We Keep Coding

sonarqube won't start with an elasticsearch error - java

Sonarqube 5.4 and java 8 here.
Tried this on both sonarqube 5.1 and with java 7 and I get the same results.
2016.03.29 10:49:23 ERROR web[o.a.c.c.C.[.[.[/]] Exception sending context initialized event to listener instance of class org.sonar.server.platform.PlatformServletContextListener
java.lang.IllegalStateException: Fail to execute ES put mapping request on indices 'rules' on type 'rule' with source '{"dynamic":false,"_id":{"path":"key"},"properties":{"debtRemFnOffset":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"_debtChar":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"_key":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"debtRemFnTypeOverloaded":{"type":"boolean"},"noteLogin":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"lang":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"id":{"type":"double"},"allTags":{"type":"multi_field","fields":{"allTags":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"words":{"type":"string","index":"analyzed","index_analyzer":"index_words","search_analyzer":"search_words"},"grams":{"type":"string","index":"analyzed","index_analyzer":"index_grams","search_analyzer":"search_grams"}}},"debtCharOverloaded":{"type":"boolean"},"ruleKey":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"createdAt":{"type":"date","format":"date_time"},"repo":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"name":{"type":"multi_field","fields":{"sort":{"type":"string","index":"analyzed","analyzer":"sortable"},"words":{"type":"string","index":"analyzed","index_analyzer":"index_words","search_analyzer":"search_words"},"name":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"grams":{"type":"string","index":"analyzed","index_analyzer":"index_grams","search_analyzer":"search_grams"}}},"debtChar":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"htmlDesc":{"type":"multi_field","fields":{"words":{"type":"string","index":"analyzed","index_analyzer":"index_words","search_analyzer":"search_words"},"htmlDesc":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"}}},"effortToFix":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"_debtRemFnOffset":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"debtRemFnType":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"key":{"type":"multi_field","fields":{"sort":{"type":"string","index":"analyzed","analyzer":"sortable"},"key":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"}}},"tags":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"templateKey":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"internalKey":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"debtSubCharOverloaded":{"type":"boolean"},"status":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"noteUpdatedAt":{"type":"date","format":"date_time"},"debtSubChar":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"mdDesc":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"noteCreatedAt":{"type":"date","format":"date_time"},"severity":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"params":{"dynamic":"true","properties":{"description":{"type":"multi_field","fields":{"words":{"type":"string","index":"analyzed","index_analyzer":"index_words","search_analyzer":"search_words"},"description":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"}}},"name":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"defaultValue":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"type":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"}},"type":"nested"},"sysTags":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"_debtRemFnCoefficient":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"_debtSubChar":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"updatedAt":{"type":"date","format":"date_time"},"_debtRemFnType":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"isTemplate":{"type":"boolean"},"markdownNote":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"},"debtRemFnCoefficient":{"index":"analyzed","index_analyzer":"keyword","search_analyzer":"whitespace","type":"string"}},"_all":{"enabled":false}}'
at org.sonar.server.es.request.ProxyPutMappingRequestBuilder.get(ProxyPutMappingRequestBuilder.java:43) ~[sonar-server-5.4.jar:na]
at org.sonar.server.es.request.ProxyPutMappingRequestBuilder.get(ProxyPutMappingRequestBuilder.java:31) ~[sonar-server-5.4.jar:na]
at org.sonar.server.search.BaseIndex.initializeIndex(BaseIndex.java:176) ~[sonar-server-5.4.jar:na]
at org.sonar.server.search.BaseIndex.start(BaseIndex.java:116) ~[sonar-server-5.4.jar:na]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_99]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_99]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_99]
at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_99]
at org.picocontainer.lifecycle.ReflectionLifecycleStrategy.invokeMethod(ReflectionLifecycleStrategy.java:110) ~[picoc
There's obviously a problem here with the embedded elasticsearch but I haven't been able to figure out it out. Any ideas?

I don't know how elastic got corrupted, but wiping the contents of /var/local/sonar/data and restoring mysql fixed it.

Related

on ubuntu 14.04, using openJDK8, When i start jprofiler, it has some error like below.
I struggle one day, at last still failed to start it.
java.lang.ExceptionInInitializerError
at java.awt.Component.<clinit>(Component.java:593)
at javax.swing.ImageIcon$2.run(ImageIcon.java:130)
at javax.swing.ImageIcon.<clinit>(ImageIcon.java:100)
at com.jprofiler.frontend.ab.a(ejt:315)
at com.jprofiler.frontend.ab.<clinit>(ejt:47)
at com.jprofiler.frontend.FrontendApplication.E(ejt:1038)
at com.jprofiler.frontend.IntegrationApplication.main(ejt:8)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:85)
at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:62)
Caused by: java.lang.NullPointerException
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1847)
at java.awt.Toolkit.loadLibraries(Toolkit.java:1633)
at java.awt.Toolkit.<clinit>(Toolkit.java:1670)
... 20 more
java.lang.NoClassDefFoundError: Could not initialize class java.awt.Toolkit
at javax.swing.ImageIcon.<init>(ImageIcon.java:198)
at javax.swing.ImageIcon.<init>(ImageIcon.java:217)
at com.ejt.framework.gui.eo.<init>(ejt:37)
at com.ejt.framework.gui.eo.a(ejt:17)
at com.jprofiler.frontend.ab.a(ejt:315)
at com.jprofiler.frontend.ab.<clinit>(ejt:47)
at com.jprofiler.frontend.FrontendApplication.E(ejt:1038)
at com.jprofiler.frontend.IntegrationApplication.main(ejt:8)
at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:62)

This a new problem with Java 8u242. It will be fixed shortly in JProfiler 11.1.1. The temporary workaround is to run JProfiler with a different JRE.
Since there is some interest, I will explain what the bug was:
The reason for this bug is that JProfiler set the private field ClassLoader.sys_paths to null to force a reevaluation of the java.library.path system property. This was a common hack to add directories to the library pack so that dependent native libraries could be loaded. Since a commit that was released as part of 8u242, the new private method ClassLoader.initLibraryPaths()has to be called after setting that field to null, otherwise no native libraries can be loaded.

I have simple grails app, it works good at my system, but it is hard to share it with other people where everyone has some different settings so i thought it woudl be good to create vagrant box so everyone coudl run it on os with same settings. Ok so let get us down to the business on guest os i can run app also(app is in shared folder) but i recive errors
Exception in thread "main" java.lang.RuntimeException: java.io.IOException: Incorrect function.
at org.grails.io.watch.WatchServiceDirectoryWatcher.addWatchDirectory(WatchServiceDirectoryWatcher.java:183)
at org.grails.io.watch.WatchServiceDirectoryWatcher.addWatchDirectory(WatchServiceDirectoryWatcher.java:153)
at org.grails.io.watch.DirectoryWatcher.addWatchDirectory(DirectoryWatcher.java:111)
at grails.boot.GrailsApp.configureDirectoryWatcher(GrailsApp.groovy:299)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springsource.loaded.ri.ReflectiveInterceptor.jlrMethodInvoke(ReflectiveInterceptor.java:1426)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:154)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:174)
at grails.boot.GrailsApp.enableDevelopmentModeWatch(GrailsApp.groovy:110)
at grails.boot.GrailsApp.run(GrailsApp.groovy:65)
at grails.boot.GrailsApp.run(GrailsApp.groovy:347)
at grails.boot.GrailsApp.run(GrailsApp.groovy:336)
at grails.boot.GrailsApp$run.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:133)
at baseapp.Application.main(Application.groovy:8)
Caused by: java.io.IOException: Incorrect function.
at sun.nio.fs.WindowsWatchService$Poller.implRegister(WindowsWatchService.java:420)
at sun.nio.fs.AbstractPoller.processRequests(AbstractPoller.java:260)
at sun.nio.fs.WindowsWatchService$Poller.run(WindowsWatchService.java:580)
at java.lang.Thread.run(Thread.java:745)
I was trying to figure out what is wrong, so my only guess based on WatchServiceDirectoryWatch.java is that grails is trying to set some dir which it will be scanning(i dont know for what?) but because project is in shared folder grails is trying to set dir to which it does not have access(guessing). My question is what cant i do to do not recive that errors?

I think you should go deeper and look at grails.boot.GrailsApp at grails.boot.GrailsApp.configureDirectoryWatcher(GrailsApp.groovy:299) which
Creates and returns a file change listener for notifying the plugin manager of changes.
and then at grails.boot.GrailsApp.enableDevelopmentModeWatch(GrailsApp.groovy:110)
which is inside a function named enableDevelopmentModeWatch.

I just tried to run Jetty 9 as non root users, using setuid feature without success for binding low port numbers.
I enabled the module setuid in the start.ini and added -Djava.library.path=/opt/jetty/lib/setuid
But I have the following stack trace when starting Jetty:
2015-06-09 16:27:27.211:WARN:oejx.XmlConfiguration:main: Config error
at | |
java.lang.reflect.InvocationTargetException in
file:/opt/jetty/etc/jetty-setuid.xml
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.jetty.start.Main.invokeMain(Main.java:321)
at org.eclipse.jetty.start.Main.start(Main.java:817)
at org.eclipse.jetty.start.Main.main(Main.java:112) Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration.set(XmlConfiguration.java:479)
at org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration.configure(XmlConfiguration.java:411)
at org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration.newObj(XmlConfiguration.java:815)
at org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration.itemValue(XmlConfiguration.java:1125)
at org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration.value(XmlConfiguration.java:1030)
at org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration.call(XmlConfiguration.java:721)
at org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration.configure(XmlConfiguration.java:417)
at org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration.configure(XmlConfiguration.java:354)
at org.eclipse.jetty.xml.XmlConfiguration.configure(XmlConfiguration.java:262)
at org.eclipse.jetty.xml.XmlConfiguration$1.run(XmlConfiguration.java:1243)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.jetty.xml.XmlConfiguration.main(XmlConfiguration.java:1174)
... 7 more Caused by: java.lang.UnsatisfiedLinkError: org.eclipse.jetty.setuid.SetUID.getpwnam(Ljava/lang/String;)Lorg/eclipse/jetty/setuid/Passwd;
at org.eclipse.jetty.setuid.SetUID.getpwnam(Native Method)
at org.eclipse.jetty.setuid.SetUIDListener.setUsername(SetUIDListener.java:53)
... 23 more
Those are the only references to this error:
dev.eclipse.org/mhonarc/lists/jetty-users/msg01657.html
groups.google.com/forum/#!topic/dropwizard-user/aap2B_U_QPo
But they are either stopped or do not show the solution.
The source code I found for the setuid package is:
https://github.com/jetty-project/codehaus-jetty-project/blob/master/jetty-setuid/modules/java/src/main/java/org/mortbay/setuid/SetUID.java
Even though I cannot be sure this is the version I am using, given this one is from a org.mortbay package, while the one Jetty 9 uses is an Eclipse one.
I tried setting -Djetty.libsetuid.path in the java args (first try-catch block), either adding the path to the $PATH variable or setting -Djava.library.path (second try-catch block) or copying the so to /lib and, finally, leaving it as it is (third try-catch block). I got the same exception stack in all the cases.
I cannot be sure if Jetty is either not finding the so file or not being able to load it, given that, if I remove all the references to the path (the cases I described latter), I still get the same error message.
I use Java7 to run Jetty.
Edit
I added the following snippet to one of my webapps as as matter of test, given that if the webapp succeed, I would know the problem is not in finding the shared object:
SetUID.setgid(1002);
SetUID.setuid(1002);
Passwd pw = SetUID.getpwuid(1002);
System.setProperty("user.name", pw.getPwName());
System.setProperty("user.home", pw.getPwDir());
I have the same UnsatisfiedLinkError as a result.
Edit2
I tried, instead, the following:
System.load(SetUID.__FILENAME);
SetUID.setgid(1002);
Which got me the following error message:
javax.servlet.ServletException: java.lang.UnsatisfiedLinkError: Native
Library /lib/libsetuid.so already loaded in another classloader
I may conclude, therefore, that the library has been loaded, at least.

Exploring the libsetuid file (nm -D /path/to/the/so), I realized that the so I was using was outdated and was not compatible with Jetty 9, the functions were named as mortbay:
root#root:~/# nm -D libsetuid.so --size-sort | less
0000000000000010 T Java_org_mortbay_setuid_SetUID_setgid
0000000000000010 T Java_org_mortbay_setuid_SetUID_setuid
0000000000000015 T Java_org_mortbay_setuid_SetUID_setumask
0000000000000018 T throwNewJavaSecurityException 0000000000000058 T
throwNewJavaException 000000000000008e T
Java_org_mortbay_setuid_SetUID_setrlimitnofiles 00000000000000a7 T
getJavaMethodId 00000000000000f5 T
Java_org_mortbay_setuid_SetUID_getrlimitnofiles 0000000000000102 T
getJavaFieldInt 0000000000000111 T setJavaFieldInt 0000000000000111 T
setJavaFieldLong 0000000000000121 T setJavaFieldString
00000000000001ba T Java_org_mortbay_setuid_SetUID_getpwuid
00000000000001e5 T Java_org_mortbay_setuid_SetUID_getpwnam
000000000000027e T Java_org_mortbay_setuid_SetUID_getgrgid
000000000000029e T Java_org_mortbay_setuid_SetUID_getgrnam
Now, I am using the shared object that already comes in the jetty download, not the one linked in the wiki.
In addition to that, looking through the code of the setuid module, I decided using the property -Djetty.libsetuid.path in my java args for indicating the absolute path of the lib, e.g., -Djetty.libsetuid.path=/opt/jetty/lib/setuid.so

I have a WebSphere 6.1 server with 3 EARs that I've recently imported and migrated in ME2015. Whenever I start my server, I'm given the following error.
(Error message that is repeated is: com.ibm.websphere.management.cmdframework.CommandMgr.getCommandMgr(Lcom/ibm/websphere/management/AdminClient;)Lcom/ibm/websphere/management/cmdframework/CommandMgr;)
The error seems to be of no consequence, because my server and apps start up and work fine. I would still like to see what the problem is. Google hasn't really yielded any results for me.
Contents of the .log file, same for each occurrence of this error:
!ENTRY com.genuitec.eclipse.blue.websphere.core 4 0 2015-06-08 09:20:41.131
!MESSAGE com.ibm.websphere.management.cmdframework.CommandMgr.getCommandMgr(Lcom/ibm/websphere/management/AdminClient;)Lcom/ibm/websphere/management/cmdframework/CommandMgr;
!STACK 0
java.lang.NoSuchMethodError: com.ibm.websphere.management.cmdframework.CommandMgr.getCommandMgr(Lcom/ibm/websphere/management/AdminClient;)Lcom/ibm/websphere/management/cmdframework/CommandMgr;
at com.genuitec.eclipse.blue.websphere.admin.proxy.WebSphereAdminClientProxy.getApplicationState(WebSphereAdminClientProxy.java:407)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at com.genuitec.eclipse.blue.websphere.admin.WebsphereAdminFactory$PassThroughProxyHandler.invoke(WebsphereAdminFactory.java:161)
at com.genuitec.eclipse.blue.websphere.admin.WebsphereAdminFactory$PassThroughProxyHandler$1.run(WebsphereAdminFactory.java:127)
at com.genuitec.eclipse.blue.websphere.admin.internal.WebSphereAdminThread.run(WebSphereAdminThread.java:55)

From your information, this is a bug in the MyEclipse code. I'll raise that. Sorry about the error message but it doesn't affect your code in any way. MyEclipse is just trying to check the start/stop state of the modules that are deployed. Looks like the method signatures changed in later releases of WebSphere.
If you're on the CI stream, that will be the quickest way of getting a fix, though I can't say exactly when that will be.

I have problem with my tomcat application, after changing the server and installing the last version of tomcat7 my application won't read/load jpg files..
I installed imageio and jai on the server, try to change java version but every time I have the same error..
Anybody have an idea?
Error: One factory fails for the operation "jpeg"
Occurs in: javax.media.jai.ThreadSafeOperationRegistry
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at javax.media.jai.FactoryCache.invoke(FactoryCache.java:122)
at javax.media.jai.OperationRegistry.invokeFactory(OperationRegistry.java:1674)
at javax.media.jai.ThreadSafeOperationRegistry.invokeFactory(ThreadSafeOperationRegistry.java:473)
at javax.media.jai.registry.RIFRegistry.create(RIFRegistry.java:332)
at com.sun.media.jai.opimage.StreamRIF.create(StreamRIF.java:102)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at javax.media.jai.FactoryCache.invoke(FactoryCache.java:122)
at javax.media.jai.OperationRegistry.invokeFactory(OperationRegistry.java:1674)
at javax.media.jai.ThreadSafeOperationRegistry.invokeFactory(ThreadSafeOperationRegistry.java:473)
at javax.media.jai.registry.RIFRegistry.create(RIFRegistry.java:332)
at javax.media.jai.RenderedOp.createInstance(RenderedOp.java:819)
at javax.media.jai.RenderedOp.createRendering(RenderedOp.java:867)
at javax.media.jai.RenderedOp.getWidth(RenderedOp.java:2179)
The whole error log can be found here -> http://paste.ubuntu.com/7653452/.
Update: The problem is related to grails plugin called ImageTools

If you look at the code for JPEGImageDecoder you'll see it depends on com.sun.image.codec.jpeg.ImageFormatException in its imports.
However, com.sun.image.codec.jpeg was removed from Java 7 onwards.
So likely the problem is that JAI is simply out of date, and you would have to use a Java 6 runtime to use it.