[ome-users] Insufficient memory running Omero server

[Paulo Almeida]

Hi Chris,

The only place where I still see the error is in WebAdmin.log, and the log is 
quiet in the 10 minutes preceding the error, so I'm not sure that will be 
useful, but I'm sending it in attachment. If it happens again I will look at 
the other logs.

Thanks
- Paulo




On Monday 12 November 2007 16:47, Chris Allan wrote:
> On 9 Nov 2007, at 19:15, Paulo Almeida wrote:
> > Hi,
>
> Hi Paulo.
>
> > I was running Omero 3.0 Beta 2.2 and I received an out of memory
> > error from
> > the server (I'm sorry, I don't have the exact error message
> > anymore). I have
> > been reading about it and a solution seems to be to allocate more
> > memory to
> > the java virtual machine. Is this common when running Omero? How
> > much memory
> > would be reasonable to use? Or do you think something else might be
> > wrong
> > that caused this? It only happened once and now the server seems
> > stable (I
> > haven't changed any memory settings, I just restarted the server).
>
> We're tracking this here:
>
> http://trac.openmicroscopy.org.uk/omero/ticket/834
>
> Not sure exactly what's causing the problem (we were just able to
> reproduce this today) but if you could "grep" your JBoss logs
> ($OMERO_HOME/jboss-4.2.1.GA/server/default/log) for "PermGen" and
> give me some of the context surrounding any lines you see come up,
> that'd be great.
>
> > - Paulo Almeida
>
> Ciao.
>
> -Chris
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 [09-11-07 15:46:41,984]  INFO - Msg: Group details [id: '0', name: 'system' Filename: ConnectionDB.java; Method name:  lookupGroups Line number: 314 
 [09-11-07 15:46:41,985]  INFO - Msg: Group details [id: '2', name: 'default' Filename: ConnectionDB.java; Method name:  lookupGroups Line number: 314 
 [09-11-07 15:46:59,247]  INFO - Msg: checkExperimenterGroup by String 'ccr' by user ID: '0' Filename: ConnectionDB.java; Method name:  checkExperimenterGroup Line number: 583 
 [09-11-07 15:46:59,322]  INFO - Msg: ExperimenterGroup 'ccr' doesn't exist Filename: ConnectionDB.java; Method name:  checkExperimenterGroup Line number: 589 
 [09-11-07 15:46:59,325]  INFO - Msg: createGroup by user ID: '0' Filename: ConnectionDB.java; Method name:  createGroup Line number: 510 
 [09-11-07 15:46:59,325]  INFO - Msg: ExperimenterGroup details [name: 'ccr', desc: 'Cell Cycle Regulation'] Filename: ConnectionDB.java; Method name:  createGroup Line number: 512 
 [09-11-07 15:47:00,918]  INFO - Msg: ExperimenterGroup created with ID: '3' Filename: ConnectionDB.java; Method name:  createGroup Line number: 515 
 [09-11-07 15:47:00,919]  INFO - Msg: lookupGroups by user ID: 0' Filename: ConnectionDB.java; Method name:  lookupGroups Line number: 310 
 [09-11-07 15:47:02,361]  INFO - Msg: Group details [id: '0', name: 'system' Filename: ConnectionDB.java; Method name:  lookupGroups Line number: 314 
 [09-11-07 15:47:02,362]  INFO - Msg: Group details [id: '2', name: 'default' Filename: ConnectionDB.java; Method name:  lookupGroups Line number: 314 
 [09-11-07 15:47:02,362]  INFO - Msg: Group details [id: '3', name: 'ccr' Filename: ConnectionDB.java; Method name:  lookupGroups Line number: 314 
 [09-11-07 15:47:10,560]  INFO - Msg: getGroup by ID '3' by user ID: 0' Filename: ConnectionDB.java; Method name:  getGroup Line number: 380 
 [09-11-07 15:47:12,108]  INFO - Msg: Group details [id: '3', name: 'ccr' Filename: ConnectionDB.java; Method name:  getGroup Line number: 382 
 [09-11-07 15:47:13,871]  INFO - Msg: lookupExperimenters by user ID: 0' Filename: ConnectionDB.java; Method name:  lookupExperimenters Line number: 326 
 [09-11-07 15:57:40,913] ERROR - Msg: Servlet.service() for servlet jsp threw exception Filename: ApplicationDispatcher.java; Method name:  invoke Line number: 719 
 java.lang.OutOfMemoryError: PermGen space
[09-11-07 15:59:10,573] ERROR - Msg: Servlet.service() for servlet Faces Servlet threw exception Filename: StandardWrapperValve.java; Method name:  invoke Line number: 271 
 java.lang.OutOfMemoryError: PermGen space
[09-11-07 15:59:47,479] ERROR - Msg: Servlet.service() for servlet jsp threw exception Filename: ApplicationDispatcher.java; Method name:  invoke Line number: 719 
 java.lang.OutOfMemoryError: PermGen space
[09-11-07 16:02:47,387]  INFO - Msg: Reading standard config org/apache/myfaces/resource/standard-faces-config.xml Filename: FacesConfigurator.java; Method name:  feedStandardConfig Line number: 159 
 [09-11-07 16:02:47,473]  INFO - Msg: Reading config jar:file:/home/paulo/software/omero/omero-3.0-Beta2.2/jboss-4.2.1.GA/server/default/tmp/deploy/tmp58403WebAdmin-exp.war/WEB-INF/lib/ajax4jsf.jar!/META-INF/faces-config.xml Filename: FacesConfigurator.java; Method name:  feedClassloaderConfigurations Line number: 379 
 [09-11-07 16:02:47,522]  INFO - Msg: Reading config jar:file:/home/paulo/software/omero/omero-3.0-Beta2.2/jboss-4.2.1.GA/server/default/tmp/deploy/tmp58403WebAdmin-exp.war/WEB-INF/lib/chartcreator.jar!/META-INF/faces-config.xml Filename: FacesConfigurator.java; Method name:  feedClassloaderConfigurations Line number: 379 
 [09-11-07 16:02:47,533]  INFO - Msg: Reading config jar:file:/home/paulo/software/omero/omero-3.0-Beta2.2/jboss-4.2.1.GA/server/default/tmp/deploy/tmp58403WebAdmin-exp.war/WEB-INF/lib/tomahawk-sandbox.jar!/META-INF/faces-config.xml Filename: FacesConfigurator.java; Method name:  feedClassloaderConfigurations Line number: 379 
 [09-11-07 16:02:47,564]  INFO - Msg: Reading config jar:file:/home/paulo/software/omero/omero-3.0-Beta2.2/jboss-4.2.1.GA/server/default/tmp/deploy/tmp58403WebAdmin-exp.war/WEB-INF/lib/tomahawk.jar!/META-INF/faces-config.xml Filename: FacesConfigurator.java; Method name:  feedClassloaderConfigurations Line number: 379 
 [09-11-07 16:02:47,599]  INFO - Msg: Reading config /WEB-INF/faces-config.xml Filename: FacesConfigurator.java; Method name:  feedWebAppConfig Line number: 540 
 [09-11-07 16:02:48,569]  INFO - Msg: MyFaces-package : myfaces-api not found. Filename: FacesConfigurator.java; Method name:  logMetaInf Line number: 207 
 [09-11-07 16:02:48,570]  INFO - Msg: MyFaces-package : myfaces-impl not found. Filename: FacesConfigurator.java; Method name:  logMetaInf Line number: 207 
 [09-11-07 16:02:48,571]  INFO - Msg: MyFaces-package : tomahawk-sandbox not found. Filename: FacesConfigurator.java; Method name:  logMetaInf Line number: 207 
 [09-11-07 16:02:48,573]  INFO - Msg: Starting up MyFaces-package : tomahawk in version : sandbox from path : file:/home/paulo/software/omero/omero-3.0-Beta2.2/jboss-4.2.1.GA/server/default/tmp/deploy/tmp58403WebAdmin-exp.war/WEB-INF/lib/tomahawk-sandbox.jar Filename: FacesConfigurator.java; Method name:  logMetaInf Line number: 199 
 [09-11-07 16:02:49,324]  INFO - Msg: Overwriting renderer with family = javax.faces.Form rendererType = javax.faces.Form renderer class = org.apache.myfaces.renderkit.html.ext.HtmlFormRenderer Filename: HtmlRenderKitImpl.java; Method name:  addRenderer Line number: 107 
 [09-11-07 16:02:49,616]  INFO - Msg: Overwriting renderer with family = javax.faces.Command rendererType = javax.faces.Button renderer class = org.apache.myfaces.renderkit.html.jsf.ExtendedHtmlButtonRenderer Filename: HtmlRenderKitImpl.java; Method name:  addRenderer Line number: 107 
 [09-11-07 16:02:49,617]  INFO - Msg: Overwriting renderer with family = javax.faces.Form rendererType = javax.faces.Form renderer class = org.apache.myfaces.renderkit.html.HtmlFormRenderer Filename: HtmlRenderKitImpl.java; Method name:  addRenderer Line number: 107 
 [09-11-07 16:02:49,637]  INFO - Msg: Overwriting renderer with family = javax.faces.Command rendererType = javax.faces.Link renderer class = org.apache.myfaces.renderkit.html.jsf.ExtendedHtmlLinkRenderer Filename: HtmlRenderKitImpl.java; Method name:  addRenderer Line number: 107 
 [09-11-07 16:02:49,675]  INFO - Msg: Serialization provider : class org.apache.myfaces.shared_impl.util.serial.DefaultSerialFactory Filename: FacesConfigurator.java; Method name:  handleSerialFactory Line number: 941