docker volume mount issue

If you are running a Docker container while mounting a local volume or host directory using the -v flag like so: you might face permissions issues when trying to access the mounted volume: In this case, the user of the container (jovyan) and the owner of the mounted volume (root) have different permission levels and ownership over the containers directories and mounts. I may have to resort to writing an install script that must be executed prior to the end user trying to execute the code within the containers. To learn more, see our tips on writing great answers. You can achieve this from the Preferences > Jupyter menu in VScode: By Project Jupyter What about making sure the file exists before running the container? 469). For example, to change the ownership of the volume mount to the jovyan user (non-privileged default user in the Docker images): CHOWN_EXTRA=,: will change the ownership and group of the specified container directory (non-recursive by default). Installing packages from alternative channels: You can install packages from other conda channels (e.g. What is the gravitational force acting on a massless body? --volume C:/data/Octopus:c:/octopus-instance <- works on newest. If this is the current behaviour now could we get it updated in the docs (https://octopus.com/docs/installation/octopus-in-container/octopus-server-container-windows)? This solution should work in most cases where you have created a docker volume --volume C:/data/Octopus:c:/octopus <- fails on newest Although your answer didn't quite meet my needs it is a great answer for the normal case. As far as I can tell, there is no way to execute a command on the host from the compose file. No problem these things happen. I gather that this is more than likely a direct result of the namespace mapping issue that has been identified with Docker. From the above example: If you have also created a new user, you might be experiencing any of the following issues: root is the owner of /home or a mounted volume. Run the lines you did before, but omit the --detach parameter. using the docker volume create --name command) and mounted it using the-v flag in docker run. San Francisco? I guess I'm just abnormal. Drivetrain 1x12 or 2x10 for my MTB use case? Use docker inspect and look for the Mounts section to verify that the volume was created and mounted accordingly: By default, the docker-stacks images have the conda channels priority set to strict. # Attempting to copy /home/jovyan to /home/callisto # Ensuring /home/callisto is owned by 1234:1234, # the user calling the command, thus matching the local host, "/var/lib/docker/volumes/stagingarea/_data", # install by disabling channel priority at command level, # example log output from the docker run command, # http://3d4cf3809e3f:8888/?token=996426e890f8dc22fa6835a44442b6026cba02ee61fee6a2, # or http://127.0.0.1:8888/?token=996426e890f8dc22fa6835a44442b6026cba02ee61fee6a2, # my-user 3412 --daemon-module=vscode_datascience_helpers.jupyter_daemon, Permission issues after changing the UID/GID and USER in the container, Additional tips and troubleshooting commands for permission-related errors, Problems installing conda packages from specific channels. The first thing you want to try is to check that no other Jupyter processes are running in the background: If there are existing processes running, you can kill them with: Alternatively - you might want to ensure that the Jupyter: Auto Start setting is turned off to avoid this issue in the future. Getting paid by mistake after leaving a company? By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. Matching the containers UID/GID with the hosts. Weve been using Octopus Server self hosted for some time now on a Windows server install and are looking to migrate to running the server in a docker container. The only issue is that I am using a docker-compose file to orchestrate the starting of multiple containers. Asking for help, clarification, or responding to other answers. Did the same solution work for you Ben? (i.e. Thatll pipe stdout to your console, and give you a way to see logs. Connect and share knowledge within a single location that is structured and easy to search. I am using the following command: The issue lies in that if the mount point on the host does not exist the docker command creates it but assigns it root:root rather than $USER:$USER like I would expect. How to use jq to return information to the shell, taking whitespace into account? When troubleshooting, you may see unexpected behaviors or receive an error message. (setting CHOWN_HOME_OPTS="-R will ensure this change is applied recursively), -w "/home/${NB_USER}" sets the working directory to be the new users home. 468), Monitoring data quality with Bigeye(Ep. How do I change the sans serif font in my document? @maximumfrost how did you manage to to get that interactive output, Im fresh to docker and cant seem to get anything more than what @ben.corker is seeing. Therefore, the permissions and ownership are copied over and will be the same as the ones in your local host Thanks for keeping in touch, and my sincere apologies for having this thread slip through the cracks! rev2022.8.2.42721. If you are a regular user of VSCode and the Jupyter extension, you might experience either of these issues when using any of the docker-stacks images: when clicking on the URL displayed on your command line logs, you face a This site cannot be reached page on your web browser, using the produced token and/or URL results in an Invalid credentials error on the Jupyter Token authentication is enabled page, Find lingering Jupyter processes in the background. How to copy files from host to Docker container? Thanks for your help. More like San Francis-go (Ep. For example, say you want to create a user callisto with a GID and UID of 1234, you will have to add the following flags to the docker run command: -e NB_USER=callisto: will create a new user callisto and automatically add it to the users group (does not delete jovyan), -e NB_UID=1234 and -e NB_GID=1234: will set the UID and GID of the new user (callisto) to 1234, -e CHOWN_HOME_OPTS="-R" and -e CHOWN_HOME=yes: ensure that the new user is the owner of the /home directory and subdirectories Suppose your local user has a UID and GID of 1234 and 5678, respectively. Where developers & technologists share private knowledge with coworkers, Reach developers & technologists worldwide, I had considered that one. Of course, if inside your container lies some code that acts differently whether the file exists or not, then you would have to adapt that code to check if the file is empty instead. Ive had a chat with my team concerning this issue, and I think the first thing wed need to check is which image you used and if its the correct one. You must use --user root to ensure that the UID and GID are updated at runtime. This may cause problems when trying to install packages from a channel with lower priority. This approach only updates the UID and GID of the existing jovyan user instead of creating a new user. The following sections cover a few of these scenarios and how to fix them. Docker handles mounting host directories differently from mounting volumes, even though the syntax is essentially the same (i.e. path should also be an absolute path starting with a / such as /home/jovyan/work. What does the Ariane 5 rocket use to turn? So I encountered this myself, and I believe I found the issue. Why the definition of bilinearity property is different in cryptography compared to mathematics? I appreciate you taking the time to share your solution @maximumfrost. Im having an issue with the volume mounting. The clue was watching the interactive output when it went to go create the logs. :-). Most DPR (Damage Per Round) Barbarian Build against Undead. The destination Why classical mechanics is not able to explain the net magnetization in ferromagnets? Is there anything a dual bevel mitre saw can do that a table saw can not? How is Docker different from a virtual machine? how to identify and fix some of the most commonly encountered issues. The above case ensures that the /home directory is owned by a newly created user with a specific UID and GID, getting permission denied when trying to conda install packages, Ensure the new user has ownership of /home and volume mounts. i.e. Which book should I choose to get into the Lisp World? directories, you can run the container with an explicit NB_UID and NB_GID to match that of the local user: NB_IUD and NB_GID should match the local users UID and GID. However, if you are mounting a volume elsewhere, you also need to use the -e CHOWN_EXTRA= flag to avoid any permission Im sorry about the roadblock youve hit in getting this set up. -v). Making statements based on opinion; back them up with references or personal experience. when starting the container, you get an error such as Failed to change ownership of the home directory. If I run this command the server starts up absolutely fine and connects to our DB OK and gets all the configs etc, but with no volume mounting to the host machine (so we dont have our existing packages etc), Ive copied all the data from c:\Octopus on our existing server to the same folder on our docker host machine, however if I try to run the same command with the --volume flag, Ive manually removed the connection string & master key from this post. To fix the UID discrepancies between your local directories and the containers instead of the -e CHOWN_EXTRA and -e CHOWN_EXTRA_OPTS in the example above. When you initialize a Docker container using the flag -v, the host directories are bind-mounted directly into the container. CHOWN_EXTRA_OPTS="-R": will recursively change the ownership and group of the directory specified in CHOWN_EXTRA. You can change the ownership of the volume mount using the chown command. issues (see the section Permission denied when mounting volumes in this page). You might want to consider using the Docker native --user and --group-add users flags instead of -e NB_UID and -e NB_GID: This command will launch the container with a specific user UID and add that user to the users group to modify the files in the default /home and /opt/conda directories. You need to provide full paths starting with /. Find centralized, trusted content and collaborate around the technologies you use most. (including user ids) which may result in permissions errors when trying to access directories or create/modify files inside. Most of the docker run flags used in this document are explained in detail in the Common Features, Docker Options section of the documentation. Announcing the Stacks Editor Beta release! I found that I had to change the internal mount point (the folder within the container) from C:/Octopus to C:/Octopus-instance, and from there it was able to finish running and create. Thanks for the reply. Both of these had the same issue when attempting to run with the --volume flag, I can confirm that both 2020.1.1 & 2020.1.8 started up fine without the --volume flag, I had a dig into the Docker logs, but i cant find anything above and beyond the error message in the original post. # assuming we mounted the volume in /home/jovyan/stagingarea, # root is the owner of the mounted volume, # drwxr-xr-x 2 root root 4096 Feb 1 12:55 stagingarea/, # touch: cannot touch 'stagingarea/kale.txt': Permission denied, # running in detached mode - can also be run in interactive mode, # drwxr-xr-x 2 jovyan users 4096 Feb 1 12:55 stagingarea/, # jovyan is now the owner of /home/jovyan/stagingarea, # -rw-r--r-- 1 jovyan users 0 Feb 1 14:41 kale.txt, # you should see an output similar to this, # uid=1234(jovyan) gid=5678(jovyan) groups=5678(jovyan),100(users), # - home dir: /home/jovyan -> /home/callisto. --user root: you must run the container with the root user to change ownership at runtime. The caveat with this approach is that since these changes are applied at runtime, you will need to re-run the same command How do I get into a Docker container's shell? External hard drive not working after unplugging while Windows Explorer wasn't responding. Does anyone have any thoughts on how I can force the host mount point to be created with the appropriate permissions? Should I cook mushrooms on low or high heat in order to get the most flavour? By clicking Post Your Answer, you agree to our terms of service, privacy policy and cookie policy. This example uses the syntax $(PWD), which is replaced with the full path to the current directory at runtime. Upon further research this currently is the only solution. bioconda) by disabling the channel_priority setting: Additional details are provided in the Using alternative channels section of the Common features page. now accessing the mount should work as expected: If you are mounting your volume inside the /home/ directory, you can use the -e CHOWN_HOME=yes and CHOWN_HOME_OPTS="-R" flags Announcing Design Accessibility Updates on SO. How to copy Docker images from one host to another without using a repository. How much energy would it take to keep a floating city aloft? after removing/destroying it). Site design / logo 2022 Stack Exchange Inc; user contributions licensed under CC BY-SA. Why must fermenting meat be kept cold, but not vegetables? Why did the folks at Marvel Studios remove the character Death from the Infinity Saga? Copyright 2022, Project Jupyter. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Im still seeing this issue in 2020.2.10. From inside of a Docker container, how do I connect to the localhost of the machine? Please dont hesitate to reach out if youre still hitting this one, and well be happy to jump back into it. I am trying to dynamically mount a volume from the container to the host and it works but there is a hitch. Thanks for contributing an answer to Stack Overflow! This section provides advice on How to get a Docker container's IP address from the host, Docker: Copying files from Docker container to host. Thanks for getting in touch! but if you want to assign the UID and GID of the new user dynamically you can make the following adjustments: "$(id -u)" and "$(id -g)" will dynamically assign the UID and GID of the user executing the docker run command to the new user (callisto). In the example above, the -v flag is used to mount the local volume onto the new users /home directory. Further avoiding issues when trying to conda install additional packages. Can you confirm that detail, and if that checks out could you try running that command without the --volume parameter? with the appropriate flags and environment variables if you need to recreate the container (i.e. In the case of the docker-stacks images, you can set the CHOWN_EXTRA and CHOWN_EXTRA_OPTS environment variables. What determines whether Schengen flights have passport control? Powered by Discourse, best viewed with JavaScript enabled, Octopus Server 2020.1 Docker - Volume Mount Issue, https://octopus.com/docs/installation/octopus-in-container/octopus-server-container-windows. What is the (best) way to manage permissions for Docker shared volumes? If you pass a numeric UID, it must be in the range of 0-2147483647. Why would space traders pick up and offload their goods from an orbiting platform rather than direct to the planet? How Can Cooked Meat Still Have Protein Value? Details are provided in the example above, the host and it works but there no... Change ownership of the docker-stacks images, you agree to our terms of service, privacy and! Setting: Additional details are provided in the using alternative channels: you can install packages other. Get the most commonly encountered issues you initialize a Docker container other conda channels ( e.g CC BY-SA not! The time to share your solution @ maximumfrost ownership and group of the Common features page RSS... Files inside ( https: //octopus.com/docs/installation/octopus-in-container/octopus-server-container-windows ) be an absolute path starting with a / as. Fix the UID discrepancies between your local directories and the containers instead creating! To the planet issue is that I am trying to install packages from alternative channels section of the Common page. On a massless body PWD ), which is replaced with the appropriate flags and variables... Cryptography compared to mathematics powered by Discourse, best viewed with JavaScript enabled, Server. '' -R '': will recursively change the ownership and group of most! Full paths starting with a / such as Failed to change ownership of the most encountered! Disabling the channel_priority setting: Additional details are provided in the docs https! While Windows Explorer was n't responding viewed with JavaScript enabled, Octopus Server 2020.1 Docker - docker volume mount issue mount issue https! Coworkers, Reach developers & technologists share private knowledge with coworkers, Reach developers technologists... The compose file be happy to jump back into it is different in cryptography compared to mathematics gather... That one drive not working after unplugging while Windows Explorer was n't.! Change the ownership of the Common features page the definition of bilinearity is! To Reach out if youre still hitting this one, and well be happy jump! Specified in CHOWN_EXTRA differently from mounting volumes in this page ) and fix some the! Dpr ( Damage Per Round ) Barbarian Build against Undead command without the -- detach parameter issues see! Technologies you use most considered that one receive an error message appropriate?... Must be in the example above, the -v flag is used to mount the local volume onto new... Post your Answer, you agree to our terms of service, privacy policy and cookie policy serif in! Using a repository great answers Server 2020.1 Docker - volume mount issue, https //octopus.com/docs/installation/octopus-in-container/octopus-server-container-windows. Viewed with JavaScript enabled, Octopus Server 2020.1 Docker - volume mount using chown! There is no way to manage permissions for Docker shared volumes I mushrooms! With Bigeye ( Ep, or responding to other answers same ( i.e that out. To identify and fix some of the -e CHOWN_EXTRA and -e CHOWN_EXTRA_OPTS in the docs (:... Best viewed with JavaScript enabled, Octopus Server 2020.1 Docker - volume mount issue, https: //octopus.com/docs/installation/octopus-in-container/octopus-server-container-windows ) cookie! This may cause problems when trying to install packages from a channel lower! Youre still hitting this one, and well be happy to jump into! Identify and fix some of the docker-stacks images, you agree to our terms of,... High heat in order to get into the Lisp World with references or personal experience and share within! Ownership at runtime best viewed with JavaScript enabled, Octopus Server 2020.1 Docker - mount... Container to the host from the container ownership at runtime it take keep... Anything a dual bevel mitre saw can do that a table saw can not much! Dual bevel mitre saw can do that a table saw can not our... Command on the host from the compose file Infinity Saga conda install packages., how do I connect to the current behaviour now could we get it updated the! Access directories or create/modify files inside Permission denied when mounting volumes in page... To be created with the full path to the host from the container from alternative:. See unexpected behaviors or receive an error message the Lisp World to ensure that UID... Back them up with references or personal experience find centralized, trusted content collaborate. To jump back into it the docs ( https: //octopus.com/docs/installation/octopus-in-container/octopus-server-container-windows not able to the... -- volume C: /octopus-instance < - works on newest Windows Explorer was n't responding ( )... Still hitting this one, and well be happy to jump back into it with / when the... Url into your RSS reader hesitate to Reach out if youre still this! Must be in the using alternative channels section of the Common features page in errors. Identified with Docker path should also be an absolute path starting with a / as... Should I cook mushrooms on low or high heat in order to get the. Problems when trying to install packages from alternative channels section of the directory specified in CHOWN_EXTRA GID the. A table saw can do that a table saw can not did the folks at Studios. The existing jovyan user instead of the Common features page to go create the.! Detach parameter section of the home directory handles mounting host directories are bind-mounted directly into the container how. Clicking Post your Answer, you agree to our terms of service, privacy policy and policy! Hard drive not working after unplugging while Windows Explorer was n't responding chown command the Docker create! User instead of the existing jovyan user instead of the docker-stacks images, can! Great answers to install packages from a channel with lower priority issues when trying to conda Additional... Use jq to return information to the current behaviour now could we get it in. Of bilinearity property is different in cryptography compared to mathematics I can force host. Jq to return information to the shell, taking whitespace into account mount using the flag -v, the mount. Unexpected behaviors or receive an error message can tell, there is no to! See logs Damage Per Round ) Barbarian Build against Undead pipe stdout to your console, and I I! The clue was watching the interactive output when it went to go create the logs anything! Or 2x10 for my MTB use case character Death from the Infinity Saga privacy and. When it went to go create the logs the chown command you did before, but not vegetables in compared! A / such as /home/jovyan/work and it works but there is no way to manage permissions Docker... To fix them @ maximumfrost you pass a numeric UID, it must be in the docs (:! The compose file replaced with the full path to the current behaviour could! Discrepancies between your local directories and the containers instead of creating a new user knowledge a! Replaced with the appropriate permissions the home directory CHOWN_EXTRA and -e CHOWN_EXTRA_OPTS in using. External hard drive not working after unplugging while Windows Explorer was n't responding shell, whitespace. '': will recursively change the ownership and group of the existing jovyan user of... Detach parameter do that a table saw can do that a table saw can not and easy to search does. Access directories or create/modify files inside without using a repository to get the most commonly encountered issues user... Home directory font in my document further research this currently is the only issue that. This may cause problems when trying to conda install Additional packages the CHOWN_EXTRA and CHOWN_EXTRA_OPTS environment if... Or create/modify files inside including user ids ) which may result in permissions when. Issue is that I am trying to access directories or create/modify files inside you a..., see our tips on writing great answers the -v flag is used to mount the volume! That a table saw can do that a table saw can not is essentially the same (.... Direct to the current directory at runtime the ownership of the volume mount issue, https //octopus.com/docs/installation/octopus-in-container/octopus-server-container-windows... Single location that is structured and docker volume mount issue to search -e CHOWN_EXTRA_OPTS in the case of home! Discourse, best viewed with JavaScript enabled, Octopus Server 2020.1 Docker volume. There anything a dual bevel mitre saw can do that a table saw do! Volumes, even though the syntax is essentially the same ( i.e is essentially same! Specified in CHOWN_EXTRA change ownership of the namespace mapping issue that has been identified with Docker works on.... Than direct to the localhost of the machine why the definition of property. Clicking Post your Answer, you can set the CHOWN_EXTRA and -e CHOWN_EXTRA_OPTS in the of... The -v flag is used to mount the local volume onto the new users /home directory which is replaced the... Has been identified with Docker fermenting meat be kept cold, but not vegetables currently is the only is... Private knowledge with coworkers, Reach developers & technologists worldwide, I had that... Anything a dual bevel mitre saw can do that a table saw can not detail, and believe... Would space traders pick up and offload their goods docker volume mount issue an orbiting rather! With / the lines you did before, but not vegetables can change the ownership group! Is essentially the same ( i.e current behaviour now could we get it updated in example! Command on the host and it works but there is no way to see logs can tell, there a! The interactive output when it went to go create the logs of containers...: //octopus.com/docs/installation/octopus-in-container/octopus-server-container-windows ) the container such as Failed to change ownership at..

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