Tomcat aborting itself

Support
1

Hi,

I have an ODK 1.4.4 installation on Amazon Linux AMI with Tomcat6. The
tomcat6 server is misbehaving, it aborts by itself sometimes and somehow
comes back by itself after a few hours. Below are the error logs. Can
someone help concerning what is going on?

Thanks,
Saad

UPLOAD TASK IN TOMCAT
RUNNING WATCHDOG TASK IN TOMCAT
KILL EXISTING WATCHDOG TASK IN TOMCAT
SCHEDULE NEW WATCHDOG TASK IN TOMCAT
RUNNING WATCHDOG TASK IN TOMCAT
EXITING WATCHDOG TASK IN TOMCAT
41435507 [task_scheduler-1] WARN
org.opendatakit.aggregate.util.BackendActionsTable - watchdog started
early: 1411064495015 vs 1411064524000
EXITING WATCHDOG TASK IN TOMCAT
41571221 [http-8080-3] ERROR
org.opendatakit.aggregate.servlet.SubmissionServlet - Unexpected
exception: Read timed out
java.net.SocketTimeoutException: Read timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:152)
at java.net.SocketInputStream.read(SocketInputStream.java:122)
at
org.apache.coyote.http11.InternalInputBuffer.fill(InternalInputBuffer.java:756)
at
org.apache.coyote.http11.InternalInputBuffer$InputStreamInputBuffer.doRead(InternalInputBuffer.java:786)
at
org.apache.coyote.http11.filters.IdentityInputFilter.doRead(IdentityInputFilter.java:116)
at
org.apache.coyote.http11.InternalInputBuffer.doRead(InternalInputBuffer.java:715)
at org.apache.coyote.Request.doRead(Request.java:427)
at
org.apache.catalina.connector.InputBuffer.realReadBytes(InputBuffer.java:304)
at
org.apache.tomcat.util.buf.ByteChunk.substract(ByteChunk.java:419)
at
org.apache.catalina.connector.InputBuffer.read(InputBuffer.java:327)
at
org.apache.catalina.connector.CoyoteInputStream.read(CoyoteInputStream.java:193)
at
org.apache.commons.fileupload.MultipartStream$ItemInputStream.makeAvailable(MultipartStream.java:999)
at
org.apache.commons.fileupload.MultipartStream$ItemInputStream.read(MultipartStream.java:903)
at java.io.FilterInputStream.read(FilterInputStream.java:133)
at
org.apache.commons.fileupload.util.LimitedInputStream.read(LimitedInputStream.java:134)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:235)
at java.io.BufferedInputStream.read(BufferedInputStream.java:254)
at
org.opendatakit.aggregate.parser.MultiPartFormData.(MultiPartFormData.java:100)
at
org.opendatakit.aggregate.servlet.SubmissionServlet.doPost(SubmissionServlet.java:223)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:643)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:723)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
at
org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
at
org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.opendatakit.common.security.spring.SecurityContextHolderAwareAuthPreservingRequestFilter.doFilter(SecurityContextHolderAwareAuthPreservingRequ
estFilter.java:66)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
at
org.opendatakit.common.security.spring.OpenIDAuthenticationFilter.doFilter(OpenIDAuthenticationFilter.java:40)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.authentication.www.DigestAuthenticationFilter.doFilter(DigestAuthenticationFilter.java:115)
at
org.opendatakit.common.security.spring.DigestAuthenticationFilter.doFilter(DigestAuthenticationFilter.java:40)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.opendatakit.common.security.spring.OutOfBandUserFilter.doFilter(OutOfBandUserFilter.java:105)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.opendatakit.common.security.spring.Oauth2ResourceFilter.doFilter(Oauth2ResourceFilter.java:354)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.access.channel.ChannelProcessingFilter.doFilter(ChannelProcessingFilter.java:144)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
at
org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
at
org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
at
org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(Authentica
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.j
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.j
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineVal
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.jav
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java
at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.proce
at
org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:48
at java.lang.Thread.run(Thread.java:745)

2

Saad,

It's probably related to sending data to the server over very slow connections.

See https://groups.google.com/forum/#!searchin/opendatakit/"Read$20timed$20out"
for ideas.

Yaw

ยทยทยท -- Need ODK services? http://nafundi.com provides form design, server setup, professional support, and software development for ODK.

On Thu, Sep 18, 2014 at 2:24 PM, Saad saad@saadaan.com wrote:

Hi,

I have an ODK 1.4.4 installation on Amazon Linux AMI with Tomcat6. The
tomcat6 server is misbehaving, it aborts by itself sometimes and somehow
comes back by itself after a few hours. Below are the error logs. Can
someone help concerning what is going on?

Thanks,
Saad

UPLOAD TASK IN TOMCAT
RUNNING WATCHDOG TASK IN TOMCAT
KILL EXISTING WATCHDOG TASK IN TOMCAT
SCHEDULE NEW WATCHDOG TASK IN TOMCAT
RUNNING WATCHDOG TASK IN TOMCAT
EXITING WATCHDOG TASK IN TOMCAT
41435507 [task_scheduler-1] WARN
org.opendatakit.aggregate.util.BackendActionsTable - watchdog started
early: 1411064495015 vs 1411064524000
EXITING WATCHDOG TASK IN TOMCAT
41571221 [http-8080-3] ERROR
org.opendatakit.aggregate.servlet.SubmissionServlet - Unexpected exception:
Read timed out
java.net.SocketTimeoutException: Read timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.read(SocketInputStream.java:152)
at java.net.SocketInputStream.read(SocketInputStream.java:122)
at
org.apache.coyote.http11.InternalInputBuffer.fill(InternalInputBuffer.java:756)
at
org.apache.coyote.http11.InternalInputBuffer$InputStreamInputBuffer.doRead(InternalInputBuffer.java:786)
at
org.apache.coyote.http11.filters.IdentityInputFilter.doRead(IdentityInputFilter.java:116)
at
org.apache.coyote.http11.InternalInputBuffer.doRead(InternalInputBuffer.java:715)
at org.apache.coyote.Request.doRead(Request.java:427)
at
org.apache.catalina.connector.InputBuffer.realReadBytes(InputBuffer.java:304)
at
org.apache.tomcat.util.buf.ByteChunk.substract(ByteChunk.java:419)
at
org.apache.catalina.connector.InputBuffer.read(InputBuffer.java:327)
at
org.apache.catalina.connector.CoyoteInputStream.read(CoyoteInputStream.java:193)
at
org.apache.commons.fileupload.MultipartStream$ItemInputStream.makeAvailable(MultipartStream.java:999)
at
org.apache.commons.fileupload.MultipartStream$ItemInputStream.read(MultipartStream.java:903)
at java.io.FilterInputStream.read(FilterInputStream.java:133)
at
org.apache.commons.fileupload.util.LimitedInputStream.read(LimitedInputStream.java:134)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:235)
at java.io.BufferedInputStream.read(BufferedInputStream.java:254)
at
org.opendatakit.aggregate.parser.MultiPartFormData.(MultiPartFormData.java:100)
at
org.opendatakit.aggregate.servlet.SubmissionServlet.doPost(SubmissionServlet.java:223)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:643)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:723)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
at
org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
at
org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.opendatakit.common.security.spring.SecurityContextHolderAwareAuthPreservingRequestFilter.doFilter(SecurityContextHolderAwareAuthPreservingRequ
estFilter.java:66)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
at
org.opendatakit.common.security.spring.OpenIDAuthenticationFilter.doFilter(OpenIDAuthenticationFilter.java:40)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.authentication.www.DigestAuthenticationFilter.doFilter(DigestAuthenticationFilter.java:115)
at
org.opendatakit.common.security.spring.DigestAuthenticationFilter.doFilter(DigestAuthenticationFilter.java:40)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.opendatakit.common.security.spring.OutOfBandUserFilter.doFilter(OutOfBandUserFilter.java:105)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.opendatakit.common.security.spring.Oauth2ResourceFilter.doFilter(Oauth2ResourceFilter.java:354)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.access.channel.ChannelProcessingFilter.doFilter(ChannelProcessingFilter.java:144)
at
org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at
org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
at
org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
at
org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
at
org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(Authentica
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.j
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.j
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineVal
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.jav
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java
at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.proce
at
org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:48
at java.lang.Thread.run(Thread.java:745)

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