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From Zakir Saifi <zakir.sa...@raxa.com>
Subject Analysis Engine Process Exception while querying ctakes Service frequently
Date Tue, 05 Mar 2019 09:41:45 GMT
Hi all,

I using Ctakes Rest Service(a Rest Server based on Apache Ctakes) for
benchmarking using *Apache Jmeter*. As I have to use it as Rest Server to
processing many clinical Text

My Configuration for BenchMarking are as follows:
I am creating 10 users(threads) each with Ramp up period (*10s*). *That
means 1 user is created after every 1 second. *
I have loop count of *5* (Number of iteration)
There is a time delay of *500ms* between each subsequent Request ( To
simulate requests as in real-time scenarios, real-users give delays between
doing different actions.)
I am also changing the *data* with each request by using data from CSV file.

I am getting following exceptions for most* of the requests* that comes to
Ctakes Rest Sever

Exception1
org.apache.uima.analysis_engine.s: Annotator processing failed.
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:280)
at
org.apache.ctakes.rest.service.CtakesRestController.getAnalyzedJSON(CtakesRestController.java:95)
at sun.reflect.GeneratedMethodAccessor157.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)
at
org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:133)
at
org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:97)
at
org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:827)
at
org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:738)
at
org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
at
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:967)
at
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:901)
at
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
at
org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:872)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:661)
at
org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
at
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
at
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
at
org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)
at
org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at
org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806)
at
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498)
at
org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NullPointerException

Exception2
05-Mar-2019 08:45:32.274 SEVERE [http-nio-8089-exec-3]
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(275)
Exception occurred
 org.apache.uima.analysis_engine.AnalysisEngineProcessException: Annotator
processing failed.
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:280)
at
org.apache.ctakes.rest.service.CtakesRestController.getAnalyzedJSON(CtakesRestController.java:95)
at sun.reflect.GeneratedMethodAccessor157.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at
org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)
at
org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:133)
at
org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:97)
at
org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:827)
at
org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:738)
at
org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
at
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:967)
at
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:901)
at
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
at
org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:872)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:661)
at
org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
at
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
at
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
at
org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)
at
org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
at
org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806)
at
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498)
at
org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NullPointerException


I have recently changed the *minimum span detection to 1 *and also not
excluding any exclusion tags in my Piper files. Since then I am seeing this
errors coming more frequently. I don't think these errors are associated
with any particular type of data to goes to ctakes Service.Because if I
increase the time between the subsequent user creation and Time delay
between the subsequent call, I am not getting any exception.

I am currently running *Ctakes Rest Server* war in a Docker Container
having tomcat image with JVM Maximum Memory of* 3 GB.*  Anyone have idea
why I am getting these exception on heavy load??




Regards
Zakir Saifi

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