[BLOG] Configuring JanusGraph for spark-yarn
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring-janusgraph-for-spark-yarn.html
Regards, Marc
On Thursday, July 6, 2017 at 4:15:37 AM UTC-4, HadoopMarc wrote:
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring- janusgraph-for-spark-yarn.html
Regards, Marc
On Thursday, July 6, 2017 at 4:15:37 AM UTC-4, HadoopMarc wrote:
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring- janusgraph-for-spark-yarn.html
Regards, Marc
It seems that we have two graph classes that need to be created:
The first is a standardjanusgraph object that runs a standard computer. This is able to perform OLTP data pushes and, I assume, standard OLTP queries. It, however, does not interface with Spark, so SparkGraphComputer cannot be used as the graph computer for its traversal object.
The second object is a HadoopGraph object that can have SparkGraphComputer activated for its associated traversal source object. This can perform appropriate map-reduced OLAP calculations, but wouldn't be good for putting information into the HBase database.
Is this accurate, or can we create a graphtraversalsource that can perform both the OLTP data inserts and utilize SparkGraphComputer? If not, could we create both objects simultaneously? Would there be conflicts between the two if there were two simultaneous traversers?
On Thursday, July 6, 2017 at 4:15:37 AM UTC-4, HadoopMarc wrote:
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring- janusgraph-for-spark-yarn.html
Regards, Marc
Your assumption about different types of graph object for OLTP and OLAP is right (at least for JanusGraph, TinkerGraph supports both). I remember examples from the gremlin user list, though, where OLTP and OLAP were mixed in the same traversal.
It is no problem to have a graph1 and a graph2 graph object simultaneously. This is also what you do in gremlin-server when you want to serve multiple graphs.
Cheers, Marc
Op zaterdag 15 juli 2017 00:24:25 UTC+2 schreef John Helmsen:
HadoopMarc,
It seems that we have two graph classes that need to be created:
The first is a standardjanusgraph object that runs a standard computer. This is able to perform OLTP data pushes and, I assume, standard OLTP queries. It, however, does not interface with Spark, so SparkGraphComputer cannot be used as the graph computer for its traversal object.
The second object is a HadoopGraph object that can have SparkGraphComputer activated for its associated traversal source object. This can perform appropriate map-reduced OLAP calculations, but wouldn't be good for putting information into the HBase database.
Is this accurate, or can we create a graphtraversalsource that can perform both the OLTP data inserts and utilize SparkGraphComputer? If not, could we create both objects simultaneously? Would there be conflicts between the two if there were two simultaneous traversers?
On Thursday, July 6, 2017 at 4:15:37 AM UTC-4, HadoopMarc wrote:
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring- janusgraph-for-spark-yarn.html
Regards, Marc
15:58:49,110 INFO SecurityManager:58 - Changing view acls to: rc15:58:49,110 INFO SecurityManager:58 - Changing modify acls to: rc15:58:49,110 INFO SecurityManager:58 - SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(rc); users with modify permissions: Set(rc)15:58:49,111 INFO Client:58 - Submitting application 25 to ResourceManager15:58:49,320 INFO YarnClientImpl:274 - Submitted application application_1500608983535_002515:58:49,321 INFO SchedulerExtensionServices:58 - Starting Yarn extension services with app application_1500608983535_0025 and attemptId None15:58:50,325 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:50,326 INFO Client:58 - client token: N/A diagnostics: N/A ApplicationMaster host: N/A ApplicationMaster RPC port: -1 queue: default start time: 1500883129115 final status: UNDEFINED tracking URL: http://dl-rc-optd-ambari-master-v-test-2.host.dataengine.com:8088/proxy/application_1500608983535_0025/ user: rc15:58:51,330 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:52,333 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:53,335 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:54,337 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:55,340 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)
15:58:56,343 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:56,802 INFO YarnSchedulerBackend$YarnSchedulerEndpoint:58 - ApplicationMaster registered as NettyRpcEndpointRef(null)15:58:56,822 INFO YarnClientSchedulerBackend:58 - Add WebUI Filter. org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter, Map(PROXY_HOSTS -> dl-rc-optd-ambari-master-v-test-1.host.dataengine.com,dl-rc-optd-ambari-master-v-test-2.host.dataengine.com, PROXY_URI_BASES -> http://dl-rc-optd-ambari-master-v-test-1.host.dataengine.com:8088/proxy/application_1500608983535_0025,http://dl-rc-optd-ambari-master-v-test-2.host.dataengine.com:8088/proxy/application_1500608983535_0025), /proxy/application_1500608983535_002515:58:56,824 INFO JettyUtils:58 - Adding filter: org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter15:58:57,346 INFO Client:58 - Application report for application_1500608983535_0025 (state: RUNNING)15:58:57,347 INFO Client:58 - client token: N/A diagnostics: N/A ApplicationMaster host: 10.200.48.154 ApplicationMaster RPC port: 0 queue: default start time: 1500883129115 final status: UNDEFINED tracking URL: http://dl-rc-optd-ambari-master-v-test-2.host.dataengine.com:8088/proxy/application_1500608983535_0025/ user: rc15:58:57,348 INFO YarnClientSchedulerBackend:58 - Application application_1500608983535_0025 has started running.15:58:57,358 INFO Utils:58 - Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 47514.15:58:57,358 INFO NettyBlockTransferService:58 - Server created on 4751415:58:57,360 INFO BlockManagerMaster:58 - Trying to register BlockManager15:58:57,363 INFO BlockManagerMasterEndpoint:58 - Registering block manager 10.200.48.112:47514 with 2.4 GB RAM, BlockManagerId(driver, 10.200.48.112, 47514)15:58:57,366 INFO BlockManagerMaster:58 - Registered BlockManager
15:58:57,585 INFO EventLoggingListener:58 - Logging events to hdfs:///spark-history/application_1500608983535_002515:59:07,177 WARN YarnSchedulerBackend$YarnSchedulerEndpoint:70 - Container marked as failed: container_e170_1500608983535_0025_01_000002 on host: dl-rc-optd-ambari-slave-v-test-1.host.dataengine.com. Exit status: 1. Diagnostics: Exception from container-launch.Container id: container_e170_1500608983535_0025_01_000002Exit code: 1Stack trace: ExitCodeException exitCode=1: at org.apache.hadoop.util.Shell.runCommand(Shell.java:576) at org.apache.hadoop.util.Shell.run(Shell.java:487) at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:753) at org.apache.hadoop.yarn.server.nodemanager.LinuxContainerExecutor.launchContainer(LinuxContainerExecutor.java:371) at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:303) at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:82) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)
Shell output: main : command provided 1main : run as user is rcmain : requested yarn user is rc
Container exited with a non-zero exit code 1
Display stack trace? [yN]15:59:57,702 WARN TransportChannelHandler:79 - Exception in connection from 10.200.48.155/10.200.48.155:50921java.io.IOException: Connection reset by peer at sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java:380) at io.netty.buffer.PooledUnsafeDirectByteBuf.setBytes(PooledUnsafeDirectByteBuf.java:313) at io.netty.buffer.AbstractByteBuf.writeBytes(AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes(NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:119) at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:111) at java.lang.Thread.run(Thread.java:748)
15:59:57,704 ERROR TransportResponseHandler:132 - Still have 1 requests outstanding when connection from 10.200.48.155/10.200.48.155:50921 is closed15:59:57,706 WARN NettyRpcEndpointRef:91 - Error sending message [message = RequestExecutors(0,0,Map())] in 1 attemptsjava.io.IOException: Connection reset by peer at sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java:380) at io.netty.buffer.PooledUnsafeDirectByteBuf.setBytes(PooledUnsafeDirectByteBuf.java:313) at io.netty.buffer.AbstractByteBuf.writeBytes(AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes(NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:119) at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:111) at java.lang.Thread.run(Thread.java:748)
在 2017年7月6日星期四 UTC+8下午4:15:37,HadoopMarc写道:
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring- janusgraph-for-spark-yarn.html
Regards, Marc
Marc - thank you for posting this. I'm trying to get this to work with our CDH 5.10.0 distribution, but have run into an issue; but first some questions. I'm using a 5 node cluster, and I think I do not need to set the zookeeper.zone.parent since the hbase configuration is in /etc/conf/hbase. Is that correct?
The error that I'm getting is:
org.apache.spark.SparkException: Job aborted due to stage
failure: Task 1 in stage 0.0 failed 4 times, most recent failure:
Lost task 1.3 in stage 0.0 (TID 10, host002, executor 1):
java.lang.ClassCastException: cannot assign instance of
java.lang.invoke.SerializedLambda to field
org.apache.spark.api.java.JavaPairRDD$$anonfun$pairFunToScalaFun$1.x$330
of type org.apache.spark.api.java.function.PairFunction in
instance of
org.apache.spark.api.java.JavaPairRDD$$anonfun$pairFunToScalaFun$1
at
java.io.ObjectStreamClass$FieldReflector.setObjFieldValues(ObjectStreamClass.java:2133)
at
java.io.ObjectStreamClass.setObjFieldValues(ObjectStreamClass.java:1305)
at
java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2238)
at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2156)
at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2014)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1536)
at
java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2232)
at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2156)
at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2014)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1536)
at
java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2232)
at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2112)
at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2014)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1536)
at
java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2232)
at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2156)
at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2014)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1536)
at
java.io.ObjectInputStream.readObject(ObjectInputStream.java:423)
at
scala.collection.immutable.$colon$colon.readObject(List.scala:362)
at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown
Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1058)
at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2123)
at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2014)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1536)
at
java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2232)
at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2156)
at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2014)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1536)
at
java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2232)
at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2156)
at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2014)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1536)
at
java.io.ObjectInputStream.readObject(ObjectInputStream.java:423)
at
org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:76)
at
org.apache.spark.serializer.JavaSerializerInstance.deserialize(JavaSerializer.scala:115)
at
org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:64)
at
org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
at org.apache.spark.scheduler.Task.run(Task.scala:89)
at
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:242)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Given this post:
https://stackoverflow.com/questions/28186607/java-lang-classcastexception-using-lambda-expressions-in-spark-job-on-remote-ser
It looks like I'm not including a necessary jar, but I'm at a loss as to which one. Any ideas?
For reference, here is part of the config:
#
# Hadoop Graph Configuration
#
gremlin.graph=org.apache.tinkerpop.gremlin.hadoop.structure.HadoopGraph
gremlin.hadoop.graphInputFormat=org.janusgraph.hadoop.formats.hbase.HBaseInputFormat
gremlin.hadoop.graphOutputFormat=org.apache.tinkerpop.gremlin.hadoop.structure.io.gryo.GryoOutputFormat
gremlin.hadoop.jarsInDistributedCache=true
gremlin.hadoop.inputLocation=none
gremlin.hadoop.outputLocation=output
#
# JanusGraph HBase InputFormat configuration
#
janusgraphmr.ioformat.conf.storage.backend=hbase
#janusgraphmr.ioformat.conf.storage.hostname=fqdn1,fqdn2,fqdn3
janusgraphmr.ioformat.conf.storage.hostname=10.22.5.63:2181,10.22.5.64:2181,10.22.5.65:2181
janusgraphmr.ioformat.conf.storage.hbase.table=TEST0.2.0
janusgraphmr.ioformat.conf.storage.hbase.region-count=5
janusgraphmr.ioformat.conf.storage.hbase.regions-per-server=18
janusgraphmr.ioformat.conf.storage.hbase.short-cf-names=false
#zookeeper.znode.parent=/hbase-unsecure
# Security configs are needed in case of a secure cluster
#zookeeper.znode.parent=/hbase-secure
#hbase.rpc.protection=privacy
#hbase.security.authentication=kerberos
#
# SparkGraphComputer with Yarn Configuration
#
spark.master=yarn-client
spark.executor.memory=512m
spark.serializer=org.apache.tinkerpop.gremlin.spark.structure.io.gryo.GryoSerializer
spark.yarn.dist.archives=/home/graph/janusgraph-0.2.0-SNAPSHOT-hadoop2.JOE/lib.zip
spark.yarn.dist.files=/opt/cloudera/parcels/CDH/jars/janusgraph-hbase-0.2.0-SNAPSHOT.jar
spark.yarn.dist.jars=/opt/cloudera/parcels/CDH/jars/janusgraph-hbase-0.2.0-SNAPSHOT.jar,/opt/cloudera/parcels/CDH/jars/spark-core_2.10-1.6.0-cdh5.10.0.jar
#spark.yarn.appMasterEnv.CLASSPATH=/etc/hadoop/conf:./lib.zip/*:
spark.yarn.appMasterEnv.CLASSPATH=/etc/haddop/conf:/etc/hbase/conf:./lib.zip/*:/opt/cloudera/parcels/CDH/jars/spark-core_2.10-1.6.0-cdh5.10.0.jar
#spark.executor.extraClassPath=/etc/hadoop/conf:/etc/hbase/conf:/home/graph/janusgraph-0.2.0-SNAPSHOT-hadoop2/janusgraph-hbase-0.2.0-SNAPSHOT.jar:./lib.zip/*
spark.driver.extraLibraryPath=/opt/cloudera/parcels/CDH/lib/hadoop/native:/opt/cloudera/parcels/CDH/lib/hadoop-0.20-mapreduce/lib/native/Linux-amd64-64
spark.executor.extraLibraryPath=/opt/cloudera/parcels/CDH/lib/hadoop/native:/opt/cloudera/parcels/CDH/lib/hadoop-0.20-mapreduce/lib/native/Linux-amd64-64
Thank you!
-Joe
--
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring-janusgraph-for-spark-yarn.html
Regards, Marc
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgra...@....
For more options, visit https://groups.google.com/d/optout.
Could this be a networking issue? Maybe a firewall is enabled, or selinux is preventing a connection?
I've been able to get this to work, but running a simple count - g.V().count() on anything but a very small graph takes a very very long time (hours). Are there any cache settings, or other resources that could be modified to better the performance?
The YARN container logs are filled withe debug lines about 'Created dirty vertex map with initial size 32', 'Created vertex cache with max size 20000', and 'Generated HBase Filter ColumnRange Filter'. Can any of these things be adjusted in the properties file? Thank you!
-Joe
hi,Thanks for your post.--I did it according to the post.But I ran into a problem.
15:58:49,110 INFO SecurityManager:58 - Changing view acls to: rc15:58:49,110 INFO SecurityManager:58 - Changing modify acls to: rc15:58:49,110 INFO SecurityManager:58 - SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(rc); users with modify permissions: Set(rc)15:58:49,111 INFO Client:58 - Submitting application 25 to ResourceManager15:58:49,320 INFO YarnClientImpl:274 - Submitted application application_1500608983535_002515:58:49,321 INFO SchedulerExtensionServices:58 - Starting Yarn extension services with app application_1500608983535_0025 and attemptId None15:58:50,325 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:50,326 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: N/AApplicationMaster RPC port: -1queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host.dataengine.com:8088/proxy/application_1500608983535_0025/user: rc15:58:51,330 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:52,333 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:53,335 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:54,337 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:55,340 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)
15:58:56,343 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:56,802 INFO YarnSchedulerBackend$YarnSchedulerEndpoint:58 - ApplicationMaster registered as NettyRpcEndpointRef(null)15:58:56,822 INFO YarnClientSchedulerBackend:58 - Add WebUI Filter. org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter, Map(PROXY_HOSTS -> dl-rc-optd-ambari-master-v-test-1.host.dataengine.com,dl-rc-optd-ambari-master-v-test-2.host.dataengine.com, PROXY_URI_BASES -> http://dl-rc-optd-ambari-master-v-test-1.host.dataengine.com:8088/proxy/application_1500608983535_0025,http://dl-rc-optd-ambari-master-v-test-2.host.dataengine.com:8088/proxy/application_1500608983535_0025), /proxy/application_1500608983535_002515:58:56,824 INFO JettyUtils:58 - Adding filter: org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter15:58:57,346 INFO Client:58 - Application report for application_1500608983535_0025 (state: RUNNING)15:58:57,347 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: 10.200.48.154ApplicationMaster RPC port: 0queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host.dataengine.com:8088/proxy/application_1500608983535_0025/user: rc15:58:57,348 INFO YarnClientSchedulerBackend:58 - Application application_1500608983535_0025 has started running.15:58:57,358 INFO Utils:58 - Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 47514.15:58:57,358 INFO NettyBlockTransferService:58 - Server created on 4751415:58:57,360 INFO BlockManagerMaster:58 - Trying to register BlockManager15:58:57,363 INFO BlockManagerMasterEndpoint:58 - Registering block manager 10.200.48.112:47514 with 2.4 GB RAM, BlockManagerId(driver, 10.200.48.112, 47514)15:58:57,366 INFO BlockManagerMaster:58 - Registered BlockManager
15:58:57,585 INFO EventLoggingListener:58 - Logging events to hdfs:///spark-history/application_1500608983535_002515:59:07,177 WARN YarnSchedulerBackend$YarnSchedulerEndpoint:70 - Container marked as failed: container_e170_1500608983535_0025_01_000002 on host: dl-rc-optd-ambari-slave-v-test-1.host.dataengine.com. Exit status: 1. Diagnostics: Exception from container-launch.Container id: container_e170_1500608983535_0025_01_000002Exit code: 1Stack trace: ExitCodeException exitCode=1:at org.apache.hadoop.util.Shell.runCommand(Shell.java:576)at org.apache.hadoop.util.Shell.run(Shell.java:487)at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:753)at org.apache.hadoop.yarn.server.nodemanager.LinuxContainerExecutor.launchContainer(LinuxContainerExecutor.java:371)at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:303)at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:82)at java.util.concurrent.FutureTask.run(FutureTask.java:266)at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)at java.lang.Thread.run(Thread.java:745)
Shell output: main : command provided 1main : run as user is rcmain : requested yarn user is rc
Container exited with a non-zero exit code 1
Display stack trace? [yN]15:59:57,702 WARN TransportChannelHandler:79 - Exception in connection from 10.200.48.155/10.200.48.155:50921java.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method)at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39)at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223)at sun.nio.ch.IOUtil.read(IOUtil.java:192)at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java:380)at io.netty.buffer.PooledUnsafeDirectByteBuf.setBytes(PooledUnsafeDirectByteBuf.java:313)at io.netty.buffer.AbstractByteBuf.writeBytes(AbstractByteBuf.java:881)at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes(NioSocketChannel.java:242)at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:119)at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511)at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468)at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382)at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354)at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:111)at java.lang.Thread.run(Thread.java:748)
15:59:57,704 ERROR TransportResponseHandler:132 - Still have 1 requests outstanding when connection from 10.200.48.155/10.200.48.155:50921 is closed15:59:57,706 WARN NettyRpcEndpointRef:91 - Error sending message [message = RequestExecutors(0,0,Map())] in 1 attemptsjava.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method)at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39)at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223)at sun.nio.ch.IOUtil.read(IOUtil.java:192)at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java:380)at io.netty.buffer.PooledUnsafeDirectByteBuf.setBytes(PooledUnsafeDirectByteBuf.java:313)at io.netty.buffer.AbstractByteBuf.writeBytes(AbstractByteBuf.java:881)at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes(NioSocketChannel.java:242)at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:119)at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511)at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468)at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382)at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354)at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:111)at java.lang.Thread.run(Thread.java:748)I am confused about that. Could you please help me?
在 2017年7月6日星期四 UTC+8下午4:15:37,HadoopMarc写道:
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring- janusgraph-for-spark-yarn.html
Regards, Marc
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgra...@....
For more options, visit https://groups.google.com/d/optout.
..., did you run the recipe on the same HDP sandbox and same Tinkerpop version? I remember (from 4 weeks ago) that copying the zookeeper.znode.parent property from the hbase configs to the janusgraph configs was essential to get janusgraph's HBaseInputFormat working (that is: read graph data for the spark tasks).
Cheers, Marc
Op maandag 24 juli 2017 10:12:13 UTC+2 schreef spi...@...:
hi,Thanks for your post.I did it according to the post.But I ran into a problem.
15:58:49,110 INFO SecurityManager:58 - Changing view acls to: rc15:58:49,110 INFO SecurityManager:58 - Changing modify acls to: rc15:58:49,110 INFO SecurityManager:58 - SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(rc); users with modify permissions: Set(rc)15:58:49,111 INFO Client:58 - Submitting application 25 to ResourceManager15:58:49,320 INFO YarnClientImpl:274 - Submitted application application_1500608983535_002515:58:49,321 INFO SchedulerExtensionServices:58 - Starting Yarn extension services with app application_1500608983535_0025 and attemptId None15:58:50,325 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:50,326 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: N/AApplicationMaster RPC port: -1queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025/ user: rc15:58:51,330 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:52,333 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:53,335 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:54,337 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:55,340 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:56,343 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:56,802 INFO YarnSchedulerBackend$YarnSchedulerEndpoint:58 - ApplicationMaster registered as NettyRpcEndpointRef(null) 15:58:56,822 INFO YarnClientSchedulerBackend:58 - Add WebUI Filter. org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter, Map(PROXY_HOSTS -> dl-rc-optd-ambari-master-v- test-1.host.dataengine.com,dl- rc-optd-ambari-master-v-test- 2.host.dataengine.com, PROXY_URI_BASES -> http://dl-rc-optd-ambari- master-v-test-1.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025,http://dl-rc-optd-ambari- master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_0025 ), /proxy/application_ 1500608983535_0025 15:58:56,824 INFO JettyUtils:58 - Adding filter: org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter 15:58:57,346 INFO Client:58 - Application report for application_1500608983535_0025 (state: RUNNING)15:58:57,347 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: 10.200.48.154ApplicationMaster RPC port: 0queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025/ user: rc15:58:57,348 INFO YarnClientSchedulerBackend:58 - Application application_1500608983535_0025 has started running.15:58:57,358 INFO Utils:58 - Successfully started service 'org.apache.spark.network.netty. NettyBlockTransferService' on port 47514. 15:58:57,358 INFO NettyBlockTransferService:58 - Server created on 4751415:58:57,360 INFO BlockManagerMaster:58 - Trying to register BlockManager15:58:57,363 INFO BlockManagerMasterEndpoint:58 - Registering block manager 10.200.48.112:47514 with 2.4 GB RAM, BlockManagerId(driver, 10.200.48.112, 47514)15:58:57,366 INFO BlockManagerMaster:58 - Registered BlockManager15:58:57,585 INFO EventLoggingListener:58 - Logging events to hdfs:///spark-history/application_1500608983535_0025 15:59:07,177 WARN YarnSchedulerBackend$YarnSchedulerEndpoint:70 - Container marked as failed: container_e170_1500608983535_ 0025_01_000002 on host: dl-rc-optd-ambari-slave-v- test-1.host.dataengine.com. Exit status: 1. Diagnostics: Exception from container-launch. Container id: container_e170_1500608983535_0025_01_000002 Exit code: 1Stack trace: ExitCodeException exitCode=1:at org.apache.hadoop.util.Shell.runCommand(Shell.java:576) at org.apache.hadoop.util.Shell.run(Shell.java:487) at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute( Shell.java:753) at org.apache.hadoop.yarn.server.nodemanager. LinuxContainerExecutor. launchContainer( LinuxContainerExecutor.java: 371) at org.apache.hadoop.yarn.server.nodemanager.containermanager. launcher.ContainerLaunch.call( ContainerLaunch.java:303) at org.apache.hadoop.yarn.server.nodemanager.containermanager. launcher.ContainerLaunch.call( ContainerLaunch.java:82) at java.util.concurrent.FutureTask.run(FutureTask. java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker( ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run( ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Shell output: main : command provided 1main : run as user is rcmain : requested yarn user is rcContainer exited with a non-zero exit code 1
Display stack trace? [yN]15:59:57,702 WARN TransportChannelHandler:79 - Exception in connection from 10.200.48.155/10.200.48.155:50921 java.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil. java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java: 380) at io.netty.buffer.PooledUnsafeDirectByteBuf. setBytes( PooledUnsafeDirectByteBuf. java:313) at io.netty.buffer.AbstractByteBuf.writeBytes( AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes( NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$ NioByteUnsafe.read( AbstractNioByteChannel.java: 119) at io.netty.channel.nio.NioEventLoop. processSelectedKey( NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop. processSelectedKeysOptimized( NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop. processSelectedKeys( NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop. java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2. run(SingleThreadEventExecutor. java:111) at java.lang.Thread.run(Thread.java:748) 15:59:57,704 ERROR TransportResponseHandler:132 - Still have 1 requests outstanding when connection from 10.200.48.155/10.200.48.155:50921 is closed 15:59:57,706 WARN NettyRpcEndpointRef:91 - Error sending message [message = RequestExecutors(0,0,Map())] in 1 attemptsjava.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil. java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java: 380) at io.netty.buffer.PooledUnsafeDirectByteBuf. setBytes( PooledUnsafeDirectByteBuf. java:313) at io.netty.buffer.AbstractByteBuf.writeBytes( AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes( NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$ NioByteUnsafe.read( AbstractNioByteChannel.java: 119) at io.netty.channel.nio.NioEventLoop. processSelectedKey( NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop. processSelectedKeysOptimized( NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop. processSelectedKeys( NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop. java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2. run(SingleThreadEventExecutor. java:111) at java.lang.Thread.run(Thread.java:748) I am confused about that. Could you please help me?
在 2017年7月6日星期四 UTC+8下午4:15:37,HadoopMarc写道:
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring- janusgraph-for-spark-yarn.html
Regards, Marc
Hi Marc - I've been able to get it to run longer, but am now getting a RowTooBigException from HBase. How does JanusGraph store data in HBase? The current max size of a row in 1GByte, which makes me think this error is covering something else up.
What I'm seeing so far in testing with a 5 server cluster - each
machine with 128G of RAM:
HBase table is 1.5G in size, split across 7 regions, and has
20,001,105 rows. To do a g.V().count() takes 2 hours and results
in 3,842,755 verticies.
Another HBase table is 5.7G in size split across 10 regions, is 57,620,276 rows, and took 6.5 hours to run the count and results in 10,859,491 nodes. When running, it looks like it hits one server very hard even though the YARN tasks are distributed across the cluster. One HBase node gets hammered.
The RowTooBigException is below. Anything to try? Thank you for
any help!
org.janusgraph.core.JanusGraphException: Could not process
individual retrieval call
at
org.janusgraph.graphdb.query.QueryUtil.processIntersectingRetrievals(QueryUtil.java:257)
at
org.janusgraph.graphdb.transaction.StandardJanusGraphTx$6.execute(StandardJanusGraphTx.java:1269)
at
org.janusgraph.graphdb.transaction.StandardJanusGraphTx$6.execute(StandardJanusGraphTx.java:1137)
at
org.janusgraph.graphdb.query.QueryProcessor$LimitAdjustingIterator.getNewIterator(QueryProcessor.java:209)
at
org.janusgraph.graphdb.query.LimitAdjustingIterator.hasNext(LimitAdjustingIterator.java:75)
at
org.janusgraph.graphdb.query.ResultSetIterator.nextInternal(ResultSetIterator.java:54)
at
org.janusgraph.graphdb.query.ResultSetIterator.next(ResultSetIterator.java:67)
at
org.janusgraph.graphdb.query.ResultSetIterator.next(ResultSetIterator.java:28)
at
com.google.common.collect.Iterators$7.computeNext(Iterators.java:651)
at
com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
at
com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
at
org.janusgraph.hadoop.formats.util.input.current.JanusGraphHadoopSetupImpl.getTypeInspector(JanusGraphHadoopSetupImpl.java:60)
at
org.janusgraph.hadoop.formats.util.JanusGraphVertexDeserializer.<init>(JanusGraphVertexDeserializer.java:55)
at
org.janusgraph.hadoop.formats.util.GiraphInputFormat.lambda$static$0(GiraphInputFormat.java:49)
at
org.janusgraph.hadoop.formats.util.GiraphInputFormat$RefCountedCloseable.acquire(GiraphInputFormat.java:100)
at
org.janusgraph.hadoop.formats.util.GiraphRecordReader.<init>(GiraphRecordReader.java:47)
at
org.janusgraph.hadoop.formats.util.GiraphInputFormat.createRecordReader(GiraphInputFormat.java:67)
at
org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>(NewHadoopRDD.scala:166)
at
org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:133)
at
org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:65)
at
org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at
org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at
org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at
org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at
org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at
org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at
org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at
org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at
org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:73)
at
org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
at
org.apache.spark.scheduler.Task.run(Task.scala:89)
at
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:242)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.janusgraph.core.JanusGraphException: Could not call
index
at
org.janusgraph.graphdb.transaction.StandardJanusGraphTx$6$6.call(StandardJanusGraphTx.java:1262)
at
org.janusgraph.graphdb.query.QueryUtil.processIntersectingRetrievals(QueryUtil.java:255)
... 34 more
Caused by: org.janusgraph.core.JanusGraphException: Could not
execute operation due to backend exception
at
org.janusgraph.diskstorage.util.BackendOperation.execute(BackendOperation.java:57)
at
org.janusgraph.diskstorage.BackendTransaction.executeRead(BackendTransaction.java:444)
at
org.janusgraph.diskstorage.BackendTransaction.indexQuery(BackendTransaction.java:395)
at
org.janusgraph.graphdb.query.graph.MultiKeySliceQuery.execute(MultiKeySliceQuery.java:51)
at
org.janusgraph.graphdb.database.IndexSerializer.query(IndexSerializer.java:529)
at
org.janusgraph.graphdb.transaction.StandardJanusGraphTx$6$6$1.lambda$call$5(StandardJanusGraphTx.java:1258)
at
org.janusgraph.graphdb.query.profile.QueryProfiler.profile(QueryProfiler.java:97)
at
org.janusgraph.graphdb.query.profile.QueryProfiler.profile(QueryProfiler.java:89)
at
org.janusgraph.graphdb.query.profile.QueryProfiler.profile(QueryProfiler.java:81)
at
org.janusgraph.graphdb.transaction.StandardJanusGraphTx$6$6$1.call(StandardJanusGraphTx.java:1258)
at
org.janusgraph.graphdb.transaction.StandardJanusGraphTx$6$6$1.call(StandardJanusGraphTx.java:1255)
at
com.google.common.cache.LocalCache$LocalManualCache$1.load(LocalCache.java:4742)
at
com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3527)
at
com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2319)
at
com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2282)
at
com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2197)
at
com.google.common.cache.LocalCache.get(LocalCache.java:3937)
at
com.google.common.cache.LocalCache$LocalManualCache.get(LocalCache.java:4739)
at
org.janusgraph.graphdb.transaction.StandardJanusGraphTx$6$6.call(StandardJanusGraphTx.java:1255)
... 35 more
Caused by: org.janusgraph.diskstorage.TemporaryBackendException:
Could not successfully complete backend operation due to repeated
temporary exceptions after PT10S
at
org.janusgraph.diskstorage.util.BackendOperation.executeDirect(BackendOperation.java:101)
at
org.janusgraph.diskstorage.util.BackendOperation.execute(BackendOperation.java:55)
... 53 more
Caused by: org.janusgraph.diskstorage.TemporaryBackendException:
Temporary failure in storage backend
at
org.janusgraph.diskstorage.hbase.HBaseKeyColumnValueStore.getHelper(HBaseKeyColumnValueStore.java:202)
at
org.janusgraph.diskstorage.hbase.HBaseKeyColumnValueStore.getSlice(HBaseKeyColumnValueStore.java:90)
at
org.janusgraph.diskstorage.keycolumnvalue.KCVSProxy.getSlice(KCVSProxy.java:77)
at
org.janusgraph.diskstorage.keycolumnvalue.KCVSProxy.getSlice(KCVSProxy.java:77)
at
org.janusgraph.diskstorage.BackendTransaction$5.call(BackendTransaction.java:398)
at
org.janusgraph.diskstorage.BackendTransaction$5.call(BackendTransaction.java:395)
at
org.janusgraph.diskstorage.util.BackendOperation.executeDirect(BackendOperation.java:69)
... 54 more
Caused by:
org.apache.hadoop.hbase.client.RetriesExhaustedException: Failed
after attempts=35, exceptions:
Sat Aug 05 07:22:03 EDT 2017,
RpcRetryingCaller{globalStartTime=1501932111280, pause=100,
retries=35},
org.apache.hadoop.hbase.regionserver.RowTooBigException:
rg.apache.hadoop.hbase.regionserver.RowTooBigException: Max row
size allowed: 1073741824, but the row is bigger than that.
at
org.apache.hadoop.hbase.regionserver.StoreScanner.next(StoreScanner.java:564)
at
org.apache.hadoop.hbase.regionserver.KeyValueHeap.next(KeyValueHeap.java:147)
at
org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.populateResult(HRegion.java:5697)
at
org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.nextInternal(HRegion.java:5856)
at
org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.nextRaw(HRegion.java:5634)
at
org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.next(HRegion.java:5611)
at
org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.next(HRegion.java:5597)
at
org.apache.hadoop.hbase.regionserver.HRegion.get(HRegion.java:6792)
at
org.apache.hadoop.hbase.regionserver.HRegion.get(HRegion.java:6770)
at
org.apache.hadoop.hbase.regionserver.RSRpcServices.get(RSRpcServices.java:2023)
at
org.apache.hadoop.hbase.protobuf.generated.ClientProtos$ClientService$2.callBlockingMethod(ClientProtos.java:33644)
at
org.apache.hadoop.hbase.ipc.RpcServer.call(RpcServer.java:2170)
at
org.apache.hadoop.hbase.ipc.CallRunner.run(CallRunner.java:109)
at
org.apache.hadoop.hbase.ipc.RpcExecutor$Handler.run(RpcExecutor.java:185)
at
org.apache.hadoop.hbase.ipc.RpcExecutor$Handler.run(RpcExecutor.java:165)
Hi ... and others, I have been offline for a few weeks enjoying a holiday and will start looking into your questions and make the suggested corrections. Thanks for following the recipes and helping others with it.--
..., did you run the recipe on the same HDP sandbox and same Tinkerpop version? I remember (from 4 weeks ago) that copying the zookeeper.znode.parent property from the hbase configs to the janusgraph configs was essential to get janusgraph's HBaseInputFormat working (that is: read graph data for the spark tasks).
Cheers, Marc
Op maandag 24 juli 2017 10:12:13 UTC+2 schreef spi...@...:hi,Thanks for your post.I did it according to the post.But I ran into a problem.
15:58:49,110 INFO SecurityManager:58 - Changing view acls to: rc15:58:49,110 INFO SecurityManager:58 - Changing modify acls to: rc15:58:49,110 INFO SecurityManager:58 - SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(rc); users with modify permissions: Set(rc)15:58:49,111 INFO Client:58 - Submitting application 25 to ResourceManager15:58:49,320 INFO YarnClientImpl:274 - Submitted application application_1500608983535_002515:58:49,321 INFO SchedulerExtensionServices:58 - Starting Yarn extension services with app application_1500608983535_0025 and attemptId None15:58:50,325 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:50,326 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: N/AApplicationMaster RPC port: -1queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025/ user: rc15:58:51,330 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:52,333 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:53,335 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:54,337 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:55,340 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)
15:58:56,343 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:56,802 INFO YarnSchedulerBackend$YarnSchedulerEndpoint:58 - ApplicationMaster registered as NettyRpcEndpointRef(null) 15:58:56,822 INFO YarnClientSchedulerBackend:58 - Add WebUI Filter. org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter, Map(PROXY_HOSTS -> dl-rc-optd-ambari-master-v- test-1.host.dataengine.com,dl- rc-optd-ambari-master-v-test- 2.host.dataengine.com, PROXY_URI_BASES -> http://dl-rc-optd-ambari- master-v-test-1.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025,http://dl-rc-optd-ambari- master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_0025 ), /proxy/application_ 1500608983535_0025 15:58:56,824 INFO JettyUtils:58 - Adding filter: org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter 15:58:57,346 INFO Client:58 - Application report for application_1500608983535_0025 (state: RUNNING)15:58:57,347 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: 10.200.48.154ApplicationMaster RPC port: 0queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025/ user: rc15:58:57,348 INFO YarnClientSchedulerBackend:58 - Application application_1500608983535_0025 has started running.15:58:57,358 INFO Utils:58 - Successfully started service 'org.apache.spark.network.netty. NettyBlockTransferService' on port 47514. 15:58:57,358 INFO NettyBlockTransferService:58 - Server created on 4751415:58:57,360 INFO BlockManagerMaster:58 - Trying to register BlockManager15:58:57,363 INFO BlockManagerMasterEndpoint:58 - Registering block manager 10.200.48.112:47514 with 2.4 GB RAM, BlockManagerId(driver, 10.200.48.112, 47514)15:58:57,366 INFO BlockManagerMaster:58 - Registered BlockManager
15:58:57,585 INFO EventLoggingListener:58 - Logging events to hdfs:///spark-history/application_1500608983535_0025 15:59:07,177 WARN YarnSchedulerBackend$YarnSchedulerEndpoint:70 - Container marked as failed: container_e170_1500608983535_ 0025_01_000002 on host: dl-rc-optd-ambari-slave-v- test-1.host.dataengine.com. Exit status: 1. Diagnostics: Exception from container-launch. Container id: container_e170_1500608983535_0025_01_000002 Exit code: 1Stack trace: ExitCodeException exitCode=1:at org.apache.hadoop.util.Shell.runCommand(Shell.java:576) at org.apache.hadoop.util.Shell.run(Shell.java:487) at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute( Shell.java:753) at org.apache.hadoop.yarn.server.nodemanager. LinuxContainerExecutor. launchContainer( LinuxContainerExecutor.java: 371) at org.apache.hadoop.yarn.server.nodemanager.containermanager. launcher.ContainerLaunch.call( ContainerLaunch.java:303) at org.apache.hadoop.yarn.server.nodemanager.containermanager. launcher.ContainerLaunch.call( ContainerLaunch.java:82) at java.util.concurrent.FutureTask.run(FutureTask. java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker( ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run( ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)
Shell output: main : command provided 1main : run as user is rcmain : requested yarn user is rc
Container exited with a non-zero exit code 1
Display stack trace? [yN]15:59:57,702 WARN TransportChannelHandler:79 - Exception in connection from 10.200.48.155/10.200.48.155:50921 java.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil. java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java: 380) at io.netty.buffer.PooledUnsafeDirectByteBuf. setBytes( PooledUnsafeDirectByteBuf. java:313) at io.netty.buffer.AbstractByteBuf.writeBytes( AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes( NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$ NioByteUnsafe.read( AbstractNioByteChannel.java: 119) at io.netty.channel.nio.NioEventLoop. processSelectedKey( NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop. processSelectedKeysOptimized( NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop. processSelectedKeys( NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop. java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2. run(SingleThreadEventExecutor. java:111) at java.lang.Thread.run(Thread.java:748)
15:59:57,704 ERROR TransportResponseHandler:132 - Still have 1 requests outstanding when connection from 10.200.48.155/10.200.48.155:50921 is closed 15:59:57,706 WARN NettyRpcEndpointRef:91 - Error sending message [message = RequestExecutors(0,0,Map())] in 1 attemptsjava.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil. java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java: 380) at io.netty.buffer.PooledUnsafeDirectByteBuf. setBytes( PooledUnsafeDirectByteBuf. java:313) at io.netty.buffer.AbstractByteBuf.writeBytes( AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes( NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$ NioByteUnsafe.read( AbstractNioByteChannel.java: 119) at io.netty.channel.nio.NioEventLoop. processSelectedKey( NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop. processSelectedKeysOptimized( NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop. processSelectedKeys( NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop. java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2. run(SingleThreadEventExecutor. java:111) at java.lang.Thread.run(Thread.java:748) I am confused about that. Could you please help me?
在 2017年7月6日星期四 UTC+8下午4:15:37,HadoopMarc写道:
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring- janusgraph-for-spark-yarn.html
Regards, Marc
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgra...@....
For more options, visit https://groups.google.com/d/optout.
You ran into terrain I have not yet covered myself. Up till now I have been using the graben1437 PR for Titan and for OLAP I adopted a poor man's approach where node id's are distributed over spark tasks and each spark executor makes its own Titan/HBase connection. This performs well, but does not have the nice abstraction of the HBaseInputFormat.
So, no clear answer to this one, but just some thoughts:
- could you try to move some regions manually and see what it does to performance?
- how do your OLAP vertex count times compare to the OLTP count times?
- how does the sum of spark task execution times compare to the yarn start-to-end time difference you reported? In other words, how much of the start-to-end time is spent in waiting for timeouts?
- unless you managed to create a vertex with > 1GB size, the RowTooBigException sounds like a bug (which you can report on Jnausgraph's github page). Hbase does not like large rows at all, so vertex/edge properties should not have blob values.
@(David Robinson): do you have any additional thoughts on this?
Cheers, Marc
Op maandag 7 augustus 2017 23:12:02 UTC+2 schreef Joseph Obernberger:
Hi Marc - I've been able to get it to run longer, but am now getting a RowTooBigException from HBase. How does JanusGraph store data in HBase? The current max size of a row in 1GByte, which makes me think this error is covering something else up.
What I'm seeing so far in testing with a 5 server cluster - each machine with 128G of RAM:
HBase table is 1.5G in size, split across 7 regions, and has 20,001,105 rows. To do a g.V().count() takes 2 hours and results in 3,842,755 verticies.Another HBase table is 5.7G in size split across 10 regions, is 57,620,276 rows, and took 6.5 hours to run the count and results in 10,859,491 nodes. When running, it looks like it hits one server very hard even though the YARN tasks are distributed across the cluster. One HBase node gets hammered.
The RowTooBigException is below. Anything to try? Thank you for any help!
org.janusgraph.core.
JanusGraphException: Could not process individual retrieval call
at org.janusgraph.graphdb.query.QueryUtil. processIntersectingRetrievals( QueryUtil.java:257)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6. execute(StandardJanusGraphTx. java:1269)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6. execute(StandardJanusGraphTx. java:1137)
at org.janusgraph.graphdb.query.QueryProcessor$ LimitAdjustingIterator. getNewIterator(QueryProcessor. java:209)
at org.janusgraph.graphdb.query.LimitAdjustingIterator. hasNext( LimitAdjustingIterator.java: 75)
at org.janusgraph.graphdb.query.ResultSetIterator. nextInternal( ResultSetIterator.java:54)
at org.janusgraph.graphdb.query.ResultSetIterator.next( ResultSetIterator.java:67)
at org.janusgraph.graphdb.query.ResultSetIterator.next( ResultSetIterator.java:28)
at com.google.common.collect.Iterators$7.computeNext( Iterators.java:651)
at com.google.common.collect.AbstractIterator. tryToComputeNext( AbstractIterator.java:143)
at com.google.common.collect.AbstractIterator.hasNext( AbstractIterator.java:138)
at org.janusgraph.hadoop.formats.util.input.current. JanusGraphHadoopSetupImpl. getTypeInspector( JanusGraphHadoopSetupImpl. java:60)
at org.janusgraph.hadoop.formats.util. JanusGraphVertexDeserializer.< init>( JanusGraphVertexDeserializer. java:55)
at org.janusgraph.hadoop.formats.util.GiraphInputFormat.lambda$ static$0(GiraphInputFormat. java:49)
at org.janusgraph.hadoop.formats.util.GiraphInputFormat$ RefCountedCloseable.acquire( GiraphInputFormat.java:100)
at org.janusgraph.hadoop.formats.util.GiraphRecordReader.<init> (GiraphRecordReader.java:47)
at org.janusgraph.hadoop.formats.util.GiraphInputFormat. createRecordReader( GiraphInputFormat.java:67)
at org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>( NewHadoopRDD.scala:166)
at org.apache.spark.rdd.NewHadoopRDD.compute( NewHadoopRDD.scala:133)
at org.apache.spark.rdd.NewHadoopRDD.compute( NewHadoopRDD.scala:65)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD. scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute( MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD. scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute( MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD. scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.scheduler.ShuffleMapTask.runTask( ShuffleMapTask.scala:73)
at org.apache.spark.scheduler.ShuffleMapTask.runTask( ShuffleMapTask.scala:41)
at org.apache.spark.scheduler.Task.run(Task.scala:89)
at org.apache.spark.executor.Executor$TaskRunner.run( Executor.scala:242)
at java.util.concurrent.ThreadPoolExecutor.runWorker( ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run( ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.janusgraph.core.JanusGraphException: Could not call index
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6.call( StandardJanusGraphTx.java: 1262)
at org.janusgraph.graphdb.query.QueryUtil. processIntersectingRetrievals( QueryUtil.java:255)
... 34 more
Caused by: org.janusgraph.core.JanusGraphException: Could not execute operation due to backend exception
at org.janusgraph.diskstorage.util.BackendOperation.execute( BackendOperation.java:57)
at org.janusgraph.diskstorage.BackendTransaction. executeRead( BackendTransaction.java:444)
at org.janusgraph.diskstorage.BackendTransaction.indexQuery( BackendTransaction.java:395)
at org.janusgraph.graphdb.query.graph.MultiKeySliceQuery. execute(MultiKeySliceQuery. java:51)
at org.janusgraph.graphdb.database.IndexSerializer. query(IndexSerializer.java: 529)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6$1. lambda$call$5( StandardJanusGraphTx.java: 1258)
at org.janusgraph.graphdb.query.profile.QueryProfiler.profile( QueryProfiler.java:97)
at org.janusgraph.graphdb.query.profile.QueryProfiler.profile( QueryProfiler.java:89)
at org.janusgraph.graphdb.query.profile.QueryProfiler.profile( QueryProfiler.java:81)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6$1. call(StandardJanusGraphTx. java:1258)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6$1. call(StandardJanusGraphTx. java:1255)
at com.google.common.cache.LocalCache$LocalManualCache$1. load(LocalCache.java:4742)
at com.google.common.cache.LocalCache$ LoadingValueReference. loadFuture(LocalCache.java: 3527)
at com.google.common.cache.LocalCache$Segment.loadSync( LocalCache.java:2319)
at com.google.common.cache.LocalCache$Segment. lockedGetOrLoad(LocalCache. java:2282)
at com.google.common.cache.LocalCache$Segment.get( LocalCache.java:2197)
at com.google.common.cache.LocalCache.get(LocalCache. java:3937)
at com.google.common.cache.LocalCache$LocalManualCache. get(LocalCache.java:4739)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6.call( StandardJanusGraphTx.java: 1255)
... 35 more
Caused by: org.janusgraph.diskstorage.TemporaryBackendException: Could not successfully complete backend operation due to repeated temporary exceptions after PT10S
at org.janusgraph.diskstorage.util.BackendOperation. executeDirect( BackendOperation.java:101)
at org.janusgraph.diskstorage.util.BackendOperation.execute( BackendOperation.java:55)
... 53 more
Caused by: org.janusgraph.diskstorage.TemporaryBackendException: Temporary failure in storage backend
at org.janusgraph.diskstorage.hbase. HBaseKeyColumnValueStore. getHelper( HBaseKeyColumnValueStore.java: 202)
at org.janusgraph.diskstorage.hbase. HBaseKeyColumnValueStore. getSlice( HBaseKeyColumnValueStore.java: 90)
at org.janusgraph.diskstorage.keycolumnvalue.KCVSProxy. getSlice(KCVSProxy.java:77)
at org.janusgraph.diskstorage.keycolumnvalue.KCVSProxy. getSlice(KCVSProxy.java:77)
at org.janusgraph.diskstorage.BackendTransaction$5.call( BackendTransaction.java:398)
at org.janusgraph.diskstorage.BackendTransaction$5.call( BackendTransaction.java:395)
at org.janusgraph.diskstorage.util.BackendOperation. executeDirect( BackendOperation.java:69)
... 54 more
Caused by: org.apache.hadoop.hbase.client. RetriesExhaustedException: Failed after attempts=35, exceptions:
Sat Aug 05 07:22:03 EDT 2017, RpcRetryingCaller{globalStartTime=1501932111280, pause=100, retries=35}, org.apache.hadoop.hbase. regionserver. RowTooBigException: rg.apache.hadoop.hbase. regionserver. RowTooBigException: Max row size allowed: 1073741824, but the row is bigger than that.
at org.apache.hadoop.hbase.regionserver.StoreScanner. next(StoreScanner.java:564)
at org.apache.hadoop.hbase.regionserver.KeyValueHeap. next(KeyValueHeap.java:147)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl. populateResult(HRegion.java: 5697)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl. nextInternal(HRegion.java: 5856)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl.nextRaw( HRegion.java:5634)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl.next( HRegion.java:5611)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl.next( HRegion.java:5597)
at org.apache.hadoop.hbase.regionserver.HRegion.get( HRegion.java:6792)
at org.apache.hadoop.hbase.regionserver.HRegion.get( HRegion.java:6770)
at org.apache.hadoop.hbase.regionserver.RSRpcServices. get(RSRpcServices.java:2023)
at org.apache.hadoop.hbase.protobuf.generated. ClientProtos$ClientService$2. callBlockingMethod( ClientProtos.java:33644)
at org.apache.hadoop.hbase.ipc.RpcServer.call(RpcServer.java: 2170)
at org.apache.hadoop.hbase.ipc.CallRunner.run(CallRunner. java:109)
at org.apache.hadoop.hbase.ipc.RpcExecutor$Handler.run( RpcExecutor.java:185)
at org.apache.hadoop.hbase.ipc.RpcExecutor$Handler.run( RpcExecutor.java:165)
On 8/6/2017 3:50 PM, HadoopMarc wrote:
Hi ... and others, I have been offline for a few weeks enjoying a holiday and will start looking into your questions and make the suggested corrections. Thanks for following the recipes and helping others with it.--
..., did you run the recipe on the same HDP sandbox and same Tinkerpop version? I remember (from 4 weeks ago) that copying the zookeeper.znode.parent property from the hbase configs to the janusgraph configs was essential to get janusgraph's HBaseInputFormat working (that is: read graph data for the spark tasks).
Cheers, Marc
Op maandag 24 juli 2017 10:12:13 UTC+2 schreef spi...@...:hi,Thanks for your post.I did it according to the post.But I ran into a problem.
15:58:49,110 INFO SecurityManager:58 - Changing view acls to: rc15:58:49,110 INFO SecurityManager:58 - Changing modify acls to: rc15:58:49,110 INFO SecurityManager:58 - SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(rc); users with modify permissions: Set(rc)15:58:49,111 INFO Client:58 - Submitting application 25 to ResourceManager15:58:49,320 INFO YarnClientImpl:274 - Submitted application application_1500608983535_002515:58:49,321 INFO SchedulerExtensionServices:58 - Starting Yarn extension services with app application_1500608983535_0025 and attemptId None15:58:50,325 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:50,326 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: N/AApplicationMaster RPC port: -1queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025/ user: rc15:58:51,330 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:52,333 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:53,335 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:54,337 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:55,340 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)
15:58:56,343 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:56,802 INFO YarnSchedulerBackend$YarnSchedulerEndpoint:58 - ApplicationMaster registered as NettyRpcEndpointRef(null) 15:58:56,822 INFO YarnClientSchedulerBackend:58 - Add WebUI Filter. org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter, Map(PROXY_HOSTS -> dl-rc-optd-ambari-master-v- test-1.host.dataengine.com,dl- rc-optd-ambari-master-v-test- 2.host.dataengine.com, PROXY_URI_BASES -> http://dl-rc-optd-ambari- master-v-test-1.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025,http://dl-rc-optd-ambari- master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_0025 ), /proxy/application_ 1500608983535_0025 15:58:56,824 INFO JettyUtils:58 - Adding filter: org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter 15:58:57,346 INFO Client:58 - Application report for application_1500608983535_0025 (state: RUNNING)15:58:57,347 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: 10.200.48.154ApplicationMaster RPC port: 0queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025/ user: rc15:58:57,348 INFO YarnClientSchedulerBackend:58 - Application application_1500608983535_0025 has started running.15:58:57,358 INFO Utils:58 - Successfully started service 'org.apache.spark.network.netty. NettyBlockTransferService' on port 47514. 15:58:57,358 INFO NettyBlockTransferService:58 - Server created on 4751415:58:57,360 INFO BlockManagerMaster:58 - Trying to register BlockManager15:58:57,363 INFO BlockManagerMasterEndpoint:58 - Registering block manager 10.200.48.112:47514 with 2.4 GB RAM, BlockManagerId(driver, 10.200.48.112, 47514)15:58:57,366 INFO BlockManagerMaster:58 - Registered BlockManager
15:58:57,585 INFO EventLoggingListener:58 - Logging events to hdfs:///spark-history/application_1500608983535_0025 15:59:07,177 WARN YarnSchedulerBackend$YarnSchedulerEndpoint:70 - Container marked as failed: container_e170_1500608983535_ 0025_01_000002 on host: dl-rc-optd-ambari-slave-v- test-1.host.dataengine.com. Exit status: 1. Diagnostics: Exception from container-launch. Container id: container_e170_1500608983535_0025_01_000002 Exit code: 1Stack trace: ExitCodeException exitCode=1:at org.apache.hadoop.util.Shell.runCommand(Shell.java:576) at org.apache.hadoop.util.Shell.run(Shell.java:487) at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute( Shell.java:753) at org.apache.hadoop.yarn.server.nodemanager. LinuxContainerExecutor. launchContainer( LinuxContainerExecutor.java: 371) at org.apache.hadoop.yarn.server.nodemanager.containermanager. launcher.ContainerLaunch.call( ContainerLaunch.java:303) at org.apache.hadoop.yarn.server.nodemanager.containermanager. launcher.ContainerLaunch.call( ContainerLaunch.java:82) at java.util.concurrent.FutureTask.run(FutureTask. java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker( ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run( ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)
Shell output: main : command provided 1main : run as user is rcmain : requested yarn user is rc
Container exited with a non-zero exit code 1
Display stack trace? [yN]15:59:57,702 WARN TransportChannelHandler:79 - Exception in connection from 10.200.48.155/10.200.48.155:50921 java.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil. java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java: 380) at io.netty.buffer.PooledUnsafeDirectByteBuf. setBytes( PooledUnsafeDirectByteBuf. java:313) at io.netty.buffer.AbstractByteBuf.writeBytes( AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes( NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$ NioByteUnsafe.read( AbstractNioByteChannel.java: 119) at io.netty.channel.nio.NioEventLoop. processSelectedKey( NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop. processSelectedKeysOptimized( NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop. processSelectedKeys( NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop. java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2. run(SingleThreadEventExecutor. java:111) at java.lang.Thread.run(Thread.java:748)
15:59:57,704 ERROR TransportResponseHandler:132 - Still have 1 requests outstanding when connection from 10.200.48.155/10.200.48.155:50921 is closed 15:59:57,706 WARN NettyRpcEndpointRef:91 - Error sending message [message = RequestExecutors(0,0,Map())] in 1 attemptsjava.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil. java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java: 380) at io.netty.buffer.PooledUnsafeDirectByteBuf. setBytes( PooledUnsafeDirectByteBuf. java:313) at io.netty.buffer.AbstractByteBuf.writeBytes( AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes( NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$ NioByteUnsafe.read( AbstractNioByteChannel.java: 119) at io.netty.channel.nio.NioEventLoop. processSelectedKey( NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop. processSelectedKeysOptimized( NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop. processSelectedKeys( NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop. java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2. run(SingleThreadEventExecutor. java:111) at java.lang.Thread.run(Thread.java:748) I am confused about that. Could you please help me?
在 2017年7月6日星期四 UTC+8下午4:15:37,HadoopMarc写道:
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring- janusgraph-for-spark-yarn.html
Regards, Marc
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgraph-use...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
Hi Marc - thank you very much for your reply. I like your idea
about moving regions manually and will try that. As to OLAP vs
OLTP (I assume Spark vs none), yes I have those times.
For a 1.5G table in HBase the count just using the gremlin shell
without using the SparkGraphComputer:
graph = JanusGraphFactory.open('conf/graph.properties')
g=graph.traversal()
g.V().count()
takes just under 1 minute. Using spark it takes about 2 hours. So something isn't right. They both return 3,842,755 vertices. When I run it with Spark, it hits one of the region servers hard - doing over 30k requests per second for those 2 hours.
-Joe
Hi Joseph,--
You ran into terrain I have not yet covered myself. Up till now I have been using the graben1437 PR for Titan and for OLAP I adopted a poor man's approach where node id's are distributed over spark tasks and each spark executor makes its own Titan/HBase connection. This performs well, but does not have the nice abstraction of the HBaseInputFormat.
So, no clear answer to this one, but just some thoughts:
- could you try to move some regions manually and see what it does to performance?
- how do your OLAP vertex count times compare to the OLTP count times?
- how does the sum of spark task execution times compare to the yarn start-to-end time difference you reported? In other words, how much of the start-to-end time is spent in waiting for timeouts?
- unless you managed to create a vertex with > 1GB size, the RowTooBigException sounds like a bug (which you can report on Jnausgraph's github page). Hbase does not like large rows at all, so vertex/edge properties should not have blob values.
@(David Robinson): do you have any additional thoughts on this?
Cheers, Marc
Op maandag 7 augustus 2017 23:12:02 UTC+2 schreef Joseph Obernberger:Hi Marc - I've been able to get it to run longer, but am now getting a RowTooBigException from HBase. How does JanusGraph store data in HBase? The current max size of a row in 1GByte, which makes me think this error is covering something else up.
What I'm seeing so far in testing with a 5 server cluster - each machine with 128G of RAM:
HBase table is 1.5G in size, split across 7 regions, and has 20,001,105 rows. To do a g.V().count() takes 2 hours and results in 3,842,755 verticies.Another HBase table is 5.7G in size split across 10 regions, is 57,620,276 rows, and took 6.5 hours to run the count and results in 10,859,491 nodes. When running, it looks like it hits one server very hard even though the YARN tasks are distributed across the cluster. One HBase node gets hammered.
The RowTooBigException is below. Anything to try? Thank you for any help!
org.janusgraph.core.
JanusGraphException: Could not process individual retrieval call
at org.janusgraph.graphdb.query.QueryUtil. processIntersectingRetrievals( QueryUtil.java:257)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6. execute(StandardJanusGraphTx. java:1269)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6. execute(StandardJanusGraphTx. java:1137)
at org.janusgraph.graphdb.query.QueryProcessor$ LimitAdjustingIterator. getNewIterator(QueryProcessor. java:209)
at org.janusgraph.graphdb.query.LimitAdjustingIterator. hasNext( LimitAdjustingIterator.java: 75)
at org.janusgraph.graphdb.query.ResultSetIterator. nextInternal( ResultSetIterator.java:54)
at org.janusgraph.graphdb.query.ResultSetIterator.next( ResultSetIterator.java:67)
at org.janusgraph.graphdb.query.ResultSetIterator.next( ResultSetIterator.java:28)
at com.google.common.collect.Iterators$7.computeNext( Iterators.java:651)
at com.google.common.collect.AbstractIterator. tryToComputeNext( AbstractIterator.java:143)
at com.google.common.collect.AbstractIterator.hasNext( AbstractIterator.java:138)
at org.janusgraph.hadoop.formats.util.input.current. JanusGraphHadoopSetupImpl. getTypeInspector( JanusGraphHadoopSetupImpl. java:60)
at org.janusgraph.hadoop.formats.util. JanusGraphVertexDeserializer.< init>( JanusGraphVertexDeserializer. java:55)
at org.janusgraph.hadoop.formats.util.GiraphInputFormat.lambda$ static$0(GiraphInputFormat. java:49)
at org.janusgraph.hadoop.formats.util.GiraphInputFormat$ RefCountedCloseable.acquire( GiraphInputFormat.java:100)
at org.janusgraph.hadoop.formats.util.GiraphRecordReader.<init> (GiraphRecordReader.java:47)
at org.janusgraph.hadoop.formats.util.GiraphInputFormat. createRecordReader( GiraphInputFormat.java:67)
at org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>( NewHadoopRDD.scala:166)
at org.apache.spark.rdd.NewHadoopRDD.compute( NewHadoopRDD.scala:133)
at org.apache.spark.rdd.NewHadoopRDD.compute( NewHadoopRDD.scala:65)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD. scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute( MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD. scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute( MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD. scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.scheduler.ShuffleMapTask.runTask( ShuffleMapTask.scala:73)
at org.apache.spark.scheduler.ShuffleMapTask.runTask( ShuffleMapTask.scala:41)
at org.apache.spark.scheduler.Task.run(Task.scala:89)
at org.apache.spark.executor.Executor$TaskRunner.run( Executor.scala:242)
at java.util.concurrent.ThreadPoolExecutor.runWorker( ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run( ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.janusgraph.core.JanusGraphException: Could not call index
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6.call( StandardJanusGraphTx.java: 1262)
at org.janusgraph.graphdb.query.QueryUtil. processIntersectingRetrievals( QueryUtil.java:255)
... 34 more
Caused by: org.janusgraph.core.JanusGraphException: Could not execute operation due to backend exception
at org.janusgraph.diskstorage.util.BackendOperation.execute( BackendOperation.java:57)
at org.janusgraph.diskstorage.BackendTransaction. executeRead( BackendTransaction.java:444)
at org.janusgraph.diskstorage.BackendTransaction.indexQuery( BackendTransaction.java:395)
at org.janusgraph.graphdb.query.graph.MultiKeySliceQuery. execute(MultiKeySliceQuery. java:51)
at org.janusgraph.graphdb.database.IndexSerializer. query(IndexSerializer.java: 529)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6$1. lambda$call$5( StandardJanusGraphTx.java: 1258)
at org.janusgraph.graphdb.query.profile.QueryProfiler.profile( QueryProfiler.java:97)
at org.janusgraph.graphdb.query.profile.QueryProfiler.profile( QueryProfiler.java:89)
at org.janusgraph.graphdb.query.profile.QueryProfiler.profile( QueryProfiler.java:81)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6$1. call(StandardJanusGraphTx. java:1258)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6$1. call(StandardJanusGraphTx. java:1255)
at com.google.common.cache.LocalCache$LocalManualCache$1. load(LocalCache.java:4742)
at com.google.common.cache.LocalCache$ LoadingValueReference. loadFuture(LocalCache.java: 3527)
at com.google.common.cache.LocalCache$Segment.loadSync( LocalCache.java:2319)
at com.google.common.cache.LocalCache$Segment. lockedGetOrLoad(LocalCache. java:2282)
at com.google.common.cache.LocalCache$Segment.get( LocalCache.java:2197)
at com.google.common.cache.LocalCache.get(LocalCache. java:3937)
at com.google.common.cache.LocalCache$LocalManualCache. get(LocalCache.java:4739)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6.call( StandardJanusGraphTx.java: 1255)
... 35 more
Caused by: org.janusgraph.diskstorage.TemporaryBackendException: Could not successfully complete backend operation due to repeated temporary exceptions after PT10S
at org.janusgraph.diskstorage.util.BackendOperation. executeDirect( BackendOperation.java:101)
at org.janusgraph.diskstorage.util.BackendOperation.execute( BackendOperation.java:55)
... 53 more
Caused by: org.janusgraph.diskstorage.TemporaryBackendException: Temporary failure in storage backend
at org.janusgraph.diskstorage.hbase. HBaseKeyColumnValueStore. getHelper( HBaseKeyColumnValueStore.java: 202)
at org.janusgraph.diskstorage.hbase. HBaseKeyColumnValueStore. getSlice( HBaseKeyColumnValueStore.java: 90)
at org.janusgraph.diskstorage.keycolumnvalue.KCVSProxy. getSlice(KCVSProxy.java:77)
at org.janusgraph.diskstorage.keycolumnvalue.KCVSProxy. getSlice(KCVSProxy.java:77)
at org.janusgraph.diskstorage.BackendTransaction$5.call( BackendTransaction.java:398)
at org.janusgraph.diskstorage.BackendTransaction$5.call( BackendTransaction.java:395)
at org.janusgraph.diskstorage.util.BackendOperation. executeDirect( BackendOperation.java:69)
... 54 more
Caused by: org.apache.hadoop.hbase.client. RetriesExhaustedException: Failed after attempts=35, exceptions:
Sat Aug 05 07:22:03 EDT 2017, RpcRetryingCaller{globalStartTime=1501932111280, pause=100, retries=35}, org.apache.hadoop.hbase. regionserver. RowTooBigException: rg.apache.hadoop.hbase. regionserver. RowTooBigException: Max row size allowed: 1073741824, but the row is bigger than that.
at org.apache.hadoop.hbase.regionserver.StoreScanner. next(StoreScanner.java:564)
at org.apache.hadoop.hbase.regionserver.KeyValueHeap. next(KeyValueHeap.java:147)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl. populateResult(HRegion.java: 5697)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl. nextInternal(HRegion.java: 5856)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl.nextRaw( HRegion.java:5634)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl.next( HRegion.java:5611)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl.next( HRegion.java:5597)
at org.apache.hadoop.hbase.regionserver.HRegion.get( HRegion.java:6792)
at org.apache.hadoop.hbase.regionserver.HRegion.get( HRegion.java:6770)
at org.apache.hadoop.hbase.regionserver.RSRpcServices. get(RSRpcServices.java:2023)
at org.apache.hadoop.hbase.protobuf.generated. ClientProtos$ClientService$2. callBlockingMethod( ClientProtos.java:33644)
at org.apache.hadoop.hbase.ipc.RpcServer.call(RpcServer.java: 2170)
at org.apache.hadoop.hbase.ipc.CallRunner.run(CallRunner. java:109)
at org.apache.hadoop.hbase.ipc.RpcExecutor$Handler.run( RpcExecutor.java:185)
at org.apache.hadoop.hbase.ipc.RpcExecutor$Handler.run( RpcExecutor.java:165)
On 8/6/2017 3:50 PM, HadoopMarc wrote:
Hi ... and others, I have been offline for a few weeks enjoying a holiday and will start looking into your questions and make the suggested corrections. Thanks for following the recipes and helping others with it.--
..., did you run the recipe on the same HDP sandbox and same Tinkerpop version? I remember (from 4 weeks ago) that copying the zookeeper.znode.parent property from the hbase configs to the janusgraph configs was essential to get janusgraph's HBaseInputFormat working (that is: read graph data for the spark tasks).
Cheers, Marc
Op maandag 24 juli 2017 10:12:13 UTC+2 schreef spi...@...:hi,Thanks for your post.I did it according to the post.But I ran into a problem.
15:58:49,110 INFO SecurityManager:58 - Changing view acls to: rc15:58:49,110 INFO SecurityManager:58 - Changing modify acls to: rc15:58:49,110 INFO SecurityManager:58 - SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(rc); users with modify permissions: Set(rc)15:58:49,111 INFO Client:58 - Submitting application 25 to ResourceManager15:58:49,320 INFO YarnClientImpl:274 - Submitted application application_1500608983535_002515:58:49,321 INFO SchedulerExtensionServices:58 - Starting Yarn extension services with app application_1500608983535_0025 and attemptId None15:58:50,325 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:50,326 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: N/AApplicationMaster RPC port: -1queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025/ user: rc15:58:51,330 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:52,333 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:53,335 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:54,337 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:55,340 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)
15:58:56,343 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:56,802 INFO YarnSchedulerBackend$YarnSchedulerEndpoint:58 - ApplicationMaster registered as NettyRpcEndpointRef(null) 15:58:56,822 INFO YarnClientSchedulerBackend:58 - Add WebUI Filter. org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter, Map(PROXY_HOSTS -> dl-rc-optd-ambari-master-v- test-1.host.dataengine.com,dl- rc-optd-ambari-master-v-test- 2.host.dataengine.com, PROXY_URI_BASES -> http://dl-rc-optd-ambari- master-v-test-1.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025,http://dl-rc-optd-ambari- master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_0025 ), /proxy/application_ 1500608983535_0025 15:58:56,824 INFO JettyUtils:58 - Adding filter: org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter 15:58:57,346 INFO Client:58 - Application report for application_1500608983535_0025 (state: RUNNING)15:58:57,347 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: 10.200.48.154ApplicationMaster RPC port: 0queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025/ user: rc15:58:57,348 INFO YarnClientSchedulerBackend:58 - Application application_1500608983535_0025 has started running.15:58:57,358 INFO Utils:58 - Successfully started service 'org.apache.spark.network.netty. NettyBlockTransferService' on port 47514. 15:58:57,358 INFO NettyBlockTransferService:58 - Server created on 4751415:58:57,360 INFO BlockManagerMaster:58 - Trying to register BlockManager15:58:57,363 INFO BlockManagerMasterEndpoint:58 - Registering block manager 10.200.48.112:47514 with 2.4 GB RAM, BlockManagerId(driver, 10.200.48.112, 47514)15:58:57,366 INFO BlockManagerMaster:58 - Registered BlockManager
15:58:57,585 INFO EventLoggingListener:58 - Logging events to hdfs:///spark-history/application_1500608983535_0025 15:59:07,177 WARN YarnSchedulerBackend$YarnSchedulerEndpoint:70 - Container marked as failed: container_e170_1500608983535_ 0025_01_000002 on host: dl-rc-optd-ambari-slave-v- test-1.host.dataengine.com. Exit status: 1. Diagnostics: Exception from container-launch. Container id: container_e170_1500608983535_0025_01_000002 Exit code: 1Stack trace: ExitCodeException exitCode=1:at org.apache.hadoop.util.Shell.runCommand(Shell.java:576) at org.apache.hadoop.util.Shell.run(Shell.java:487) at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute( Shell.java:753) at org.apache.hadoop.yarn.server.nodemanager. LinuxContainerExecutor. launchContainer( LinuxContainerExecutor.java: 371) at org.apache.hadoop.yarn.server.nodemanager.containermanager. launcher.ContainerLaunch.call( ContainerLaunch.java:303) at org.apache.hadoop.yarn.server.nodemanager.containermanager. launcher.ContainerLaunch.call( ContainerLaunch.java:82) at java.util.concurrent.FutureTask.run(FutureTask. java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker( ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run( ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)
Shell output: main : command provided 1main : run as user is rcmain : requested yarn user is rc
Container exited with a non-zero exit code 1
Display stack trace? [yN]15:59:57,702 WARN TransportChannelHandler:79 - Exception in connection from 10.200.48.155/10.200.48.155:50921 java.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil. java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java: 380) at io.netty.buffer.PooledUnsafeDirectByteBuf. setBytes( PooledUnsafeDirectByteBuf. java:313) at io.netty.buffer.AbstractByteBuf.writeBytes( AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes( NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$ NioByteUnsafe.read( AbstractNioByteChannel.java: 119) at io.netty.channel.nio.NioEventLoop. processSelectedKey( NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop. processSelectedKeysOptimized( NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop. processSelectedKeys( NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop. java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2. run(SingleThreadEventExecutor. java:111) at java.lang.Thread.run(Thread.java:748)
15:59:57,704 ERROR TransportResponseHandler:132 - Still have 1 requests outstanding when connection from 10.200.48.155/10.200.48.155:50921 is closed 15:59:57,706 WARN NettyRpcEndpointRef:91 - Error sending message [message = RequestExecutors(0,0,Map())] in 1 attemptsjava.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil. java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java: 380) at io.netty.buffer.PooledUnsafeDirectByteBuf. setBytes( PooledUnsafeDirectByteBuf. java:313) at io.netty.buffer.AbstractByteBuf.writeBytes( AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes( NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$ NioByteUnsafe.read( AbstractNioByteChannel.java: 119) at io.netty.channel.nio.NioEventLoop. processSelectedKey( NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop. processSelectedKeysOptimized( NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop. processSelectedKeys( NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop. java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2. run(SingleThreadEventExecutor. java:111) at java.lang.Thread.run(Thread.java:748) I am confused about that. Could you please help me?
在 2017年7月6日星期四 UTC+8下午4:15:37,HadoopMarc写道:
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring- janusgraph-for-spark-yarn.html
Regards, Marc
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgraph-use...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgra...@....
For more options, visit https://groups.google.com/d/optout.
But when I am trying to execute the following where cluster is mapr and spark on yarn
plugin activated: tinkerpop.tinkergraph
gremlin> graph = GraphFactory.open('conf/hadoop-graph/hadoop-load.properties')
==>hadoopgraph[gryoinputformat->nulloutputformat]
gremlin> g = graph.traversal(computer(SparkGraphComputer))
==>graphtraversalsource[hadoopgraph[gryoinputformat->nulloutputformat], sparkgraphcomputer]
gremlin> g.V().count()
hadoop-load.properties ( I tried all different combinations as commented below each time its the same error)
#
# SparkGraphComputer Configuration
#
spark.master=yarn-client
spark.yarn.queue=cmp
mapred.job.queue.name=cmp
#spark.driver.allowMultipleContexts=true
#spark.executor.memory=4g
#spark.ui.port=20000
spark.serializer=org.apache.spark.serializer.KryoSerializer
spark.yarn.appMasterEnv.CLASSPATH=$CLASSPATH:/opt/mapr/hadoop/hadoop-2.7.0/etc/hadoop:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/common/lib/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/common/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/hdfs:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/hdfs/lib/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/hdfs/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/yarn/lib/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/yarn/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/mapreduce/lib/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/mapreduce/*:/contrib/capacity-scheduler/*.jar:/opt/mapr/lib/kvstore*.jar:/opt/mapr/lib/libprotodefs*.jar:/opt/mapr/lib/baseutils*.jar:/opt/mapr/lib/maprutil*.jar:/opt/mapr/lib/json-20080701.jar:/opt/mapr/lib/flexjson-2.1.jar
#spark.executor.instances=10
#spark.executor.cores=2
#spark.executor.CoarseGrainedExecutorBackend.cores=2
#spark.executor.CoarseGrainedExecutorBackend.driver=FIXME
#spark.executor.CoarseGrainedExecutorBackend.stopping=false
#spark.streaming.stopGracefullyOnShutdown=true
#spark.yarn.driver.memoryOverhead=4g
#spark.yarn.executor.memoryOverhead=1024
#spark.yarn.am.extraJavaOptions=-Dhdp.version=2.3.0.0-2557
--------------------------------------------------------------------------------------------------------------
yarn log
------------------------------------------------------------------------------------------------------------
When the last command is executed, driver abruptly shuts down in yarn container and shuts down the spark context too with following error from Yarn logs
Container: container_e27_1501284102300_47651_01_000008 on abcd.com_8039
LogType:stderr
Log Upload Time:Mon Jul 31 14:08:42 -0700 2017
LogLength:2441
Log Contents:
17/07/31 14:08:05 INFO executor.CoarseGrainedExecutorBackend: Registered signal handlers for [TERM, HUP, INT]
17/07/31 14:08:05 INFO spark.SecurityManager: Changing view acls to: cmphs
17/07/31 14:08:05 INFO spark.SecurityManager: Changing modify acls to: cmphs
17/07/31 14:08:05 INFO spark.SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(cmphs); users with modify permissions: Set(cmphs)
17/07/31 14:08:06 INFO spark.SecurityManager: Changing view acls to: cmphs
17/07/31 14:08:06 INFO spark.SecurityManager: Changing modify acls to: cmphs
17/07/31 14:08:06 INFO spark.SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(cmphs); users with modify permissions: Set(cmphs)
17/07/31 14:08:06 INFO slf4j.Slf4jLogger: Slf4jLogger started
17/07/31 14:08:06 INFO Remoting: Starting remoting
17/07/31 14:08:06 INFO Remoting: Remoting started; listening on addresses :[akka.tcp://sparkExecutorActorSystem@...:36376]
17/07/31 14:08:06 INFO util.Utils: Successfully started service 'sparkExecutorActorSystem' on port 36376.
17/07/31 14:08:06 INFO storage.DiskBlockManager: Created local directory at /tmp/hadoop-mapr/nm-local-dir/usercache/cmphs/appcache/application_1501284102300_47651/blockmgr-244e0062-016e-4402-85c9-69f2ab9ef9d2
17/07/31 14:08:06 INFO storage.MemoryStore: MemoryStore started with capacity 2.7 GB
17/07/31 14:08:06 INFO executor.CoarseGrainedExecutorBackend: Connecting to driver: spark://CoarseGrainedScheduler@...:43768
17/07/31 14:08:06 INFO executor.CoarseGrainedExecutorBackend: Successfully registered with driver
17/07/31 14:08:06 INFO executor.Executor: Starting executor ID 7 on host abcd.com
17/07/31 14:08:06 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 44208.
17/07/31 14:08:06 INFO netty.NettyBlockTransferService: Server created on 44208
17/07/31 14:08:06 INFO storage.BlockManagerMaster: Trying to register BlockManager
17/07/31 14:08:06 INFO storage.BlockManagerMaster: Registered BlockManager
17/07/31 14:08:41 INFO executor.CoarseGrainedExecutorBackend: Driver commanded a shutdown
17/07/31 14:08:41 INFO storage.MemoryStore: MemoryStore cleared
17/07/31 14:08:41 INFO storage.BlockManager: BlockManager stopped
17/07/31 14:08:41 INFO util.ShutdownHookManager: Shutdown hook called
End of LogType:stderr
LogType:stdout
Log Upload Time:Mon Jul 31 14:08:42 -0700 2017
LogLength:0
Log Contents:
End of LogType:stdout
I am stuck wit h this error , request help here.
Could you let us know a little more about your configuration? What is your storage backend for JanusGraph (HBase/Cassandra)? I actually do not see an error in your log, but at the very least you'll need to defein spark.executor.extraClassPath to point to the various jars required. Are there other logs you can look at such as the container logs for YARN?
I assume you've see Marc's blog post:
http://yaaics.blogspot.com/2017/07/configuring-janusgraph-for-spark-yarn.html
-Joe
Hi Marc,--
Request your help, I am runnign Janusgraph with maprdb as backend, I have successfuly been able to create GodofGraphs example on M7 as backend
But when I am trying to execute the following where cluster is mapr and spark on yarn
plugin activated: tinkerpop.tinkergraph
gremlin> graph = GraphFactory.open('conf/hadoop-graph/hadoop-load.properties')
==>hadoopgraph[gryoinputformat->nulloutputformat]
gremlin> g = graph.traversal(computer(SparkGraphComputer))
==>graphtraversalsource[hadoopgraph[gryoinputformat->nulloutputformat], sparkgraphcomputer]
gremlin> g.V().count()
hadoop-load.properties ( I tried all different combinations as commented below each time its the same error)
#
# SparkGraphComputer Configuration
#
spark.master=yarn-client
spark.yarn.queue=cmp
mapred.job.queue.name=cmp
#spark.driver.allowMultipleContexts=true
#spark.executor.memory=4g
#spark.ui.port=20000
spark.serializer=org.apache.spark.serializer.KryoSerializer
spark.yarn.appMasterEnv.CLASSPATH=$CLASSPATH:/opt/mapr/hadoop/hadoop-2.7.0/etc/hadoop:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/common/lib/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/common/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/hdfs:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/hdfs/lib/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/hdfs/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/yarn/lib/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/yarn/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/mapreduce/lib/*:/opt/mapr/hadoop/hadoop-2.7.0/share/hadoop/mapreduce/*:/contrib/capacity-scheduler/*.jar:/opt/mapr/lib/kvstore*.jar:/opt/mapr/lib/libprotodefs*.jar:/opt/mapr/lib/baseutils*.jar:/opt/mapr/lib/maprutil*.jar:/opt/mapr/lib/json-20080701.jar:/opt/mapr/lib/flexjson-2.1.jar
#spark.executor.instances=10
#spark.executor.cores=2
#spark.executor.CoarseGrainedExecutorBackend.cores=2
#spark.executor.CoarseGrainedExecutorBackend.driver=FIXME
#spark.executor.CoarseGrainedExecutorBackend.stopping=false
#spark.streaming.stopGracefullyOnShutdown=true
#spark.yarn.driver.memoryOverhead=4g
#spark.yarn.executor.memoryOverhead=1024
#spark.yarn.am.extraJavaOptions=-Dhdp.version=2.3.0.0-2557
--------------------------------------------------------------------------------------------------------------
yarn log
------------------------------------------------------------------------------------------------------------
When the last command is executed, driver abruptly shuts down in yarn container and shuts down the spark context too with following error from Yarn logs
Container: container_e27_1501284102300_47651_01_000008 on abcd.com_8039
LogType:stderr
Log Upload Time:Mon Jul 31 14:08:42 -0700 2017
LogLength:2441
Log Contents:
17/07/31 14:08:05 INFO executor.CoarseGrainedExecutorBackend: Registered signal handlers for [TERM, HUP, INT]
17/07/31 14:08:05 INFO spark.SecurityManager: Changing view acls to: cmphs
17/07/31 14:08:05 INFO spark.SecurityManager: Changing modify acls to: cmphs
17/07/31 14:08:05 INFO spark.SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(cmphs); users with modify permissions: Set(cmphs)
17/07/31 14:08:06 INFO spark.SecurityManager: Changing view acls to: cmphs
17/07/31 14:08:06 INFO spark.SecurityManager: Changing modify acls to: cmphs
17/07/31 14:08:06 INFO spark.SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(cmphs); users with modify permissions: Set(cmphs)
17/07/31 14:08:06 INFO slf4j.Slf4jLogger: Slf4jLogger started
17/07/31 14:08:06 INFO Remoting: Starting remoting
17/07/31 14:08:06 INFO Remoting: Remoting started; listening on addresses :[akka.tcp://sparkExecutorActorSystem@...:36376]
17/07/31 14:08:06 INFO util.Utils: Successfully started service 'sparkExecutorActorSystem' on port 36376.
17/07/31 14:08:06 INFO storage.DiskBlockManager: Created local directory at /tmp/hadoop-mapr/nm-local-dir/usercache/cmphs/appcache/application_1501284102300_47651/blockmgr-244e0062-016e-4402-85c9-69f2ab9ef9d2
17/07/31 14:08:06 INFO storage.MemoryStore: MemoryStore started with capacity 2.7 GB
17/07/31 14:08:06 INFO executor.CoarseGrainedExecutorBackend: Connecting to driver: spark://CoarseGrainedScheduler@...:43768
17/07/31 14:08:06 INFO executor.CoarseGrainedExecutorBackend: Successfully registered with driver
17/07/31 14:08:06 INFO executor.Executor: Starting executor ID 7 on host abcd.com
17/07/31 14:08:06 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 44208.
17/07/31 14:08:06 INFO netty.NettyBlockTransferService: Server created on 44208
17/07/31 14:08:06 INFO storage.BlockManagerMaster: Trying to register BlockManager
17/07/31 14:08:06 INFO storage.BlockManagerMaster: Registered BlockManager
17/07/31 14:08:41 INFO executor.CoarseGrainedExecutorBackend: Driver commanded a shutdown
17/07/31 14:08:41 INFO storage.MemoryStore: MemoryStore cleared
17/07/31 14:08:41 INFO storage.BlockManager: BlockManager stopped
17/07/31 14:08:41 INFO util.ShutdownHookManager: Shutdown hook called
End of LogType:stderrLogType:stdout
Log Upload Time:Mon Jul 31 14:08:42 -0700 2017
LogLength:0
Log Contents:
End of LogType:stdout
I am stuck wit h this error , request help here.
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgra...@....
For more options, visit https://groups.google.com/d/optout.
Hi Marc - I did try splitting regions. What happens when I run the SparkGraphComputer job, is that it seems to hit one region server hard, then moves onto the next; appears to run serially. All that said, I think the big issue is that running with Spark for a count takes 2 hours and running without takes 2 minutes. Perhaps the SparkGraphComputer is not the tool to be used for handling large graphs? Although, I'm not sure what the purpose is then?
For reference, here is my Hadoop configuration file using Cloudera CDH 5.10.0 and JanusGraph 0.1.0:
Config:
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#
# Hadoop Graph Configuration
#
gremlin.graph=org.apache.tinkerpop.gremlin.hadoop.structure.HadoopGraph
gremlin.hadoop.graphInputFormat=org.janusgraph.hadoop.formats.hbase.HBaseInputFormat
gremlin.hadoop.graphOutputFormat=org.apache.tinkerpop.gremlin.hadoop.structure.io.gryo.GryoOutputFormat
gremlin.hadoop.memoryOutputFormat=org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat
gremlin.hadoop.memoryOutputFormat=org.apache.tinkerpop.gremlin.hadoop.structure.io.gryo.GryoOutputFormat
gremlin.hadoop.deriveMemory=false
gremlin.hadoop.jarsInDistributedCache=true
gremlin.hadoop.inputLocation=none
gremlin.hadoop.outputLocation=output
log4j.rootLogger=WARNING, STDOUT
log4j.logger.deng=WARNING
log4j.appender.STDOUT=org.apache.log4j.ConsoleAppender
org.slf4j.simpleLogger.defaultLogLevel=warn
#
# JanusGraph HBase InputFormat configuration
#
janusgraphmr.ioformat.conf.storage.backend=hbase
janusgraphmr.ioformat.conf.storage.hostname=host003:2181,host004:2181,host005:2181
janusgraphmr.ioformat.conf.storage.hbase.table=Large2
janusgraphmr.ioformat.conf.storage.hbase.region-count=5
janusgraphmr.ioformat.conf.storage.hbase.regions-per-server=5
janusgraphmr.ioformat.conf.storage.hbase.short-cf-names=false
# Security configs are needed in case of a secure cluster
zookeeper.znode.parent=/hbase
#
# SparkGraphComputer with Yarn Configuration
#
#spark.master=yarn-client
spark.executor.extraJavaOptions=-XX:ReservedCodeCacheSize=100M
-XX:MaxMetaspaceSize=256m -XX:CompressedClassSpaceSize=256m
-Dlogback.configurationFile=logback.xml
spark.driver.extraJavaOptons=-XX:ReservedCodeCacheSize=100M
-XX:MaxMetaspaceSize=256m -XX:CompressedClassSpaceSize=256m
spark.master=yarn-cluster
spark.executor.memory=10240m
spark.serializer=org.apache.tinkerpop.gremlin.spark.structure.io.gryo.GryoSerializer
spark.yarn.dist.archives=/home/graph/janusgraph-0.1.0-SNAPSHOT-hadoop2/lib.zip
spark.yarn.dist.files=/opt/cloudera/parcels/CDH/jars/janusgraph-hbase-0.1.0-SNAPSHOT.jar,/home/graph/janusgraph-0.1.0-SNAPSHOT-hadoop2/conf/logback.xml
spark.yarn.dist.jars=/opt/cloudera/parcels/CDH/jars/janusgraph-hbase-0.1.0-SNAPSHOT.jar
spark.yarn.appMasterEnv.CLASSPATH=/etc/haddop/conf:/etc/hbase/conf:./lib.zip/*
spark.executor.extraLibraryPath=/opt/cloudera/parcels/CDH/lib/hadoop/native:/opt/cloudera/parcels/CDH/lib/hadoop-0.20-mapreduce/lib/native/Linux-amd64-64
spark.akka.frameSize=1024
spark.kyroserializer.buffer.max=1600m
spark.network.timeout=90000
spark.executor.heartbeatInterval=100000
spark.cores.max=64
#
# Relevant configs from spark-defaults.conf
#
spark.authenticate=false
spark.dynamicAllocation.enabled=true
spark.dynamicAllocation.executorIdleTimeout=60
spark.dynamicAllocation.minExecutors=0
spark.dynamicAllocation.schedulerBacklogTimeout=1
spark.eventLog.enabled=true
spark.serializer=org.apache.spark.serializer.KryoSerializer
spark.shuffle.service.enabled=true
spark.shuffle.service.port=7337
spark.ui.killEnabled=true
spark.executor.extraClassPath=/opt/cloudera/parcels/CDH/jars/janusgraph-hbase-0.1.0-SNAPSHOT.jar:./lib.zip/*:\
/opt/cloudera/parcels/CDH/lib/hbase/bin/../conf:\
/opt/cloudera/parcels/CDH/lib/hbase/bin/..:\
/opt/cloudera/parcels/CDH/lib/spark/assembly/lib/spark-assembly.jar:\
/usr/lib/jvm/java-openjdk/jre/lib/rt.jar:\
/opt/cloudera/parcels/CDH/lib/hbase/bin/../lib/*:\
/etc/hadoop/conf:\
/etc/hbase/conf:\
/opt/cloudera/parcels/CDH/lib/hadoop/libexec/../../hadoop/lib/*:\
/opt/cloudera/parcels/CDH/lib/hadoop/libexec/../../hadoop/.//*:\
/opt/cloudera/parcels/CDH/lib/hadoop/libexec/../../hadoop-yarn/lib/*:\
/opt/cloudera/parcels/CDH/lib/hadoop/libexec/../../hadoop-yarn/.//*
spark.eventLog.dir=hdfs://host001:8020/user/spark/applicationHistory
spark.yarn.historyServer.address=http://host001:18088
spark.yarn.jar=local:/opt/cloudera/parcels/CDH-5.10.0-1.cdh5.10.0.p0.41/lib/spark/lib/spark-assembly.jar
spark.driver.extraLibraryPath=/opt/cloudera/parcels/CDH-5.10.0-1.cdh5.10.0.p0.41/lib/hadoop/lib/native
spark.executor.extraLibraryPath=/opt/cloudera/parcels/CDH-5.10.0-1.cdh5.10.0.p0.41/lib/hadoop/lib/native
spark.yarn.am.extraLibraryPath=/opt/cloudera/parcels/CDH-5.10.0-1.cdh5.10.0.p0.41/lib/hadoop/lib/native
spark.yarn.config.gatewayPath=/opt/cloudera/parcels
spark.yarn.config.replacementPath={{HADOOP_COMMON_HOME}}/../../..
spark.master=yarn-client
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Joe
Hi Joseph,--
You ran into terrain I have not yet covered myself. Up till now I have been using the graben1437 PR for Titan and for OLAP I adopted a poor man's approach where node id's are distributed over spark tasks and each spark executor makes its own Titan/HBase connection. This performs well, but does not have the nice abstraction of the HBaseInputFormat.
So, no clear answer to this one, but just some thoughts:
- could you try to move some regions manually and see what it does to performance?
- how do your OLAP vertex count times compare to the OLTP count times?
- how does the sum of spark task execution times compare to the yarn start-to-end time difference you reported? In other words, how much of the start-to-end time is spent in waiting for timeouts?
- unless you managed to create a vertex with > 1GB size, the RowTooBigException sounds like a bug (which you can report on Jnausgraph's github page). Hbase does not like large rows at all, so vertex/edge properties should not have blob values.
@(David Robinson): do you have any additional thoughts on this?
Cheers, Marc
Op maandag 7 augustus 2017 23:12:02 UTC+2 schreef Joseph Obernberger:Hi Marc - I've been able to get it to run longer, but am now getting a RowTooBigException from HBase. How does JanusGraph store data in HBase? The current max size of a row in 1GByte, which makes me think this error is covering something else up.
What I'm seeing so far in testing with a 5 server cluster - each machine with 128G of RAM:
HBase table is 1.5G in size, split across 7 regions, and has 20,001,105 rows. To do a g.V().count() takes 2 hours and results in 3,842,755 verticies.Another HBase table is 5.7G in size split across 10 regions, is 57,620,276 rows, and took 6.5 hours to run the count and results in 10,859,491 nodes. When running, it looks like it hits one server very hard even though the YARN tasks are distributed across the cluster. One HBase node gets hammered.
The RowTooBigException is below. Anything to try? Thank you for any help!
org.janusgraph.core.
JanusGraphException: Could not process individual retrieval call
at org.janusgraph.graphdb.query.QueryUtil. processIntersectingRetrievals( QueryUtil.java:257)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6. execute(StandardJanusGraphTx. java:1269)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6. execute(StandardJanusGraphTx. java:1137)
at org.janusgraph.graphdb.query.QueryProcessor$ LimitAdjustingIterator. getNewIterator(QueryProcessor. java:209)
at org.janusgraph.graphdb.query.LimitAdjustingIterator. hasNext( LimitAdjustingIterator.java: 75)
at org.janusgraph.graphdb.query.ResultSetIterator. nextInternal( ResultSetIterator.java:54)
at org.janusgraph.graphdb.query.ResultSetIterator.next( ResultSetIterator.java:67)
at org.janusgraph.graphdb.query.ResultSetIterator.next( ResultSetIterator.java:28)
at com.google.common.collect.Iterators$7.computeNext( Iterators.java:651)
at com.google.common.collect.AbstractIterator. tryToComputeNext( AbstractIterator.java:143)
at com.google.common.collect.AbstractIterator.hasNext( AbstractIterator.java:138)
at org.janusgraph.hadoop.formats.util.input.current. JanusGraphHadoopSetupImpl. getTypeInspector( JanusGraphHadoopSetupImpl. java:60)
at org.janusgraph.hadoop.formats.util. JanusGraphVertexDeserializer.< init>( JanusGraphVertexDeserializer. java:55)
at org.janusgraph.hadoop.formats.util.GiraphInputFormat.lambda$ static$0(GiraphInputFormat. java:49)
at org.janusgraph.hadoop.formats.util.GiraphInputFormat$ RefCountedCloseable.acquire( GiraphInputFormat.java:100)
at org.janusgraph.hadoop.formats.util.GiraphRecordReader.<init> (GiraphRecordReader.java:47)
at org.janusgraph.hadoop.formats.util.GiraphInputFormat. createRecordReader( GiraphInputFormat.java:67)
at org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>( NewHadoopRDD.scala:166)
at org.apache.spark.rdd.NewHadoopRDD.compute( NewHadoopRDD.scala:133)
at org.apache.spark.rdd.NewHadoopRDD.compute( NewHadoopRDD.scala:65)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD. scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute( MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD. scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute( MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD. scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.scheduler.ShuffleMapTask.runTask( ShuffleMapTask.scala:73)
at org.apache.spark.scheduler.ShuffleMapTask.runTask( ShuffleMapTask.scala:41)
at org.apache.spark.scheduler.Task.run(Task.scala:89)
at org.apache.spark.executor.Executor$TaskRunner.run( Executor.scala:242)
at java.util.concurrent.ThreadPoolExecutor.runWorker( ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run( ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.janusgraph.core.JanusGraphException: Could not call index
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6.call( StandardJanusGraphTx.java: 1262)
at org.janusgraph.graphdb.query.QueryUtil. processIntersectingRetrievals( QueryUtil.java:255)
... 34 more
Caused by: org.janusgraph.core.JanusGraphException: Could not execute operation due to backend exception
at org.janusgraph.diskstorage.util.BackendOperation.execute( BackendOperation.java:57)
at org.janusgraph.diskstorage.BackendTransaction. executeRead( BackendTransaction.java:444)
at org.janusgraph.diskstorage.BackendTransaction.indexQuery( BackendTransaction.java:395)
at org.janusgraph.graphdb.query.graph.MultiKeySliceQuery. execute(MultiKeySliceQuery. java:51)
at org.janusgraph.graphdb.database.IndexSerializer. query(IndexSerializer.java: 529)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6$1. lambda$call$5( StandardJanusGraphTx.java: 1258)
at org.janusgraph.graphdb.query.profile.QueryProfiler.profile( QueryProfiler.java:97)
at org.janusgraph.graphdb.query.profile.QueryProfiler.profile( QueryProfiler.java:89)
at org.janusgraph.graphdb.query.profile.QueryProfiler.profile( QueryProfiler.java:81)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6$1. call(StandardJanusGraphTx. java:1258)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6$1. call(StandardJanusGraphTx. java:1255)
at com.google.common.cache.LocalCache$LocalManualCache$1. load(LocalCache.java:4742)
at com.google.common.cache.LocalCache$ LoadingValueReference. loadFuture(LocalCache.java: 3527)
at com.google.common.cache.LocalCache$Segment.loadSync( LocalCache.java:2319)
at com.google.common.cache.LocalCache$Segment. lockedGetOrLoad(LocalCache. java:2282)
at com.google.common.cache.LocalCache$Segment.get( LocalCache.java:2197)
at com.google.common.cache.LocalCache.get(LocalCache. java:3937)
at com.google.common.cache.LocalCache$LocalManualCache. get(LocalCache.java:4739)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6.call( StandardJanusGraphTx.java: 1255)
... 35 more
Caused by: org.janusgraph.diskstorage.TemporaryBackendException: Could not successfully complete backend operation due to repeated temporary exceptions after PT10S
at org.janusgraph.diskstorage.util.BackendOperation. executeDirect( BackendOperation.java:101)
at org.janusgraph.diskstorage.util.BackendOperation.execute( BackendOperation.java:55)
... 53 more
Caused by: org.janusgraph.diskstorage.TemporaryBackendException: Temporary failure in storage backend
at org.janusgraph.diskstorage.hbase. HBaseKeyColumnValueStore. getHelper( HBaseKeyColumnValueStore.java: 202)
at org.janusgraph.diskstorage.hbase. HBaseKeyColumnValueStore. getSlice( HBaseKeyColumnValueStore.java: 90)
at org.janusgraph.diskstorage.keycolumnvalue.KCVSProxy. getSlice(KCVSProxy.java:77)
at org.janusgraph.diskstorage.keycolumnvalue.KCVSProxy. getSlice(KCVSProxy.java:77)
at org.janusgraph.diskstorage.BackendTransaction$5.call( BackendTransaction.java:398)
at org.janusgraph.diskstorage.BackendTransaction$5.call( BackendTransaction.java:395)
at org.janusgraph.diskstorage.util.BackendOperation. executeDirect( BackendOperation.java:69)
... 54 more
Caused by: org.apache.hadoop.hbase.client. RetriesExhaustedException: Failed after attempts=35, exceptions:
Sat Aug 05 07:22:03 EDT 2017, RpcRetryingCaller{globalStartTime=1501932111280, pause=100, retries=35}, org.apache.hadoop.hbase. regionserver. RowTooBigException: rg.apache.hadoop.hbase. regionserver. RowTooBigException: Max row size allowed: 1073741824, but the row is bigger than that.
at org.apache.hadoop.hbase.regionserver.StoreScanner. next(StoreScanner.java:564)
at org.apache.hadoop.hbase.regionserver.KeyValueHeap. next(KeyValueHeap.java:147)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl. populateResult(HRegion.java: 5697)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl. nextInternal(HRegion.java: 5856)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl.nextRaw( HRegion.java:5634)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl.next( HRegion.java:5611)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl.next( HRegion.java:5597)
at org.apache.hadoop.hbase.regionserver.HRegion.get( HRegion.java:6792)
at org.apache.hadoop.hbase.regionserver.HRegion.get( HRegion.java:6770)
at org.apache.hadoop.hbase.regionserver.RSRpcServices. get(RSRpcServices.java:2023)
at org.apache.hadoop.hbase.protobuf.generated. ClientProtos$ClientService$2. callBlockingMethod( ClientProtos.java:33644)
at org.apache.hadoop.hbase.ipc.RpcServer.call(RpcServer.java: 2170)
at org.apache.hadoop.hbase.ipc.CallRunner.run(CallRunner. java:109)
at org.apache.hadoop.hbase.ipc.RpcExecutor$Handler.run( RpcExecutor.java:185)
at org.apache.hadoop.hbase.ipc.RpcExecutor$Handler.run( RpcExecutor.java:165)
On 8/6/2017 3:50 PM, HadoopMarc wrote:
Hi ... and others, I have been offline for a few weeks enjoying a holiday and will start looking into your questions and make the suggested corrections. Thanks for following the recipes and helping others with it.--
..., did you run the recipe on the same HDP sandbox and same Tinkerpop version? I remember (from 4 weeks ago) that copying the zookeeper.znode.parent property from the hbase configs to the janusgraph configs was essential to get janusgraph's HBaseInputFormat working (that is: read graph data for the spark tasks).
Cheers, Marc
Op maandag 24 juli 2017 10:12:13 UTC+2 schreef spi...@...:hi,Thanks for your post.I did it according to the post.But I ran into a problem.
15:58:49,110 INFO SecurityManager:58 - Changing view acls to: rc15:58:49,110 INFO SecurityManager:58 - Changing modify acls to: rc15:58:49,110 INFO SecurityManager:58 - SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(rc); users with modify permissions: Set(rc)15:58:49,111 INFO Client:58 - Submitting application 25 to ResourceManager15:58:49,320 INFO YarnClientImpl:274 - Submitted application application_1500608983535_002515:58:49,321 INFO SchedulerExtensionServices:58 - Starting Yarn extension services with app application_1500608983535_0025 and attemptId None15:58:50,325 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:50,326 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: N/AApplicationMaster RPC port: -1queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025/ user: rc15:58:51,330 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:52,333 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:53,335 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:54,337 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:55,340 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)
15:58:56,343 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:56,802 INFO YarnSchedulerBackend$YarnSchedulerEndpoint:58 - ApplicationMaster registered as NettyRpcEndpointRef(null) 15:58:56,822 INFO YarnClientSchedulerBackend:58 - Add WebUI Filter. org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter, Map(PROXY_HOSTS -> dl-rc-optd-ambari-master-v- test-1.host.dataengine.com,dl- rc-optd-ambari-master-v-test- 2.host.dataengine.com, PROXY_URI_BASES -> http://dl-rc-optd-ambari- master-v-test-1.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025,http://dl-rc-optd-ambari- master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_0025 ), /proxy/application_ 1500608983535_0025 15:58:56,824 INFO JettyUtils:58 - Adding filter: org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter 15:58:57,346 INFO Client:58 - Application report for application_1500608983535_0025 (state: RUNNING)15:58:57,347 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: 10.200.48.154ApplicationMaster RPC port: 0queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025/ user: rc15:58:57,348 INFO YarnClientSchedulerBackend:58 - Application application_1500608983535_0025 has started running.15:58:57,358 INFO Utils:58 - Successfully started service 'org.apache.spark.network.netty. NettyBlockTransferService' on port 47514. 15:58:57,358 INFO NettyBlockTransferService:58 - Server created on 4751415:58:57,360 INFO BlockManagerMaster:58 - Trying to register BlockManager15:58:57,363 INFO BlockManagerMasterEndpoint:58 - Registering block manager 10.200.48.112:47514 with 2.4 GB RAM, BlockManagerId(driver, 10.200.48.112, 47514)15:58:57,366 INFO BlockManagerMaster:58 - Registered BlockManager
15:58:57,585 INFO EventLoggingListener:58 - Logging events to hdfs:///spark-history/application_1500608983535_0025 15:59:07,177 WARN YarnSchedulerBackend$YarnSchedulerEndpoint:70 - Container marked as failed: container_e170_1500608983535_ 0025_01_000002 on host: dl-rc-optd-ambari-slave-v- test-1.host.dataengine.com. Exit status: 1. Diagnostics: Exception from container-launch. Container id: container_e170_1500608983535_0025_01_000002 Exit code: 1Stack trace: ExitCodeException exitCode=1:at org.apache.hadoop.util.Shell.runCommand(Shell.java:576) at org.apache.hadoop.util.Shell.run(Shell.java:487) at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute( Shell.java:753) at org.apache.hadoop.yarn.server.nodemanager. LinuxContainerExecutor. launchContainer( LinuxContainerExecutor.java: 371) at org.apache.hadoop.yarn.server.nodemanager.containermanager. launcher.ContainerLaunch.call( ContainerLaunch.java:303) at org.apache.hadoop.yarn.server.nodemanager.containermanager. launcher.ContainerLaunch.call( ContainerLaunch.java:82) at java.util.concurrent.FutureTask.run(FutureTask. java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker( ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run( ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)
Shell output: main : command provided 1main : run as user is rcmain : requested yarn user is rc
Container exited with a non-zero exit code 1
Display stack trace? [yN]15:59:57,702 WARN TransportChannelHandler:79 - Exception in connection from 10.200.48.155/10.200.48.155:50921 java.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil. java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java: 380) at io.netty.buffer.PooledUnsafeDirectByteBuf. setBytes( PooledUnsafeDirectByteBuf. java:313) at io.netty.buffer.AbstractByteBuf.writeBytes( AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes( NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$ NioByteUnsafe.read( AbstractNioByteChannel.java: 119) at io.netty.channel.nio.NioEventLoop. processSelectedKey( NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop. processSelectedKeysOptimized( NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop. processSelectedKeys( NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop. java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2. run(SingleThreadEventExecutor. java:111) at java.lang.Thread.run(Thread.java:748)
15:59:57,704 ERROR TransportResponseHandler:132 - Still have 1 requests outstanding when connection from 10.200.48.155/10.200.48.155:50921 is closed 15:59:57,706 WARN NettyRpcEndpointRef:91 - Error sending message [message = RequestExecutors(0,0,Map())] in 1 attemptsjava.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil. java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java: 380) at io.netty.buffer.PooledUnsafeDirectByteBuf. setBytes( PooledUnsafeDirectByteBuf. java:313) at io.netty.buffer.AbstractByteBuf.writeBytes( AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes( NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$ NioByteUnsafe.read( AbstractNioByteChannel.java: 119) at io.netty.channel.nio.NioEventLoop. processSelectedKey( NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop. processSelectedKeysOptimized( NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop. processSelectedKeys( NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop. java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2. run(SingleThreadEventExecutor. java:111) at java.lang.Thread.run(Thread.java:748) I am confused about that. Could you please help me?
在 2017年7月6日星期四 UTC+8下午4:15:37,HadoopMarc写道:
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring- janusgraph-for-spark-yarn.html
Regards, Marc
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgraph-use...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgra...@....
For more options, visit https://groups.google.com/d/optout.
Glad to see you testing the recipes for MapR and Cloudera respectively! I am sure that you realized by now that getting this to work is like walking through a minefield. If you deviate from the known path, the odds for getting through are dim, and no one wants to be in your vicinity. So, if you see a need to deviate (which there may be for the hadoop distributions you use), you will need your mine sweeper, that is, put the logging level to DEBUG for relevant java packages.
This is where you deviated:
- for Gari: you put all kinds of MapR lib folders on the applications master's classpath (other classpath configs are not visible from your post)
- for Joe: you put all kinds of Cloudera lib folders on the executors classpath (worst of all the spark-assembly.jar)
Probably, you experience all kinds of mismatches in netty libraries which slows down or even kills all comms between the yarn containers. The philosophy of the recipes really is to only add the minimum number of conf folders and jars to the Tinkerpop/Janusgraph distribution and see from there if any libraries are missing.
At my side, it has become apparent that I should at least add to the recipes:
- proof of work for a medium-sized graph (say 10M vertices and edges)
- configs for the number of executors present in the OLAP job (instead of relying on spark default number of 2)
So, still some work to do!
Cheers, Marc
Op woensdag 9 augustus 2017 19:16:23 UTC+2 schreef Joseph Obernberger:
Hi Marc - I did try splitting regions. What happens when I run the SparkGraphComputer job, is that it seems to hit one region server hard, then moves onto the next; appears to run serially. All that said, I think the big issue is that running with Spark for a count takes 2 hours and running without takes 2 minutes. Perhaps the SparkGraphComputer is not the tool to be used for handling large graphs? Although, I'm not sure what the purpose is then?
For reference, here is my Hadoop configuration file using Cloudera CDH 5.10.0 and JanusGraph 0.1.0:
Config:
Thanks very much for any input / further dialog!
------------------------------------------------------------ ------------------------------ ------------------------------ ------------------------------ ---------------------------
#
# Hadoop Graph Configuration
#
gremlin.graph=org.apache.tinkerpop.gremlin.hadoop. structure.HadoopGraph
gremlin.hadoop.graphInputFormat=org. janusgraph.hadoop.formats. hbase.HBaseInputFormat
gremlin.hadoop.graphOutputFormat=org.apache. tinkerpop.gremlin.hadoop. structure.io.gryo. GryoOutputFormat
gremlin.hadoop.memoryOutputFormat=org.apache. hadoop.mapreduce.lib.output. SequenceFileOutputFormat
gremlin.hadoop.memoryOutputFormat=org.apache. tinkerpop.gremlin.hadoop. structure.io.gryo. GryoOutputFormat
gremlin.hadoop.deriveMemory=false
gremlin.hadoop.jarsInDistributedCache=true
gremlin.hadoop.inputLocation=none
gremlin.hadoop.outputLocation=output
log4j.rootLogger=WARNING, STDOUT
log4j.logger.deng=WARNING
log4j.appender.STDOUT=org.apache.log4j.ConsoleAppender
org.slf4j.simpleLogger.defaultLogLevel=warn
#
# JanusGraph HBase InputFormat configuration
#
janusgraphmr.ioformat.conf.storage.backend=hbase
janusgraphmr.ioformat.conf.storage.hostname=host003:2181, host004:2181,host005:2181
janusgraphmr.ioformat.conf.storage.hbase.table=Large2
janusgraphmr.ioformat.conf.storage.hbase.region-count=5
janusgraphmr.ioformat.conf.storage.hbase.regions-per- server=5
janusgraphmr.ioformat.conf.storage.hbase.short-cf-names= false
# Security configs are needed in case of a secure cluster
zookeeper.znode.parent=/hbase
#
# SparkGraphComputer with Yarn Configuration
#
#spark.master=yarn-client
spark.executor.extraJavaOptions=-XX: ReservedCodeCacheSize=100M -XX:MaxMetaspaceSize=256m -XX:CompressedClassSpaceSize= 256m -Dlogback.configurationFile= logback.xml
spark.driver.extraJavaOptons=-XX:ReservedCodeCacheSize=100M -XX:MaxMetaspaceSize=256m -XX:CompressedClassSpaceSize= 256m
spark.master=yarn-cluster
spark.executor.memory=10240m
spark.serializer=org.apache.tinkerpop.gremlin.spark. structure.io.gryo. GryoSerializer
spark.yarn.dist.archives=/home/graph/janusgraph-0.1.0- SNAPSHOT-hadoop2/lib.zip
spark.yarn.dist.files=/opt/cloudera/parcels/CDH/jars/ janusgraph-hbase-0.1.0- SNAPSHOT.jar,/home/graph/ janusgraph-0.1.0-SNAPSHOT- hadoop2/conf/logback.xml
spark.yarn.dist.jars=/opt/cloudera/parcels/CDH/jars/ janusgraph-hbase-0.1.0- SNAPSHOT.jar
spark.yarn.appMasterEnv.CLASSPATH=/etc/haddop/conf:/ etc/hbase/conf:./lib.zip/*
spark.executor.extraLibraryPath=/opt/ cloudera/parcels/CDH/lib/ hadoop/native:/opt/cloudera/ parcels/CDH/lib/hadoop-0.20- mapreduce/lib/native/Linux- amd64-64
spark.akka.frameSize=1024
spark.kyroserializer.buffer.max=1600m
spark.network.timeout=90000
spark.executor.heartbeatInterval=100000
spark.cores.max=64
#
# Relevant configs from spark-defaults.conf
#
spark.authenticate=false
spark.dynamicAllocation.enabled=true
spark.dynamicAllocation.executorIdleTimeout=60
spark.dynamicAllocation.minExecutors=0
spark.dynamicAllocation.schedulerBacklogTimeout=1
spark.eventLog.enabled=true
spark.serializer=org.apache.spark.serializer. KryoSerializer
spark.shuffle.service.enabled=true
spark.shuffle.service.port=7337
spark.ui.killEnabled=true
spark.executor.extraClassPath=/opt/cloudera/parcels/CDH/ jars/janusgraph-hbase-0.1.0- SNAPSHOT.jar:./lib.zip/*:\
/opt/cloudera/parcels/CDH/lib/hbase/bin/../conf:\
/opt/cloudera/parcels/CDH/lib/hbase/bin/..:\
/opt/cloudera/parcels/CDH/lib/spark/assembly/lib/spark- assembly.jar:\
/usr/lib/jvm/java-openjdk/jre/lib/rt.jar:\
/opt/cloudera/parcels/CDH/lib/hbase/bin/../lib/*:\
/etc/hadoop/conf:\
/etc/hbase/conf:\
/opt/cloudera/parcels/CDH/lib/hadoop/libexec/../../hadoop/ lib/*:\
/opt/cloudera/parcels/CDH/lib/hadoop/libexec/../../hadoop/./ /*:\
/opt/cloudera/parcels/CDH/lib/hadoop/libexec/../../hadoop- yarn/lib/*:\
/opt/cloudera/parcels/CDH/lib/hadoop/libexec/../../hadoop- yarn/.//*
spark.eventLog.dir=hdfs://host001:8020/user/spark/ applicationHistory
spark.yarn.historyServer.address=http://host001:18088
spark.yarn.jar=local:/opt/cloudera/parcels/CDH-5.10.0-1. cdh5.10.0.p0.41/lib/spark/lib/ spark-assembly.jar
spark.driver.extraLibraryPath=/opt/cloudera/parcels/CDH-5. 10.0-1.cdh5.10.0.p0.41/lib/ hadoop/lib/native
spark.executor.extraLibraryPath=/opt/ cloudera/parcels/CDH-5.10.0-1. cdh5.10.0.p0.41/lib/hadoop/ lib/native
spark.yarn.am.extraLibraryPath=/opt/ cloudera/parcels/CDH-5.10.0-1. cdh5.10.0.p0.41/lib/hadoop/ lib/native
spark.yarn.config.gatewayPath=/opt/cloudera/parcels
spark.yarn.config.replacementPath={{HADOOP_ COMMON_HOME}}/../../..
spark.master=yarn-client
------------------------------------------------------------ ------------------------------ ------------------------------ ------------------------------ ---------------------------
-Joe
On 8/8/2017 3:17 AM, HadoopMarc wrote:
Hi Joseph,--
You ran into terrain I have not yet covered myself. Up till now I have been using the graben1437 PR for Titan and for OLAP I adopted a poor man's approach where node id's are distributed over spark tasks and each spark executor makes its own Titan/HBase connection. This performs well, but does not have the nice abstraction of the HBaseInputFormat.
So, no clear answer to this one, but just some thoughts:
- could you try to move some regions manually and see what it does to performance?
- how do your OLAP vertex count times compare to the OLTP count times?
- how does the sum of spark task execution times compare to the yarn start-to-end time difference you reported? In other words, how much of the start-to-end time is spent in waiting for timeouts?
- unless you managed to create a vertex with > 1GB size, the RowTooBigException sounds like a bug (which you can report on Jnausgraph's github page). Hbase does not like large rows at all, so vertex/edge properties should not have blob values.
@(David Robinson): do you have any additional thoughts on this?
Cheers, Marc
Op maandag 7 augustus 2017 23:12:02 UTC+2 schreef Joseph Obernberger:Hi Marc - I've been able to get it to run longer, but am now getting a RowTooBigException from HBase. How does JanusGraph store data in HBase? The current max size of a row in 1GByte, which makes me think this error is covering something else up.
What I'm seeing so far in testing with a 5 server cluster - each machine with 128G of RAM:
HBase table is 1.5G in size, split across 7 regions, and has 20,001,105 rows. To do a g.V().count() takes 2 hours and results in 3,842,755 verticies.Another HBase table is 5.7G in size split across 10 regions, is 57,620,276 rows, and took 6.5 hours to run the count and results in 10,859,491 nodes. When running, it looks like it hits one server very hard even though the YARN tasks are distributed across the cluster. One HBase node gets hammered.
The RowTooBigException is below. Anything to try? Thank you for any help!
org.janusgraph.core.
JanusGraphException: Could not process individual retrieval call
at org.janusgraph.graphdb.query.QueryUtil. processIntersectingRetrievals( QueryUtil.java:257)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6. execute(StandardJanusGraphTx. java:1269)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6. execute(StandardJanusGraphTx. java:1137)
at org.janusgraph.graphdb.query.QueryProcessor$ LimitAdjustingIterator. getNewIterator(QueryProcessor. java:209)
at org.janusgraph.graphdb.query.LimitAdjustingIterator. hasNext( LimitAdjustingIterator.java: 75)
at org.janusgraph.graphdb.query.ResultSetIterator. nextInternal( ResultSetIterator.java:54)
at org.janusgraph.graphdb.query.ResultSetIterator.next( ResultSetIterator.java:67)
at org.janusgraph.graphdb.query.ResultSetIterator.next( ResultSetIterator.java:28)
at com.google.common.collect.Iterators$7.computeNext( Iterators.java:651)
at com.google.common.collect.AbstractIterator. tryToComputeNext( AbstractIterator.java:143)
at com.google.common.collect.AbstractIterator.hasNext( AbstractIterator.java:138)
at org.janusgraph.hadoop.formats.util.input.current. JanusGraphHadoopSetupImpl. getTypeInspector( JanusGraphHadoopSetupImpl. java:60)
at org.janusgraph.hadoop.formats.util. JanusGraphVertexDeserializer.< init>( JanusGraphVertexDeserializer. java:55)
at org.janusgraph.hadoop.formats.util.GiraphInputFormat.lambda$ static$0(GiraphInputFormat. java:49)
at org.janusgraph.hadoop.formats.util.GiraphInputFormat$ RefCountedCloseable.acquire( GiraphInputFormat.java:100)
at org.janusgraph.hadoop.formats.util.GiraphRecordReader.<init> (GiraphRecordReader.java:47)
at org.janusgraph.hadoop.formats.util.GiraphInputFormat. createRecordReader( GiraphInputFormat.java:67)
at org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>( NewHadoopRDD.scala:166)
at org.apache.spark.rdd.NewHadoopRDD.compute( NewHadoopRDD.scala:133)
at org.apache.spark.rdd.NewHadoopRDD.compute( NewHadoopRDD.scala:65)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD. scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute( MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD. scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute( MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD. scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.scheduler.ShuffleMapTask.runTask( ShuffleMapTask.scala:73)
at org.apache.spark.scheduler.ShuffleMapTask.runTask( ShuffleMapTask.scala:41)
at org.apache.spark.scheduler.Task.run(Task.scala:89)
at org.apache.spark.executor.Executor$TaskRunner.run( Executor.scala:242)
at java.util.concurrent.ThreadPoolExecutor.runWorker( ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run( ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.janusgraph.core.JanusGraphException: Could not call index
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6.call( StandardJanusGraphTx.java: 1262)
at org.janusgraph.graphdb.query.QueryUtil. processIntersectingRetrievals( QueryUtil.java:255)
... 34 more
Caused by: org.janusgraph.core.JanusGraphException: Could not execute operation due to backend exception
at org.janusgraph.diskstorage.util.BackendOperation.execute( BackendOperation.java:57)
at org.janusgraph.diskstorage.BackendTransaction. executeRead( BackendTransaction.java:444)
at org.janusgraph.diskstorage.BackendTransaction.indexQuery( BackendTransaction.java:395)
at org.janusgraph.graphdb.query.graph.MultiKeySliceQuery. execute(MultiKeySliceQuery. java:51)
at org.janusgraph.graphdb.database.IndexSerializer. query(IndexSerializer.java: 529)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6$1. lambda$call$5( StandardJanusGraphTx.java: 1258)
at org.janusgraph.graphdb.query.profile.QueryProfiler.profile( QueryProfiler.java:97)
at org.janusgraph.graphdb.query.profile.QueryProfiler.profile( QueryProfiler.java:89)
at org.janusgraph.graphdb.query.profile.QueryProfiler.profile( QueryProfiler.java:81)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6$1. call(StandardJanusGraphTx. java:1258)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6$1. call(StandardJanusGraphTx. java:1255)
at com.google.common.cache.LocalCache$LocalManualCache$1. load(LocalCache.java:4742)
at com.google.common.cache.LocalCache$ LoadingValueReference. loadFuture(LocalCache.java: 3527)
at com.google.common.cache.LocalCache$Segment.loadSync( LocalCache.java:2319)
at com.google.common.cache.LocalCache$Segment. lockedGetOrLoad(LocalCache. java:2282)
at com.google.common.cache.LocalCache$Segment.get( LocalCache.java:2197)
at com.google.common.cache.LocalCache.get(LocalCache. java:3937)
at com.google.common.cache.LocalCache$LocalManualCache. get(LocalCache.java:4739)
at org.janusgraph.graphdb.transaction. StandardJanusGraphTx$6$6.call( StandardJanusGraphTx.java: 1255)
... 35 more
Caused by: org.janusgraph.diskstorage.TemporaryBackendException: Could not successfully complete backend operation due to repeated temporary exceptions after PT10S
at org.janusgraph.diskstorage.util.BackendOperation. executeDirect( BackendOperation.java:101)
at org.janusgraph.diskstorage.util.BackendOperation.execute( BackendOperation.java:55)
... 53 more
Caused by: org.janusgraph.diskstorage.TemporaryBackendException: Temporary failure in storage backend
at org.janusgraph.diskstorage.hbase. HBaseKeyColumnValueStore. getHelper( HBaseKeyColumnValueStore.java: 202)
at org.janusgraph.diskstorage.hbase. HBaseKeyColumnValueStore. getSlice( HBaseKeyColumnValueStore.java: 90)
at org.janusgraph.diskstorage.keycolumnvalue.KCVSProxy. getSlice(KCVSProxy.java:77)
at org.janusgraph.diskstorage.keycolumnvalue.KCVSProxy. getSlice(KCVSProxy.java:77)
at org.janusgraph.diskstorage.BackendTransaction$5.call( BackendTransaction.java:398)
at org.janusgraph.diskstorage.BackendTransaction$5.call( BackendTransaction.java:395)
at org.janusgraph.diskstorage.util.BackendOperation. executeDirect( BackendOperation.java:69)
... 54 more
Caused by: org.apache.hadoop.hbase.client. RetriesExhaustedException: Failed after attempts=35, exceptions:
Sat Aug 05 07:22:03 EDT 2017, RpcRetryingCaller{globalStartTime=1501932111280, pause=100, retries=35}, org.apache.hadoop.hbase. regionserver. RowTooBigException: rg.apache.hadoop.hbase. regionserver. RowTooBigException: Max row size allowed: 1073741824, but the row is bigger than that.
at org.apache.hadoop.hbase.regionserver.StoreScanner. next(StoreScanner.java:564)
at org.apache.hadoop.hbase.regionserver.KeyValueHeap. next(KeyValueHeap.java:147)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl. populateResult(HRegion.java: 5697)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl. nextInternal(HRegion.java: 5856)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl.nextRaw( HRegion.java:5634)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl.next( HRegion.java:5611)
at org.apache.hadoop.hbase.regionserver.HRegion$ RegionScannerImpl.next( HRegion.java:5597)
at org.apache.hadoop.hbase.regionserver.HRegion.get( HRegion.java:6792)
at org.apache.hadoop.hbase.regionserver.HRegion.get( HRegion.java:6770)
at org.apache.hadoop.hbase.regionserver.RSRpcServices. get(RSRpcServices.java:2023)
at org.apache.hadoop.hbase.protobuf.generated. ClientProtos$ClientService$2. callBlockingMethod( ClientProtos.java:33644)
at org.apache.hadoop.hbase.ipc.RpcServer.call(RpcServer.java: 2170)
at org.apache.hadoop.hbase.ipc.CallRunner.run(CallRunner. java:109)
at org.apache.hadoop.hbase.ipc.RpcExecutor$Handler.run( RpcExecutor.java:185)
at org.apache.hadoop.hbase.ipc.RpcExecutor$Handler.run( RpcExecutor.java:165)
On 8/6/2017 3:50 PM, HadoopMarc wrote:
Hi ... and others, I have been offline for a few weeks enjoying a holiday and will start looking into your questions and make the suggested corrections. Thanks for following the recipes and helping others with it.--
..., did you run the recipe on the same HDP sandbox and same Tinkerpop version? I remember (from 4 weeks ago) that copying the zookeeper.znode.parent property from the hbase configs to the janusgraph configs was essential to get janusgraph's HBaseInputFormat working (that is: read graph data for the spark tasks).
Cheers, Marc
Op maandag 24 juli 2017 10:12:13 UTC+2 schreef spi...@...:hi,Thanks for your post.I did it according to the post.But I ran into a problem.
15:58:49,110 INFO SecurityManager:58 - Changing view acls to: rc15:58:49,110 INFO SecurityManager:58 - Changing modify acls to: rc15:58:49,110 INFO SecurityManager:58 - SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(rc); users with modify permissions: Set(rc)15:58:49,111 INFO Client:58 - Submitting application 25 to ResourceManager15:58:49,320 INFO YarnClientImpl:274 - Submitted application application_1500608983535_002515:58:49,321 INFO SchedulerExtensionServices:58 - Starting Yarn extension services with app application_1500608983535_0025 and attemptId None15:58:50,325 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:50,326 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: N/AApplicationMaster RPC port: -1queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025/ user: rc15:58:51,330 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:52,333 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:53,335 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:54,337 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:55,340 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)
15:58:56,343 INFO Client:58 - Application report for application_1500608983535_0025 (state: ACCEPTED)15:58:56,802 INFO YarnSchedulerBackend$YarnSchedulerEndpoint:58 - ApplicationMaster registered as NettyRpcEndpointRef(null) 15:58:56,822 INFO YarnClientSchedulerBackend:58 - Add WebUI Filter. org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter, Map(PROXY_HOSTS -> dl-rc-optd-ambari-master-v- test-1.host.dataengine.com,dl- rc-optd-ambari-master-v-test- 2.host.dataengine.com, PROXY_URI_BASES -> http://dl-rc-optd-ambari- master-v-test-1.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025,http://dl-rc-optd-ambari- master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_0025 ), /proxy/application_ 1500608983535_0025 15:58:56,824 INFO JettyUtils:58 - Adding filter: org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter 15:58:57,346 INFO Client:58 - Application report for application_1500608983535_0025 (state: RUNNING)15:58:57,347 INFO Client:58 -client token: N/Adiagnostics: N/AApplicationMaster host: 10.200.48.154ApplicationMaster RPC port: 0queue: defaultstart time: 1500883129115final status: UNDEFINEDtracking URL: http://dl-rc-optd-ambari-master-v-test-2.host. dataengine.com:8088/proxy/ application_1500608983535_ 0025/ user: rc15:58:57,348 INFO YarnClientSchedulerBackend:58 - Application application_1500608983535_0025 has started running.15:58:57,358 INFO Utils:58 - Successfully started service 'org.apache.spark.network.netty. NettyBlockTransferService' on port 47514. 15:58:57,358 INFO NettyBlockTransferService:58 - Server created on 4751415:58:57,360 INFO BlockManagerMaster:58 - Trying to register BlockManager15:58:57,363 INFO BlockManagerMasterEndpoint:58 - Registering block manager 10.200.48.112:47514 with 2.4 GB RAM, BlockManagerId(driver, 10.200.48.112, 47514)15:58:57,366 INFO BlockManagerMaster:58 - Registered BlockManager
15:58:57,585 INFO EventLoggingListener:58 - Logging events to hdfs:///spark-history/application_1500608983535_0025 15:59:07,177 WARN YarnSchedulerBackend$YarnSchedulerEndpoint:70 - Container marked as failed: container_e170_1500608983535_ 0025_01_000002 on host: dl-rc-optd-ambari-slave-v- test-1.host.dataengine.com. Exit status: 1. Diagnostics: Exception from container-launch. Container id: container_e170_1500608983535_0025_01_000002 Exit code: 1Stack trace: ExitCodeException exitCode=1:at org.apache.hadoop.util.Shell.runCommand(Shell.java:576) at org.apache.hadoop.util.Shell.run(Shell.java:487) at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute( Shell.java:753) at org.apache.hadoop.yarn.server.nodemanager. LinuxContainerExecutor. launchContainer( LinuxContainerExecutor.java: 371) at org.apache.hadoop.yarn.server.nodemanager.containermanager. launcher.ContainerLaunch.call( ContainerLaunch.java:303) at org.apache.hadoop.yarn.server.nodemanager.containermanager. launcher.ContainerLaunch.call( ContainerLaunch.java:82) at java.util.concurrent.FutureTask.run(FutureTask. java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker( ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run( ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)
Shell output: main : command provided 1main : run as user is rcmain : requested yarn user is rc
Container exited with a non-zero exit code 1
Display stack trace? [yN]15:59:57,702 WARN TransportChannelHandler:79 - Exception in connection from 10.200.48.155/10.200.48.155:50921 java.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil. java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java: 380) at io.netty.buffer.PooledUnsafeDirectByteBuf. setBytes( PooledUnsafeDirectByteBuf. java:313) at io.netty.buffer.AbstractByteBuf.writeBytes( AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes( NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$ NioByteUnsafe.read( AbstractNioByteChannel.java: 119) at io.netty.channel.nio.NioEventLoop. processSelectedKey( NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop. processSelectedKeysOptimized( NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop. processSelectedKeys( NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop. java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2. run(SingleThreadEventExecutor. java:111) at java.lang.Thread.run(Thread.java:748)
15:59:57,704 ERROR TransportResponseHandler:132 - Still have 1 requests outstanding when connection from 10.200.48.155/10.200.48.155:50921 is closed 15:59:57,706 WARN NettyRpcEndpointRef:91 - Error sending message [message = RequestExecutors(0,0,Map())] in 1 attemptsjava.io.IOException: Connection reset by peerat sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil. java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:192) at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java: 380) at io.netty.buffer.PooledUnsafeDirectByteBuf. setBytes( PooledUnsafeDirectByteBuf. java:313) at io.netty.buffer.AbstractByteBuf.writeBytes( AbstractByteBuf.java:881) at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes( NioSocketChannel.java:242) at io.netty.channel.nio.AbstractNioByteChannel$ NioByteUnsafe.read( AbstractNioByteChannel.java: 119) at io.netty.channel.nio.NioEventLoop. processSelectedKey( NioEventLoop.java:511) at io.netty.channel.nio.NioEventLoop. processSelectedKeysOptimized( NioEventLoop.java:468) at io.netty.channel.nio.NioEventLoop. processSelectedKeys( NioEventLoop.java:382) at io.netty.channel.nio.NioEventLoop.run(NioEventLoop. java:354) at io.netty.util.concurrent.SingleThreadEventExecutor$2. run(SingleThreadEventExecutor. java:111) at java.lang.Thread.run(Thread.java:748) I am confused about that. Could you please help me?
在 2017年7月6日星期四 UTC+8下午4:15:37,HadoopMarc写道:
Readers wanting to run OLAP queries on a real spark-yarn cluster might want to check my recent post:
http://yaaics.blogspot.nl/2017/07/configuring- janusgraph-for-spark-yarn.html
Regards, Marc
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgraph-use...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgraph-use...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
Marc - thank you. I've updated the classpath and removed nearly all of the CDH jars; had to keep chimera and some of the HBase libs in there. Apart from those and all the jars in lib.zip, it is working as it did before. The reason I turned DEBUG off was because it was producing 100+GBytes of logs. Nearly all of which are things like:
18:04:29 DEBUG
org.janusgraph.diskstorage.hbase.HBaseKeyColumnValueStore -
Generated HBase Filter ColumnRangeFilter [\x10\xC0, \x10\xC1)
18:04:29 DEBUG
org.janusgraph.graphdb.transaction.StandardJanusGraphTx - Guava
vertex cache size: requested=20000 effective=20000 (min=100)
18:04:29 DEBUG
org.janusgraph.graphdb.transaction.vertexcache.GuavaVertexCache -
Created dirty vertex map with initial size 32
18:04:29 DEBUG
org.janusgraph.graphdb.transaction.vertexcache.GuavaVertexCache -
Created vertex cache with max size 20000
18:04:29 DEBUG
org.janusgraph.diskstorage.hbase.HBaseKeyColumnValueStore -
Generated HBase Filter ColumnRangeFilter [\x10\xC2, \x10\xC3)
18:04:29 DEBUG
org.janusgraph.graphdb.transaction.StandardJanusGraphTx - Guava
vertex cache size: requested=20000 effective=20000 (min=100)
18:04:29 DEBUG
org.janusgraph.graphdb.transaction.vertexcache.GuavaVertexCache -
Created dirty vertex map with initial size 32
18:04:29 DEBUG
org.janusgraph.graphdb.transaction.vertexcache.GuavaVertexCache -
Created vertex cache with max size 20000
Here are the spark properties; notice the nice and small extraClassPath! :)
Name |
Value |
gremlin.graph |
org.apache.tinkerpop.gremlin.hadoop.structure.HadoopGraph |
gremlin.hadoop.deriveMemory |
false |
gremlin.hadoop.graphReader |
org.janusgraph.hadoop.formats.hbase.HBaseInputFormat |
gremlin.hadoop.graphWriter |
org.apache.tinkerpop.gremlin.hadoop.structure.io.gryo.GryoOutputFormat |
gremlin.hadoop.graphWriter.hasEdges |
false |
gremlin.hadoop.inputLocation |
none |
gremlin.hadoop.jarsInDistributedCache |
true |
gremlin.hadoop.memoryOutputFormat |
org.apache.tinkerpop.gremlin.hadoop.structure.io.gryo.GryoOutputFormat |
gremlin.hadoop.outputLocation |
output |
janusgraphmr.ioformat.conf.storage.backend |
hbase |
janusgraphmr.ioformat.conf.storage.hbase.region-count |
5 |
janusgraphmr.ioformat.conf.storage.hbase.regions-per-server |
5 |
janusgraphmr.ioformat.conf.storage.hbase.short-cf-names |
false |
janusgraphmr.ioformat.conf.storage.hbase.table |
TEST0.2.0 |
janusgraphmr.ioformat.conf.storage.hostname |
10.22.5.65:2181 |
log4j.appender.STDOUT |
org.apache.log4j.ConsoleAppender |
log4j.logger.deng |
WARNING |
log4j.rootLogger |
STDOUT |
org.slf4j.simpleLogger.defaultLogLevel |
warn |
spark.akka.frameSize |
1024 |
spark.app.id |
application_1502118729859_0041 |
spark.app.name |
Apache TinkerPop's Spark-Gremlin |
spark.authenticate |
false |
spark.cores.max |
64 |
spark.driver.appUIAddress |
|
spark.driver.extraJavaOptons |
-XX:ReservedCodeCacheSize=100M -XX:MaxMetaspaceSize=256m -XX:CompressedClassSpaceSize=256m |
spark.driver.extraLibraryPath |
/opt/cloudera/parcels/CDH-5.10.0-1.cdh5.10.0.p0.41/lib/hadoop/lib/native |
spark.driver.host |
10.22.5.61 |
spark.driver.port |
38529 |
spark.dynamicAllocation.enabled |
true |
spark.dynamicAllocation.executorIdleTimeout |
60 |
spark.dynamicAllocation.minExecutors |
0 |
spark.dynamicAllocation.schedulerBacklogTimeout |
1 |
spark.eventLog.dir |
hdfs://host001:8020/user/spark/applicationHistory |
spark.eventLog.enabled |
true |
spark.executor.extraClassPath |
/opt/cloudera/parcels/CDH/jars/janusgraph-hbase-0.2.0-SNAPSHOT.jar:./lib.zip/*:/opt/cloudera/parcels/CDH/lib/hbase/bin/../lib/*:/etc/hbase/conf: |
spark.executor.extraJavaOptions |
-XX:ReservedCodeCacheSize=100M -XX:MaxMetaspaceSize=256m -XX:CompressedClassSpaceSize=256m -Dlogback.configurationFile=logback.xml |
spark.executor.extraLibraryPath |
/opt/cloudera/parcels/CDH-5.10.0-1.cdh5.10.0.p0.41/lib/hadoop/lib/native |
spark.executor.heartbeatInterval |
100000 |
spark.executor.id |
driver |
spark.executor.memory |
10240m |
spark.externalBlockStore.folderName |
spark-27dac3f3-dfbc-4f32-b52d-ececdbcae0db |
spark.kyroserializer.buffer.max |
1600m |
spark.master |
yarn-client |
spark.network.timeout |
90000 |
spark.org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter.param.PROXY_HOSTS |
host005 |
spark.org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter.param.PROXY_URI_BASES |
|
spark.scheduler.mode |
FIFO |
spark.serializer |
org.apache.spark.serializer.KryoSerializer |
spark.shuffle.service.enabled |
true |
spark.shuffle.service.port |
7337 |
spark.ui.filters |
org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter |
spark.ui.killEnabled |
true |
spark.yarn.am.extraLibraryPath |
/opt/cloudera/parcels/CDH-5.10.0-1.cdh5.10.0.p0.41/lib/hadoop/lib/native |
spark.yarn.appMasterEnv.CLASSPATH |
/etc/haddop/conf:/etc/hbase/conf:./lib.zip/* |
spark.yarn.config.gatewayPath |
/opt/cloudera/parcels |
spark.yarn.config.replacementPath |
{{HADOOP_COMMON_HOME}}/../../.. |
spark.yarn.dist.archives |
/home/graph/janusgraph-0.2.0-SNAPSHOT-hadoop2.JOE/lib.zip |
spark.yarn.dist.files |
/home/graph/janusgraph-0.2.0-SNAPSHOT-hadoop2.JOE/conf/logback.xml |
spark.yarn.dist.jars |
/opt/cloudera/parcels/CDH/jars/janusgraph-hbase-0.2.0-SNAPSHOT.jar |
spark.yarn.historyServer.address |
|
zookeeper.znode.parent |
/hbase |
-Joe
Hi Gari and Joe,
Glad to see you testing the recipes for MapR and Cloudera respectively! I am sure that you realized by now that getting this to work is like walking through a minefield. If you deviate from the known path, the odds for getting through are dim, and no one wants to be in your vicinity. So, if you see a need to deviate (which there may be for the hadoop distributions you use), you will need your mine sweeper, that is, put the logging level to DEBUG for relevant java packages.
This is where you deviated:
- for Gari: you put all kinds of MapR lib folders on the applications master's classpath (other classpath configs are not visible from your post)
- for Joe: you put all kinds of Cloudera lib folders on the executors classpath (worst of all the spark-assembly.jar)
Probably, you experience all kinds of mismatches in netty libraries which slows down or even kills all comms between the yarn containers. The philosophy of the recipes really is to only add the minimum number of conf folders and jars to the Tinkerpop/Janusgraph distribution and see from there if any libraries are missing.
At my side, it has become apparent that I should at least add to the recipes:
- proof of work for a medium-sized graph (say 10M vertices and edges)
- configs for the number of executors present in the OLAP job (instead of relying on spark default number of 2)
So, still some work to do!
Cheers, Marc
Another thing to try (only tested on Tinkerpop, not on JanusGraph): create the traversalsource as follows:
g = graph.traversal().withComputer(new Computer().graphComputer(SparkGraphComputer).workers(100))
With HadoopGraph this helps hdfs files with very large or no partitions to be split across tasks; I did not check the effect yet for HBaseInputFormat in JanusGraph. And did you add spark.executor.instances=10 (or some suitable number) to your config? And did you check in the RM ui or Spark history server whether these executors were really allocated and started?
More later,
Marc
Op donderdag 10 augustus 2017 00:13:09 UTC+2 schreef Joseph Obernberger:
Marc - thank you. I've updated the classpath and removed nearly all of the CDH jars; had to keep chimera and some of the HBase libs in there. Apart from those and all the jars in lib.zip, it is working as it did before. The reason I turned DEBUG off was because it was producing 100+GBytes of logs. Nearly all of which are things like:
18:04:29 DEBUG org.janusgraph.diskstorage.
Do those mean anything to you? I've turned it back on for running with smaller graph sizes, but so far I don't see anything helpful there apart from an exception about not setting HADOOP_HOME.hbase.HBaseKeyColumnValueStore - Generated HBase Filter ColumnRangeFilter [\x10\xC0, \x10\xC1)
18:04:29 DEBUG org.janusgraph.graphdb.transaction. StandardJanusGraphTx - Guava vertex cache size: requested=20000 effective=20000 (min=100)
18:04:29 DEBUG org.janusgraph.graphdb.transaction.vertexcache. GuavaVertexCache - Created dirty vertex map with initial size 32
18:04:29 DEBUG org.janusgraph.graphdb.transaction.vertexcache. GuavaVertexCache - Created vertex cache with max size 20000
18:04:29 DEBUG org.janusgraph.diskstorage.hbase.HBaseKeyColumnValueStore - Generated HBase Filter ColumnRangeFilter [\x10\xC2, \x10\xC3)
18:04:29 DEBUG org.janusgraph.graphdb.transaction. StandardJanusGraphTx - Guava vertex cache size: requested=20000 effective=20000 (min=100)
18:04:29 DEBUG org.janusgraph.graphdb.transaction.vertexcache. GuavaVertexCache - Created dirty vertex map with initial size 32
18:04:29 DEBUG org.janusgraph.graphdb.transaction.vertexcache. GuavaVertexCache - Created vertex cache with max size 20000
Here are the spark properties; notice the nice and small extraClassPath! :)
Name
Value
gremlin.graph
org.apache.tinkerpop.gremlin.
hadoop.structure.HadoopGraph gremlin.hadoop.deriveMemory
false
gremlin.hadoop.graphReader
org.janusgraph.hadoop.formats.
hbase.HBaseInputFormat gremlin.hadoop.graphWriter
org.apache.tinkerpop.gremlin.
hadoop.structure.io.gryo. GryoOutputFormat gremlin.hadoop.graphWriter.
hasEdges false
gremlin.hadoop.inputLocation
none
gremlin.hadoop.
jarsInDistributedCache true
gremlin.hadoop.
memoryOutputFormat org.apache.tinkerpop.gremlin.
hadoop.structure.io.gryo. GryoOutputFormat gremlin.hadoop.outputLocation
output
janusgraphmr.ioformat.conf.
storage.backend hbase
janusgraphmr.ioformat.conf.
storage.hbase.region-count 5
janusgraphmr.ioformat.conf.
storage.hbase.regions-per- server 5
janusgraphmr.ioformat.conf.
storage.hbase.short-cf-names false
janusgraphmr.ioformat.conf.
storage.hbase.table TEST0.2.0
janusgraphmr.ioformat.conf.
storage.hostname log4j.appender.STDOUT
org.apache.log4j.
ConsoleAppender log4j.logger.deng
WARNING
log4j.rootLogger
STDOUT
org.slf4j.simpleLogger.
defaultLogLevel warn
spark.akka.frameSize
1024
application_1502118729859_0041
Apache TinkerPop's Spark-Gremlin
spark.authenticate
false
spark.cores.max
64
spark.driver.appUIAddress
spark.driver.extraJavaOptons
-XX:ReservedCodeCacheSize=100M -XX:MaxMetaspaceSize=256m -XX:CompressedClassSpaceSize=
256m spark.driver.extraLibraryPath
/opt/cloudera/parcels/CDH-5.
10.0-1.cdh5.10.0.p0.41/lib/ hadoop/lib/native spark.driver.host
10.22.5.61
spark.driver.port
38529
spark.dynamicAllocation.
enabled true
spark.dynamicAllocation.
executorIdleTimeout 60
spark.dynamicAllocation.
minExecutors 0
spark.dynamicAllocation.
schedulerBacklogTimeout 1
spark.eventLog.dir
hdfs://host001:8020/user/
spark/applicationHistory spark.eventLog.enabled
true
spark.executor.extraClassPath
/opt/cloudera/parcels/CDH/
jars/janusgraph-hbase-0.2.0- SNAPSHOT.jar:./lib.zip/*:/opt/ cloudera/parcels/CDH/lib/ hbase/bin/../lib/*:/etc/hbase/ conf: spark.executor.
extraJavaOptions -XX:ReservedCodeCacheSize=100M -XX:MaxMetaspaceSize=256m -XX:CompressedClassSpaceSize=
256m -Dlogback.configurationFile= logback.xml spark.executor.
extraLibraryPath /opt/cloudera/parcels/CDH-5.
10.0-1.cdh5.10.0.p0.41/lib/ hadoop/lib/native spark.executor.
heartbeatInterval 100000
driver
spark.executor.memory
10240m
spark.externalBlockStore.
folderName spark-27dac3f3-dfbc-4f32-b52d-
ececdbcae0db spark.kyroserializer.buffer.
max 1600m
spark.master
yarn-client
spark.network.timeout
90000
spark.org.apache.hadoop.yarn.
server.webproxy.amfilter. AmIpFilter.param.PROXY_HOSTS host005
spark.org.apache.hadoop.yarn.
server.webproxy.amfilter. AmIpFilter.param.PROXY_URI_ BASES spark.scheduler.mode
FIFO
spark.serializer
org.apache.spark.serializer.
KryoSerializer spark.shuffle.service.enabled
true
spark.shuffle.service.port
7337
spark.ui.filters
org.apache.hadoop.yarn.server.
webproxy.amfilter.AmIpFilter spark.ui.killEnabled
true
spark.yarn.am.extraLibraryPath
/opt/cloudera/parcels/CDH-5.
10.0-1.cdh5.10.0.p0.41/lib/ hadoop/lib/native spark.yarn.appMasterEnv.
CLASSPATH /etc/haddop/conf:/etc/hbase/
conf:./lib.zip/* spark.yarn.config.gatewayPath
/opt/cloudera/parcels
spark.yarn.config.
replacementPath {{HADOOP_COMMON_HOME}}/../../.
. spark.yarn.dist.archives
/home/graph/janusgraph-0.2.0-
SNAPSHOT-hadoop2.JOE/lib.zip spark.yarn.dist.files
/home/graph/janusgraph-0.2.0-
SNAPSHOT-hadoop2.JOE/conf/ logback.xml spark.yarn.dist.jars
/opt/cloudera/parcels/CDH/
jars/janusgraph-hbase-0.2.0- SNAPSHOT.jar spark.yarn.historyServer.
address zookeeper.znode.parent
/hbase
-Joe
On 8/9/2017 3:33 PM, HadoopMarc wrote:
Hi Gari and Joe,
Glad to see you testing the recipes for MapR and Cloudera respectively! I am sure that you realized by now that getting this to work is like walking through a minefield. If you deviate from the known path, the odds for getting through are dim, and no one wants to be in your vicinity. So, if you see a need to deviate (which there may be for the hadoop distributions you use), you will need your mine sweeper, that is, put the logging level to DEBUG for relevant java packages.
This is where you deviated:
- for Gari: you put all kinds of MapR lib folders on the applications master's classpath (other classpath configs are not visible from your post)
- for Joe: you put all kinds of Cloudera lib folders on the executors classpath (worst of all the spark-assembly.jar)
Probably, you experience all kinds of mismatches in netty libraries which slows down or even kills all comms between the yarn containers. The philosophy of the recipes really is to only add the minimum number of conf folders and jars to the Tinkerpop/Janusgraph distribution and see from there if any libraries are missing.
At my side, it has become apparent that I should at least add to the recipes:
- proof of work for a medium-sized graph (say 10M vertices and edges)
- configs for the number of executors present in the OLAP job (instead of relying on spark default number of 2)
So, still some work to do!
Cheers, Marc
Thank you Marc.
I did not set spark.executor.instances, but I do have spark.cores.max set to 64 and within YARN, it is configured to allow has much RAM/cores for our 5 server cluster. When I run a job on a table that has 61 regions, I see that 43 tasks are started and running on all 5 nodes in the Spark UI (and running top on each of the servers). If I lower the amount of RAM (heap) that each tasks has (currently set to 10G), they fail with OutOfMemory exceptions. It still hits one HBase node very hard and cycles through them. While that may be a reason for a performance issue, it doesn't explain the massive number of calls that HBase receives for a count job, and why using SparkGraphComputer takes so much more time.
Running with your command below appears to not alter the
behavior. I did run a job last night with DEBUG turned on, but it
produced too much logging filling up the log directory on 3 of the
5 nodes before stopping.
Thanks again Marc!
-Joe
Hi Joe,--
Another thing to try (only tested on Tinkerpop, not on JanusGraph): create the traversalsource as follows:
g = graph.traversal().withComputer(new Computer().graphComputer(SparkGraphComputer).workers(100))
With HadoopGraph this helps hdfs files with very large or no partitions to be split across tasks; I did not check the effect yet for HBaseInputFormat in JanusGraph. And did you add spark.executor.instances=10 (or some suitable number) to your config? And did you check in the RM ui or Spark history server whether these executors were really allocated and started?
More later,
Marc
Op donderdag 10 augustus 2017 00:13:09 UTC+2 schreef Joseph Obernberger:Marc - thank you. I've updated the classpath and removed nearly all of the CDH jars; had to keep chimera and some of the HBase libs in there. Apart from those and all the jars in lib.zip, it is working as it did before. The reason I turned DEBUG off was because it was producing 100+GBytes of logs. Nearly all of which are things like:
18:04:29 DEBUG org.janusgraph.diskstorage.
Do those mean anything to you? I've turned it back on for running with smaller graph sizes, but so far I don't see anything helpful there apart from an exception about not setting HADOOP_HOME.hbase.HBaseKeyColumnValueStore - Generated HBase Filter ColumnRangeFilter [\x10\xC0, \x10\xC1)
18:04:29 DEBUG org.janusgraph.graphdb.transaction. StandardJanusGraphTx - Guava vertex cache size: requested=20000 effective=20000 (min=100)
18:04:29 DEBUG org.janusgraph.graphdb.transaction.vertexcache. GuavaVertexCache - Created dirty vertex map with initial size 32
18:04:29 DEBUG org.janusgraph.graphdb.transaction.vertexcache. GuavaVertexCache - Created vertex cache with max size 20000
18:04:29 DEBUG org.janusgraph.diskstorage.hbase.HBaseKeyColumnValueStore - Generated HBase Filter ColumnRangeFilter [\x10\xC2, \x10\xC3)
18:04:29 DEBUG org.janusgraph.graphdb.transaction. StandardJanusGraphTx - Guava vertex cache size: requested=20000 effective=20000 (min=100)
18:04:29 DEBUG org.janusgraph.graphdb.transaction.vertexcache. GuavaVertexCache - Created dirty vertex map with initial size 32
18:04:29 DEBUG org.janusgraph.graphdb.transaction.vertexcache. GuavaVertexCache - Created vertex cache with max size 20000
Here are the spark properties; notice the nice and small extraClassPath! :)
Name
Value
gremlin.graph
org.apache.tinkerpop.gremlin.
hadoop.structure.HadoopGraph gremlin.hadoop.deriveMemory
false
gremlin.hadoop.graphReader
org.janusgraph.hadoop.formats.
hbase.HBaseInputFormat gremlin.hadoop.graphWriter
org.apache.tinkerpop.gremlin.
hadoop.structure.io.gryo. GryoOutputFormat gremlin.hadoop.graphWriter.
hasEdges false
gremlin.hadoop.inputLocation
none
gremlin.hadoop.
jarsInDistributedCache true
gremlin.hadoop.
memoryOutputFormat org.apache.tinkerpop.gremlin.
hadoop.structure.io.gryo. GryoOutputFormat gremlin.hadoop.outputLocation
output
janusgraphmr.ioformat.conf.
storage.backend hbase
janusgraphmr.ioformat.conf.
storage.hbase.region-count 5
janusgraphmr.ioformat.conf.
storage.hbase.regions-per- server 5
janusgraphmr.ioformat.conf.
storage.hbase.short-cf-names false
janusgraphmr.ioformat.conf.
storage.hbase.table TEST0.2.0
janusgraphmr.ioformat.conf.
storage.hostname log4j.appender.STDOUT
org.apache.log4j.
ConsoleAppender log4j.logger.deng
WARNING
log4j.rootLogger
STDOUT
org.slf4j.simpleLogger.
defaultLogLevel warn
spark.akka.frameSize
1024
application_1502118729859_0041
Apache TinkerPop's Spark-Gremlin
spark.authenticate
false
spark.cores.max
64
spark.driver.appUIAddress
spark.driver.extraJavaOptons
-XX:ReservedCodeCacheSize=100M -XX:MaxMetaspaceSize=256m -XX:CompressedClassSpaceSize=
256m spark.driver.extraLibraryPath
/opt/cloudera/parcels/CDH-5.
10.0-1.cdh5.10.0.p0.41/lib/ hadoop/lib/native spark.driver.host
10.22.5.61
spark.driver.port
38529
spark.dynamicAllocation.
enabled true
spark.dynamicAllocation.
executorIdleTimeout 60
spark.dynamicAllocation.
minExecutors 0
spark.dynamicAllocation.
schedulerBacklogTimeout 1
spark.eventLog.dir
hdfs://host001:8020/user/
spark/applicationHistory spark.eventLog.enabled
true
spark.executor.extraClassPath
/opt/cloudera/parcels/CDH/
jars/janusgraph-hbase-0.2.0- SNAPSHOT.jar:./lib.zip/*:/opt/ cloudera/parcels/CDH/lib/ hbase/bin/../lib/*:/etc/hbase/ conf: spark.executor.
extraJavaOptions -XX:ReservedCodeCacheSize=100M -XX:MaxMetaspaceSize=256m -XX:CompressedClassSpaceSize=
256m -Dlogback.configurationFile= logback.xml spark.executor.
extraLibraryPath /opt/cloudera/parcels/CDH-5.
10.0-1.cdh5.10.0.p0.41/lib/ hadoop/lib/native spark.executor.
heartbeatInterval 100000
driver
spark.executor.memory
10240m
spark.externalBlockStore.
folderName spark-27dac3f3-dfbc-4f32-b52d-
ececdbcae0db spark.kyroserializer.buffer.
max 1600m
spark.master
yarn-client
spark.network.timeout
90000
spark.org.apache.hadoop.yarn.
server.webproxy.amfilter. AmIpFilter.param.PROXY_HOSTS host005
spark.org.apache.hadoop.yarn.
server.webproxy.amfilter. AmIpFilter.param.PROXY_URI_ BASES spark.scheduler.mode
FIFO
spark.serializer
org.apache.spark.serializer.
KryoSerializer spark.shuffle.service.enabled
true
spark.shuffle.service.port
7337
spark.ui.filters
org.apache.hadoop.yarn.server.
webproxy.amfilter.AmIpFilter spark.ui.killEnabled
true
spark.yarn.am.extraLibraryPath
/opt/cloudera/parcels/CDH-5.
10.0-1.cdh5.10.0.p0.41/lib/ hadoop/lib/native spark.yarn.appMasterEnv.
CLASSPATH /etc/haddop/conf:/etc/hbase/
conf:./lib.zip/* spark.yarn.config.gatewayPath
/opt/cloudera/parcels
spark.yarn.config.
replacementPath {{HADOOP_COMMON_HOME}}/../../.
. spark.yarn.dist.archives
/home/graph/janusgraph-0.2.0-
SNAPSHOT-hadoop2.JOE/lib.zip spark.yarn.dist.files
/home/graph/janusgraph-0.2.0-
SNAPSHOT-hadoop2.JOE/conf/ logback.xml spark.yarn.dist.jars
/opt/cloudera/parcels/CDH/
jars/janusgraph-hbase-0.2.0- SNAPSHOT.jar spark.yarn.historyServer.
address zookeeper.znode.parent
/hbase
-Joe
On 8/9/2017 3:33 PM, HadoopMarc wrote:
Hi Gari and Joe,
Glad to see you testing the recipes for MapR and Cloudera respectively! I am sure that you realized by now that getting this to work is like walking through a minefield. If you deviate from the known path, the odds for getting through are dim, and no one wants to be in your vicinity. So, if you see a need to deviate (which there may be for the hadoop distributions you use), you will need your mine sweeper, that is, put the logging level to DEBUG for relevant java packages.
This is where you deviated:
- for Gari: you put all kinds of MapR lib folders on the applications master's classpath (other classpath configs are not visible from your post)
- for Joe: you put all kinds of Cloudera lib folders on the executors classpath (worst of all the spark-assembly.jar)
Probably, you experience all kinds of mismatches in netty libraries which slows down or even kills all comms between the yarn containers. The philosophy of the recipes really is to only add the minimum number of conf folders and jars to the Tinkerpop/Janusgraph distribution and see from there if any libraries are missing.
At my side, it has become apparent that I should at least add to the recipes:
- proof of work for a medium-sized graph (say 10M vertices and edges)
- configs for the number of executors present in the OLAP job (instead of relying on spark default number of 2)
So, still some work to do!
Cheers, Marc
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgra...@....
For more options, visit https://groups.google.com/d/optout.
Hi Joe,
To shed some more light on the running figures you presented, I ran some tests on my own cluster:
1. I loaded the default janusgraph-hbase table with the following simple script from the console:
graph=JanusGraphFactory.open(" conf/janusgraph-hbase. properties")
g = graph.traversal()
m = 1200L
n = 10000L
(0L..<m).each{
(0L..<n).each{
v1 = g.addV().id().next()
v2 = g.addV().id().next()
g.V(v1).addE('link1').to(g.V(v 2)).next()
g.V(v1).addE('link2').to(g.V(v 2)).next()
}
g.tx().commit()
}
This scipt runs about 20(?) minutes and results in 24M vertices and edges committed to the graph.
2. I did an OLTP g.V().count() on this graph from the console: 11 minutes first time, 10 minutes second time
3. I ran OLAP jobs on this graph using janusgraph-hhbase in two ways:
a) with g = graph.traversal().withComputer(SparkGraphComputer)
b) with g = graph.traversal().withComputer(new Computer().graphComputer(SparkGraphComputer).workers(10))
the properties file was as in the recipe, with the exception of:
spark.executor.memory=4096m # smaller values might work, but the 512m from the recipe is definitely too small
spark.executor.instances=4
#spark.executor.cores not set, so default value 1
This resulted in the following running times:
a) stage 0,1,2 => 12min, 12min, 3s => 24min total
b) stage 0,1,2 => 18min, 1min, 86ms => 19 min total
Discussion:
- HBase is not an easy source for OLAP: HBase wants large regions for efficiency (configurable, but typically 2-20GB), while mapreduce inputformats (like janusgraph's HBaseInputFormat) take regions as inputsplits by default. This means that only a few executors will read from HBase unless the HBaseInputFormat is extended to split a region's keyspace into multiple inputsplits. This mismatch between the numbers of regions and spark executors is a potential JanusGraph issue. Examples exist to improve on this, e.g.
org.apache.hadoop.hbase.mapreduce.RowCounter
- For spark stages after stage 0 (reading from HBase), increasing the number of spark tasks with the "workers()" setting helps optimizing the parallelization. This means that for larger traversals than just a vertex count, the parallelization with spark will really pay off.
- I did not try to repeat your settings with a large number of cores. Various sources discourage the use of spark.executor.cores values larger than 5, e.g. https://blog.cloudera.com/blog/2015/03/how-to-tune-your-apache-spark-jobs-part-2/, https://stackoverflow.com/questions/37871194/how-to-tune-spark-executor-number-cores-and-executor-memory
Cheers, Marc
Op donderdag 10 augustus 2017 15:40:21 UTC+2 schreef Joseph Obernberger:
Thank you Marc.
I did not set spark.executor.instances, but I do have spark.cores.max set to 64 and within YARN, it is configured to allow has much RAM/cores for our 5 server cluster. When I run a job on a table that has 61 regions, I see that 43 tasks are started and running on all 5 nodes in the Spark UI (and running top on each of the servers). If I lower the amount of RAM (heap) that each tasks has (currently set to 10G), they fail with OutOfMemory exceptions. It still hits one HBase node very hard and cycles through them. While that may be a reason for a performance issue, it doesn't explain the massive number of calls that HBase receives for a count job, and why using SparkGraphComputer takes so much more time.
Running with your command below appears to not alter the behavior. I did run a job last night with DEBUG turned on, but it produced too much logging filling up the log directory on 3 of the 5 nodes before stopping.
Thanks again Marc!
-Joe
On 8/10/2017 7:33 AM, HadoopMarc wrote:
Hi Joe,--
Another thing to try (only tested on Tinkerpop, not on JanusGraph): create the traversalsource as follows:
g = graph.traversal().withComputer(new Computer().graphComputer( SparkGraphComputer).workers( 100))
With HadoopGraph this helps hdfs files with very large or no partitions to be split across tasks; I did not check the effect yet for HBaseInputFormat in JanusGraph. And did you add spark.executor.instances=10 (or some suitable number) to your config? And did you check in the RM ui or Spark history server whether these executors were really allocated and started?
More later,
Marc
Op donderdag 10 augustus 2017 00:13:09 UTC+2 schreef Joseph Obernberger:Marc - thank you. I've updated the classpath and removed nearly all of the CDH jars; had to keep chimera and some of the HBase libs in there. Apart from those and all the jars in lib.zip, it is working as it did before. The reason I turned DEBUG off was because it was producing 100+GBytes of logs. Nearly all of which are things like:
18:04:29 DEBUG org.janusgraph.diskstorage.
Do those mean anything to you? I've turned it back on for running with smaller graph sizes, but so far I don't see anything helpful there apart from an exception about not setting HADOOP_HOME.hbase.HBaseKeyColumnValueStore - Generated HBase Filter ColumnRangeFilter [\x10\xC0, \x10\xC1)
18:04:29 DEBUG org.janusgraph.graphdb.transaction. StandardJanusGraphTx - Guava vertex cache size: requested=20000 effective=20000 (min=100)
18:04:29 DEBUG org.janusgraph.graphdb.transaction.vertexcache. GuavaVertexCache - Created dirty vertex map with initial size 32
18:04:29 DEBUG org.janusgraph.graphdb.transaction.vertexcache. GuavaVertexCache - Created vertex cache with max size 20000
18:04:29 DEBUG org.janusgraph.diskstorage.hbase.HBaseKeyColumnValueStore - Generated HBase Filter ColumnRangeFilter [\x10\xC2, \x10\xC3)
18:04:29 DEBUG org.janusgraph.graphdb.transaction. StandardJanusGraphTx - Guava vertex cache size: requested=20000 effective=20000 (min=100)
18:04:29 DEBUG org.janusgraph.graphdb.transaction.vertexcache. GuavaVertexCache - Created dirty vertex map with initial size 32
18:04:29 DEBUG org.janusgraph.graphdb.transaction.vertexcache. GuavaVertexCache - Created vertex cache with max size 20000
Here are the spark properties; notice the nice and small extraClassPath! :)
Name
Value
gremlin.graph
org.apache.tinkerpop.gremlin.
hadoop.structure.HadoopGraph gremlin.hadoop.deriveMemory
false
gremlin.hadoop.graphReader
org.janusgraph.hadoop.formats.
hbase.HBaseInputFormat gremlin.hadoop.graphWriter
org.apache.tinkerpop.gremlin.
hadoop.structure.io.gryo. GryoOutputFormat gremlin.hadoop.graphWriter.
hasEdges false
gremlin.hadoop.inputLocation
none
gremlin.hadoop.
jarsInDistributedCache true
gremlin.hadoop.
memoryOutputFormat org.apache.tinkerpop.gremlin.
hadoop.structure.io.gryo. GryoOutputFormat gremlin.hadoop.outputLocation
output
janusgraphmr.ioformat.conf.
storage.backend hbase
janusgraphmr.ioformat.conf.
storage.hbase.region-count 5
janusgraphmr.ioformat.conf.
storage.hbase.regions-per- server 5
janusgraphmr.ioformat.conf.
storage.hbase.short-cf-names false
janusgraphmr.ioformat.conf.
storage.hbase.table TEST0.2.0
janusgraphmr.ioformat.conf.
storage.hostname log4j.appender.STDOUT
org.apache.log4j.
ConsoleAppender log4j.logger.deng
WARNING
log4j.rootLogger
STDOUT
org.slf4j.simpleLogger.
defaultLogLevel warn
spark.akka.frameSize
1024
application_1502118729859_0041
Apache TinkerPop's Spark-Gremlin
spark.authenticate
false
spark.cores.max
64
spark.driver.appUIAddress
spark.driver.extraJavaOptons
-XX:ReservedCodeCacheSize=100M -XX:MaxMetaspaceSize=256m -XX:CompressedClassSpaceSize=
256m spark.driver.extraLibraryPath
/opt/cloudera/parcels/CDH-5.
10.0-1.cdh5.10.0.p0.41/lib/ hadoop/lib/native spark.driver.host
10.22.5.61
spark.driver.port
38529
spark.dynamicAllocation.
enabled true
spark.dynamicAllocation.
executorIdleTimeout 60
spark.dynamicAllocation.
minExecutors 0
spark.dynamicAllocation.
schedulerBacklogTimeout 1
spark.eventLog.dir
hdfs://host001:8020/user/
spark/applicationHistory spark.eventLog.enabled
true
spark.executor.extraClassPath
/opt/cloudera/parcels/CDH/
jars/janusgraph-hbase-0.2.0- SNAPSHOT.jar:./lib.zip/*:/opt/ cloudera/parcels/CDH/lib/ hbase/bin/../lib/*:/etc/hbase/ conf: spark.executor.
extraJavaOptions -XX:ReservedCodeCacheSize=100M -XX:MaxMetaspaceSize=256m -XX:CompressedClassSpaceSize=
256m -Dlogback.configurationFile= logback.xml spark.executor.
extraLibraryPath /opt/cloudera/parcels/CDH-5.
10.0-1.cdh5.10.0.p0.41/lib/ hadoop/lib/native spark.executor.
heartbeatInterval 100000
driver
spark.executor.memory
10240m
spark.externalBlockStore.
folderName spark-27dac3f3-dfbc-4f32-b52d-
ececdbcae0db spark.kyroserializer.buffer.
max 1600m
spark.master
yarn-client
spark.network.timeout
90000
spark.org.apache.hadoop.yarn.
server.webproxy.amfilter. AmIpFilter.param.PROXY_HOSTS host005
spark.org.apache.hadoop.yarn.
server.webproxy.amfilter. AmIpFilter.param.PROXY_URI_ BASES spark.scheduler.mode
FIFO
spark.serializer
org.apache.spark.serializer.
KryoSerializer spark.shuffle.service.enabled
true
spark.shuffle.service.port
7337
spark.ui.filters
org.apache.hadoop.yarn.server.
webproxy.amfilter.AmIpFilter spark.ui.killEnabled
true
spark.yarn.am.extraLibraryPath
/opt/cloudera/parcels/CDH-5.
10.0-1.cdh5.10.0.p0.41/lib/ hadoop/lib/native spark.yarn.appMasterEnv.
CLASSPATH /etc/haddop/conf:/etc/hbase/
conf:./lib.zip/* spark.yarn.config.gatewayPath
/opt/cloudera/parcels
spark.yarn.config.
replacementPath {{HADOOP_COMMON_HOME}}/../../.
. spark.yarn.dist.archives
/home/graph/janusgraph-0.2.0-
SNAPSHOT-hadoop2.JOE/lib.zip spark.yarn.dist.files
/home/graph/janusgraph-0.2.0-
SNAPSHOT-hadoop2.JOE/conf/ logback.xml spark.yarn.dist.jars
/opt/cloudera/parcels/CDH/
jars/janusgraph-hbase-0.2.0- SNAPSHOT.jar spark.yarn.historyServer.
address zookeeper.znode.parent
/hbase
-Joe
On 8/9/2017 3:33 PM, HadoopMarc wrote:
Hi Gari and Joe,
Glad to see you testing the recipes for MapR and Cloudera respectively! I am sure that you realized by now that getting this to work is like walking through a minefield. If you deviate from the known path, the odds for getting through are dim, and no one wants to be in your vicinity. So, if you see a need to deviate (which there may be for the hadoop distributions you use), you will need your mine sweeper, that is, put the logging level to DEBUG for relevant java packages.
This is where you deviated:
- for Gari: you put all kinds of MapR lib folders on the applications master's classpath (other classpath configs are not visible from your post)
- for Joe: you put all kinds of Cloudera lib folders on the executors classpath (worst of all the spark-assembly.jar)
Probably, you experience all kinds of mismatches in netty libraries which slows down or even kills all comms between the yarn containers. The philosophy of the recipes really is to only add the minimum number of conf folders and jars to the Tinkerpop/Janusgraph distribution and see from there if any libraries are missing.
At my side, it has become apparent that I should at least add to the recipes:
- proof of work for a medium-sized graph (say 10M vertices and edges)
- configs for the number of executors present in the OLAP job (instead of relying on spark default number of 2)
So, still some work to do!
Cheers, Marc
You received this message because you are subscribed to the Google Groups "JanusGraph users list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to janusgraph-use...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.