tmp*./tmp
> *fs.har.impl.disable.cache*true*dfs.safemode.threshold.pct*0.999f
> *mapred.skip.reduce.max.skip.groups*0*dfs.namenode.handler.count*10
> *dfs.blockreport.initialDelay*0*mapred.heartbeats.in.second*100
> *mapred.tasktracker.dns.nameserver*default*io.sort.factor*10
> *mapred.task.timeout*600000*giraph.maxWorkers*1
> *mapred.max.tracker.failures*4*hadoop.rpc.socket.factory.class.default*
> org.apache.hadoop.net.StandardSocketFactory
> *mapred.job.tracker.jobhistory.lru.cache.size*5*fs.hdfs.impl*
> org.apache.hadoop.hdfs.DistributedFileSystem
> *mapred.queue.default.acl-administer-jobs**
> *dfs.block.access.key.update.interval*600
> *mapred.skip.map.auto.incr.proc.count*true
> *mapreduce.job.complete.cancel.delegation.tokens*true
> *io.mapfile.bloom.size*1048576*mapreduce.reduce.shuffle.connect.timeout*
> 180000*dfs.safemode.extension*30000
> *mapred.jobtracker.blacklist.fault-timeout-window*180
> *tasktracker.http.threads*40*mapred.job.shuffle.merge.percent*0.66
> *mapreduce.inputformat.class*org.apache.giraph.bsp.BspInputFormat
> *fs.ftp.impl*org.apache.hadoop.fs.ftp.FTPFileSystem*user.name
> <http://user.name>*hduser*mapred.output.compress*false
> *io.bytes.per.checksum*512*giraph.isStaticGraph*true
> *mapred.healthChecker.script.timeout*600000
> *topology.node.switch.mapping.impl*
> org.apache.hadoop.net.ScriptBasedMapping
> *dfs.https.server.keystore.resource*ssl-server.xml
> *mapred.reduce.slowstart.completed.maps*0.05*mapred.reduce.max.attempts*4
> *fs.ramfs.impl*org.apache.hadoop.fs.InMemoryFileSystem
> *dfs.block.access.token.lifetime*600*dfs.name.edits.dir*${dfs.name.dir}
> *mapred.skip.map.max.skip.records*0*mapred.cluster.map.memory.mb*-1
> *hadoop.security.group.mapping*
> org.apache.hadoop.security.ShellBasedUnixGroupsMapping
> *mapred.job.tracker.persist.jobstatus.dir*/jobtracker/jobsInfo*mapred.jar*
> hdfs://localhost:54310
> /app/hadoop/tmp/mapred/staging/hduser/.staging/job_201312051827_0001/job.jar
> *dfs.block.size*67108864*fs.s3.buffer.dir*${hadoop.tmp.dir}/s3
> *job.end.retry.attempts*0*fs.file.impl*
> org.apache.hadoop.fs.LocalFileSystem*mapred.local.dir.minspacestart*0
> *mapred.output.compression.type*RECORD*dfs.datanode.ipc.address*
> 0.0.0.0:50020*dfs.permissions*true*topology.script.number.args*100
> *io.mapfile.bloom.error.rate*0.005*mapred.cluster.max.reduce.memory.mb*-1
> *mapred.max.tracker.blacklists*4*mapred.task.profile.maps*0-2
> *dfs.datanode.https.address*0.0.0.0:50475*mapred.userlog.retain.hours*24
> *dfs.secondary.http.address*0.0.0.0:50090*dfs.replication.max*512
> *mapred.job.tracker.persist.jobstatus.active*false
> *hadoop.security.authorization*false*local.cache.size*10737418240
> *dfs.namenode.delegation.token.renew-interval*86400000
> *mapred.min.split.size*0*mapred.map.tasks*2*mapred.child.java.opts*
> -Xmx4000m*mapreduce.job.counters.limit*120
> *dfs.https.client.keystore.resource*ssl-client.xml*mapred.job.queue.name
> <http://mapred.job.queue.name>*default*dfs.https.address*0.0.0.0:50470
> *mapred.job.tracker.retiredjobs.cache.size*1000
> *dfs.balance.bandwidthPerSec*1048576*ipc.server.listen.queue.size*128
> *mapred.inmem.merge.threshold*1000*job.end.retry.interval*30000
> *mapred.skip.attempts.to.start.skipping*2*fs.checkpoint.dir*
> ${hadoop.tmp.dir}/dfs/namesecondary*mapred.reduce.tasks*0
> *mapred.merge.recordsBeforeProgress*10000*mapred.userlog.limit.kb*0
> *mapred.job.reduce.memory.mb*-1*dfs.max.objects*0
> *webinterface.private.actions*false*io.sort.spill.percent*0.80
> *mapred.job.shuffle.input.buffer.percent*0.70*mapred.job.name
> <http://mapred.job.name>*Giraph:
> org.apache.giraph.examples.MyShortestPaths*dfs.datanode.dns.nameserver*
> default*mapred.map.tasks.speculative.execution*false
> *hadoop.util.hash.type*murmur*dfs.blockreport.intervalMsec*3600000
> *mapred.map.max.attempts*0*mapreduce.job.acl-view-job*
> *dfs.client.block.write.retries*3*mapred.job.tracker.handler.count*10
> *mapreduce.reduce.shuffle.read.timeout*180000
> *mapred.tasktracker.expiry.interval*600000*dfs.https.enable*false
> *mapred.jobtracker.maxtasks.per.job*-1
> *mapred.jobtracker.job.history.block.size*3145728
> *giraph.useOutOfCoreGiraph*true*keep.failed.task.files*false
> *mapreduce.outputformat.class*org.apache.giraph.bsp.BspOutputFormat
> *dfs.datanode.failed.volumes.tolerated*0*ipc.client.tcpnodelay*false
> *mapred.task.profile.reduces*0-2*mapred.output.compression.codec*
> org.apache.hadoop.io.compress.DefaultCodec*io.map.index.skip*0
> *mapred.working.dir*hdfs://localhost:54310/user/hduser
> *ipc.server.tcpnodelay*false
> *mapred.jobtracker.blacklist.fault-bucket-width*15
> *dfs.namenode.delegation.key.update-interval*86400000
> *mapred.used.genericoptionsparser*true*mapred.mapper.new-api*true
> *mapred.job.map.memory.mb*-1*giraph.vertex.input.dir*hdfs://localhost:
> 54310/user/hduser/output*dfs.default.chunk.view.size*32768
> *hadoop.logfile.size*10000000*mapred.reduce.tasks.speculative.execution*
> true*mapreduce.job.dir*hdfs://localhost:54310
> /app/hadoop/tmp/mapred/staging/hduser/.staging/job_201312051827_0001
> *mapreduce.tasktracker.outofband.heartbeat*false
> *mapreduce.reduce.input.limit*-1*dfs.datanode.du.reserved*0
> *hadoop.security.authentication*simple*fs.checkpoint.period*3600
> *dfs.web.ugi*webuser,webgroup*mapred.job.reuse.jvm.num.tasks*1
> *mapred.jobtracker.completeuserjobs.maximum*100*dfs.df.interval*60000
> *dfs.data.dir*${hadoop.tmp.dir}/dfs/data
> *mapred.task.tracker.task-controller*
> org.apache.hadoop.mapred.DefaultTaskController*giraph.minWorkers*1
> *fs.s3.maxRetries*4*dfs.datanode.dns.interface*default
> *mapred.cluster.max.map.memory.mb*-1*dfs.support.append*false
> *mapreduce.job.acl-modify-job*
> *dfs.permissions.supergroup*supergroup*mapred.local.dir*
> ${hadoop.tmp.dir}/mapred/local*fs.hftp.impl*
> org.apache.hadoop.hdfs.HftpFileSystem*fs.trash.interval*0
> *fs.s3.sleepTimeSeconds*10*dfs.replication.min*1
> *mapred.submit.replication*10*fs.har.impl*
> org.apache.hadoop.fs.HarFileSystem*mapred.map.output.compression.codec*
> org.apache.hadoop.io.compress.DefaultCodec
> *mapred.tasktracker.dns.interface*default
> *dfs.namenode.decommission.interval*30*dfs.http.address*0.0.0.0:50070
> *dfs.heartbeat.interval*3*mapred.job.tracker*localhost:54311
> *mapreduce.job.submithost*hduser*io.seqfile.sorter.recordlimit*1000000
> *giraph.vertexInputFormatClass*
> org.apache.giraph.examples.MyShortestPaths$MyInputFormat*dfs.name.dir*
> ${hadoop.tmp.dir}/dfs/name*mapred.line.input.format.linespermap*1
> *mapred.jobtracker.taskScheduler*
> org.apache.hadoop.mapred.JobQueueTaskScheduler*dfs.datanode.http.address*
> 0.0.0.0:50075*mapred.local.dir.minspacekill*0*dfs.replication.interval*3
> *io.sort.record.percent*0.05*fs.kfs.impl*
> org.apache.hadoop.fs.kfs.KosmosFileSystem*mapred.temp.dir*
> ${hadoop.tmp.dir}/mapred/temp*mapred.tasktracker.reduce.tasks.maximum*2
> *mapreduce.job.user.classpath.first*true*dfs.replication*1
> *fs.checkpoint.edits.dir*${fs.checkpoint.dir}*giraph.computationClass*
> org.apache.giraph.examples.MyShortestPaths
> *mapred.tasktracker.tasks.sleeptime-before-sigkill*5000
> *mapred.job.reduce.input.buffer.percent*0.0
> *mapred.tasktracker.indexcache.mb*10*mapreduce.job.split.metainfo.maxsize*
> 10000000*hadoop.logfile.count*10*mapred.skip.reduce.auto.incr.proc.count*
> true*mapreduce.job.submithostaddress*127.0.1.1
> *io.seqfile.compress.blocksize*1000000*fs.s3.block.size*67108864
> *mapred.tasktracker.taskmemorymanager.monitoring-interval*5000
> *giraph.minPercentResponded*100.0*mapred.queue.default.state*RUNNING
> *mapred.acls.enabled*false*mapreduce.jobtracker.staging.root.dir*
> ${hadoop.tmp.dir}/mapred/staging*mapred.queue.names*default
> *dfs.access.time.precision*3600000*fs.hsftp.impl*
> org.apache.hadoop.hdfs.HsftpFileSystem*mapred.task.tracker.http.address*
> 0.0.0.0:50060*mapred.reduce.parallel.copies*5*io.seqfile.lazydecompress*
> true*mapred.output.dir*/user/hduser/output/shortestpaths*io.sort.mb*100
> *ipc.client.connection.maxidletime*10000*mapred.compress.map.output*false
> *hadoop.security.uid.cache.secs*14400*mapred.task.tracker.report.address*
> 127.0.0.1:0*mapred.healthChecker.interval*60000*ipc.client.kill.max*10
> *ipc.client.connect.max.retries*10*ipc.ping.interval*300000
> *mapreduce.user.classpath.first*true*mapreduce.map.class*
> org.apache.giraph.graph.GraphMapper*fs.s3.impl*
> org.apache.hadoop.fs.s3.S3FileSystem*mapred.user.jobconf.limit*5242880
> *mapred.job.tracker.http.address*0.0.0.0:50030*io.file.buffer.size*4096
> *mapred.jobtracker.restart.recover*false*io.serializations*
> org.apache.hadoop.io.serializer.WritableSerialization
> *dfs.datanode.handler.count*3*mapred.reduce.copy.backoff*300
> *mapred.task.profile*false*dfs.replication.considerLoad*true
> *jobclient.output.filter*FAILED
> *dfs.namenode.delegation.token.max-lifetime*604800000
> *mapred.tasktracker.map.tasks.maximum*4*io.compression.codecs*
> org.apache.hadoop.io.compress.DefaultCodec,org.apache.hadoop.io.compress.GzipCodec,org.apache.hadoop.io.compress.BZip2Codec
> *fs.checkpoint.size*67108864
>
> Additionally, if I have more than one worker I get an Exception, too? Are
> my configurations wrong?
>
>
> best regards,
> Sebastian
>
>

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