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cytomine / Cytomine-IMS

Cytomine-IMS: Image Management System
GNU Lesser General Public License v2.1
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Image upload failure : v2.0.0 #35

Open yasushinj opened 2 years ago

yasushinj commented 2 years ago

IMS : v2.0.0 Core : v3.2.0 Ubuntu 20.04 Docker :20.10.12

From the front-end, upon Image upload, image was marked as deployed in green (assuming success), but the image does not show on the viewer. Both Core/IMS does not create catallan.out, so the only way is to run docker logs to get a log from tomcat. At least, catalina.out is not found under /user/local/tomcat/log. The catalina log with a timestamp and it only writes startup log, no subsequent log was written to the file.

It may be an issue on log rotation.

I can see a log from core, but need to use docker logs core, but no processing log was produced on ims:v2.0.0 and the log stops after startup. From docker logs core, it shows an error to get image from ims sever. It looks like it is having a communication issue with ims server.

yasushi@x1-gen3:~$ docker exec -it ims /bin/bash root@340ee8cea518:/usr/local/tomcat# ls -l logs/ total 196 -rw-r----- 1 root root 4616 Mar 3 16:10 catalina.2022-03-03.log -rw-r----- 1 root root 0 Mar 3 16:10 host-manager.2022-03-03.log -rw-r----- 1 root root 412 Mar 3 16:10 localhost.2022-03-03.log -rw-r----- 1 root root 4041 Mar 3 16:44 localhost_access_log.2022-03-03.txt -rw-r----- 1 root root 0 Mar 3 16:10 manager.2022-03-03.log -rw-r----- 1 root root 181690 Mar 3 16:44 stacktrace.log

yasushi@x1-gen3:~$ docker logs ims mv: cannot stat '/tmp/setenv.sh': No such file or directory 03-Mar-2022 16:10:02.026 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat/9.0.54 03-Mar-2022 16:10:02.028 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Sep 28 2021 13:51:49 UTC 03-Mar-2022 16:10:02.028 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 9.0.54.0 03-Mar-2022 16:10:02.028 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux 03-Mar-2022 16:10:02.028 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 5.14.0-1024-oem 03-Mar-2022 16:10:02.028 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64 03-Mar-2022 16:10:02.028 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/local/openjdk-8/jre 03-Mar-2022 16:10:02.028 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_302-b08 03-Mar-2022 16:10:02.028 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation 03-Mar-2022 16:10:02.028 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/tomcat 03-Mar-2022 16:10:02.028 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/tomcat 03-Mar-2022 16:10:02.029 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties 03-Mar-2022 16:10:02.030 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager 03-Mar-2022 16:10:02.030 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048 03-Mar-2022 16:10:02.030 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources 03-Mar-2022 16:10:02.030 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027 03-Mar-2022 16:10:02.030 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs= 03-Mar-2022 16:10:02.030 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/tomcat 03-Mar-2022 16:10:02.030 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/tomcat 03-Mar-2022 16:10:02.030 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp 03-Mar-2022 16:10:02.031 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent The Apache Tomcat Native library which allows using OpenSSL was not found on the java.library.path: [/usr/local/lib/openslide-java:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib] 03-Mar-2022 16:10:02.260 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"] 03-Mar-2022 16:10:02.279 INFO [main] org.apache.catalina.startup.Catalina.load Server initialization in [389] milliseconds 03-Mar-2022 16:10:02.305 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina] 03-Mar-2022 16:10:02.305 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat/9.0.54] 03-Mar-2022 16:10:02.325 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deploying web application archive [/usr/local/tomcat/webapps/ROOT.war] 03-Mar-2022 16:10:05.910 INFO [main] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time. log4j:WARN No appenders could be found for logger (net.bull.javamelody). log4j:WARN Please initialize the log4j system properly. log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info. External configuration file : [file:/root/.grails/ims-config.groovy] Found configuration file ? true External configuration file : [file:/root/.grails/ims-config.groovy] Found configuration file ? true 03-Mar-2022 16:10:12.369 INFO [main] org.apache.catalina.startup.HostConfig.deployWAR Deployment of web application archive [/usr/local/tomcat/webapps/ROOT.war] has finished in [10,044] ms 03-Mar-2022 16:10:12.371 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"] 03-Mar-2022 16:10:12.379 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [10099] milliseconds

== docker logs core ==

3-03-2022 16:17:30,448 ERROR ImageServerService - 03-03-2022 16:17:30,448 ERROR ImageServerService - 03-03-2022 16:17:30,448 ERROR ImageServerService - groovyx.net.http.HttpResponseException: at groovyx.net.http.HTTPBuilder.defaultFailureHandler(HTTPBuilder.java:652) 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:498) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:324) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1207) at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1110) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1074) at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1110) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1016) at groovy.lang.Closure.call(Closure.java:423) at groovyx.net.http.HTTPBuilder.doRequest(HTTPBuilder.java:508) at groovyx.net.http.HTTPBuilder.get(HTTPBuilder.java:292) at groovyx.net.http.HTTPBuilder$get.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120) at be.cytomine.middleware.ImageServerService.makeRequest(ImageServerService.groovy:344) at be.cytomine.middleware.ImageServerService.makeRequest(ImageServerService.groovy) at be.cytomine.middleware.ImageServerService.this$3$makeRequest(ImageServerService.groovy) at be.cytomine.middleware.ImageServerService$this$3$makeRequest$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:49) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:149) at be.cytomine.middleware.ImageServerService.thumb(ImageServerService.groovy:163) at be.cytomine.middleware.ImageServerService$thumb$1.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:49) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:145) at be.cytomine.middleware.ImageServerService.thumb(ImageServerService.groovy:135) at be.cytomine.middleware.ImageServerService$thumb$0.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:49) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:133) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:145) at be.cytomine.middleware.ImageServerService.thumb(ImageServerService.groovy:131) at be.cytomine.middleware.ImageServerService$$FastClassBySpringCGLIB$$216a4334.invoke() at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204) at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:640) at be.cytomine.middleware.ImageServerService$$EnhancerBySpringCGLIB$$e87d2c74.thumb() at be.cytomine.middleware.ImageServerService$thumb.call(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:120) at be.cytomine.api.image.RestImageInstanceController.thumb(RestImageInstanceController.groovy:234) 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:498) at org.codehaus.groovy.grails.web.servlet.mvc.MixedGrailsControllerHelper.invoke(MixedGrailsControllerHelper.java:154) at org.codehaus.groovy.grails.web.servlet.mvc.AbstractGrailsControllerHelper.handleAction(AbstractGrailsControllerHelper.java:375) at org.codehaus.groovy.grails.web.servlet.mvc.AbstractGrailsControllerHelper.executeAction(AbstractGrailsControllerHelper.java:252) at org.codehaus.groovy.grails.web.servlet.mvc.AbstractGrailsControllerHelper.handleURI(AbstractGrailsControllerHelper.java:205) at org.codehaus.groovy.grails.web.servlet.mvc.AbstractGrailsControllerHelper.handleURI(AbstractGrailsControllerHelper.java:126) at org.codehaus.groovy.grails.web.servlet.mvc.SimpleGrailsController.handleRequest(SimpleGrailsController.java:72) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:50) at org.codehaus.groovy.grails.web.servlet.GrailsDispatcherServlet.doDispatch(GrailsDispatcherServlet.java:347) 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:655) at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837) at javax.servlet.http.HttpServlet.service(HttpServlet.java:764) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:227) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at grails.plugin.cache.web.filter.PageFragmentCachingFilter.doFilter(PageFragmentCachingFilter.java:198) at grails.plugin.cache.web.filter.AbstractFilter.doFilter(AbstractFilter.java:63) 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:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:101) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:101) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:101) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:711) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:459) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:385) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:313) at org.codehaus.groovy.grails.web.mapping.UrlMappingUtils.forwardRequestForUrlMappingInfo(UrlMappingUtils.java:178) at org.codehaus.groovy.grails.web.mapping.UrlMappingUtils.forwardRequestForUrlMappingInfo(UrlMappingUtils.java:144) at org.codehaus.groovy.grails.web.mapping.UrlMappingUtils.forwardRequestForUrlMappingInfo(UrlMappingUtils.java:135) at org.codehaus.groovy.grails.web.mapping.filter.UrlMappingsFilter.doFilterInternal(UrlMappingsFilter.java:216) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.authentication.switchuser.SwitchUserFilter.doFilter(SwitchUserFilter.java:181) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118) at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) at grails.plugin.springsecurity.web.filter.GrailsAnonymousAuthenticationFilter.doFilter(GrailsAnonymousAuthenticationFilter.java:53) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) at org.springframework.security.web.authentication.rememberme.RememberMeAuthenticationFilter.doFilter(RememberMeAuthenticationFilter.java:146) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) at javax.servlet.FilterChain$doFilter$0.call(Unknown Source) at cytomine.web.APIAuthentificationFilters.doFilter(APIAuthentificationFilters.groovy:46) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199) at grails.plugin.springsecurity.web.authentication.RequestHolderAuthenticationFilter.doFilter(RequestHolderAuthenticationFilter.java:49) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) at grails.plugin.springsecurity.web.authentication.logout.MutableLogoutFilter.doFilter(MutableLogoutFilter.java:82) at org.springframework.security.web.FilterChainProxy$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.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:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.codehaus.groovy.grails.web.servlet.mvc.GrailsWebRequestFilter.doFilterInternal(GrailsWebRequestFilter.java:69) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.codehaus.groovy.grails.web.filters.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:67) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) 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:189) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:162) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:197) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:540) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:135) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:687) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:357) at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:382) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:895) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1722) at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191) at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:748)