[GIRAPH-1026] New Out-of-core mechanism does not work

• Type: Bug
• Status: Resolved
• Priority: Major
• Resolution: Fixed
• Affects Version/s: 1.3.0
• Fix Version/s: 1.2.0
• Assignee: Hassan Eslami
• Reporter: Max Garmash
• Created: 04/Aug/15 11:35
• Updated: 14/Oct/16 00:58
• Resolved: 20/May/16 22:42

Description

After releasing new OOC mechanism we tried to test it on our data and it failed.

Our environment:
4x (CPU 6 cores / 12 threads, RAM 64GB)

We can successfully process about 75 millions of vertices.
With 100-120M vertices it fails like this:

2015-08-04 12:35:21,000 INFO  [AMRM Callback Handler Thread] yarn.GiraphApplicationMaster (GiraphApplicationMaster.java:onContainersCompleted(574)) - Got container status for containerID=container_1438068521412_0193_01_000005, state=COMPLETE, exitStatus=-104, diagnostics=Container [pid=6700,containerID=container_1438068521412_0193_01_000005] is running beyond physical memory limits. Current usage: 20.3 GB of 20 GB physical memory used; 22.4 GB of 42 GB virtual memory used. Killing container.
Dump of the process-tree for container_1438068521412_0193_01_000005 :
	|- PID PPID PGRPID SESSID CMD_NAME USER_MODE_TIME(MILLIS) SYSTEM_TIME(MILLIS) VMEM_USAGE(BYTES) RSSMEM_USAGE(PAGES) FULL_CMD_LINE
	|- 6704 6700 6700 6700 (java) 78760 20733 24033841152 5317812 java -Xmx20480M -Xms20480M -cp .:${CLASSPATH}:./*:$HADOOP_CLIENT_CONF_DIR:$HADOOP_CONF_DIR:$HADOOP_COMMON_HOME/*:$HADOOP_COMMON_HOME/lib/*:$HADOOP_HDFS_HOME/*:$HADOOP_HDFS_HOME/lib/*:$HADOOP_YARN_HOME/*:$HADOOP_YARN_HOME/lib/*:$HADOOP_MAPRED_HOME/*:$HADOOP_MAPRED_HOME/lib/*:$MR2_CLASSPATH:./*:/etc/hadoop/conf.cloudera.yarn:/run/cloudera-scm-agent/process/264-yarn-NODEMANAGER:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop/lib/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-hdfs/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-hdfs/lib/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-yarn/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-yarn/lib/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-mapreduce/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-mapreduce/lib/*::./*:/etc/hadoop/conf.cloudera.yarn:/run/cloudera-scm-agent/process/264-yarn-NODEMANAGER:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop/lib/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-hdfs/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-hdfs/lib/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-yarn/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-yarn/lib/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-mapreduce/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-mapreduce/lib/*::./*:/etc/hadoop/conf.cloudera.yarn:/run/cloudera-scm-agent/process/264-yarn-NODEMANAGER:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop/lib/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-hdfs/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-hdfs/lib/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-yarn/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-yarn/lib/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-mapreduce/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-mapreduce/lib/*: org.apache.giraph.yarn.GiraphYarnTask 1438068521412 193 5 1 
	|- 6700 6698 6700 6700 (bash) 0 0 14376960 433 /bin/bash -c java -Xmx20480M -Xms20480M -cp .:${CLASSPATH}:./*:$HADOOP_CLIENT_CONF_DIR:$HADOOP_CONF_DIR:$HADOOP_COMMON_HOME/*:$HADOOP_COMMON_HOME/lib/*:$HADOOP_HDFS_HOME/*:$HADOOP_HDFS_HOME/lib/*:$HADOOP_YARN_HOME/*:$HADOOP_YARN_HOME/lib/*:$HADOOP_MAPRED_HOME/*:$HADOOP_MAPRED_HOME/lib/*:$MR2_CLASSPATH:./*:/etc/hadoop/conf.cloudera.yarn:/run/cloudera-scm-agent/process/264-yarn-NODEMANAGER:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop/lib/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-hdfs/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-hdfs/lib/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-yarn/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-yarn/lib/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-mapreduce/*:/opt/cloudera/parcels/CDH-5.4.4-1.cdh5.4.4.p0.4/lib/hadoop-mapreduce/lib/*: org.apache.giraph.yarn.GiraphYarnTask 1438068521412 193 5 1 1>/var/log/hadoop-yarn/container/application_1438068521412_0193/container_1438068521412_0193_01_000005/task-5-stdout.log 2>/var/log/hadoop-yarn/container/application_1438068521412_0193/container_1438068521412_0193_01_000005/task-5-stderr.log  

Container killed on request. Exit code is 143
Container exited with a non-zero exit code 143

Logs from container

2015-08-04 12:34:51,258 INFO  [netty-server-worker-4] handler.RequestDecoder (RequestDecoder.java:channelRead(74)) - decode: Server window metrics MBytes/sec received = 12.5315, MBytesReceived = 380.217, ave received req MBytes = 0.007, secs waited = 30.34
2015-08-04 12:35:16,258 INFO  [check-memory] ooc.CheckMemoryCallable (CheckMemoryCallable.java:call(221)) - call: Memory is very limited now. Calling GC manually. freeMemory = 924.27MB

We are running our job like this:

hadoop jar giraph-examples-1.2.0-SNAPSHOT-for-hadoop-2.6.0-cdh5.4.4-jar-with-dependencies.jar \
 org.apache.giraph.GiraphRunner \
 -Dgiraph.yarn.task.heap.mb=20480 \
 -Dgiraph.isStaticGraph=true \
 -Dgiraph.useOutOfCoreGraph=true \
 -Dgiraph.logLevel=info \
 -Dgiraph.weightedPageRank.superstepCount=5 \
 ru.isys.WeightedPageRankComputation \
 -vif ru.isys.CrawlerInputFormat \
 -vip /tmp/bigdata/input \
 -vof org.apache.giraph.io.formats.IdWithValueTextOutputFormat \
 -op /tmp/giraph \
 -w 6 \
 -yj giraph-examples-1.2.0-SNAPSHOT-for-hadoop-2.6.0-cdh5.4.4-jar-with-dependencies.jar

Issue Links

• relates to: GIRAPH-1022 Out-of-core mechanism for input superstep and graph data