Failed to start container
engti opened this issue · 6 comments
Thanks for putting this up. I was really looking forward to something like this.
I am able to install on GCP instance with Ubuntu 18.04, connect via browser, and then login. The issue arises when I try to enter into the Rstudio and VSCode page. It responds for both with "Container not found". Would appreciate any help you could provide.
I looked at a related issue #2
And out there the user had copied the folder and thus there were issue with the image name. I followed the readme and used gitclone, but still I am facing issues.
When I do docker images I get the following
REPOSITORY TAG IMAGE ID CREATED SIZE
shinystudio_rstudio_rshiny_vscode latest 4ffba85c4489 11 minutes ago 4.57GB
shinystudio_shinyproxy latest a9a78357ee2b 20 minutes ago 503MB
shinystudio_influxdb latest 3c7cc3dac046 20 minutes ago 258MB
rocker/verse latest a832931679ea 35 hours ago 3.21GB
influxdb latest f0656e147345 2 weeks ago 258MB
openjdk 8-jre b5ee13f1fc07 2 weeks ago 443MB
The error message when trying to access Rstudio is the following.
`Status code: 500
Message: Failed to start container
Stack Trace:
eu.openanalytics.containerproxy.ContainerProxyException: Failed to start container
at eu.openanalytics.containerproxy.backend.AbstractContainerBackend.startProxy(AbstractContainerBackend.java:110)
at eu.openanalytics.containerproxy.service.ProxyService.startProxy(ProxyService.java:213)
at eu.openanalytics.shinyproxy.controllers.AppController.getOrStart(AppController.java:100)
at eu.openanalytics.shinyproxy.controllers.AppController.startApp(AppController.java:68)
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.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:209)
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:102)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:870)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:776)
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:991)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:925)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:978)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:881)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:855)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at io.undertow.servlet.handlers.ServletHandler.handleRequest(ServletHandler.java:74)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:129)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:119)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:158)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:200)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:357)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:270)
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131)
at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:200)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at io.undertow.servlet.core.ManagedFilter.doFilter(ManagedFilter.java:61)
at io.undertow.servlet.handlers.FilterHandler$FilterChainImpl.doFilter(FilterHandler.java:131)
at io.undertow.servlet.handlers.FilterHandler.handleRequest(FilterHandler.java:84)
at io.undertow.servlet.handlers.security.ServletSecurityRoleHandler.handleRequest(ServletSecurityRoleHandler.java:62)
at io.undertow.servlet.handlers.ServletChain$1.handleRequest(ServletChain.java:64)
at io.undertow.servlet.handlers.ServletDispatchingHandler.handleRequest(ServletDispatchingHandler.java:36)
at io.undertow.server.handlers.PathHandler.handleRequest(PathHandler.java:94)
at eu.openanalytics.containerproxy.util.ProxyMappingManager$ProxyPathHandler.handleRequest(ProxyMappingManager.java:159)
at io.undertow.servlet.handlers.security.SSLInformationAssociationHandler.handleRequest(SSLInformationAssociationHandler.java:131)
at io.undertow.servlet.handlers.security.ServletAuthenticationCallHandler.handleRequest(ServletAuthenticationCallHandler.java:57)
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43)
at io.undertow.security.handlers.AbstractConfidentialityHandler.handleRequest(AbstractConfidentialityHandler.java:46)
at io.undertow.servlet.handlers.security.ServletConfidentialityConstraintHandler.handleRequest(ServletConfidentialityConstraintHandler.java:64)
at io.undertow.security.handlers.AuthenticationMechanismsHandler.handleRequest(AuthenticationMechanismsHandler.java:60)
at io.undertow.servlet.handlers.security.CachedAuthenticatedSessionHandler.handleRequest(CachedAuthenticatedSessionHandler.java:77)
at io.undertow.security.handlers.AbstractSecurityContextAssociationHandler.handleRequest(AbstractSecurityContextAssociationHandler.java:43)
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43)
at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43)
at io.undertow.servlet.handlers.ServletInitialHandler.handleFirstRequest(ServletInitialHandler.java:292)
at io.undertow.servlet.handlers.ServletInitialHandler.access$100(ServletInitialHandler.java:81)
at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:138)
at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:135)
at io.undertow.servlet.core.ServletRequestContextThreadSetupAction$1.call(ServletRequestContextThreadSetupAction.java:48)
at io.undertow.servlet.core.ContextClassLoaderSetupAction$1.call(ContextClassLoaderSetupAction.java:43)
at io.undertow.servlet.handlers.ServletInitialHandler.dispatchRequest(ServletInitialHandler.java:272)
at io.undertow.servlet.handlers.ServletInitialHandler.access$000(ServletInitialHandler.java:81)
at io.undertow.servlet.handlers.ServletInitialHandler$1.handleRequest(ServletInitialHandler.java:104)
at io.undertow.server.Connectors.executeRootHandler(Connectors.java:336)
at io.undertow.server.HttpServerExchange$1.run(HttpServerExchange.java:830)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: com.spotify.docker.client.exceptions.DockerRequestException: Request error: POST unix://localhost:80/containers/26c0f051ed4099d98b75c49bf6c08a7da9980498b195dfc10dbd51260c9b4159/start: 500, body: {"message":"error while creating mount source path '/srv/shinystudio/content/sites/8080': mkdir /srv/shinystudio: read-only file system"}
at com.spotify.docker.client.DefaultDockerClient.propagate(DefaultDockerClient.java:2702)
at com.spotify.docker.client.DefaultDockerClient.request(DefaultDockerClient.java:2663)
at com.spotify.docker.client.DefaultDockerClient.containerAction(DefaultDockerClient.java:700)
at com.spotify.docker.client.DefaultDockerClient.containerAction(DefaultDockerClient.java:685)
at com.spotify.docker.client.DefaultDockerClient.startContainer(DefaultDockerClient.java:680)
at eu.openanalytics.containerproxy.backend.docker.DockerEngineBackend.startContainer(DockerEngineBackend.java:83)
at eu.openanalytics.containerproxy.backend.AbstractContainerBackend.doStartProxy(AbstractContainerBackend.java:126)
at eu.openanalytics.containerproxy.backend.AbstractContainerBackend.startProxy(AbstractContainerBackend.java:107)
... 95 more
Caused by: javax.ws.rs.InternalServerErrorException: HTTP 500 Internal Server Error
at org.glassfish.jersey.client.JerseyInvocation.convertToException(JerseyInvocation.java:1098)
at org.glassfish.jersey.client.JerseyInvocation.translate(JerseyInvocation.java:883)
at org.glassfish.jersey.client.JerseyInvocation.access$500(JerseyInvocation.java:99)
at org.glassfish.jersey.client.JerseyInvocation$2.completed(JerseyInvocation.java:840)
at org.glassfish.jersey.client.ClientRuntime.processResponse(ClientRuntime.java:227)
at org.glassfish.jersey.client.ClientRuntime.access$200(ClientRuntime.java:85)
at org.glassfish.jersey.client.ClientRuntime$2.lambda$response$0(ClientRuntime.java:178)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:272)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:268)
at org.glassfish.jersey.internal.Errors.process(Errors.java:316)
at org.glassfish.jersey.internal.Errors.process(Errors.java:298)
at org.glassfish.jersey.internal.Errors.process(Errors.java:268)
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:312)
at org.glassfish.jersey.client.ClientRuntime$2.response(ClientRuntime.java:178)
at org.glassfish.jersey.apache.connector.ApacheConnector$1.run(ApacheConnector.java:491)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at jersey.repackaged.com.google.common.util.concurrent.MoreExecutors$DirectExecutorService.execute(MoreExecutors.java:299)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
at jersey.repackaged.com.google.common.util.concurrent.AbstractListeningExecutorService.submit(AbstractListeningExecutorService.java:50)
at jersey.repackaged.com.google.common.util.concurrent.AbstractListeningExecutorService.submit(AbstractListeningExecutorService.java:37)
at org.glassfish.jersey.apache.connector.ApacheConnector.apply(ApacheConnector.java:487)
at org.glassfish.jersey.client.ClientRuntime.lambda$null$3(ClientRuntime.java:187)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:272)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:268)
at org.glassfish.jersey.internal.Errors.process(Errors.java:316)
at org.glassfish.jersey.internal.Errors.process(Errors.java:298)
at org.glassfish.jersey.internal.Errors.process(Errors.java:268)
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:312)
at org.glassfish.jersey.client.ClientRuntime.lambda$createRunnableForAsyncProcessing$4(ClientRuntime.java:163)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
... 3 more`
It looks like the pertinent error is:
error while creating mount source path '/srv/shinystudio/content/sites/8080': mkdir /srv/shinystudio: read-only file system
It is important that the account you use for setup be a non-root user with sudoer access. The command to setup ShinyStudio is control.sh setup and should be run without elevation (sudo).
If you want to change the mountpoint, you can do so with an argument, control.sh setup /path/to/mountpoint.
Thanks for getting back to me so quickly.
I did try that initially, but it gave me the error listed below. Googling is telling me that I need to add docker to the sudo group. But using sudo usermod -aG docker ${USER} asks for the password. And since this is a GCP instance i am connecting with ssh key. So not sure where password is.
Anyway, if the above is the pertinent error. I will see what else I can do to fix it. Thanks again
ubuntu@spark-instance3:~/ShinyStudio$ ./control.sh setup
*** Stopping
Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Get http://%2Fvar%2Frun%2Fdocker.sock/v1.39/containers/json?filters=%7B%22network%22%3A%7B%22shinystudio-net%22%3Atrue%7D%7D: dial unix /var/run/docker.sock: connect: permission denied
"docker stop" requires at least 1 argument.
See 'docker stop --help'.
Usage: docker stop [OPTIONS] CONTAINER [CONTAINER...]
Stop one or more running containers
Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Get http://%2Fvar%2Frun%2Fdocker.sock/v1.39/containers/json?all=1&filters=%7B%22network%22%3A%7B%22shinystudio-net%22%3Atrue%7D%7D: dial unix /var/run/docker.sock: connect: permission denied
"docker rm" requires at least 1 argument.
See 'docker rm --help'.
Usage: docker rm [OPTIONS] CONTAINER [CONTAINER...]
Remove one or more containers
ERROR: Couldn't connect to Docker daemon - you might need to run docker-machine start default.
*** Building
ERROR: Couldn't connect to Docker daemon - you might need to run docker-machine start default.
*** Starting
ERROR: Couldn't connect to Docker daemon - you might need to run docker-machine start default.
Okay, I managed to get docker to not require sudo.
And the setup script ran just fine. But when I go to the rstudio and vscode app, I still get error 500 Failed to start container.
And this line still exists in the log {"message":"error while creating mount source path '/srv/shinystudio/content/sites/8080': mkdir /srv/shinystudio: read-only file system"}
Any more avenues I can chase down?
You can either manually create the destination directory sudo mkdir -p /srv/shinystudio/content/sites/8080 and ensure the current user owns it sudo chown -R /srv/shinystudio, or specify the mountpoint be in a directory the current user owns, e.g., control.sh setup "${HOME}/shinystudio".
Awesome. It worked.
Thank you so much. Much appreciated.
Glad to help. Look forward to a rendition of ShinyStudio that can be served via DockerHub for easier setup.