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| jeckels responded: |
2009-05-11 09:25 |
Hi Rich,
I haven't heard any other reports of this problem yet. I can't reproduce it on my local machine or on labkey.org. Can you reproduce it on this folder:
https://www.labkey.org/project/home/CPAS/demo/begin.view?
Also, are there any other errors under Admin Console->View All Site Errors?
Thanks,
Josh |
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| greener responded: |
2009-05-11 10:51 |
I will look into reproducing on the labkey server. Pasted below is the view all site errors output. Thanks -Rich
ERROR ExceptionUtil 2009-05-10 14:27:21,459 http-8443-Processor25 : Unhandled exception: 500: Unexpected server error
java.lang.OutOfMemoryError: Java heap space
at jxl.write.biff.MemoryDataOutput.write(MemoryDataOutput.java:72)
at jxl.write.biff.File.write(File.java:149)
at jxl.write.biff.SheetWriter.write(SheetWriter.java:569)
at jxl.write.biff.WritableSheetImpl.write(WritableSheetImpl.java:1431)
at jxl.write.biff.WritableWorkbookImpl.write(WritableWorkbookImpl.java:915)
at org.labkey.api.data.ExcelWriter.closeWorkbook(ExcelWriter.java:417)
at org.labkey.api.data.ExcelWriter.write(ExcelWriter.java:351)
at org.labkey.ms2.MS2Controller.compareRuns(MS2Controller.java:2123)
at org.labkey.ms2.MS2Controller.access$5000(MS2Controller.java:87)
at org.labkey.ms2.MS2Controller$ExportCompareToExcel.export(MS2Controller.java:1818)
at org.labkey.ms2.MS2Controller$ExportCompareToExcel.export(MS2Controller.java:1814)
at org.labkey.api.action.ExportAction.getView(ExportAction.java:41)
at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:61)
at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:162)
at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:336)
at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:689)
at org.labkey.api.view.ViewServlet.service(ViewServlet.java:139)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:124)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:647)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:101)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
ERROR ExceptionUtil 2009-05-10 14:29:35,248 http-8443-Processor23 : Unhandled exception: 500: Unexpected server error
java.lang.OutOfMemoryError: Java heap space
at jxl.write.biff.MemoryDataOutput.write(MemoryDataOutput.java:72)
at jxl.write.biff.File.write(File.java:149)
at jxl.write.biff.SheetWriter.write(SheetWriter.java:569)
at jxl.write.biff.WritableSheetImpl.write(WritableSheetImpl.java:1431)
at jxl.write.biff.WritableWorkbookImpl.write(WritableWorkbookImpl.java:915)
at org.labkey.api.data.ExcelWriter.closeWorkbook(ExcelWriter.java:417)
at org.labkey.api.data.ExcelWriter.write(ExcelWriter.java:351)
at org.labkey.ms2.MS2Controller.compareRuns(MS2Controller.java:2123)
at org.labkey.ms2.MS2Controller.access$5000(MS2Controller.java:87)
at org.labkey.ms2.MS2Controller$ExportCompareToExcel.export(MS2Controller.java:1818)
at org.labkey.ms2.MS2Controller$ExportCompareToExcel.export(MS2Controller.java:1814)
at org.labkey.api.action.ExportAction.getView(ExportAction.java:41)
at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:61)
at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:162)
at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:336)
at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:689)
at org.labkey.api.view.ViewServlet.service(ViewServlet.java:139)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:124)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:647)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:101)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
ERROR ExceptionUtil 2009-05-10 14:30:55,788 http-8443-Processor20 : Unhandled exception: 500: Unexpected server error
java.lang.IllegalStateException
at org.apache.catalina.connector.ResponseFacade.reset(ResponseFacade.java:308)
at javax.servlet.ServletResponseWrapper.reset(ServletResponseWrapper.java:183)
at org.labkey.api.data.ExcelWriter.getOutputStream(ExcelWriter.java:361)
at org.labkey.api.data.ExcelWriter.write(ExcelWriter.java:344)
at org.labkey.api.query.QueryView.exportToExcel(QueryView.java:1124)
at org.labkey.api.query.QueryView.exportToExcel(QueryView.java:1108)
at org.labkey.api.action.QueryViewAction.getView(QueryViewAction.java:74)
at org.labkey.ms2.MS2Controller$RunListHandlerAction.getView(MS2Controller.java:1981)
at org.labkey.ms2.MS2Controller$CompareProteinProphetQueryAction.getView(MS2Controller.java:1556)
at org.labkey.ms2.MS2Controller$CompareProteinProphetQueryAction.getView(MS2Controller.java:1544)
at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:61)
at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:162)
at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:336)
at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:689)
at org.labkey.api.view.ViewServlet.service(ViewServlet.java:139)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:124)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:647)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:101)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:542)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870)
at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685)
at java.lang.Thread.run(Unknown Source) |
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| jeckels responded: |
2009-05-11 11:12 |
Hi Rich,
Those OutOfMemoryErrors are likely related. How big is your heap size right now? You can find it by going to Admin Console->Memory Usage. The first line of text should be Total Heap Memory, and include the maximum size.
Thanks,
Josh |
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| greener responded: |
2009-05-11 11:41 |
Pasted below, where can I increase the heap size in tomcat/labkey server? Thanks -Rich
Total Heap Memory init = 0; used = 882,038,448; committed = 1,022,230,528; max = 1,034,027,008
Total Non-heap Memory init = 19,136,512; used = 55,817,552; committed = 55,836,672; max = 117,440,512
Code Cache Non-heap memory init = 2,359,296; used = 7,850,048; committed = 7,864,320; max = 50,331,648 |
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| greener responded: |
2009-05-11 15:53 |
increased heap memory from 1024m to 1750m in tomcat by setting
export CATALINA_OPTS="-Djavax.net.debug=ssl,handshake,trustmanager -Xmx1750m"
now
Total Heap Memory init = 0; used = 57,006,272; committed = 169,672,704; max = 1,767,047,168
Total Non-heap Memory init = 19,136,512; used = 54,933,880; committed = 67,305,472; max = 117,440,512
and restarting services, still receiving the same bug however and error below, any other thoughts on what could be the problem? Thanks -Rich
ERROR ExceptionUtil 2009-05-11 15:40:03,760 http-8443-Processor21 : Unhandled exception: 500: Unexpected server error
java.lang.IllegalStateException
at org.apache.catalina.connector.ResponseFacade.reset(ResponseFacade.java:308)
at javax.servlet.ServletResponseWrapper.reset(ServletResponseWrapper.java:183)
at org.labkey.api.data.ExcelWriter.getOutputStream(ExcelWriter.java:361)
at org.labkey.api.data.ExcelWriter.write(ExcelWriter.java:344)
at org.labkey.api.query.QueryView.exportToExcel(QueryView.java:1124)
at org.labkey.api.query.QueryView.exportToExcel(QueryView.java:1108)
at org.labkey.api.action.QueryViewAction.getView(QueryViewAction.java:74)
at org.labkey.ms2.MS2Controller$RunListHandlerAction.getView(MS2Controller.java:1981)
at org.labkey.ms2.MS2Controller$CompareProteinProphetQueryAction.getView(MS2Controller.java:1556)
at org.labkey.ms2.MS2Controller$CompareProteinProphetQueryAction.getView(MS2Controller.java:1544)
at org.labkey.api.action.SimpleViewAction.handleRequest(SimpleViewAction.java:61)
at org.labkey.api.action.BaseViewAction.handleRequestInternal(BaseViewAction.java:162)
at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
at org.labkey.api.action.SpringActionController.handleRequest(SpringActionController.java:336)
at org.labkey.api.module.DefaultModule.dispatch(DefaultModule.java:689)
at org.labkey.api.view.ViewServlet.service(ViewServlet.java:139)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.api.data.TransactionFilter.doFilter(TransactionFilter.java:36)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.core.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:124)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.api.module.ModuleLoader.doFilter(ModuleLoader.java:647)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.labkey.api.security.AuthFilter.doFilter(AuthFilter.java:101)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:542)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870)
at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
at org.apache.tomcat.util.threads.ThreadP |
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| jeckels responded: |
2009-05-20 14:36 |
Hi Rich,
I think I've tracked down the root problem here. It affects queries that take longer than a certain amount of time. I'll work on a fix for 9.2.
Thanks,
Josh |
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| edwin.lowe responded: |
2009-09-15 16:50 |
Just checking to see if this issue has been fixed in 9.2. I've come across the same issue. |
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| jeckels responded: |
2009-09-15 16:52 |
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