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Posted to dev@giraph.apache.org by "Alexandre Fonseca (JIRA)" <ji...@apache.org> on 2014/02/03 18:30:08 UTC
[jira] [Updated] (GIRAPH-788) Giraph job suspends with exceptions
when out-of-core options are set
[ https://issues.apache.org/jira/browse/GIRAPH-788?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Alexandre Fonseca updated GIRAPH-788:
-------------------------------------
Attachment: GIRAPH-788.patch
Stumbled across this same issue today with exactly the same stacktrace.
Function getOrCreatePartition(id) in DiskBackedPartitionStore:228-238 is the parent in the stacktrace of the NPR. Looking at the code:
{code:java}
Partition<I, V, E> partition =
pool.submit(new GetPartition(id)).get();
if (partition == null) {
Partition<I, V, E> newPartition =
conf.createPartition(id, context);
pool.submit(
new AddPartition(id, newPartition)).get();
return newPartition;
} else {
return partition;
}
{/code}
it is obvious that the intent is getting a partition if it exists or adding a new one if it doesn't. However, in the call() method of GetPartition (DiskBackedPartitionStore:695), the states HashMap is accessed directly without any ID check. Since states are only created for existing partitions, the result of this access is a null pointer. Switching on that null pointer causes the NPR:
{code:java}
while (partition == null) {
wLock.lock();
try {
State pState = states.get(id);
switch (pState) {
{/code}
By adding a check before this direct access for the existence of the partition, I was able to circumvent the NPR and obtain the expected result. This patch implements that check and was tested against a 5-node Hadoop 2.2.0 cluster using both MR2 and YARN executions.
> Giraph job suspends with exceptions when out-of-core options are set
> --------------------------------------------------------------------
>
> Key: GIRAPH-788
> URL: https://issues.apache.org/jira/browse/GIRAPH-788
> Project: Giraph
> Issue Type: Bug
> Components: mapreduce
> Affects Versions: 1.0.0
> Environment: uses hadoop 0.20.203.0 with 32 cluster nodes
> Giraph release-1.0 pulled Oct. 29. 2013.
> Reporter: Byungnam Lim
> Attachments: GIRAPH-788.patch
>
>
> When I run my code with out-of-core graph/message options OFF, it's fine. But when out-of-core graph/message options ON, then some workers give me exception messages like below and whole tasks suspends.
> {noformat}
> java.lang.IllegalStateException: run: Caught an unrecoverable exception waitFor: ExecutionException occurred while waiting for org.apache.giraph.utils.ProgressableUtils$FutureWaitable@3c7659ab
> at org.apache.giraph.graph.GraphMapper.run(GraphMapper.java:101)
> at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:763)
> at org.apache.hadoop.mapred.MapTask.run(MapTask.java:369)
> at org.apache.hadoop.mapred.Child$4.run(Child.java:259)
> at java.security.AccessController.doPrivileged(Native Method)
> at javax.security.auth.Subject.doAs(Subject.java:415)
> at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1059)
> at org.apache.hadoop.mapred.Child.main(Child.java:253)
> Caused by: java.lang.IllegalStateException: waitFor: ExecutionException occurred while waiting for org.apache.giraph.utils.ProgressableUtils$FutureWaitable@3c7659ab
> at org.apache.giraph.utils.ProgressableUtils.waitFor(ProgressableUtils.java:181)
> at org.apache.giraph.utils.ProgressableUtils.waitForever(ProgressableUtils.java:139)
> at org.apache.giraph.utils.ProgressableUtils.waitForever(ProgressableUtils.java:124)
> at org.apache.giraph.utils.ProgressableUtils.getFutureResult(ProgressableUtils.java:87)
> at org.apache.giraph.utils.ProgressableUtils.getResultsWithNCallables(ProgressableUtils.java:221)
> at org.apache.giraph.worker.BspServiceWorker.loadInputSplits(BspServiceWorker.java:283)
> at org.apache.giraph.worker.BspServiceWorker.loadVertices(BspServiceWorker.java:327)
> at org.apache.giraph.worker.BspServiceWorker.setup(BspServiceWorker.java:508)
> at org.apache.giraph.graph.GraphTaskManager.execute(GraphTaskManager.java:246)
> at org.apache.giraph.graph.GraphMapper.run(GraphMapper.java:91)
> ... 7 more
> Caused by: java.util.concurrent.ExecutionException: java.lang.IllegalStateException: getOrCreatePartition: cannot retrieve partition 6
> at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:262)
> at java.util.concurrent.FutureTask.get(FutureTask.java:119)
> at org.apache.giraph.utils.ProgressableUtils$FutureWaitable.waitFor(ProgressableUtils.java:300)
> at org.apache.giraph.utils.ProgressableUtils.waitFor(ProgressableUtils.java:173)
> ... 16 more
> Caused by: java.lang.IllegalStateException: getOrCreatePartition: cannot retrieve partition 6
> at org.apache.giraph.partition.DiskBackedPartitionStore.getOrCreatePartition(DiskBackedPartitionStore.java:243)
> at org.apache.giraph.comm.requests.SendWorkerVerticesRequest.doRequest(SendWorkerVerticesRequest.java:110)
> at org.apache.giraph.comm.netty.NettyWorkerClientRequestProcessor.doRequest(NettyWorkerClientRequestProcessor.java:482)
> at org.apache.giraph.comm.netty.NettyWorkerClientRequestProcessor.sendVertexRequest(NettyWorkerClientRequestProcessor.java:276)
> at org.apache.giraph.worker.VertexInputSplitsCallable.readInputSplit(VertexInputSplitsCallable.java:172)
> at org.apache.giraph.worker.InputSplitsCallable.loadInputSplit(InputSplitsCallable.java:267)
> at org.apache.giraph.worker.InputSplitsCallable.call(InputSplitsCallable.java:211)
> at org.apache.giraph.worker.InputSplitsCallable.call(InputSplitsCallable.java:60)
> at org.apache.giraph.utils.LogStacktraceCallable.call(LogStacktraceCallable.java:51)
> at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
> at java.util.concurrent.FutureTask.run(FutureTask.java:166)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
> at java.lang.Thread.run(Thread.java:722)
> Caused by: java.util.concurrent.ExecutionException: java.lang.NullPointerException
> at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:252)
> at java.util.concurrent.FutureTask.get(FutureTask.java:111)
> at org.apache.giraph.partition.DiskBackedPartitionStore.getOrCreatePartition(DiskBackedPartitionStore.java:228)
> ... 13 more
> Caused by: java.lang.NullPointerException
> at org.apache.giraph.partition.DiskBackedPartitionStore$GetPartition.call(DiskBackedPartitionStore.java:692)
> at org.apache.giraph.partition.DiskBackedPartitionStore$GetPartition.call(DiskBackedPartitionStore.java:658)
> at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
> at java.util.concurrent.FutureTask.run(FutureTask.java:166)
> at org.apache.giraph.partition.DiskBackedPartitionStore$DirectExecutorService.execute(DiskBackedPartitionStore.java:972)
> at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:132)
> ... 14 more
> {noformat}
> This exception occurs when superstep = -1.
> Strange things are that i) when I give option to run the job with equal or less than 10 workers, or ii ) when I run one of the example codes in giraph-examples - particularly, SimpleShortestPath with 32 workers, the job finishes fine. The exceptions only occur when I run my own code with larger than 10 workers. Then it goes out of the way.
> I found that there was a similar - yet as far as I know, the very same problem before in GIRAPH-462, but the issue is marked as 'Resolved' and 'Fixed'. Does this issue really fixed and am I just doing wrong?
> My input size was 75 MBytes with about 1 million nodes but I tested and found this problem does not depends on the input sizes.
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