I'm running apache-jena-fuseki-3.13-1 and just found tdb2.tdbcompact from its bin-directory. I should run tdb2.tdbcompact nightly to prevent my jena-fuseki from running out of disk space, but now I get error message( Failed to get a lock: file) when running it:
miettinj#ramen:~/jena> ./apache-jena-3.13.1/bin/tdb2.tdbcompact --loc=./apache-jena-fuseki- 3.13.1/run/databases/test_TDB2
org.apache.jena.dboe.DBOpEnvException: Failed to get a lock: file='/srv/work/miettinj/jena/apache-jena-fuseki-3.13.1/run/databases/test_TDB2/tdb.lock': held by process 6136
ps -x|grep 6136
6136 ? Sl 30:48 /usr/lib64/jvm/java/bin/java -Xmx1200M -cp /srv/work/miettinj/jena/apache-jena-fuseki-3.13.1/fuseki-server.jar
"held by process 6136"
Another process is using the database. Compaction has to happen from the process using the database.
Apache Jena Fuseki Jena 3.17.0 added a function endpoint so that the administrator can ask for compaction on a running Fuseki server.
Related
I want to build Docker image with jib Gradle plugin in Windows, and use a Windows docker client to load it into my WSL 2 container running dockerd, and use WSL 2 as server. Resource-wise I think this is the lightest solution. .
On WSL 2 side, I run dockerd service in Ubuntu 20 on WSL 2, and it's listening on [::]:2375. TLS disabled(--tls=false), only http.
On Windows side, I only downloaded the Docker client(static client, from https://download.docker.com/win/static/stable/x86_64/), and added the dynamic WSL 2 container IP into the insecure-registry in daemon.json. This file is put in the same dir of docker.exe client.
On Intellij IDEA side, I use gradle 5.2.1 wrapper, and jib plugin 3.2.1. I configure jib as follows:
jib {
dockerClient.executable = 'E:\\coding\\environment\\docker\\docker.exe'
dockerClient.environment = [ DOCKER_HOST: '172.21.169.180:2375',
DOCKER_INSECURE_REGISTRIES: "172.21.169.180:5000"]
from.image = 'docker://mini/java#sha256:d3ded1fd0df592c33185d930d976304994bbc539c7bf70a6091cb3da0f7e11fa'
to.image = 'spring-plugins-demo'
container.mainClass = 'dev.westerngun.oldway.ApplicationV1'
}
I know it can connect to dockerd in my WSL 2, because before I add the dynamic IP of Ubuntu the error was not able to connect to daemon. Now it can load the base image and start building.
Then, when I run jibDockerBuild --stacktrace, I see this error:
Execution failed for task ':jibDockerBuild'.
> com.google.cloud.tools.jib.plugins.common.BuildStepsExecutionException: C:\Users\WESTER~1\AppData\Local\Temp\16164656866093264693\33e3f3775358985441c3bea658f06f5307326c83f9c0bcbf8aa4acb327abffde\layer.tar: �ͻ���û���������Ȩ��
* Try:
Run with --info or --debug option to get more log output. Run with --scan to get full insights.
* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':jibDockerBuild'.
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$2.accept(ExecuteActionsTaskExecuter.java:121)
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$2.accept(ExecuteActionsTaskExecuter.java:117)
at org.gradle.internal.Try$Failure.ifSuccessfulOrElse(Try.java:184)
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:110)
at org.gradle.api.internal.tasks.execution.ResolveIncrementalChangesTaskExecuter.execute(ResolveIncrementalChangesTaskExecuter.java:84)
at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:91)
at org.gradle.api.internal.tasks.execution.ResolveBeforeExecutionStateTaskExecuter.execute(ResolveBeforeExecutionStateTaskExecuter.java:74)
at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:109)
at org.gradle.api.internal.tasks.execution.ResolveBeforeExecutionOutputsTaskExecuter.execute(ResolveBeforeExecutionOutputsTaskExecuter.java:67)
at org.gradle.api.internal.tasks.execution.ResolveAfterPreviousExecutionStateTaskExecuter.execute(ResolveAfterPreviousExecutionStateTaskExecuter.java:46)
at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:93)
at org.gradle.api.internal.tasks.execution.FinalizePropertiesTaskExecuter.execute(FinalizePropertiesTaskExecuter.java:45)
at org.gradle.api.internal.tasks.execution.ResolveTaskExecutionModeExecuter.execute(ResolveTaskExecutionModeExecuter.java:94)
at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:57)
at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:56)
at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:36)
at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.executeTask(EventFiringTaskExecuter.java:63)
at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:49)
at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:46)
at org.gradle.internal.operations.DefaultBuildOperationExecutor$CallableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:416)
at org.gradle.internal.operations.DefaultBuildOperationExecutor$CallableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:406)
at org.gradle.internal.operations.DefaultBuildOperationExecutor$1.execute(DefaultBuildOperationExecutor.java:165)
at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:250)
at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:158)
at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:102)
at org.gradle.internal.operations.DelegatingBuildOperationExecutor.call(DelegatingBuildOperationExecutor.java:36)
at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter.execute(EventFiringTaskExecuter.java:46)
at org.gradle.execution.plan.LocalTaskNodeExecutor.execute(LocalTaskNodeExecutor.java:43)
at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:355)
at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:343)
at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:336)
at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:322)
at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker$1.execute(DefaultPlanExecutor.java:134)
at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker$1.execute(DefaultPlanExecutor.java:129)
at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.execute(DefaultPlanExecutor.java:202)
at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.executeNextNode(DefaultPlanExecutor.java:193)
at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.run(DefaultPlanExecutor.java:129)
at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
Caused by: org.gradle.internal.UncheckedException: com.google.cloud.tools.jib.plugins.common.BuildStepsExecutionException: C:\Users\WESTER~1\AppData\Local\Temp\16164656866093264693\33e3f3775358985441c3bea658f06f5307326c83f9c0bcbf8aa4acb327abffde\layer.tar: �ͻ���û���������Ȩ��
at org.gradle.internal.UncheckedException.throwAsUncheckedException(UncheckedException.java:67)
at org.gradle.internal.UncheckedException.throwAsUncheckedException(UncheckedException.java:41)
at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:106)
at org.gradle.api.internal.project.taskfactory.StandardTaskAction.doExecute(StandardTaskAction.java:48)
at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:41)
at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:28)
at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:705)
at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:672)
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$4.run(ExecuteActionsTaskExecuter.java:338)
at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:402)
at org.gradle.internal.operations.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:394)
at org.gradle.internal.operations.DefaultBuildOperationExecutor$1.execute(DefaultBuildOperationExecutor.java:165)
at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:250)
at org.gradle.internal.operations.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:158)
at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:92)
at org.gradle.internal.operations.DelegatingBuildOperationExecutor.run(DelegatingBuildOperationExecutor.java:31)
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:327)
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:312)
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.access$200(ExecuteActionsTaskExecuter.java:75)
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$TaskExecution.execute(ExecuteActionsTaskExecuter.java:158)
at org.gradle.internal.execution.impl.steps.ExecuteStep.execute(ExecuteStep.java:46)
at org.gradle.internal.execution.impl.steps.CancelExecutionStep.execute(CancelExecutionStep.java:34)
at org.gradle.internal.execution.impl.steps.TimeoutStep.executeWithoutTimeout(TimeoutStep.java:69)
at org.gradle.internal.execution.impl.steps.TimeoutStep.execute(TimeoutStep.java:49)
at org.gradle.internal.execution.impl.steps.CatchExceptionStep.execute(CatchExceptionStep.java:34)
at org.gradle.internal.execution.impl.steps.CreateOutputsStep.execute(CreateOutputsStep.java:49)
at org.gradle.internal.execution.impl.steps.SnapshotOutputStep.execute(SnapshotOutputStep.java:42)
at org.gradle.internal.execution.impl.steps.SnapshotOutputStep.execute(SnapshotOutputStep.java:28)
at org.gradle.internal.execution.impl.steps.CacheStep.executeWithoutCache(CacheStep.java:133)
at org.gradle.internal.execution.impl.steps.CacheStep.lambda$execute$5(CacheStep.java:83)
at org.gradle.internal.execution.impl.steps.CacheStep.execute(CacheStep.java:82)
at org.gradle.internal.execution.impl.steps.CacheStep.execute(CacheStep.java:37)
at org.gradle.internal.execution.impl.steps.PrepareCachingStep.execute(PrepareCachingStep.java:33)
at org.gradle.internal.execution.impl.steps.StoreSnapshotsStep.execute(StoreSnapshotsStep.java:38)
at org.gradle.internal.execution.impl.steps.StoreSnapshotsStep.execute(StoreSnapshotsStep.java:23)
at org.gradle.internal.execution.impl.steps.SkipUpToDateStep.executeBecause(SkipUpToDateStep.java:95)
at org.gradle.internal.execution.impl.steps.SkipUpToDateStep.lambda$execute$0(SkipUpToDateStep.java:88)
at org.gradle.internal.execution.impl.steps.SkipUpToDateStep.execute(SkipUpToDateStep.java:52)
at org.gradle.internal.execution.impl.steps.SkipUpToDateStep.execute(SkipUpToDateStep.java:36)
at org.gradle.internal.execution.impl.DefaultWorkExecutor.execute(DefaultWorkExecutor.java:34)
at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:109)
... 37 more
Caused by: com.google.cloud.tools.jib.plugins.common.BuildStepsExecutionException: C:\Users\WESTER~1\AppData\Local\Temp\16164656866093264693\33e3f3775358985441c3bea658f06f5307326c83f9c0bcbf8aa4acb327abffde\layer.tar: �ͻ���û���������Ȩ��
at com.google.cloud.tools.jib.plugins.common.JibBuildRunner.runBuild(JibBuildRunner.java:285)
at com.google.cloud.tools.jib.gradle.BuildDockerTask.buildDocker(BuildDockerTask.java:126)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:103)
... 75 more
Caused by: java.nio.file.FileSystemException: C:\Users\WESTER~1\AppData\Local\Temp\16164656866093264693\33e3f3775358985441c3bea658f06f5307326c83f9c0bcbf8aa4acb327abffde\layer.tar: �ͻ���û���������Ȩ��
at com.google.cloud.tools.jib.tar.TarExtractor.extract(TarExtractor.java:93)
at com.google.cloud.tools.jib.tar.TarExtractor.extract(TarExtractor.java:49)
at com.google.cloud.tools.jib.builder.steps.LocalBaseImageSteps.cacheDockerImageTar(LocalBaseImageSteps.java:217)
at com.google.cloud.tools.jib.builder.steps.LocalBaseImageSteps.lambda$retrieveDockerDaemonLayersStep$0(LocalBaseImageSteps.java:133)
at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:131)
at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:74)
at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:82)
The error message in Chinese is
C:\Users\WESTER~1\AppData\Local\Temp\16164656866093264693\33e3f3775358985441c3bea658f06f5307326c83f9c0bcbf8aa4acb327abffde\layer.tar: 客户端没有所需的特权。
And I think it can be translated into "A required permission is not held by the client".
I suspect this is because my user is not added to docker-user group, as stated here. But, I uninstalled Docker toolbox and I don't see this group anymore, as it sets DOCKER_HOST and interferes with my setup. Secondly, I don't have Local Users and Group available, seems Windows 10 Home edition does not have it.
Should I try to install gpedit in my Home Edition, add the group and try? But without Docker toolbox, I doubt it would work. Docker documentation explains here that it creates the group and configure it to ensure separation of permissions between root/admin and non-root/non-admin users; I think only creating that group will not work. https://docs.docker.com/desktop/windows/permission-requirements/
But, when I use docker.exe to connect to WSL 2 and save a tar file to C:\Users\WESTER~1\AppData\Local\Temp, it works. The tar file is created and not corrupted. So I think it's not a permission error; anyone can access that dir.
Windows bundled bsd-tar.exe has nothing to do with it; renaming the tar.exe in System32 and build, the error is the same.
It is solved when I run cmd as admin and cd to project dir and do gradlew jibDockerBuild. Image built and loaded into WSL 2 daemon successfully. It is indeed file system permission error.
Although still very strange(as I allowed the permission to everyone on that folder), but at least this is one workaround.
Another workaround, even better:
As per https://github.com/microsoft/WSL/issues/4983, I changed the jib config to set docker host to be http://[::1]:2375, and suddenly it works. Seems only ipv6 is bind.
Now not only the host is reachable, even permission error disappears; no insecure_registries settings needed, neither.
I've recently installed Jenkins on a cheap VM on Azure. The specs are very low, since I use this server for testing the setup: 1vCPU & 1GB RAM. There will usually only be 1 build at the same time, with a max. of 3, in very rare occassions.
During the build process from Jenkins quite frequently my server would crash completely and stay so for +- 10 - 15 minutes until being able to be used again.
I checked the processes on the server and this is the result:
The full line is like this:
/etc/alternatives/java -Dcom.sun.akuma.Daemon=daemonized -Djava.awt.headless=true -DJENKINS_HOME=/var/lib/jenkins -jar /usr/lib/jenkins/jenkins.war --logfile=/var/log/jenkins/jenkins.log --webroot=/var/cache/jenkins/war --daemon --httpPort=8080 --debug=5 --handlerCountMax=100 --handlerCountMaxIdle=20
It is the same for every single one of those daemons, not a single parameter is different.
Is this normal behavior, and is this the reason why my server is crashing? Or are my specs just too low for Jenkins to run on to?
Thanks in advance!
EDIT:
My jenkins.log file looks pretty normal except for one NullPointerException that keeps coming back up:
2020-01-08 12:43:17.702+0000 [id=148] WARNING h.ExpressionFactory2$JexlExpression#evaluate: Caught exception evaluating: h.filterDescriptors(it,attrs.descriptors) in /configure. Reason: java.lang.NullPointerException: Descriptor list is null for context 'class hudson.model.Hudson' in thread 'Handling GET /configure from 85.154.65.124 : qtp2085857771-148 Jenkins/configure.jelly GlobalLibraries/config.jelly LibraryConfiguration/config.jelly SCMRetriever/DescriptorImpl/config.jelly MultiSCM/DescriptorImpl/config.jelly'
java.lang.NullPointerException: Descriptor list is null for context 'class hudson.model.Hudson' in thread 'Handling GET /configure from 85.154.65.124 : qtp2085857771-148 Jenkins/configure.jelly GlobalLibraries/config.jelly LibraryConfiguration/config.jelly SCMRetriever/DescriptorImpl/config.jelly MultiSCM/DescriptorImpl/config.jelly'
at hudson.model.DescriptorVisibilityFilter.apply(DescriptorVisibilityFilter.java:73)
...
Version : spring-cloud-dataflow-server-yarn-1.2.2.RELEASE
Issue : All OOTB / Custom Task Apps seem to be NOT working with Yarn Deployer (I Specifically tested with timestamp-task-1.3.0.RELEASE and a hello world Custom Task built per the reference doc).
We have a Yarn cluster where all the streams that we have deployed are running fine which rules out any issue with hadoop/yarn cluster. The moment we try to deploy a task, the task exits with code 0 with below message logged in Yarn Container/AppMaster stdout
2018-09-19 18:04:20.782 DEBUG 22625 --- [ask-scheduler-2] o.s.yarn.am.allocate.AbstractAllocator : completed container: container_1536919363436_0805_01_000002 with status=ContainerStatus: [ContainerId: container_1536919363436_0805_01_000002, State: COMPLETE, Diagnostics: Exception from container-launch.
Container id: container_1536919363436_0805_01_000002
Exit code: 1
Stack trace: ExitCodeException exitCode=1:
at org.apache.hadoop.util.Shell.runCommand(Shell.java:545)
at org.apache.hadoop.util.Shell.run(Shell.java:456)
at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:722)
at org.apache.hadoop.yarn.server.nodemanager.DefaultContainerExecutor.launchContainer(DefaultContainerExecutor.java:211)
at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:302)
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:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Container exited with a non-zero exit code 1
, ExitStatus: 1, ]
Full AppMaster Log can be found here and corresponding servers.yml can be found here
Any help is Appreciated.
I am answering my own question -- our yarn server had log aggregation enabled and hence container logs weren't displayed immediately and I had to grep through the aggregated logs to find out why custom tasks weren't launching. Once we (temporarily) disabled log aggregation in yarn, custom task's Container.stdout and Container.stderror were visible under log directory configured in yarn-site.xml
I have been trying to use use neo4j community in a container and am getting errors. I think this might more a docker usage issues rather than neo4j usage.
I have built a container image from https://github.com/neo4j/docker-neo4j-publish 2.3.9, 3.3.3, 3.3.4 and 3.3.5 (only differences being some new ports in later versions). I have even pulled a native 3.3.3 from dockerhub.com
mkdir /tmp/data
chmod 777 /tmp/data
docker run --detach=true --name=neo4j --publish=7474:7474 --publish=7687:7687 --publish=7473:7473 --volume=/tmp/data:/data neo4j:3.3.3
docker exec -it neo4j find / -name '*.log'
and although it seems to be working with
neo4j> CREATE (n);
0 rows available after 50 ms, consumed after another 0 ms
Added 1 nodes
neo4j> CREATE (m),(o);
0 rows available after 15 ms, consumed after another 0 ms
Added 2 nodes
neo4j> MATCH (n) RETURN n;
+----+
| n |
+----+
| () |
| () |
| () |
+----+
3 rows available after 21 ms, consumed after another 8 ms
I actually get errors like this:
docker exec -it neo4j neo4j status
Neo4j is not running
Now this one looks like I am mistakenly trying to start another instance of Neo4j over a running instance:
docker exec -it neo4j neo4j console
Active database: graph.db
Directories in use:
home: /var/lib/neo4j
config: /var/lib/neo4j/conf
logs: /var/lib/neo4j/logs
plugins: /var/lib/neo4j/plugins
import: /var/lib/neo4j/import
data: /var/lib/neo4j/data
certificates: /var/lib/neo4j/certificates
run: /var/lib/neo4j/run
Starting Neo4j.
2018-04-15 06:30:13.119+0000 WARN Unknown config option: causal_clustering.discovery_listen_address
2018-04-15 06:30:13.123+0000 WARN Unknown config option: causal_clustering.raft_advertised_address
2018-04-15 06:30:13.123+0000 WARN Unknown config option: causal_clustering.raft_listen_address
2018-04-15 06:30:13.123+0000 WARN Unknown config option: ha.host.coordination
2018-04-15 06:30:13.124+0000 WARN Unknown config option: causal_clustering.transaction_advertised_address
2018-04-15 06:30:13.124+0000 WARN Unknown config option: causal_clustering.discovery_advertised_address
2018-04-15 06:30:13.124+0000 WARN Unknown config option: ha.host.data
2018-04-15 06:30:13.124+0000 WARN Unknown config option: causal_clustering.transaction_listen_address
2018-04-15 06:30:13.146+0000 INFO ======== Neo4j 3.3.3 ========
2018-04-15 06:30:13.186+0000 INFO Starting...
2018-04-15 06:30:13.997+0000 INFO Bolt enabled on 0.0.0.0:7687.
2018-04-15 06:30:14.094+0000 ERROR Failed to start Neo4j: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase#44a59da3' was successfully initialized, but failed to start. Please see the attached cause exception "Store and its lock file has been locked by another process: /var/lib/neo4j/data/databases/graph.db/store_lock. Please ensure no other process is using this database, and that the directory is writable (required even for read-only access)". Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase#44a59da3' was successfully initialized, but failed to start. Please see the attached cause exception "Store and its lock file has been locked by another process: /var/lib/neo4j/data/databases/graph.db/store_lock. Please ensure no other process is using this database, and that the directory is writable (required even for read-only access)".
org.neo4j.server.ServerStartupException: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabase#44a59da3' was successfully initialized, but failed to start. Please see the attached cause exception "Store and its lock file has been locked by another process: /var/lib/neo4j/data/databases/graph.db/store_lock. Please ensure no other process is using this database, and that the directory is writable (required even for read-only access)".
Does anybody have experience with Neo4j's docker implementation? Is it a single threaded issue meaning I need to call the CLI tools differently from the container?
The neo4j status command only works if you've started neo4j with neo4j start. Start creates a neo4j.pid file that status uses to see if neo4j is running. Starting under docker uses the console option instead of the start option. This does not create the PID file, so the status doesn't work. But that hardly matters, because neo4j is just about the only process running; if neo4j dies, the container will exit. If docker ps -a says that the container is up, then neo4j is up.
I have written my own hadoop program and I can run using pseudo distribute mode in my own laptop, however, when I put the program in the cluster which can run example jar of hadoop, it by default launches the local job though I indicate the hdfs file path, below is the output, give suggestions?
./hadoop -jar MyRandomForest_oob_distance.jar hdfs://montana-01:8020/user/randomforest/input/genotype1.txt hdfs://montana-01:8020/user/randomforest/input/phenotype1.txt hdfs://montana-01:8020/user/randomforest/output1_distance/ hdfs://montana-01:8020/user/randomforest/input/genotype101.txt hdfs://montana-01:8020/user/randomforest/input/phenotype101.txt 33 500 1
12/03/16 16:21:25 INFO jvm.JvmMetrics: Initializing JVM Metrics with processName=JobTracker, sessionId=
12/03/16 16:21:25 WARN mapred.JobClient: Use GenericOptionsParser for parsing the arguments. Applications should implement Tool for the same.
12/03/16 16:21:25 INFO mapred.JobClient: Running job: job_local_0001
12/03/16 16:21:25 INFO mapred.MapTask: io.sort.mb = 100
12/03/16 16:21:25 INFO mapred.MapTask: data buffer = 79691776/99614720
12/03/16 16:21:25 INFO mapred.MapTask: record buffer = 262144/327680
12/03/16 16:21:25 WARN mapred.LocalJobRunner: job_local_0001
java.io.FileNotFoundException: File /user/randomforest/input/genotype1.txt does not exist.
at org.apache.hadoop.fs.RawLocalFileSystem.getFileStatus(RawLocalFileSystem.java:361)
at org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:245)
at org.apache.hadoop.fs.ChecksumFileSystem$ChecksumFSInputChecker.<init>(ChecksumFileSystem.java:125)
at org.apache.hadoop.fs.ChecksumFileSystem.open(ChecksumFileSystem.java:283)
at org.apache.hadoop.fs.FileSystem.open(FileSystem.java:356)
at Data.Data.loadData(Data.java:103)
at MapReduce.DearMapper.loadData(DearMapper.java:261)
at MapReduce.DearMapper.setup(DearMapper.java:332)
at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:142)
at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:621)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:305)
at org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:177)
12/03/16 16:21:26 INFO mapred.JobClient: map 0% reduce 0%
12/03/16 16:21:26 INFO mapred.JobClient: Job complete: job_local_0001
12/03/16 16:21:26 INFO mapred.JobClient: Counters: 0
Total Running time is: 1 secs
LocalJobRunner has been chosen as your configuration most probably has the mapred.job.tracker property set to local or has not been set at all (in which case the default is local). To check, go to "wherever you extracted/installed hadoop"/etc/hadoop/ and see if the file mapred-site.xml exists (for me it did not, a file called mapped-site.xml.template was there). In that file (or create it if it doesn't exist) make sure it has the following property:
<configuration>
<property>
<name>mapreduce.framework.name</name>
<value>yarn</value>
</property>
</configuration>
See the source for org.apache.hadoop.mapred.JobClient.init(JobConf)
What is the value of this configuration property in the hadoop configuration on the machine you are submitting this from? Also confirm that the hadoop executable you are running references this configuration (and that you don't have 2+ installations configured differently) - type which hadoop and trace any symlinks you come across.
Alternatively you can override this when you submit your job, if you know the JobTracker host and port number using the -jt option:
hadoop jar MyRandomForest_oob_distance.jar -jt hostname:port hdfs://montana-01:8020/user/randomforest/input/genotype1.txt hdfs://montana-01:8020/user/randomforest/input/phenotype1.txt hdfs://montana-01:8020/user/randomforest/output1_distance/ hdfs://montana-01:8020/user/randomforest/input/genotype101.txt hdfs://montana-01:8020/user/randomforest/input/phenotype101.txt 33 500 1
If you're using Hadoop 2 and your job is running locally instead of on the cluster, ensure that you have setup mapred-site.xml to contain the mapreduce.framework.name property with a value of yarn. You also need to set up an aux-service in yarn-site.xml
Checkout the Cloudera Hadoop 2 operator migration blog for more information.
I had the same problem that every mapreduce v2 (mrv2) or yarn task only ran with the mapred.LocalJobRunner
INFO mapred.LocalJobRunner: Starting task: attempt_local284299729_0001_m_000000_0
The Resourcemanager and Nodemanagers were accessible and the mapreduce.framework.name was set to yarn.
Setting the HADOOP_MAPRED_HOME before executing the job fixed the problem for me.
export HADOOP_MAPRED_HOME=/usr/lib/hadoop-mapreduce
cheers
dan