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$DirectExecutorService.execute(DiskBackedPartitionStore.java:972) at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:132) ... 14 more Thanks, Sebastian 2013/12/5 Rob Vesse <rve...@dotnetrdf.org> > Sebastian > > You've made a minor typo in the configuration setting which means you > haven't actually enabled out of core graph mode. > > You have *giraph.useOutOfCoreGiraph *when it should be > *giraph.useOutOfCoreGraph > *– note that the last word is Graph not Giraph > > Rob > > From: Sebastian Stipkovic <sebastian.stipko...@gmail.com> > Reply-To: <user@giraph.apache.org> > Date: Thursday, 5 December 2013 20:39 > To: <user@giraph.apache.org> > Subject: out of core option > > Hello, > > I had setup giraph 1.1.0 with hadoop-0.20.203.0rc1 on a single > node cluster. It computes a tiny graph successful. But if the > input graph is huge (5 GB), I get an OutOfMemory(Garbage Collector) > exception, although I had turned on the out-of-memory-option. The job with > out-of-memory-option works only well with a tiny graph (0.9 GB). What is > Wrong? Does I have to do furthermore configurations? > > My Configurations are as follows: > > > namevalue*fs.s3n.impl*org.apache.hadoop.fs.s3native.NativeS3FileSystem > *mapred.task.cache.levels*2*giraph.vertexOutputFormatClass* > org.apache.giraph.examples.MyShortestPaths$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 > >