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Permlink Replies: 12 - Pages: 1 - Last Post: Jun 6, 2008 2:15 PM Last Post By: arnold
pts2

Posts: 50
Registered: 6/1/08
all sorts of errors on startup...
Posted: Jun 3, 2008 5:11 AM
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Can anyone help me understand these (and how to fix them)?:

after starting the run.jar, I get things like:

22:56:46,844 ERROR MainDeployer Could not create deployment: file:/Users/lab/Documents/dcm4chee-mysql-2.13.4/server/default/deploy/dcm4chee-xdsquery.sar
org.jboss.deployment.DeploymentException: - nested throwable: (java.lang.reflect.UndeclaredThrowableException)
at org.jboss.system.ServiceConfigurator.install(ServiceConfigurator.java:196)
(plus a whole bunch of other 'at org...' etc., then:

Caused by: java.lang.reflect.UndeclaredThrowableException
at org.jboss.system.ServiceCreator.install(ServiceCreator.java:236)
at org.jboss.system.ServiceConfigurator.internalInstall(ServiceConfigurator.java:451)
at org.jboss.system.ServiceConfigurator.install(ServiceConfigurator.java:171)
... 81 more
Caused by: java.lang.ExceptionInInitializerError
at org.dcm4chex.xds.query.mbean.XDSStoredQuery.<clinit>(XDSStoredQuery.java:124)
at org.dcm4chex.xds.query.mbean.XDSQueryService.<init>(XDSQueryService.java:86)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:494)
at org.jboss.mx.server.MBeanServerImpl.instantiate(MBeanServerImpl.java:1233)
at org.jboss.mx.server.MBeanServerImpl.instantiate(MBeanServerImpl.java:286)
at org.jboss.system.ServiceCreator.install(ServiceCreator.java:170)
... 83 more
Caused by: java.lang.RuntimeException: Cannot create "omar.home" directory: ../server/default/conf/omar
at org.freebxml.omar.common.AbstractProperties.initHomeDir(AbstractProperties.java:66)
at org.freebxml.omar.common.AbstractProperties.initOmarHomeDir(AbstractProperties.java:89)
at org.freebxml.omar.common.CommonProperties.initProperties(CommonProperties.java:48)
at org.freebxml.omar.common.CommonProperties.<init>(CommonProperties.java:38)
at org.freebxml.omar.common.CommonProperties.getInstance(CommonProperties.java:61)
at org.freebxml.omar.common.CommonResourceBundle.getInstance(CommonResourceBundle.java:48)
at org.freebxml.omar.common.BindingUtility.<clinit>(BindingUtility.java:105)
... 92 more
22:56:46,932 INFO STDOUT no object for null
22:56:46,933 INFO STDOUT no object for null
22:56:46,947 INFO STDOUT no object for null
22:56:46,961 INFO STDOUT no object for {urn:jboss:bean-deployer}supplyType
22:56:46,968 INFO STDOUT no object for {urn:jboss:bean-deployer}dependsType

Then a bit later:

22:56:53,563 ERROR MainDeployer Could not create deployment: file:/Users/lab/Documents/dcm4chee-mysql-2.13.4/server/default/deploy/dcm4chee-rid-service.xml
org.jboss.deployment.DeploymentException: - nested throwable: (java.lang.reflect.InvocationTargetException)
at org.jboss.system.ServiceConfigurator.install(ServiceConfigurator.java:196)
at org.jboss.system.ServiceController.install(ServiceController.java:226)
(etc.)

I'm not sure what would be helpful to anyone of you, so I'll just put the "caused by" lines:

Caused by: java.lang.reflect.InvocationTargetException
Caused by: javax.management.MBeanException
Caused by: javax.management.MBeanRegistrationException: preRegister() failed:
Caused by: javax.management.RuntimeMBeanException
Caused by: org.dcm4chex.archive.exceptions.ConfigurationException: No such ImageWriter - com.sun.media.imageioimpl.plugins.jpeg.CLibJPEGImageWriter

a bit later:

22:56:54,343 WARN BasicMBeanRegistry javax.management.MBeanRegistrationException: preRegister() failed:
22:56:54,343 INFO WADOService Registration is not done -> stop
22:56:54,343 ERROR MainDeployer Could not create deployment: file:/Users/lab/Documents/dcm4chee-mysql-2.13.4/server/default/deploy/dcm4chee-wado-service.xml
org.jboss.deployment.DeploymentException: - nested throwable: (java.lang.reflect.InvocationTargetException)

Caused by: java.lang.reflect.InvocationTargetException
Caused by: javax.management.MBeanException
Caused by: javax.management.MBeanRegistrationException: preRegister() failed:
Caused by: javax.management.RuntimeMBeanException
Caused by: org.dcm4chex.archive.exceptions.ConfigurationException: No such ImageWriter - com.sun.media.imageioimpl.plugins.jpeg.CLibJPEGImageWriter

Finally, near the end:

      • Incompletely deployed packages ---
org.jboss.deployment.DeploymentInfo@b3276079 { url=file:/Users/lab/Documents/dcm4chee-mysql-2.13.4/server/default/deploy/dcm4chee-xdsquery.sar }
deployer: org.jboss.deployment.SARDeployer@ddcd5f
status: Deployment FAILED reason: - nested throwable: (java.lang.reflect.UndeclaredThrowableException)
state: FAILED
watch: file:/Users/lab/Documents/dcm4chee-mysql-2.13.4/server/default/deploy/dcm4chee-xdsquery.sar
altDD: null
lastDeployed: 1212461806787
lastModified: 1212461805000
mbeans:

org.jboss.deployment.DeploymentInfo@843f5c52 { url=file:/Users/lab/Documents/dcm4chee-mysql-2.13.4/server/default/deploy/dcm4chee-rid-service.xml }
deployer: org.jboss.deployment.SARDeployer@ddcd5f
status: Deployment FAILED reason: - nested throwable: (java.lang.reflect.InvocationTargetException)
state: FAILED
watch: file:/Users/lab/Documents/dcm4chee-mysql-2.13.4/server/default/deploy/dcm4chee-rid-service.xml
altDD: null
lastDeployed: 1212461813002
lastModified: 1212461812000
mbeans:

org.jboss.deployment.DeploymentInfo@e945bac8 { url=file:/Users/lab/Documents/dcm4chee-mysql-2.13.4/server/default/deploy/dcm4chee-wado-service.xml }
deployer: org.jboss.deployment.SARDeployer@ddcd5f
status: Deployment FAILED reason: - nested throwable: (java.lang.reflect.InvocationTargetException)
state: FAILED
watch: file:/Users/lab/Documents/dcm4chee-mysql-2.13.4/server/default/deploy/dcm4chee-wado-service.xml
altDD: null
lastDeployed: 1212461814325
lastModified: 1212461814000
mbeans:

WTF? Any help would be appreciated. Complete reinstall? OK, but how to backup what I have already put in the database (or am I screwed? -- see my thread trying to understand how to backup things so they can be recovered...)

Thanks, Tom
justin

Posts: 184
Registered: 11/16/07
Re: all sorts of errors on startup...
Posted: Jun 3, 2008 6:29 AM   in response to: pts2 in response to: pts2
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Tom,

It would be helpful if you could provide some basic details about what you're trying to accomplish and what type of system you have. Is this an upgrade? What OS? What database?

The exception suggests that you may not have permissions to create a directory in ../server/default/conf/. Please verify that you have the ability to write to this directory.

Justin
arnold

Posts: 1,373
Registered: 11/15/07
Re: all sorts of errors on startup...
Posted: Jun 3, 2008 6:32 AM   in response to: pts2 in response to: pts2
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looks like you cannot create folders inside your installation directory. please check your permissions.
pts2

Posts: 50
Registered: 6/1/08
Re: all sorts of errors on startup...
Posted: Jun 3, 2008 6:46 AM   in response to: pts2 in response to: pts2
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OK, figured out some of it..

I needed to change the files for the ImageWriterClass. That fixed the RID/WADO service bails.

I also seem to have heap problems. Is this something that more ram would help with? If I send too many files at once, it gets confused. It also doesn't like to show 1000 lines (one for each slice image) in the web interface.

-Tom
pts2

Posts: 50
Registered: 6/1/08
Re: all sorts of errors on startup...
Posted: Jun 3, 2008 6:52 AM   in response to: arnold in response to: arnold
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Yes, thanks. I fixed that. It still doesn't like large files sent (from Osirix) to the pacs. It seems to keep running up against memory heap limits... I set them up to 1024m, but that doesn't seem to be enough. I guess it needs more heap space for bigger image series??

We are (trying) to construct a database of high-resolution research CT (and other) scans. We have ~2500 scans so far, and are trying to use dcm4chee + Osirix for our installation. Many of the scans are >1000 slices. I'm trying to get the thing running reliably on a quad-xeon Mac Pro (with only 2 GB of RAM).

-Tom
pts2

Posts: 50
Registered: 6/1/08
Re: all sorts of errors on startup...
Posted: Jun 3, 2008 7:03 AM   in response to: pts2 in response to: pts2
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What sort of heap space requirements do we need? It seems to constantly bail accepting incoming scan series greater than ~1000 images. Is this normal? This will seriously crimp our ability to use it if we can't figure out a workaround.

-Tom
arnold

Posts: 1,373
Registered: 11/15/07
Re: all sorts of errors on startup...
Posted: Jun 3, 2008 7:13 AM   in response to: pts2 in response to: pts2
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can you post a log with your problem. as always the more RAM you have the better :) you can modify the Xmx/Xms parameters in run.conf
pts2

Posts: 50
Registered: 6/1/08
Re: all sorts of errors on startup...
Posted: Jun 3, 2008 9:49 PM   in response to: arnold in response to: arnold
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OK, so I'm sending a series from Osirix to the dcm4chee. It is going fine. ~1000 images (1 full series) seem to have been transferred. No errors. I then send another one. It immediately seems to be going slower. While it is doing this, I switch to look at the dcm4chee-web interface. I press 'folder' again to refresh (to try to see the first series I sent). At this point it starts giving errors in the log. The web interface bails and gives this:

HTTP Status 500 -

type Exception report

message

description The server encountered an internal error () that prevented it from fulfilling this request.

exception

javax.servlet.ServletException: Servlet execution threw an exception
org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:96)
root cause

java.lang.OutOfMemoryError: Java heap space
org.apache.xpath.VariableStack.<init>(VariableStack.java:73)
org.apache.xpath.XPathContext.<init>(XPathContext.java:448)
org.apache.xalan.transformer.TransformerImpl.<init>(TransformerImpl.java:397)
org.apache.xalan.templates.StylesheetRoot.newTransformer(StylesheetRoot.java:196)
org.infohazard.maverick.transform.XSLTransform$Step.go(XSLTransform.java:323)
org.infohazard.maverick.opt.view.DomifyViewFactory$DomifyView.go(DomifyViewFactory.java:116)
org.infohazard.maverick.flow.ViewWithTransforms.go(ViewWithTransforms.java:57)
org.infohazard.maverick.flow.ViewShunted.go(ViewShunted.java:38)
org.infohazard.maverick.flow.CommandBase.go(CommandBase.java:79)
org.infohazard.maverick.Dispatcher.service(Dispatcher.java:345)
javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:96)
note The full stack trace of the root cause is available in the JBossWeb/2.0.1.GA logs.

JBossWeb/2.0.1.GA

The log (output of the 'run.jar' window):

(just where things go bad)
...
15:39:21,647 INFO FsmImpl received pc-17 299:C_STORE_RQ with Dataset
class: 1.2.840.10008.5.1.4.1.1.2/CT Image Storage
inst: 1.3.12.2.1107.5.1.4.54314.30000007020412314242100004456/?
15:39:22,235 INFO StoreScpService M-WRITE file:/Users/lab/Documents/dcm4chee-mysql-2.13.5/server/default/archive/2008/6/3/15/EB21B38A/878403EE/87840F30
15:39:22,538 INFO StoreScpService Add missing Issuer Of Patient ID for Patient ID 29-43-379 (torso)
15:39:22,538 INFO StorageBean inserting instance FileMetaInfo[uid=1.3.12.2.1107.5.1.4.54314.30000007020412314242100004456
class=1.2.840.10008.5.1.4.1.1.2/CT Image Storage
ts=1.2.840.10008.1.2.1/Explicit VR Little Endian
impl=1.2.40.0.13.1.1-dcm4che-1.4.17]
15:39:25,477 INFO InstanceBean Created Instancepk=11354, iuid=1.3.12.2.1107.5.1.4.54314.30000007020412314242100004456, cuid=1.2.840.10008.5.1.4.1.1.2, series->ejb/Series:28
15:39:27,239 WARN TxConnectionManager Connection error occured: org.jboss.resource.connectionmanager.TxConnectionManager$TxConnectionEventListener@2c92d4state=NORMAL mc=org.jboss.resource.adapter.jdbc.local.LocalManagedConnection@3aa93d handles=1 lastUse=1212521961942 permit=true trackByTx=true mcp=org.jboss.resource.connectionmanager.JBossManagedConnectionPool$OnePool@a6905a context=org.jboss.resource.connectionmanager.InternalManagedConnectionPool@4f1805 xaResource=org.jboss.resource.connectionmanager.TxConnectionManager$LocalXAResource@b1ea44 txSync=null
15:39:30,754 INFO FileSystemMgtService Check for unreferenced private files to delete
15:39:36,320 WARN LocalManagedConnectionFactory Error notifying of connection error for listener: org.jboss.resource.connectionmanager.TxConnectionManager$TxConnectionEventListener@2c92d4state=NORMAL mc=org.jboss.resource.adapter.jdbc.local.LocalManagedConnection@3aa93d handles=1 lastUse=1212521961942 permit=true trackByTx=true mcp=org.jboss.resource.connectionmanager.JBossManagedConnectionPool$OnePool@a6905a context=org.jboss.resource.connectionmanager.InternalManagedConnectionPool@4f1805 xaResource=org.jboss.resource.connectionmanager.TxConnectionManager$LocalXAResource@b1ea44 txSync=null
java.lang.OutOfMemoryError: Java heap space
15:39:37,500 ERROR LogInterceptor] TransactionRolledbackLocalException in method: public abstract org.dcm4chex.archive.ejb.interfaces.FileLocal org.dcm4chex.archive.ejb.interfaces.FileLocalHome.create(java.lang.String,java.lang.String,long,byte[,int,org.dcm4chex.archive.ejb.interfaces.InstanceLocal,org.dcm4chex.archive.ejb.interfaces.FileSystemLocal) throws javax.ejb.CreateException, causedBy:
15:39:44,837 WARN loggerI18N http://com.arjuna.ats.internal.jta.transaction.arjunacore.enliststarterror http://com.arjuna.ats.internal.jta.transaction.arjunacore.enliststarterror TransactionImple.enlistResource - XAResource.start returned: XAException.XAER_PROTO for < 131075, 31, 29, 1--7da4adea:c543:4844d091:15335-7da4adea:c543:4844d091:15337 >
15:39:46,012 ERROR STDERR org.jboss.resource.connectionmanager.JBossLocalXAException: Trying to start a new tx when old is not complete! old: < 131075, 31, 29, 1--7da4adea:c543:4844d091:1532a-7da4adea:c543:4844d091:1532c >, new < 131075, 31, 29, 1--7da4adea:c543:4844d091:15335-7da4adea:c543:4844d091:15337 >, flags 0
15:39:46,307 ERROR TxConnectionManager There is something wrong with the pooling?
java.lang.IllegalStateException: afterCompletion called with wrong tx! Expected: TxSync3688651{tx=TransactionImple < ac, BasicAction: -7da4adea:c543:4844d091:1532a status: ActionStatus.ABORTED > wasTrackByTx=true enlisted=true}, actual: TxSync5326683{tx=TransactionImple < ac, BasicAction: -7da4adea:c543:4844d091:15335 status: ActionStatus.ABORT_ONLY > wasTrackByTx=true enlisted=false}
at org.jboss.resource.connectionmanager.TxConnectionManager$TxConnectionEventListener$TransactionSynchronization.afterCompletion(TxConnectionManager.java:819)
at org.jboss.resource.connectionmanager.TransactionSynchronizer.invokeAfter(TransactionSynchronizer.java:301)
at org.jboss.resource.connectionmanager.TransactionSynchronizer.afterCompletion(TransactionSynchronizer.java:265)
at com.arjuna.ats.internal.jta.resources.arjunacore.SynchronizationImple.afterCompletion(SynchronizationImple.java:136)
http://etc...

then, a bit later:

15:39:46,895 ERROR STDERR at org.jboss.resource.connectionmanager.TxConnectionManager$LocalXAResource.start(TxConnectionManager.java:886)
15:39:55,969 ERROR LogInterceptor] Unexpected Error in method: public abstract org.dcm4che.data.Dataset org.dcm4chex.archive.ejb.interfaces.Storage.store(org.dcm4che.data.Dataset,long,java.lang.String,long,byte[,boolean) throws org.dcm4che.net.DcmServiceException,java.rmi.RemoteException
java.lang.OutOfMemoryError: Java heap space
15:39:55,969 ERROR STDERR at com.arjuna.ats.internal.jta.transaction.arjunacore.TransactionImple.enlistResource(TransactionImple.java:776)
15:39:56,264 WARN StoreScpService failed to update DB with entries for received 2008/6/3/15/EB21B38A/878403EE/87840F30 - retry
java.rmi.ServerError: Unexpected Error; nested exception is:
java.lang.OutOfMemoryError: Java heap space
at org.jboss.ejb.plugins.LogInterceptor.handleException(LogInterceptor.java:434)
at org.jboss.ejb.plugins.LogInterceptor.invoke(LogInterceptor.java:209)
at org.jboss.ejb.plugins.ProxyFactoryFinderInterceptor.invoke(ProxyFactoryFinderInterceptor.java:138)
at org.jboss.ejb.SessionContainer.internalInvoke(SessionContainer.java:648)

and a bit later:

Caused by: java.lang.OutOfMemoryError: Java heap space
15:39:56,264 ERROR STDERR at com.arjuna.ats.internal.jta.transaction.arjunacore.TransactionImple.enlistResource(TransactionImple.java:499)
15:39:56,855 ERROR STDERR at org.jboss.resource.connectionmanager.TxConnectionManager$TxConnectionEventListener$TransactionSynchronization.enlist(TxConnectionManager.java:773)
15:39:57,148 ERROR STDERR at org.jboss.resource.connectionmanager.TxConnectionManager$TxConnectionEventListener.enlist(TxConnectionManager.java:564)
15:39:57,149 ERROR STDERR at org.jboss.resource.connectionmanager.TxConnectionManager.managedConnectionReconnected(TxConnectionManager.java:337)
15:39:57,149 ERROR STDERR at org.jboss.resource.connectionmanager.BaseConnectionManager2.reconnectManagedConnection(BaseConnectionManager2.java:518)
15:39:57,150 ERROR STDERR at org.jboss.resource.connectionmanager.BaseConnectionManager2.allocateConnection(BaseConnectionManager2.java:399)
15:39:57,444 ERROR STDERR at org.jboss.resource.connectionmanager.BaseConnectionManager2$ConnectionManagerProxy.allocateConnection(BaseConnectionManager2.java:842)
15:39:57,445 ERROR STDERR at org.jboss.resource.adapter.jdbc.WrapperDataSource.getConnection(WrapperDataSource.java:88)
15:39:57,446 ERROR STDERR at org.jboss.ejb.plugins.cmp.jdbc.JDBCAbstractQueryCommand.execute(JDBCAbstractQueryCommand.java:225)
etc....

Does this help? It basically does fine accepting ~ 1 series, then starts complaining about memory heap. After I restart the 'run.jar', it works for ~ 1 large series and bails again. ??? Any ideas?

-Tom

pts2

Posts: 50
Registered: 6/1/08
Re: all sorts of errors on startup...
Posted: Jun 3, 2008 9:51 PM   in response to: pts2 in response to: pts2
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sorry about the formatting of my post of parts of the log. I have no idea why some is lined out, and others became hyperlinked!

-Tom
damien

Posts: 1,891
Registered: 11/15/07
Re: all sorts of errors on startup...
Posted: Jun 3, 2008 10:22 PM   in response to: pts2 in response to: pts2
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It's because the forum software uses some wiki-style markup. When typing a message in "Plain Text" mode, look at the right hand side of the screen and you'll see a little sidebar with the markup guide. The log snippets have characters in them that coincide to the markup. Sometimes it is better to post log files and snippets as attachments to the message.
pts2

Posts: 50
Registered: 6/1/08
Re: all sorts of errors on startup...
Posted: Jun 4, 2008 6:53 AM   in response to: damien in response to: damien
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OK, do you need me to repost the log messages, or are they sufficient as is to diagnose the problem?

-Tom
damien

Posts: 1,891
Registered: 11/15/07
Re: all sorts of errors on startup...
Posted: Jun 4, 2008 1:33 PM   in response to: pts2 in response to: pts2
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No need to repost.
arnold

Posts: 1,373
Registered: 11/15/07
Re: all sorts of errors on startup...
Posted: Jun 6, 2008 2:15 PM   in response to: pts2 in response to: pts2
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Did you try to give more memory to dcm4chee as you get an out of memory error ?
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