SQL deadlock detected

[dave J]

Every once in a while, I would get a 500 server error when setting an attribute through pyxnat.  It seems i've finally been able to re-create the problem.

Has anybody else seen this?  it seems to happen if you try and change attributes at to fast of rate. 

I have this in my xdat.log:

2015-05-27 11:32:38,757 [http-8080-57] ERROR org.nrg.xft.db.DBAction - 

org.postgresql.util.PSQLException: ERROR: deadlock detected

  Detail: Process 6085 waits for ShareLock on transaction 11439771; blocked by process 6088.

Process 6088 waits for ShareLock on transaction 11439773; blocked by process 6085.

  Hint: See server log for query details.

  Where: SQL statement "UPDATE adir_MRExperiment_meta_data SET last_modified=NOW(), modified=1 WHERE meta_data_id=current_row.meta_data_id"

PL/pgSQL function "update_ls_adir_mrexperiment" line 18 at SQL statement

SQL statement "SELECT update_ls_adir_MRExperiment( $1, $2)"

PL/pgSQL function "update_ls_xnat_imagesessiondata" line 15 at PERFORM

SQL statement "SELECT update_ls_xnat_imageSessionData(current_row.image_session_id, $2)"

PL/pgSQL function "update_ls_ext_xnat_imagescandata" line 14 at PERFORM

SQL statement "SELECT update_ls_ext_xnat_imageScanData( $1, $2)"

PL/pgSQL function "update_ls_ext_xnat_mrscandata" line 24 at PERFORM

SQL statement "SELECT update_ls_ext_xnat_mrScanData( $1, $2)"

PL/pgSQL function "update_ls_adir_mrscan" line 24 at PERFORM

SQL statement "SELECT update_ls_adir_MRScan( $1, $2)"

PL/pgSQL function "update_ls_xnat_mrscandata" line 15 at PERFORM

        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2102)

        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1835)

        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257)

        at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:500)

        at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:374)

        at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:366)

        at org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)

        at org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:264)

        at org.nrg.xft.db.PoolDBUtils.execute(PoolDBUtils.java:914)

        at org.nrg.xft.db.PoolDBUtils.executeNonSelectQuery(PoolDBUtils.java:325)

        at org.nrg.xft.db.PoolDBUtils.ExecuteNonSelectQuery(PoolDBUtils.java:352)

        at org.nrg.xft.db.DBAction.PerformUpdateTriggers(DBAction.java:3816)

        at org.nrg.xft.db.DBAction.StoreItem(DBAction.java:137)

        at org.nrg.xft.XFTItem.save(XFTItem.java:5769)

        at org.nrg.xft.ItemWrapper.save(ItemWrapper.java:368)

        at org.nrg.xft.utils.SaveItemHelper.save(SaveItemHelper.java:65)

        at org.nrg.xft.utils.SaveItemHelper.authorizedSave(SaveItemHelper.java:421)

        at org.nrg.xnat.restlet.resources.SubjAssessmentResource.handlePut(SubjAssessmentResource.java:520)

        at org.restlet.Finder.handle(Finder.java:359)

        at org.restlet.Filter.doHandle(Filter.java:150)

        at org.restlet.Filter.handle(Filter.java:195)

        at org.restlet.Router.handle(Router.java:504)

        at org.restlet.Filter.doHandle(Filter.java:150)

        at org.restlet.Filter.handle(Filter.java:195)

        at org.restlet.Filter.doHandle(Filter.java:150)

        at org.restlet.Filter.handle(Filter.java:195)

        at org.restlet.Router.handle(Router.java:504)

        at org.restlet.Filter.doHandle(Filter.java:150)

        at org.restlet.Filter.handle(Filter.java:195)

        at org.restlet.Filter.doHandle(Filter.java:150)

        at org.restlet.Filter.handle(Filter.java:195)

        at org.restlet.Filter.doHandle(Filter.java:150)

        at com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:130)

        at org.restlet.Filter.handle(Filter.java:195)

        at org.restlet.Filter.doHandle(Filter.java:150)

        at org.restlet.Filter.handle(Filter.java:195)

        at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:124)

        at com.noelios.restlet.application.ApplicationHelper.handle(ApplicationHelper.java:112)

        at org.restlet.Application.handle(Application.java:341)

        at org.restlet.Filter.doHandle(Filter.java:150)

        at org.restlet.Filter.handle(Filter.java:195)

        at org.restlet.Router.handle(Router.java:504)

        at org.restlet.Filter.doHandle(Filter.java:150)

        at org.restlet.Filter.handle(Filter.java:195)

        at org.restlet.Router.handle(Router.java:504)

        at org.restlet.Filter.doHandle(Filter.java:150)

        at com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:130)

        at org.restlet.Filter.handle(Filter.java:195)

        at org.restlet.Filter.doHandle(Filter.java:150)

        at org.restlet.Filter.handle(Filter.java:195)

        at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:124)

        at org.restlet.Component.handle(Component.java:673)

        at org.restlet.Server.handle(Server.java:331)

        at com.noelios.restlet.ServerHelper.handle(ServerHelper.java:68)

        at com.noelios.restlet.http.HttpServerHelper.handle(HttpServerHelper.java:147)

        at com.noelios.restlet.ext.servlet.ServerServlet.service(ServerServlet.java:881)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

        at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:206)

        at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:179)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

        at org.nrg.xnat.restlet.util.UpdateExpirationCookie.doFilter(UpdateExpirationCookie.java:38)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:369)

        at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:109)

        at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:83)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:97)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:100)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:78)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.nrg.xnat.security.XnatArcSpecFilter.doFilter(XnatArcSpecFilter.java:40)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:54)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:35)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.nrg.xnat.security.XnatBasicAuthenticationFilter.doFilter(XnatBasicAuthenticationFilter.java:134)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:187)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:105)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.springframework.security.web.session.ConcurrentSessionFilter.doFilter(ConcurrentSessionFilter.java:109)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.nrg.xnat.security.XnatExpiredPasswordFilter.doFilter(XnatExpiredPasswordFilter.java:83)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:79)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.springframework.security.web.access.channel.ChannelProcessingFilter.doFilter(ChannelProcessingFilter.java:109)

        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)

        at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:168)

        at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)

        at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)

        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(AuthenticatorBase.java:465)

        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)

        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)

        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)

        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)

        at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:857)

        at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)

        at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)

        at java.lang.Thread.run(Thread.java:701)

[Tim Olsen]

What version of XNAT are you on?  I saw something like this in some load testing and fixed it at some point, but it might be a different issue.

 

Tim

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[dave J]

Tag 1.6.3 plus some customizations.