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fresh2dev / ShinyStudio

A fully Dockerized, self-hosted development environment for teams. Develop where you serve.
https://hub.docker.com/r/dm3ll3n/shinystudio
MIT License
242 stars 40 forks source link

Failed to start container #6

Closed engti closed 5 years ago

engti commented 5 years ago

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 https://github.com/dm3ll3n/ShinyStudio/issues/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`

fresh2dev commented 5 years ago

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.

engti commented 5 years ago

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.

engti commented 5 years ago

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?

fresh2dev commented 5 years ago

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".

engti commented 5 years ago

Awesome. It worked.

Thank you so much. Much appreciated.

fresh2dev commented 5 years ago

Glad to help. Look forward to a rendition of ShinyStudio that can be served via DockerHub for easier setup.