java permission error on first run of newly installed Neo4J server - java

I'm setting up a new server for an application (node.js with Neo4j 1.8.3) that hasn't been used for a while. I installed Oracle JDK 7 (latest), which might explain this issue, as it's not recommended
for 1.8.3, will retest with JDK 6 tomorrow.
I installed Neo4J 1.8.3 on Thursday, on Ubuntu 14.04 running on Linode. Today I reviewed the log file (neo4j.0.0.log) and saw the following error:
Oct 02, 2014 5:02:48 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
After that there are numerous errors as follows:
WARNING: java.io.IOException: No such file or directory
Oct 02, 2014 12:00:46 PM java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode
This discussion seems relevant,
java system preferences under different users in linux
But before trying this I wanted to ask here. Is this a known problem with a standard solution?

Related

Issue in Jenkins installation plugins

I am facing issue while installing any of the Jenkins plugins suggested.
Actually after downloading,Jenkins.war file(which is latest 2.141) when i tried to execute the jar with
java -jar jenkins.war so it gave me an error of Jenkins require java 8 but you are using 10. Also,it says that java class version 54.0 is running,but it requires java 52.0.
But I was able to resolve this issue by setting --enable-future-java flag.
java -jar jenkins.war --enable-future-java flag
Now,after writing this command,jenkins is up and running but i am unable to install the plugins.
Also,im cmd prompt after the Jenkins is upa d running.There is one error also.
PFB :-
Sep 17, 2018 4:38:49 PM hudson.WebAppMain$3 run
INFO: Jenkins is fully up and running
[31mSep 17, 2018 4:39:02 PM hudson.model.UpdateSite updateData
SEVERE: ERROR: SHA-512 based signature in the update center doesn't match with the certificate in 'update site 'default''
[0mSep 17, 2018 4:39:02 PM hudson.model.AsyncPeriodicWork$1 run
INFO: Finished Download metadata. 15,407 ms
You need to add a flag which allows starting Jenkins with unsupported Java versions. You can do some google research on this.
If we change the Jenkins war file version from 2.141 to 2.814 then it is suitable with Java 10 and works fine for plugins installation of Jenkins

Jelastic GC agent does not work with Tomcat 8.5.x

I use Jelastic platform from different providers: dogado.de (Jelastic version is 4.6.2) and mirhosting.com (Jelastic version is 4.6.1). I have some environments on both platforms. These environments have next configuration:
Java 8
Apache Tomcat 8.5.3
MySQL 5.7.10
The Tomcat prints next info to the log file:
Server version: Apache Tomcat/8.5.3
Server number: 8.5.3.0
OS Name: Linux
OS Version: 2.6.32-042stab113.21
Architecture: amd64
Java Home: /usr/java/jdk1.8.0_72/jre
JVM Version: 1.8.0_72-b15
JVM Vendor: Oracle Corporation
CATALINA_BASE: /opt/repo/versions/8.5.3
CATALINA_HOME: /opt/repo/versions/8.5.3
I'm trying to enable Jelastic GC agent. So I changed the conf/variables.conf file, so now it contains next lines:
-javaagent:/opt/repo/versions/8.5.3/lib/jelastic-gc-agent.jar=debug=true,period=60
It means that the debug mode should be enabled now and the agent must print every 60 seconds the info about memory releasing. For previous Tomcat version (7.0.39; on the same platform, but another environment) it looks like this:
Jul 14, 2016 6:08:30 PM com.jelastic.java.gc.JelasticGCAgent$1 run
INFO: JelasticGCAgent - Start Full GC : [free memory] : 181834896 bytes
Jul 14, 2016 6:08:30 PM com.jelastic.java.gc.JelasticGCAgent$1 run
INFO: JelasticGCAgent - Finish Full GC : [free memory] : 74885120 bytes
But it does not work for Tomcat 8: memory usage is not changing at all time, there are no any new messages in the log file. I asked supports of these providers how to fix this issue, but the issue still there. And even more it looks like a bug in Jelastic agent or in the whole platform.
Did anybody face with the same issue already? Any known ways to fix it? Maybe I need to use another jar files?
Any ideas are welcome and of course I want to ask Jelastic team about this problem.
It seems to be a problem with configuration file for variables parsing.
As a workaround:
log into your Tomcat node via SSH
navigate to /opt/repo/versions/8.5.3/bin/
edit variablesparser.sh file and change the third line from
CONFFILE='/opt/repo/versions/${Version}/conf/variables.conf'
to
CONFFILE="/opt/repo/versions/${Version}/conf/variables.conf"
restart Tomcat

neo4j failing to start after disk full

i had the /var disk full on my debian server and neo4j stopped as expected. I freed up the space on the disk but the neo4j server does not start throwing the error given below in the logs. I don't have any java or neo4j process running on the server that i may kill.
Things were stable with my neo4j setup for the past 6 months with around 1000 nodes. I am little novice on the java side so please let me know if i have missed out on anything basic.
Output on command line: service neo4j-service restart
Restarting Neo4j Graph Database: neo4jWARNING: Max 1024 open files
allowed, minimum of 40 000 recommended. See the Neo4j manual. WARNING!
You are using an unsupported Java runtime.
* Please use Oracle(R) Java(TM) 7 to run Neo4j Server. Download "Java Platform (JDK) 7" from:
http://www.oracle.com/technetwork/java/javase/downloads/index.html
* Please see http://docs.neo4j.org/ for Neo4j Server installation instructions. Using additional JVM arguments: -server
-XX:+DisableExplicitGC -Dorg.neo4j.server.properties=conf/neo4j-server.properties -Djava.util.logging.config.file=conf/logging.properties -Dlog4j.configuration=file:conf/log4j.properties -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled Starting Neo4j Server...WARNING: not changing user process [4733]... waiting for
server to be ready..... Failed to start within 120 seconds. Neo4j
Server may have failed to start, please check the logs. failed!
Logfile:
Sep 26, 2014 3:31:38 PM org.neo4j.server.logging.Logger log
SEVERE: Failed to start Neo Server on port [7474]
Sep 26, 2014 3:33:00 PM org.neo4j.server.logging.Logger log
WARNING: You are using an unsupported Java runtime. Please use Oracle(R) Java(TM) Runtime Environment 7.
Sep 26, 2014 3:33:00 PM org.neo4j.server.logging.Logger log
INFO: Setting startup timeout to: 120000ms based on -1
Sep 26, 2014 3:33:03 PM org.neo4j.server.logging.Logger log
SEVERE:
org.neo4j.server.ServerStartupException: Starting Neo4j Server failed: Error starting org.neo4j.kernel.EmbeddedGraphDatabase, /var/lib/neo4j/data/graph.db
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:218)
at org.neo4j.server.Bootstrapper.start(Bootstrapper.java:87)
at org.neo4j.server.Bootstrapper.main(Bootstrapper.java:50)
Caused by: java.lang.RuntimeException: Error starting org.neo4j.kernel.EmbeddedGraphDatabase, /var/lib/neo4j/data/graph.db
at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:330)
at org.neo4j.kernel.EmbeddedGraphDatabase.<init>(EmbeddedGraphDatabase.java:63)
at org.neo4j.graphdb.factory.GraphDatabaseFactory$1.newDatabase(GraphDatabaseFactory.java:92)
at org.neo4j.graphdb.factory.GraphDatabaseBuilder.newGraphDatabase(GraphDatabaseBuilder.java:198)
at org.neo4j.kernel.impl.recovery.StoreRecoverer.recover(StoreRecoverer.java:115)
at org.neo4j.server.preflight.PerformRecoveryIfNecessary.run(PerformRecoveryIfNecessary.java:59)
at org.neo4j.server.preflight.PreFlightTasks.run(PreFlightTasks.java:70)
at org.neo4j.server.AbstractNeoServer.runPreflightTasks(AbstractNeoServer.java:333)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:152)
... 2 more
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.impl.transaction.TxManager#61615142' was successfully initialized, but failed to start. Please see attached cause exception.
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:509)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:115)
at org.neo4j.kernel.InternalAbstractGraphDatabase.run(InternalAbstractGraphDatabase.java:307)
... 10 more
Caused by: org.neo4j.graphdb.TransactionFailureException: Unable to start TM
at org.neo4j.kernel.impl.transaction.TxManager.openLog(TxManager.java:824)
at org.neo4j.kernel.impl.transaction.TxManager.start(TxManager.java:198)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:503)
... 12 more
Caused by: java.io.IOException: Branch[����] found for [GlobalId[NENEOK|5930761323375553953|5569093129887285248|13248], BranchId[ ]] but no record list found in map
at org.neo4j.kernel.impl.transaction.TxLog.readBranchAddRecordInto(TxLog.java:520)
at org.neo4j.kernel.impl.transaction.TxLog.getDanglingRecords(TxLog.java:440)
at org.neo4j.kernel.impl.transaction.TxLog.recreateActiveTransactionState(TxLog.java:133)
at org.neo4j.kernel.impl.transaction.TxLog.<init>(TxLog.java:128)
at org.neo4j.kernel.impl.transaction.TxManager.openLog(TxManager.java:796)
... 14 more
Sep 26, 2014 3:33:03 PM org.neo4j.server.logging.Logger log
SEVERE: Failed to start Neo Server on port [7474]
I am using an openjdk 1.7 runtime environment which i think i should upgrade but i don't understand what is the cause of the error since everything was working fine before. Thanks for any help!
You should never ever manually modify anything inside the graph.db directory unless you're 100% sure what you're doing.
To prevent the datastore directory from continuously growing check your setting for keep_logical_logs in neo4j.properties, see http://docs.neo4j.org/chunked/stable/configuration-logical-logs.html.
Unless you require logical logs for online backup or cluster synchronization, you might be save deleting nioneo_logical.log.v* files. Make sure to have a backup first!
Also check your settings for open file limits, http://docs.neo4j.org/chunked/stable/linux-performance-guide.html#_setting_the_number_of_open_files.
There used to be a outdated version of Neo4j having a bug that might corrupt your datastore when running out of disc space. If that has happened to you either need to manually fix it on a binary level (which requires a lot of knowledge on Neo4j internals) or restore a previous backup from a time before you run out of disc.

tomcat not starting

suddenly for some reason tomcat server is not runnin/starting/stopping.
below is the result I get when i run the startup command,
C:\Program Files\jasperserver-3.5.0\apache-tomcat\bin>startup
Using CATALINA_BASE: C:\Program Files\jasperserver-3.5.0\apache-tomcat
Using CATALINA_HOME: C:\Program Files\jasperserver-3.5.0\apache-tomcat
Using CATALINA_TMPDIR: C:\Program Files\jasperserver-3.5.0\apache-tomcat\temp
Using JRE_HOME: C:\PROGRA~1\JASPER~1.0\java\jre
The tomcat window pops up for a split of a second and goes away.
(I have another java instance installed under c:\program files)
Help!!!
Update:
Logs from catalina file
Mar 22, 2011 3:41:50 AM org.apache.coyote.http11.Http11BaseProtocol init
INFO: Initializing Coyote HTTP/1.1 on http-8080
Mar 22, 2011 3:41:50 AM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 1017 ms
Mar 22, 2011 3:41:51 AM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
Mar 22, 2011 3:41:51 AM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/5.5.20
Mar 22, 2011 3:41:51 AM org.apache.catalina.core.StandardHost start
INFO: XML validation disabled
Mar 22, 2011 3:42:06 AM org.apache.coyote.http11.Http11BaseProtocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Mar 22, 2011 3:42:06 AM org.apache.jk.common.ChannelSocket init
INFO: JK: ajp13 listening on /0.0.0.0:8009
Mar 22, 2011 3:42:06 AM org.apache.jk.server.JkMain start
INFO: Jk running ID=0 time=0/43 config=null
Mar 22, 2011 3:42:06 AM org.apache.catalina.storeconfig.StoreLoader load
INFO: Find registry server-registry.xml at classpath resource
Mar 22, 2011 3:42:06 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 15374 ms
Use catalina.bat run instead of startup.bat. Then the window won't go away and you can see what's going on
In my case that was a problem with final slash in %CATALINA_HOME% path: final slash should not be there!
C:\tomcat\8.0.30 - correct
C:\tomcat\8.0.30\ - wrong
See http://blackandwhitecomputer.blogspot.de/2015/09/tomcat-debug-cannot-startup.html
Honestly, I had not expected modern applications may be depended on final slash in environment variable path!
I ran into a similar problem. I open cmd prompt and cd to tomcat\bin\startup.bat. The issue was my JRE_HOME not defined in the environment variables. I added and it worked.
I had the same problem and I solved it this way:
First, following #ykaganovich suggestions, I tried to start the server using the catalina.bat start command; it did not solve the problem, but at least it showed a log that specified the error, which was really helpful.
In my case, the log said that the problem was because of the java versión. I had the JAVA_HOME variable pointing to the JDK7, but my tomcat version needed it to point to the JDK8.
I changed the JAVA_HOME variable to point to JDK8 (instead of JDK7) and then , when I executed the catalina.bat start command again, it worked perfectly and the server started. I hope my suggestion could be helpful to someone.
Hmm it's very strange problem because in the log you have that server started, so try this:
restart computer :) - the best solution for strange situations
change tomcat port
close every unnecessary applications: skype, ip phones etc (I've encountered similar problem someday and application ip phone "softly" blocked this port ("softly" - in tomcat log everything was OK but in reality webapp doesn't work)
Add tomcat in your eclipse and start it from there. Configure tomcat as 'Use Tomcat installation'. It will work
Had same problem with apache Tomcat 9 version.
Solution very simple.
Apache Tomcat 9 is supported by Java 8 and later versions.
So, i had JRE_HOME with JRE7 path, I binded it to new JRE8 and everything works fine.
Different versions of Apache Tomcat are available for different versions of the Servlet and JSP specifications. The mapping between the specifications and the respective Apache Tomcat versions is:
Hope this will work for you guys, cheers!
If Tomcat was earlier working fine and Tomcat not starting happens unexpectedly, it's because some other process has started using the port you were using Tomcat on. In my case, I had shutdown Tomcat and was trying to run my servlet directly from Eclipse. So Eclipse took control of the port. After I closed Eclipse and tried restarting Tomcat (with startup.bat), everything worked fine.
ykaganovich's answer helped me track down my issue.
Non of the solutions above worked for me.
I found my way out by removing my current tomcat and replace it with a new one and setting up again my workspace.
I hope this may help someone
Open up the Tomcat users file (tomcat-users.xml)and check that you've closed all your speech marks. That is what fixed it for me.
Now double-check the role names:
<tomcat-users>
<role rolename="admin" />
<role rolename="manager" />
<user username="admin" password="secret" roles="admin,manager" />
</tomcat-users>
Finally, execute startup.bat file from bin
Try to open Tomcat7w.exe or follow the below steps.
(I have installed Tomcat under folder C:\Program Files\Apache Software Foundation\Tomcat 7.0)
open command prompt as Administrator
run --> "C:\Program Files\Apache Software Foundation\Tomcat 7.0\bin\Tomcat7w.exe" //MS//
now you can see icon in the system tray
double click on icon and start/stop

Google App Engine - How to get demos to work?

I'm embarrassed to have to ask this, but I can't for the life of me figure out what I'm doing wrong.
I've downloaded the appengine-java-sdk-1.4.2 via the eclipse 3.6 plugin as per the instructions on Installing the Java SDK page. I am running Mac OSX 10.5.8 with JRE version 1.5.0_26. I have made the dev_appserver.sh file executable (chmod u+x dev_appserver.sh) and when I attempt to start the app server with one of the demos via the command
bin/dev_appserver.sh demos/guestbook/war/
I get the following output, but the server does not start up:
2011-03-13 17:52:43.404 java[839:80f] [Java CocoaComponent compatibility mode]: Enabled
2011-03-13 17:52:43.405 java[839:80f] [Java CocoaComponent compatibility mode]: Setting timeout for SWT to 0.100000
********************************************************
Warning: Future versions of the Dev App Server will require Java 1.6 or later. Please upgrade your JRE.
********************************************************
Mar 13, 2011 9:52:44 PM com.google.apphosting.utils.jetty.JettyLogger info
INFO: Logging to JettyLogger(null) via com.google.apphosting.utils.jetty.JettyLogger
Mar 13, 2011 9:52:44 PM com.google.apphosting.utils.config.AppEngineWebXmlReader readAppEngineWebXml
INFO: Successfully processed /Applications/eclipse_3.6/plugins/com.google.appengine.eclipse.sdkbundle.1.4.2_1.4.2.v201102111811/appengine-java-sdk-1.4.2/demos/guestbook/war/WEB-INF/appengine-web.xml
Mar 13, 2011 9:52:44 PM com.google.apphosting.utils.config.AbstractConfigXmlReader readConfigXml
INFO: Successfully processed /Applications/eclipse_3.6/plugins/com.google.appengine.eclipse.sdkbundle.1.4.2_1.4.2.v201102111811/appengine-java-sdk-1.4.2/demos/guestbook/war/WEB-INF/web.xml
I see the warning about upgrading the JRE, but I don't think this is the problem, as there are no exceptions reported. It just won't start up. I've tried creating a hello world app from within Eclipse using the plugin and running as Web server, but that also spits out the same text but does not start up the web server.
Any idea what I'm doing wrong and how to remedy the problem?
By changing the line in dev_appserver.sh to
/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Commands/java -ea -cp "$JAR_FILE" \
com.google.appengine.tools.KickStart \
com.google.appengine.tools.development.DevAppServerMain $*
instead of using the default java (which is set to 1.5.0_26 as I mentioned earlier) the web server starts up.
I had the same problem and simply tried running Eclipse as Administrator and then debugging worked fine.

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