SocketInputStream.socketRead0 stuck thread and huge memory leak on jdbc query - java

We are using:
Oracle JDK 8
Tomcat 7
PostgreSQL 9.4.1208
The database is located on a different machine.
Previously we used FreeBSD with openjdk 7. After switching to debian and oracle jdk 8, we noticed the problem described below.
Very very rarely the thread gets stuck at socketRead0 native method while communicating with database. Not only it is stuck but also generates huge memory leak (700MB - 4GB) in a very short amount of time. There is no correlation between the query and problem (it happens at random queries).
After analyzing heap dump with MAT I found that the whole leak is concentrated in byte[] varaible directly referenced by stucked thread - native memory leak. The variable does not change (once it leaks it stays the same).
The leaked variable contains information from database so it managed to connect to db, but somehow got stuck.
I downloaded openjdk source and took a look at the socketRead0 native method. It indeed allocates byte[] on heap.
To sum up - there is some problem in socketRead0 call, which never returns nor throw exception. It casuse the thread to stay in RUNNABLE state keeping huge amount of garbage in the byte[] variable allocated on the heap.
Here is the stack trace:
java.lang.Thread.State: RUNNABLE
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.socketRead(SocketInputStream.java:116)
at java.net.SocketInputStream.read(SocketInputStream.java:170)
at java.net.SocketInputStream.read(SocketInputStream.java:141)
at org.postgresql.core.VisibleBufferedInputStream.read(VisibleBufferedInputStream.java:217)
at org.postgresql.core.PGStream.Receive(PGStream.java:468)
at org.postgresql.core.PGStream.ReceiveTupleV3(PGStream.java:373)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1879)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:173)
- locked <7bf011e1> (a org.postgresql.core.v3.QueryExecutorImpl)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:645)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:495)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:380)
at org.springframework.jdbc.core.JdbcTemplate$1.doInPreparedStatement(JdbcTemplate.java:646)
at org.springframework.jdbc.core.JdbcTemplate.execute(JdbcTemplate.java:589)
at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:639)
at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:664)
at org.springframework.jdbc.core.JdbcTemplate.query(JdbcTemplate.java:704)
at org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate.query(NamedParameterJdbcTemplate.java:181)
at org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate.query(NamedParameterJdbcTemplate.java:187)
at com.myproject.SomeController(SomeController.java:34)
at org.springframework.web.servlet.HandlerExecutionChain.applyPreHandle(HandlerExecutionChain.java:134)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:928)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:867)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:953)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:855)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:829)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:106)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:176)
at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:145)
at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:92)
at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:394)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.springframework.mobile.device.DeviceResolverRequestFilter.doFilterInternal(DeviceResolverRequestFilter.java:60)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:106)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
at org.apache.catalina.valves.StuckThreadDetectionValve.invoke(StuckThreadDetectionValve.java:221)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.ha.session.JvmRouteBinderValve.invoke(JvmRouteBinderValve.java:218)
at org.apache.catalina.ha.tcp.ReplicationValve.invoke(ReplicationValve.java:333)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
at org.apache.coyote.ajp.AjpAprProcessor.process(AjpAprProcessor.java:188)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2516)
at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2505)
- locked <6039befe> (a org.apache.tomcat.util.net.AprEndpoint$AprSocketWrapper)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)

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at com.owera.xaps.web.app.Output.deliverResponse(Output.java:140)
at com.owera.xaps.web.app.Main.doImpl(Main.java:183)
at com.owera.xaps.web.app.Main.doGet(Main.java:94)
at com.owera.xaps.web.app.Main.doPost(Main.java:84)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
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at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:313)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1152)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:622)
at java.lang.Thread.run(Thread.java:748)
Any idea / help
Bill, you will have to analyse thread dumps and will have to go through your application code once. It seems objects are not getting GC.
But before that, to prove this analogy, you can try to double your Memory.
In your catalina.sh/catalina.bat (depending on OS) please try to modify your -Xmx, -Xms and -XX:MaxPermSize and observe if it has any impact on your server uptime.

Jenkins publish over SSH giving an error when I try to save new credentials

I am using Jenkins with publish over ssh plug-in. I have been able to do this successfully for many of my projects. I currently have 12 different server configurations and I will need to keep adding more.
But when I am trying to add a new configuration for server credentials and I get the error below. I am able to test the connection successfully. I believe that there might be a limit to the number of credentials that can be added to the plug in.
I have done some researching online but I cannot find much info on this problem. I am more or less lost with java debugging. I am at a blocker due to not being able to setup the automated jobs for this project.
Any help would be greatly appreciated: even in just guiding me through some of the debugging process.
Thanks so much for your time!
Here is the error message I received:
A problem occurred while processing the request. Please check our bug tracker to see if a similar problem has already been reported. If it is already reported, please vote and put a comment on it to let us gauge the impact of the problem. If you think this is a new issue, please file a new issue. When you file an issue, make sure to add the entire stack trace, along with the version of Jenkins and relevant plugins. The users list might be also useful in understanding what has happened.
Stack trace
javax.servlet.ServletException: java.lang.NullPointerException
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:796)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:876)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:649)
at org.kohsuke.stapler.Stapler.service(Stapler.java:238)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:132)
at hudson.util.PluginServletFilter.doFilter(PluginServletFilter.java:123)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at hudson.security.csrf.CrumbFilter.doFilter(CrumbFilter.java:49)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:84)
at hudson.security.UnwrapSecurityExceptionFilter.doFilter(UnwrapSecurityExceptionFilter.java:51)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at jenkins.security.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:117)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.providers.anonymous.AnonymousProcessingFilter.doFilter(AnonymousProcessingFilter.java:125)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.ui.rememberme.RememberMeProcessingFilter.doFilter(RememberMeProcessingFilter.java:142)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:271)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at jenkins.security.BasicHeaderProcessor.doFilter(BasicHeaderProcessor.java:93)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:249)
at hudson.security.HttpSessionContextIntegrationFilter2.doFilter(HttpSessionContextIntegrationFilter2.java:67)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at hudson.security.ChainedServletFilter.doFilter(ChainedServletFilter.java:76)
at hudson.security.HudsonFilter.doFilter(HudsonFilter.java:171)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.kohsuke.stapler.compression.CompressionFilter.doFilter(CompressionFilter.java:49)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at hudson.util.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:81)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.kohsuke.stapler.DiagnosticThreadNameFilter.doFilter(DiagnosticThreadNameFilter.java:30)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:614)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
at org.apache.coyote.ajp.AjpAprProcessor.process(AjpAprProcessor.java:188)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625)
at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2522)
at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2511)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
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at hudson.model.Descriptor.getConfigFile(Descriptor.java:797)
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at com.google.jenkins.plugins.googlecontainerregistryauth.GoogleContainerRegistryCredentialGlobalConfig.configure(GoogleContainerRegistryCredentialGlobalConfig.java:63)
at jenkins.model.Jenkins.configureDescriptor(Jenkins.java:2956)
at jenkins.model.Jenkins.doConfigSubmit(Jenkins.java:2919)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.kohsuke.stapler.Function$InstanceFunction.invoke(Function.java:298)
at org.kohsuke.stapler.Function.bindAndInvoke(Function.java:161)
at org.kohsuke.stapler.Function.bindAndInvokeAndServeResponse(Function.java:96)
at org.kohsuke.stapler.MetaClass$1.doDispatch(MetaClass.java:121)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:53)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:746)
... 61 more
The stacktrace suggests that this is caused by an issue that was fixed in the Google Container Registry Auth plugin.
Try upgrading to version 0.3 of that plugin, which contains the fix.

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at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
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at org.apache.catalina.filters.CorsFilter.handleNonCORS(CorsFilter.java:438)
at org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:179)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
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at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
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Exception:
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at org.apache.jasper.servlet.JspServletWrapper.getServlet(JspServletWrapper.java:177)
at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:369)
at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:390)
at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:334)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at com.framepool.web.filters.RequestFilter.doFilter(RequestFilter.java:177)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at com.framepool.web.filters.RequestAttributesFilter.doFilter(RequestAttributesFilter.java:146)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
at org.apache.struts.action.RequestProcessor.doForward(RequestProcessor.java:1054)
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at com.framepool.web.ValidableActionServlet.doGet(ValidableActionServlet.java:59)
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at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at com.framepool.web.filters.RequestFilter.doFilter(RequestFilter.java:177)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at com.framepool.web.filters.RequestAttributesFilter.doFilter(RequestAttributesFilter.java:146)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
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at com.framepool.web.filters.DomainRedirectFilter.doFilter(DomainRedirectFilter.java:86)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at com.framepool.web.filters.XSSFilter.doFilter(XSSFilter.java:39)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: org.apache.jsp.frame_jsp
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at org.apache.jasper.servlet.JasperLoader.loadClass(JasperLoader.java:132)
at org.apache.jasper.servlet.JasperLoader.loadClass(JasperLoader.java:63)
at org.apache.catalina.core.DefaultInstanceManager.newInstance(DefaultInstanceManager.java:145)
at org.apache.jasper.servlet.JspServletWrapper.getServlet(JspServletWrapper.java:172)
... 66 more
The solution is to remove the eclipse/tomcat scratch dir completely. Searching for .class files takes very long and doesn't give any result.
The scratch dir can be found in /.metadata/.plugins/org.eclipse.wst.server.core there you can find a folder called tmp0. Removing this folder resolved my problem.
Start back at the basics. The only two reasons for ClassNotFoundException are that the class does not exist, or the configuration of the runtime does not include the correct pointer to where the class exists.
Figure out where your development system expects class files to be for your project. Someone well-versed in eclipse could tell you exactly where this is configured, or the various places where it can be configured, I can't off the top of my head. Depending on how you're running Tomcat, it might not be an eclipse thing; running Tomcat as a separate program would decouple it from eclipse config, for instance.
Another possible way to do this is, when it is working, search the entire disk for the .class file for the class that shows up missing (or one of them, you aren't clear about whether it is always the same file). There may be multiple copies of it, note them all. The next time it isn't working, do the same search.
I am assuming you do not package the class files into jars in the development environment. If that's so, then the two searches should tell you where the class file is supposed to be but is not. Perhaps you can work backwards from there to figure out why it seems random, which process is supposed to put it there but does not.
I don't think it is actually random, and I don't think it's eclipse. I think out of the 10-20 times you clean and restart something different is going on. I hope you have verified, too, that you are not running out of disk space or ignoring logs that would indicate compilation problems.

An established connection was aborted by the software in your host machine tomcat jackson

Below is a stacktrace I get when my rest service tries to fetch a large data set (database and tomcat are on my local machine, so everything is local). It works on smaller ones, but in some cases user wants a lot of data. I checked similar problems posted here, but there seems to be none like mine.
My questions are
1. Why does it fail to display a response?
2. Is response size limited somehow on tomcat? Maybe there is a timeout or something like that?
3. Maybe it is Jackson that fails to do its job. If it is Jackson - can it be caused by annotations like #JsonBackReference and #JsonManagedReference?
4. What can I do to fix it?
ClientAbortException: java.io.IOException: An established connection was aborted by the software in your host machine
at org.apache.catalina.connector.OutputBuffer.realWriteBytes(OutputBuffer.java:413)
at org.apache.tomcat.util.buf.ByteChunk.flushBuffer(ByteChunk.java:480)
at org.apache.tomcat.util.buf.ByteChunk.append(ByteChunk.java:366)
at org.apache.catalina.connector.OutputBuffer.writeBytes(OutputBuffer.java:438)
at org.apache.catalina.connector.OutputBuffer.write(OutputBuffer.java:426)
at org.apache.catalina.connector.CoyoteOutputStream.write(CoyoteOutputStream.java:91)
at com.fasterxml.jackson.core.json.UTF8JsonGenerator._flushBuffer(UTF8JsonGenerator.java:1862)
at com.fasterxml.jackson.core.json.UTF8JsonGenerator._writeBytes(UTF8JsonGenerator.java:1132)
at com.fasterxml.jackson.core.json.UTF8JsonGenerator._writeFieldName(UTF8JsonGenerator.java:270)
at com.fasterxml.jackson.core.json.UTF8JsonGenerator.writeFieldName(UTF8JsonGenerator.java:249)
at com.fasterxml.jackson.databind.ser.BeanPropertyWriter.serializeAsField(BeanPropertyWriter.java:539)
at com.fasterxml.jackson.databind.ser.std.BeanSerializerBase.serializeFields(BeanSerializerBase.java:644)
at com.fasterxml.jackson.databind.ser.BeanSerializer.serialize(BeanSerializer.java:152)
at com.fasterxml.jackson.databind.ser.std.CollectionSerializer.serializeContents(CollectionSerializer.java:117)
at com.fasterxml.jackson.databind.ser.std.CollectionSerializer.serializeContents(CollectionSerializer.java:23)
at com.fasterxml.jackson.databind.ser.std.AsArraySerializerBase.serialize(AsArraySerializerBase.java:183)
at com.fasterxml.jackson.databind.ser.BeanPropertyWriter.serializeAsField(BeanPropertyWriter.java:541)
at com.fasterxml.jackson.databind.ser.std.BeanSerializerBase.serializeFields(BeanSerializerBase.java:644)
at com.fasterxml.jackson.databind.ser.BeanSerializer.serialize(BeanSerializer.java:152)
at com.fasterxml.jackson.databind.ser.std.CollectionSerializer.serializeContents(CollectionSerializer.java:117)
at com.fasterxml.jackson.databind.ser.std.CollectionSerializer.serializeContents(CollectionSerializer.java:23)
at com.fasterxml.jackson.databind.ser.std.AsArraySerializerBase.serialize(AsArraySerializerBase.java:183)
at com.fasterxml.jackson.databind.ser.BeanPropertyWriter.serializeAsField(BeanPropertyWriter.java:541)
at com.fasterxml.jackson.databind.ser.std.BeanSerializerBase.serializeFields(BeanSerializerBase.java:644)
at com.fasterxml.jackson.databind.ser.BeanSerializer.serialize(BeanSerializer.java:152)
at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:114)
at com.fasterxml.jackson.databind.ObjectMapper.writeValue(ObjectMapper.java:1837)
at org.springframework.http.converter.json.MappingJackson2HttpMessageConverter.writeInternal(MappingJackson2HttpMessageConverter.java:253)
at org.springframework.http.converter.AbstractHttpMessageConverter.write(AbstractHttpMessageConverter.java:208)
at org.springframework.web.servlet.mvc.method.annotation.AbstractMessageConverterMethodProcessor.writeWithMessageConverters(AbstractMessageConverterMethodProcessor.java:143)
at org.springframework.web.servlet.mvc.method.annotation.AbstractMessageConverterMethodProcessor.writeWithMessageConverters(AbstractMessageConverterMethodProcessor.java:89)
at org.springframework.web.servlet.mvc.method.annotation.RequestResponseBodyMethodProcessor.handleReturnValue(RequestResponseBodyMethodProcessor.java:193)
at org.springframework.web.method.support.HandlerMethodReturnValueHandlerComposite.handleReturnValue(HandlerMethodReturnValueHandlerComposite.java:71)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:122)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:749)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:689)
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:83)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:938)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:870)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:961)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:852)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:620)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:186)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:177)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:683)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1720)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1679)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: An established connection was aborted by the software in your host machine
at sun.nio.ch.SocketDispatcher.write0(Native Method)
at sun.nio.ch.SocketDispatcher.write(Unknown Source)
at sun.nio.ch.IOUtil.writeFromNativeBuffer(Unknown Source)
at sun.nio.ch.IOUtil.write(Unknown Source)
at sun.nio.ch.SocketChannelImpl.write(Unknown Source)
at org.apache.tomcat.util.net.NioChannel.write(NioChannel.java:123)
at org.apache.tomcat.util.net.NioBlockingSelector.write(NioBlockingSelector.java:101)
at org.apache.tomcat.util.net.NioSelectorPool.write(NioSelectorPool.java:174)
at org.apache.coyote.http11.InternalNioOutputBuffer.writeToSocket(InternalNioOutputBuffer.java:163)
at org.apache.coyote.http11.InternalNioOutputBuffer.flushBuffer(InternalNioOutputBuffer.java:242)
at org.apache.coyote.http11.InternalNioOutputBuffer.addToBB(InternalNioOutputBuffer.java:213)
at org.apache.coyote.http11.InternalNioOutputBuffer.access$000(InternalNioOutputBuffer.java:41)
at org.apache.coyote.http11.InternalNioOutputBuffer$SocketOutputBuffer.doWrite(InternalNioOutputBuffer.java:268)
at org.apache.coyote.http11.filters.ChunkedOutputFilter.doWrite(ChunkedOutputFilter.java:119)
at org.apache.coyote.http11.AbstractOutputBuffer.doWrite(AbstractOutputBuffer.java:192)
at org.apache.coyote.Response.doWrite(Response.java:520)
at org.apache.catalina.connector.OutputBuffer.realWriteBytes(OutputBuffer.java:408)
... 69 more
2014-09-15 17:35:31 ERROR ExceptionHandlerExceptionResolver:343 - Failed to invoke #ExceptionHandler method: public void com.acxiom.listkey.metadata.exceptions.GlobalExceptionHandler.handleInternalException(java.lang.Exception)
java.lang.IllegalStateException: Cannot call sendError() after the response has been committed
at org.apache.catalina.connector.ResponseFacade.sendError(ResponseFacade.java:450)
at javax.servlet.http.HttpServletResponseWrapper.sendError(HttpServletResponseWrapper.java:119)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.setResponseStatus(ServletInvocableHandlerMethod.java:141)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:106)
at org.springframework.web.servlet.mvc.method.annotation.ExceptionHandlerExceptionResolver.doResolveHandlerMethodException(ExceptionHandlerExceptionResolver.java:340)
at org.springframework.web.servlet.handler.AbstractHandlerMethodExceptionResolver.doResolveException(AbstractHandlerMethodExceptionResolver.java:60)
at org.springframework.web.servlet.handler.AbstractHandlerExceptionResolver.resolveException(AbstractHandlerExceptionResolver.java:138)
at org.springframework.web.servlet.handler.HandlerExceptionResolverComposite.resolveException(HandlerExceptionResolverComposite.java:75)
at org.springframework.web.servlet.DispatcherServlet.processHandlerException(DispatcherServlet.java:1161)
at org.springframework.web.servlet.DispatcherServlet.processDispatchResult(DispatcherServlet.java:998)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:952)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:870)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:961)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:852)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:620)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:186)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.springframework.orm.jpa.support.OpenEntityManagerInViewFilter.doFilterInternal(OpenEntityManagerInViewFilter.java:177)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:683)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1720)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1679)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Unknown Source)
below is the code (in controller) that returns the response to client:
#RequestMapping(method = RequestMethod.GET)
#ResponseBody
public String getSelections(#RequestParam Integer systemId, #RequestParam String listCode)
throws JsonProcessingException {
SelectionsDTO selectionsDTO = new SelectionsDTO(systemSelectionService.findSelections(systemId, listCode));
String retVal = objectMapper.writeValueAsString(selectionsDTO);
return retVal;
}
as you can see I have even tried to marshall it to string before returning, to exclude jackson as the reason of failure. It does not matter if I return collection of my DTOs or string. It fails the same way. I have debugged it and I checked the size of the message that was written to output successfully (it is around 2,15MB). In my opinion size of the message is the failure cause.
Eh... after hours of debugging and thinking - the answer turned out to be the most obvious one - both clients I have been using were closing the connection (probably timeout). It worked in wget and postman while using swagger and advanced rest client caused the exception to be thrown.
The reason might be connection timeout of http request.
If you are using Tomcat server you can set the timeout in server.xml.
-1 indicates no timeout.
<Connector connectionTimeout="-1" port="8989" protocol="HTTP/1.1" redirectPort="8443"/>
reference : https://tomcat.apache.org/tomcat-7.0-doc/config/http.html
If you are using ColdFusion, you can also set a page's requestTimeOut to override the server setting.
Per https://helpx.adobe.com/coldfusion/cfml-reference/coldfusion-tags/tags-r-s/cfsetting.html, "If you specify 0 as the value, timeout is disabled for the request".
<cfsetting requestTimeOut="0">
cfscript: setting requestTimeOut="0";

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