Insight fails to retrieve thumbnails using 4.3.3
Posted: Thu Nov 24, 2011 9:27 amHi,
I experience difficulties with retrieving images thumbnails using insight when expanding dataset. The issue seems not linked to a particular dataset. Apparently one can open a few dataset (1-3) then the waiting sign last forever leading to hanging of insight (and sometimes reporting deconnexion of the server). This affects Mac (snow leaopard), Windows (Win 7 64 bits) and linux (Debian squeeze). This is not a network issue since it also happen when running the client directly on the server. All server and client use 4.3.3 omero and server runs Debian squeeze. The server does not experience strong load or disk filling. The only error reported are in Blitz-0.log (see below). Sever has a 12 TB disk, full at 77 %. Restarting the omero server (I mean the process) does provide any change. I increased the memory of the server but it does not help either (see diff between etc/grid/template.xmlby default and changed). Interestingly, importing and matlab client does not suffer from significant delays in running. In the same line, opening project in insight does not has delay either. It seems specific to thumbnails as far as I can judge.
Interestingly, the webclient suffer of the same issue.
It seems to affect data imported with 4.3.3 or 4.3.0 / 4.3.1 with patch mentionned in viewtopic.php?f=5&t=750
But not data imported using 4.2.2
All suggestions to work around this issue are welcome.
Thank you!
Jacques
****************************** excerpts of Blitz-0.log *************************************
jacques@cedre-5a:~$ tail -2000l /var/log/omero/Blitz-0.log | grep -A 10 -B 10 ERROR
2011-11-24 07:52:05,005 INFO [ ome.io.nio.PixelsService] (l.Server-9) Pixel buffer file exists returning read-only ROMIO pixel buffer.
2011-11-24 07:52:05,006 INFO [ omeis.providers.re.Renderer] (l.Server-9) Enabling alphaless rendering.
2011-11-24 07:52:05,006 INFO [ omeis.providers.re.Renderer] (l.Server-9) Enabling primary color rendering.
2011-11-24 07:52:05,006 INFO [ omeis.providers.re.Renderer] (l.Server-9) Using: 'omeis.providers.re.GreyScaleStrategy' rendering strategy.
2011-11-24 07:52:05,006 INFO [ ome.io.nio.RomioPixelBuffer] (l.Server-9) Retrieving plane: 0x0x0
2011-11-24 07:52:05,011 INFO [ ome.logic.JavaImageScalingService] (l.Server-9) Scaling to: 96x96
2011-11-24 07:52:05,021 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1322117525011] time[10] tag[java-image-scaling.resampleOp]
2011-11-24 07:52:05,024 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1322117524987] time[37] tag[omero._createThumbnail]
2011-11-24 07:52:05,123 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1322117356787] time[168336] tag[omero.call.success.ome.services.ThumbnailBean.getThumbnailByLongestSideSet]
2011-11-24 07:52:05,123 INFO [ ome.services.util.ServiceHandler] (l.Server-9) Rslt: {195787=[-1, -40, -1, ... 1 more], 195788=[-1, -40, -1, ... 1 more], 195789=[-1, -40, -1, ... 1 more], ... 3 more}
2011-11-24 07:52:05,123 ERROR [ ome.services.util.ServiceHandler] (l.Server-9) Method interface ome.api.ThumbnailStore.getThumbnailByLongestSideSet invocation took 168336
2011-11-24 07:52:05,393 INFO [ ome.services.util.ServiceHandler] (l.Server-4) Meth: interface ome.api.IAdmin.getEventContext
2011-11-24 07:52:05,393 INFO [ ome.services.util.ServiceHandler] (l.Server-4) Args: ()
2011-11-24 07:52:05,394 INFO [ ome.security.basic.EventHandler] (l.Server-4) Auth: user=2,group=3,event=null(User),sess=a722fdeb-ee6d-41d5-aecd-38d81cbafcbf
2011-11-24 07:52:05,395 INFO [ ome.services.util.ServiceHandler] (-thread-19) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload(a722fdeb-ee6d-41d5-aecd-38d81cbafcbf)
2011-11-24 07:52:05,395 INFO [ ome.services.util.ServiceHandler] (-thread-19) Args: [null, InternalSF@1816971292]
2011-11-24 07:52:05,401 INFO [ ome.security.basic.EventHandler] (-thread-19) Auth: user=0,group=0,event=null(Sessions),sess=5788f1af-6017-46cb-ac97-779957235d4e
2011-11-24 07:52:05,414 INFO [ org.perf4j.TimingLogger] (-thread-19) start[1322117525395] time[19] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2011-11-24 07:52:05,414 INFO [ ome.services.util.ServiceHandler] (-thread-19) Rslt: (ome.model.meta.Experimenter:Id_2, ome.model.meta.ExperimenterGroup:Id_3, [1, 0, 153, 3, 53], ... 4 more)
2011-11-24 07:52:05,415 INFO [ org.perf4j.TimingLogger] (l.Server-4) start[1322117525393] time[22] tag[omero.call.success.ome.logic.AdminImpl.getEventContext]
2011-11-24 07:52:05,415 INFO [ ome.services.util.ServiceHandler] (l.Server-4) Rslt: ome.system.SimpleEventContext@78692862
--
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Removed servant from adapter: 70170556-7a04-4196-a04d-94e4fd4e4057omero.api.IMetadata
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Unregistered servant:a722fdeb-ee6d-41d5-aecd-38d81cbafcbf/70170556-7a04-4196-a04d-94e4fd4e4057omero.api.IConfig(omero.api._IConfigTie@238e4547)
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Removed servant from adapter: 70170556-7a04-4196-a04d-94e4fd4e4057omero.api.IConfig
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Unregistered servant:a722fdeb-ee6d-41d5-aecd-38d81cbafcbf/93b2654c-2dca-4a16-95f5-2ba4957a2fb7omero.api.IAdmin(omero.api._IAdminTie@6fa607fc)
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Removed servant from adapter: 93b2654c-2dca-4a16-95f5-2ba4957a2fb7omero.api.IAdmin
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Unregistered servant:a722fdeb-ee6d-41d5-aecd-38d81cbafcbf/70170556-7a04-4196-a04d-94e4fd4e4057omero.api.IUpdate(omero.api._IUpdateTie@2bd0d357)
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Removed servant from adapter: 70170556-7a04-4196-a04d-94e4fd4e4057omero.api.IUpdate
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Unregistered servant:a722fdeb-ee6d-41d5-aecd-38d81cbafcbf/93b2654c-2dca-4a16-95f5-2ba4957a2fb7omero.api.IConfig(omero.api._IConfigTie@7548b029)
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Removed servant from adapter: 93b2654c-2dca-4a16-95f5-2ba4957a2fb7omero.api.IConfig
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ThumbnailStoreI] (l.Server-2) NoSuchElementException: Login is already gone
2011-11-24 08:02:41,217 ERROR [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Error destroying servant: 81:14:9f:a5:-74e95fe1:133d2613380:-7fe6omero.api.ThumbnailStore=ome.services.blitz.impl.ThumbnailStoreI@504235d2
java.lang.RuntimeException: omero.InternalException
serverStackTrace = "java.util.NoSuchElementException
at java.util.LinkedList.remove(LinkedList.java:788)
at java.util.LinkedList.removeLast(LinkedList.java:144)
at ome.security.basic.CurrentDetails.logout(CurrentDetails.java:180)
at ome.security.basic.BasicSecurityWiring.logout(BasicSecurityWiring.java:110)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
--
2011-11-24 08:06:00,012 INFO [ ome.services.blitz.fire.SessionManagerI] (3-thread-3) Performing requestHeartbeats
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Session already removed. Cleaning up blitz state.
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-7) Session already removed. Cleaning up blitz state.
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) doDestroy(ServiceFactoryI(session-9b6cefab-aedb-4691-8d78-2a500a5bfe91/29f15fa0-f321-4444-88c8-9fe7c081975e))
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-7) doDestroy(ServiceFactoryI(session-c3368f86-1f4f-415b-8ad1-bcc999fb29bb/29f15fa0-f321-4444-88c8-9fe7c081975e))
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Unregistered servant:29f15fa0-f321-4444-88c8-9fe7c081975e/9b6cefab-aedb-4691-8d78-2a500a5bfe91omero.api.IContainer(omero.api._IContainerTie@7fdcab3f)
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Removed servant from adapter: 9b6cefab-aedb-4691-8d78-2a500a5bfe91omero.api.IContainer
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Unregistered servant:29f15fa0-f321-4444-88c8-9fe7c081975e/9b6cefab-aedb-4691-8d78-2a500a5bfe91omero.api.IMetadata(omero.api._IMetadataTie@7a37ef7f)
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Removed servant from adapter: 9b6cefab-aedb-4691-8d78-2a500a5bfe91omero.api.IMetadata
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ThumbnailStoreI] (l.Server-6) NoSuchElementException: Login is already gone
2011-11-24 08:07:41,217 ERROR [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Error destroying servant: 81:14:9f:a5:-74e95fe1:133d2613380:-7fe4omero.api.ThumbnailStore=ome.services.blitz.impl.ThumbnailStoreI@31b86d22
java.lang.RuntimeException: omero.InternalException
serverStackTrace = "java.util.NoSuchElementException
at java.util.LinkedList.remove(LinkedList.java:788)
at java.util.LinkedList.removeLast(LinkedList.java:144)
at ome.security.basic.CurrentDetails.logout(CurrentDetails.java:180)
at ome.security.basic.BasicSecurityWiring.logout(BasicSecurityWiring.java:110)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
************************* etc/grid/template.xml modification ************************
***************
*** 172,191 ****
<option>-Xbootclasspath/a:${JPROFILER_AGENT}</option>
</target>
<target name="Blitz-hprof">
<option>-agentlib:hprof=cpu=samples,cutoff=0,thread=y,interval=1,depth=50,force=y,file=${OMERO_LOGS}Blitz-${index}.hprof</option>
</target>
! <option>-Xmx512M</option>
<!--
MaxPermSize needs to be set for most operating systems using Hibernate 3.3+
with any largish heap size. The value below should be sufficient for most
cases. The value will be added to the "-Xmx" value for the total memory used
by the JVM (here: 512+128 = 640MB).
See #4670
-->
! <option>-XX:MaxPermSize=128m</option>
<target name="memcfg">
<option>${omero.blitz.maxmemory}</option>
<option>${omero.blitz.permgen}</option>
</target>
<option>-Djava.awt.headless=true</option>
--- 172,191 ----
<option>-Xbootclasspath/a:${JPROFILER_AGENT}</option>
</target>
<target name="Blitz-hprof">
<option>-agentlib:hprof=cpu=samples,cutoff=0,thread=y,interval=1,depth=50,force=y,file=${OMERO_LOGS}Blitz-${index}.hprof</option>
</target>
! <option>-Xmx2048M</option>
<!--
MaxPermSize needs to be set for most operating systems using Hibernate 3.3+
with any largish heap size. The value below should be sufficient for most
cases. The value will be added to the "-Xmx" value for the total memory used
by the JVM (here: 512+128 = 640MB).
See #4670
-->
! <option>-XX:MaxPermSize=512m</option>
<target name="memcfg">
<option>${omero.blitz.maxmemory}</option>
<option>${omero.blitz.permgen}</option>
</target>
<option>-Djava.awt.headless=true</option>
***************
*** 239,249 ****
<server-template id="PixelDataTemplate">
<parameter name="index"/>
<parameter name="dir"/>
<parameter name="config" default="default"/>
<server id="PixelData-${index}" exe="${JAVA}" activation="always" pwd="${OMERO_HOME}">
! <option>-Xmx256M</option>
<option>-Djava.awt.headless=true</option>
<option>-Dlog4j.configuration=${OMERO_ETC}log4j-indexing.xml</option>
<option>-Domero.logfile=${OMERO_LOGFILE}</option>
<option>-Domero.name=PixelData-${index}</option>
<option>-jar</option>
--- 239,249 ----
<server-template id="PixelDataTemplate">
<parameter name="index"/>
<parameter name="dir"/>
<parameter name="config" default="default"/>
<server id="PixelData-${index}" exe="${JAVA}" activation="always" pwd="${OMERO_HOME}">
! <option>-Xmx6144M</option>
<option>-Djava.awt.headless=true</option>
<option>-Dlog4j.configuration=${OMERO_ETC}log4j-indexing.xml</option>
<option>-Domero.logfile=${OMERO_LOGFILE}</option>
<option>-Domero.name=PixelData-${index}</option>
<option>-jar</option>
I experience difficulties with retrieving images thumbnails using insight when expanding dataset. The issue seems not linked to a particular dataset. Apparently one can open a few dataset (1-3) then the waiting sign last forever leading to hanging of insight (and sometimes reporting deconnexion of the server). This affects Mac (snow leaopard), Windows (Win 7 64 bits) and linux (Debian squeeze). This is not a network issue since it also happen when running the client directly on the server. All server and client use 4.3.3 omero and server runs Debian squeeze. The server does not experience strong load or disk filling. The only error reported are in Blitz-0.log (see below). Sever has a 12 TB disk, full at 77 %. Restarting the omero server (I mean the process) does provide any change. I increased the memory of the server but it does not help either (see diff between etc/grid/template.xmlby default and changed). Interestingly, importing and matlab client does not suffer from significant delays in running. In the same line, opening project in insight does not has delay either. It seems specific to thumbnails as far as I can judge.
Interestingly, the webclient suffer of the same issue.
It seems to affect data imported with 4.3.3 or 4.3.0 / 4.3.1 with patch mentionned in viewtopic.php?f=5&t=750
But not data imported using 4.2.2
All suggestions to work around this issue are welcome.
Thank you!
Jacques
****************************** excerpts of Blitz-0.log *************************************
jacques@cedre-5a:~$ tail -2000l /var/log/omero/Blitz-0.log | grep -A 10 -B 10 ERROR
2011-11-24 07:52:05,005 INFO [ ome.io.nio.PixelsService] (l.Server-9) Pixel buffer file exists returning read-only ROMIO pixel buffer.
2011-11-24 07:52:05,006 INFO [ omeis.providers.re.Renderer] (l.Server-9) Enabling alphaless rendering.
2011-11-24 07:52:05,006 INFO [ omeis.providers.re.Renderer] (l.Server-9) Enabling primary color rendering.
2011-11-24 07:52:05,006 INFO [ omeis.providers.re.Renderer] (l.Server-9) Using: 'omeis.providers.re.GreyScaleStrategy' rendering strategy.
2011-11-24 07:52:05,006 INFO [ ome.io.nio.RomioPixelBuffer] (l.Server-9) Retrieving plane: 0x0x0
2011-11-24 07:52:05,011 INFO [ ome.logic.JavaImageScalingService] (l.Server-9) Scaling to: 96x96
2011-11-24 07:52:05,021 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1322117525011] time[10] tag[java-image-scaling.resampleOp]
2011-11-24 07:52:05,024 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1322117524987] time[37] tag[omero._createThumbnail]
2011-11-24 07:52:05,123 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1322117356787] time[168336] tag[omero.call.success.ome.services.ThumbnailBean.getThumbnailByLongestSideSet]
2011-11-24 07:52:05,123 INFO [ ome.services.util.ServiceHandler] (l.Server-9) Rslt: {195787=[-1, -40, -1, ... 1 more], 195788=[-1, -40, -1, ... 1 more], 195789=[-1, -40, -1, ... 1 more], ... 3 more}
2011-11-24 07:52:05,123 ERROR [ ome.services.util.ServiceHandler] (l.Server-9) Method interface ome.api.ThumbnailStore.getThumbnailByLongestSideSet invocation took 168336
2011-11-24 07:52:05,393 INFO [ ome.services.util.ServiceHandler] (l.Server-4) Meth: interface ome.api.IAdmin.getEventContext
2011-11-24 07:52:05,393 INFO [ ome.services.util.ServiceHandler] (l.Server-4) Args: ()
2011-11-24 07:52:05,394 INFO [ ome.security.basic.EventHandler] (l.Server-4) Auth: user=2,group=3,event=null(User),sess=a722fdeb-ee6d-41d5-aecd-38d81cbafcbf
2011-11-24 07:52:05,395 INFO [ ome.services.util.ServiceHandler] (-thread-19) Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload(a722fdeb-ee6d-41d5-aecd-38d81cbafcbf)
2011-11-24 07:52:05,395 INFO [ ome.services.util.ServiceHandler] (-thread-19) Args: [null, InternalSF@1816971292]
2011-11-24 07:52:05,401 INFO [ ome.security.basic.EventHandler] (-thread-19) Auth: user=0,group=0,event=null(Sessions),sess=5788f1af-6017-46cb-ac97-779957235d4e
2011-11-24 07:52:05,414 INFO [ org.perf4j.TimingLogger] (-thread-19) start[1322117525395] time[19] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2011-11-24 07:52:05,414 INFO [ ome.services.util.ServiceHandler] (-thread-19) Rslt: (ome.model.meta.Experimenter:Id_2, ome.model.meta.ExperimenterGroup:Id_3, [1, 0, 153, 3, 53], ... 4 more)
2011-11-24 07:52:05,415 INFO [ org.perf4j.TimingLogger] (l.Server-4) start[1322117525393] time[22] tag[omero.call.success.ome.logic.AdminImpl.getEventContext]
2011-11-24 07:52:05,415 INFO [ ome.services.util.ServiceHandler] (l.Server-4) Rslt: ome.system.SimpleEventContext@78692862
--
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Removed servant from adapter: 70170556-7a04-4196-a04d-94e4fd4e4057omero.api.IMetadata
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Unregistered servant:a722fdeb-ee6d-41d5-aecd-38d81cbafcbf/70170556-7a04-4196-a04d-94e4fd4e4057omero.api.IConfig(omero.api._IConfigTie@238e4547)
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Removed servant from adapter: 70170556-7a04-4196-a04d-94e4fd4e4057omero.api.IConfig
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Unregistered servant:a722fdeb-ee6d-41d5-aecd-38d81cbafcbf/93b2654c-2dca-4a16-95f5-2ba4957a2fb7omero.api.IAdmin(omero.api._IAdminTie@6fa607fc)
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Removed servant from adapter: 93b2654c-2dca-4a16-95f5-2ba4957a2fb7omero.api.IAdmin
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Unregistered servant:a722fdeb-ee6d-41d5-aecd-38d81cbafcbf/70170556-7a04-4196-a04d-94e4fd4e4057omero.api.IUpdate(omero.api._IUpdateTie@2bd0d357)
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Removed servant from adapter: 70170556-7a04-4196-a04d-94e4fd4e4057omero.api.IUpdate
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Unregistered servant:a722fdeb-ee6d-41d5-aecd-38d81cbafcbf/93b2654c-2dca-4a16-95f5-2ba4957a2fb7omero.api.IConfig(omero.api._IConfigTie@7548b029)
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Removed servant from adapter: 93b2654c-2dca-4a16-95f5-2ba4957a2fb7omero.api.IConfig
2011-11-24 08:02:41,216 INFO [ ome.services.blitz.impl.ThumbnailStoreI] (l.Server-2) NoSuchElementException: Login is already gone
2011-11-24 08:02:41,217 ERROR [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-2) Error destroying servant: 81:14:9f:a5:-74e95fe1:133d2613380:-7fe6omero.api.ThumbnailStore=ome.services.blitz.impl.ThumbnailStoreI@504235d2
java.lang.RuntimeException: omero.InternalException
serverStackTrace = "java.util.NoSuchElementException
at java.util.LinkedList.remove(LinkedList.java:788)
at java.util.LinkedList.removeLast(LinkedList.java:144)
at ome.security.basic.CurrentDetails.logout(CurrentDetails.java:180)
at ome.security.basic.BasicSecurityWiring.logout(BasicSecurityWiring.java:110)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
--
2011-11-24 08:06:00,012 INFO [ ome.services.blitz.fire.SessionManagerI] (3-thread-3) Performing requestHeartbeats
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Session already removed. Cleaning up blitz state.
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-7) Session already removed. Cleaning up blitz state.
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) doDestroy(ServiceFactoryI(session-9b6cefab-aedb-4691-8d78-2a500a5bfe91/29f15fa0-f321-4444-88c8-9fe7c081975e))
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-7) doDestroy(ServiceFactoryI(session-c3368f86-1f4f-415b-8ad1-bcc999fb29bb/29f15fa0-f321-4444-88c8-9fe7c081975e))
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Unregistered servant:29f15fa0-f321-4444-88c8-9fe7c081975e/9b6cefab-aedb-4691-8d78-2a500a5bfe91omero.api.IContainer(omero.api._IContainerTie@7fdcab3f)
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Removed servant from adapter: 9b6cefab-aedb-4691-8d78-2a500a5bfe91omero.api.IContainer
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Unregistered servant:29f15fa0-f321-4444-88c8-9fe7c081975e/9b6cefab-aedb-4691-8d78-2a500a5bfe91omero.api.IMetadata(omero.api._IMetadataTie@7a37ef7f)
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Removed servant from adapter: 9b6cefab-aedb-4691-8d78-2a500a5bfe91omero.api.IMetadata
2011-11-24 08:07:41,216 INFO [ ome.services.blitz.impl.ThumbnailStoreI] (l.Server-6) NoSuchElementException: Login is already gone
2011-11-24 08:07:41,217 ERROR [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Error destroying servant: 81:14:9f:a5:-74e95fe1:133d2613380:-7fe4omero.api.ThumbnailStore=ome.services.blitz.impl.ThumbnailStoreI@31b86d22
java.lang.RuntimeException: omero.InternalException
serverStackTrace = "java.util.NoSuchElementException
at java.util.LinkedList.remove(LinkedList.java:788)
at java.util.LinkedList.removeLast(LinkedList.java:144)
at ome.security.basic.CurrentDetails.logout(CurrentDetails.java:180)
at ome.security.basic.BasicSecurityWiring.logout(BasicSecurityWiring.java:110)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
************************* etc/grid/template.xml modification ************************
***************
*** 172,191 ****
<option>-Xbootclasspath/a:${JPROFILER_AGENT}</option>
</target>
<target name="Blitz-hprof">
<option>-agentlib:hprof=cpu=samples,cutoff=0,thread=y,interval=1,depth=50,force=y,file=${OMERO_LOGS}Blitz-${index}.hprof</option>
</target>
! <option>-Xmx512M</option>
<!--
MaxPermSize needs to be set for most operating systems using Hibernate 3.3+
with any largish heap size. The value below should be sufficient for most
cases. The value will be added to the "-Xmx" value for the total memory used
by the JVM (here: 512+128 = 640MB).
See #4670
-->
! <option>-XX:MaxPermSize=128m</option>
<target name="memcfg">
<option>${omero.blitz.maxmemory}</option>
<option>${omero.blitz.permgen}</option>
</target>
<option>-Djava.awt.headless=true</option>
--- 172,191 ----
<option>-Xbootclasspath/a:${JPROFILER_AGENT}</option>
</target>
<target name="Blitz-hprof">
<option>-agentlib:hprof=cpu=samples,cutoff=0,thread=y,interval=1,depth=50,force=y,file=${OMERO_LOGS}Blitz-${index}.hprof</option>
</target>
! <option>-Xmx2048M</option>
<!--
MaxPermSize needs to be set for most operating systems using Hibernate 3.3+
with any largish heap size. The value below should be sufficient for most
cases. The value will be added to the "-Xmx" value for the total memory used
by the JVM (here: 512+128 = 640MB).
See #4670
-->
! <option>-XX:MaxPermSize=512m</option>
<target name="memcfg">
<option>${omero.blitz.maxmemory}</option>
<option>${omero.blitz.permgen}</option>
</target>
<option>-Djava.awt.headless=true</option>
***************
*** 239,249 ****
<server-template id="PixelDataTemplate">
<parameter name="index"/>
<parameter name="dir"/>
<parameter name="config" default="default"/>
<server id="PixelData-${index}" exe="${JAVA}" activation="always" pwd="${OMERO_HOME}">
! <option>-Xmx256M</option>
<option>-Djava.awt.headless=true</option>
<option>-Dlog4j.configuration=${OMERO_ETC}log4j-indexing.xml</option>
<option>-Domero.logfile=${OMERO_LOGFILE}</option>
<option>-Domero.name=PixelData-${index}</option>
<option>-jar</option>
--- 239,249 ----
<server-template id="PixelDataTemplate">
<parameter name="index"/>
<parameter name="dir"/>
<parameter name="config" default="default"/>
<server id="PixelData-${index}" exe="${JAVA}" activation="always" pwd="${OMERO_HOME}">
! <option>-Xmx6144M</option>
<option>-Djava.awt.headless=true</option>
<option>-Dlog4j.configuration=${OMERO_ETC}log4j-indexing.xml</option>
<option>-Domero.logfile=${OMERO_LOGFILE}</option>
<option>-Domero.name=PixelData-${index}</option>
<option>-jar</option>
