In the docker vignette/documentation, they give an example with a shiny app, but don't exactly specify what their parameters mean. Some of them are self explanatory, but others aren't. More specifically:
https://rstudio.github.io/renv/articles/docker.html
RENV_PATHS_CACHE_HOST=/opt/local/renv/cache
RENV_PATHS_CACHE_CONTAINER=/renv/cache
docker run --rm \
-e "RENV_PATHS_CACHE=${RENV_PATHS_CACHE_CONTAINER}" \
-v "${RENV_PATHS_CACHE_HOST}:${RENV_PATHS_CACHE_CONTAINER}" \
-p 14618:14618 \
R -s -e 'renv::restore(); shiny::runApp(host = "0.0.0.0", port = 14618)'
What is RENV_PATHS_CACHE_HOST?
And is RENV_PATHS_CACHE_CONTAINER the location of where my cache will be upon running the image instance/container?
I'm not entirely sure how to use this example, but feel I'll need it.
The example here tries to demonstrate how one might mount an renv cache from the host filesystem on to a Docker container.
In this case, RENV_PATHS_CACHE_HOST points to a (theoretical) cache directory on the host filesystem, at /opt/local/renv/cache, whereas RENV_PATHS_CACHE_CONTAINER points to the location in the container where the host cache will be visible.
Related
I use the geospatial rocker2 image to deploy Rstudio for development and a Shiny app for production. By using a single image, I have a consistent package library, credentials and database connections. I would like to use this same image to serve a plumber API.
Using the standard plumber.R example and the standard plumber Docker example I have tried to serve it as follows:
docker run -v `pwd`/app/plumber.R:/plumber.R --name plumber --restart=unless-stopped \
-p 8000:8000 my_rocker2_fork/geospatial Rscript /plumber.R
Success, kind of. The plumber.R file is clearly being sourced, but it is not being "plumbed":
Another issue is that the container continually restarts (this is the output of docker ps - please ignore the node.js container running):
One more oddity is that port 8000 isn't shown. Sometimes it is, sometimes it isn't. I think this is related to the restarting behaviour.
My code isn't plumbed, because I don't have the Entrypoint that is standard in the rstudio/plumber Dockerfile, and I don't think I want this Entrypoint, as it may cause issues with Rstudio Server and the Shiny app that are also in this image. Therefore, I think it is probably optimal to "plumb" by expanding the Rscript command at the end of my Docker run statement:
docker run -v `pwd`/app/plumber.R:/plumber.R -p 8000:8000 my_rocker2_fork/geospatial \
'Rscript pr("/plumber.R") %>% pr_run(port = 8000)' &
However, this fails because of all the special characters (like the pipe operator). How can I serve plumber code with an arbitrary Dockerfile without an Entrypoint?
The answer is simple! Call a script that sets the plumbing in motion, e.g.
docker run -v `pwd`/app/plumb_start.R:/plumb_start.R -p 8000:8000 my_rocker2_fork/geospatial \
Rscript plumb_start.R
Where plumb_start.R contains:
pr("plumber.R") %>% pr_run(port=8000)
Make sure that you also expose port 8000 in the Dockerfile.
I'm working on a read the docs documentation where I use docker. To customize it, I d like to share the css folder between the container and host, in order to avoid building always a new image to see the changes. The goal is, that I can just refresh the browser and see the changes.
I tried something like this, but it doesn't work:
docker run -v ~/docs/source/_static/css:/docs/source/_static/css -p 80:80 -it my-docu:latest
What is wrong in this command?
The path of the folder I'd like to share is:
Documents/my-documentation/docs/source/_static/css
Thanks for your help!
I'm guessing that the ~ does not resolve correctly. The tilde character ("~") refers to the home directory of your user; usually something like /home/your_username.
In your case, it sounds like your document isn't in this directory anyway.
Try:
docker run -v Documents/my-documentation/docs/source/_static/css:/docs/source/_static/css -p 80:80 -it my-docu:latest
I have no mac to test with, but I suspect the command should be as below (Documents is a subfolder to inside your home directory denoted by ~)
docker run -v ~/Documents/my-documentation/docs/source/_static/css:/docs/source/_static/css -p 80:80 -it my-docu:latest
In your OP you mount the host folder ~/docs/source/_static/css, which does not make sense if your files are in Documents/my-documentation/docs/source/_static/css as that would correspond to ~/Documents/my-documentation/docs/source/_static/css
Keep in mind that Docker is still running inside a VM on Mac, so you will need to give a host path that is valid on that VM
What you can do to get a better view of the situation is to start an interactive container where you mount the root file system of the host vm root into /mnt/vm-root. That way you can see what paths are available to mount and how they should be formatted when you pass them using the -v flag to the docker run command
docker run --rm -it -w /mnt/vm-root -v /:/mnt/vm-root ubuntu:latest bash
I'm trying to put my shiny app in docker container. My shiny app works totally fine on my local computer. But after dockerize my shiny app, I always have error message on my localhost like The application failed to start. The application exited during initialization..
I have no idea why that happens. I'm new to docker. How can I find the error logs when I run the docker image? I need the log to know what goes wrong.
Here is my dockfile:
# Install R version 3.6
FROM r-base:3.6.0
# Install Ubuntu packages
RUN apt-get update && apt-get install -y \
sudo \
gdebi-core \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev/unstable \
libxt-dev \
libssl-dev
# Download and install ShinyServer (latest version)
RUN wget --no-verbose https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/VERSION -O "version.txt" && \
VERSION=$(cat version.txt) && \
wget --no-verbose "https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
gdebi -n ss-latest.deb && \
rm -f version.txt ss-latest.deb
# Install R packages that are required
# TODO: add further package if you need!
RUN R -e "install.packages(c( 'tidyverse', 'ggplot2','shiny','shinydashboard', 'DT', 'plotly', 'RColorBrewer'), repos='http://cran.rstudio.com/')"
# Copy configuration files into the Docker image
COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
COPY /app /srv/shiny-server/
# Make the ShinyApp available at port 80
EXPOSE 80
# Copy further configuration files into the Docker image
COPY shiny-server.sh /usr/bin/shiny-server.sh
CMD ["/usr/bin/shiny-server.sh"]
I built image and ran like below:
docker build -t myshinyapp .
docker run -p 80:80 myshinyapp
Usually the logs for any (live or dead) container can be found by just using:
docker logs full-container-name
or
docker logs CONTAINERID
(replacing the actual ID of your container)
As first said, this usually works as well even for stopped (not still removed) containers, which you can list with:
docker container ls -a
or just
docker ps -a
However, sometimes you won't even have a log, since the container was never created at all (which I think, by experience, fits more to your case)
And it can be happening simply because the docker engine is unable to allocate all of the resources that your service definition is requiring to have available.
The application failed to start. The application exited during initialization
is usually reflect of your docker engine being unable to get the required resources.
And the most common case for that, is just as simple as your host ports:
If you have another service (being dockerized or not) using (for example) that port that you want to use for your service (in your case, port 80) then Docker would just be unable to start your container.
So... in short... the easiest fix for that situation (and your first try whenever you face this kind of issues) is just to bind any other port from your host (say: 8080), to that 80 port that your service will be listening to internally (inside your container):
docker run -p 8080:80 myshinyapp
The same principle applies to unallocatable volumes (e.g.: trying to bind a volume as read-only that doesn't actually exist in the host)
As an aside comment/trick:
Since you're not setting a name for your container, you will need to use the container id instead when looking for its logs.
But instead of typing (or copy-pasting) the full container id (usually something like: 1283c66babea or even larger) you can just type in a few first digits instead, and it will still work as expected:
docker logs 1283c6 or docker logs 1283 or even docker logs 128
(of course... as long as you don't have any other 128***** container)
The idea is simple, I need to send a signal from a container to another one to restart nginx.
Connect to the nginx container from the first one in ssh is a good solution?
Do you have other recommended ways for this?
I don't recommend installing ssh, Docker containers are not virtual machines, And should respect microservices architecture to benefit from many advantages it provides.
In order to send signal from one container to another, You can use docker API.
First you need to share /var/run/docker.sock between required containers.
docker run -d --name control -v /var/run/docker.sock:/var/run/docker.sock <Control Container>
to send signal to a container named nginx you can do the following:
echo -e "POST /containers/nginx/kill?signal=HUP HTTP/1.0\r\n" | \
nc -U /var/run/docker.sock
Another option is using a custom image, with a custom script, that checks nginx config files and if the hash is changed sends reload signal. This way, each time you change config, nginx will automatically reload, or You can reload manually using comments. these kind of scripts are common among kubernetes users. Following is an example:
nginx "$#"
oldcksum=`cksum /etc/nginx/conf.d/default.conf`
inotifywait -e modify,move,create,delete -mr --timefmt '%d/%m/%y %H:%M' --format '%T' \
/etc/nginx/conf.d/ | while read date time; do
newcksum=`cksum /etc/nginx/conf.d/default.conf`
if [ "$newcksum" != "$oldcksum" ]; then
echo "At ${time} on ${date}, config file update detected."
oldcksum=$newcksum
nginx -s reload
fi
done
Don't forget to install inotifywait package.
This question is inspired by Can you run GUI apps in a docker container?.
The basic idea is to run apps with audio and ui (vlc, firefox, skype, ...)
I was searching for docker containers using pulseaudio but all containers I found where using pulseaudio streaming over tcp.
(security sandboxing of the applications)
https://gist.github.com/hybris42/ce429de428e5af3a344a
https://github.com/jlund/docker-chrome-pulseaudio
https://github.com/tomparys/docker-skype-pulseaudio
In my case I would prefere playing audio from an app inside the container directly to my host pulseaudio. (without ssh tunneling and bloated docker images)
Pulseaudio because my qt app is using it ;)
it took me some time until i found out what is needed. (Ubuntu)
we start with the docker run command docker run -ti --rm myContainer sh -c "echo run something"
ALSA:
we need /dev/snd and some hardware access as it looks like.
when we put this together we have
docker run -ti --rm \
-v /dev/snd:/dev/snd \
--lxc-conf='lxc.cgroup.devices.allow = c 116:* rwm' \
myContainer sh -c "echo run something"`
In new docker versions without lxc flags you shoud use this:
docker run -ti --rm \
-v /dev/snd:/dev/snd \
--privileged \
myContainer sh -c "echo run something"`
PULSEAUDIO:
update: it may be enought to mount the pulseaudio socket within the container using -v option. this depends on your version and prefered access method. see other answers for the socket method.
Here we need basically /dev/shm, /etc/machine-id and /run/user/$uid/pulse. But that is not all (maybe because of Ubuntu and how they did it in the past). The envirorment variable XDG_RUNTIME_DIR has to be the same in the host system and in your docker container. You may also need /var/lib/dbus because some apps are accessing the machine id from here (may only containing a symbolic link to the 'real' machine id). And at least you may need the hidden home folder ~/.pulse for some temp data (i am not sure about this).
docker run -ti --rm \
-v /dev/shm:/dev/shm \
-v /etc/machine-id:/etc/machine-id \
-v /run/user/$uid/pulse:/run/user/$uid/pulse \
-v /var/lib/dbus:/var/lib/dbus \
-v ~/.pulse:/home/$dockerUsername/.pulse \
myContainer sh -c "echo run something"
In new docker versions you might need to add --privileged.
Of course you can combine both together and use it together with xServer ui forwarding like here: https://stackoverflow.com/a/28971413/2835523
Just to mention:
you can handle most of this (all without the used id) in the dockerfile
using uid=$(id -u) to get the user id and gid with id -g
creating a docker user with this id
create user script:
mkdir -p /home/$dockerUsername && \
echo "$dockerUsername:x:${uid}:${gid}:$dockerUsername,,,:/home/$dockerUsername:/bin/bash" >> /etc/passwd && \
echo "$dockerUsername:x:${uid}:" >> /etc/group && \
mkdir /etc/sudoers.d && \
echo "$dockerUsername ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/$dockerUsername && \
chmod 0440 /etc/sudoers.d/$dockerUsername && \
chown ${uid}:${gid} -R /home/$dockerUsername
Inspired by the links you've posted, I was able to create the following solution. It is as lightweight as I could get it. However, I'm not sure if it is (1) secure, and (2) entirely fits your use-case (as it still uses the network).
Install paprefson your host system, e.g. using sudo apt-get install paprefs on an Ubuntu machine.
Launch PulseAudio Preferences, go to the "Network Server" tab, and check the "Enable network access to local sound devices" checkbox [1]
Restart your computer. (Only restarting Pulseaudio didn't work for me on Ubuntu 14.10)
Install Pulseaudio in your container, e.g. sudo apt-get install -y pulseaudio
In your container, run export "PULSE_SERVER=tcp:<host IP address>:<host Pulseaudio port>". For example, export "PULSE_SERVER=tcp:172.16.86.13:4713" [2]. You can find out your IP address using ifconfig and the Pulseaudio port using pax11publish [1].
That's it. Step 5 should probably be automated if the IP address and Pulseaudio port are subject to change. Additionally, I'm not sure if Docker permanently stores environment variables like PULSE_SERVER: If it doesn't then you have to initialize it after each container start.
Suggestions to make my approach even better would be greatly appreciated, since I'm currently working on a similar problem as the OP.
References:
[1] https://github.com/jlund/docker-chrome-pulseaudio
[2] https://github.com/jlund/docker-chrome-pulseaudio/blob/master/Dockerfile
UPDATE (and probably the better solution):
This also works using a Unix socket instead of a TCP socket:
Start the container with -v /run/user/$UID/pulse/native:/path/to/pulseaudio/socket
In the container, run export "PULSE_SERVER=unix:/path/to/pulseaudio/socket"
The /path/to/pulseaudio/socket can be anything, for testing purposes I used /home/user/pulse.
Maybe it will even work with the same path as on the host (taking care of the $UID part) as the default socket, this way the ultimate solution would be -v /run/user/$UID/pulse/native:/run/user/<UID in container>/pulse; I haven't tested this however.
After trying most of the solutions described here I found only PulseAudio over network to be really working. However you can make it safe by keeping the authentication.
Install paprefs (on host machine):
$ apt-get install paprefs
Launch paprefs (PulseAudio Preferences) > Network Server > [X] Enable network access to local sound devices.
Restart PulseAudio:
$ service pulseaudio restart
Check it worked or restart machine:
$ (pax11publish || xprop -root PULSE_SERVER) | grep -Eo 'tcp:[^ ]*'
tcp:myhostname:4713
Now use that socket:
$ docker run \
-e PULSE_SERVER=tcp:$(hostname -i):4713 \
-e PULSE_COOKIE=/run/pulse/cookie \
-v ~/.config/pulse/cookie:/run/pulse/cookie \
...
Check that the user running inside the container has access to the cookie file ~/.config/pulse/cookie.
To test it works:
$ apt-get install mplayer
$ mplayer /usr/share/sounds/alsa/Front_Right.wav
For more info may check Docker Mopidy project.
Assuming pulseaudio is installed on host and in image, one can provide pulseaudio sound over tcp with only a few steps. pulseaudio does not need to be restarted, and no configuration has to be done on host or in image either. This way it is included in x11docker, without the need of VNC or SSH:
First, find a free tcp port:
read LOWERPORT UPPERPORT < /proc/sys/net/ipv4/ip_local_port_range
while : ; do
PULSE_PORT="`shuf -i $LOWERPORT-$UPPERPORT -n 1`"
ss -lpn | grep -q ":$PULSE_PORT " || break
done
Get ip adress of docker daemon. I always find it being 172.17.42.1/16
ip -4 -o a | grep docker0 | awk '{print $4}'
Load pulseaudio tcp module, authenticate connection to docker ip:
PULSE_MODULE_ID=$(pactl load-module module-native-protocol-tcp port=$PULSE_PORT auth-ip-acl=172.17.42.1/16)
On docker run, create environment variable PULSE_SERVER
docker run -e PULSE_SERVER=tcp:172.17.42.1:$PULSE_PORT yourimage
Afterwards, unload tcp module. (Note: for unknown reasons, unloading this module can stop pulseaudio daemon on host):
pactl unload-module $PULSE_MODULE_ID
Edit: How-To for ALSA and Pulseaudio in container
I managed to dockerize a Java game in the following ways, effectively passing through the game's sound.
This approach requires building an image, making sure the app has all the dependencies it'll need, in this case, pulseaudio and x11. If you're sure your images has everything it needs, you may procees as stated in the previous answers.
Here, we need to build the image, then we can actually launch it.
docker build -t my-unciv-image . # Run from directory where Dockerfile is
docker run --name unciv # image name\
--device /dev/dri \
-e DISPLAY=$DISPLAY \
-e PULSE_SERVER=unix:/run/user/1000/pulse/native \
--privileged \
-u $(id -u):$(id -g) \
-v /path/to/Unciv:/App \
-v /run/user/$(id -u)/pulse:/run/user/(id -u)/pulse \
-v /tmp/.X11-unix:/tmp/.X11-unix \
-w /App \
my-unciv-image \
java -jar /App/Unciv.jar
In the second command the following is specified:
--name: a name is given to the container
--device: video device*
-e: required environment vars
DISPLAY: the display number
PULSE_SERVER: PulseAudio audio server socket
--privileged: run ip privileged*, so it can access all devices
-v: Mounted volumes:
Path to the game mounted into /App in the container**
Audio server socke
Display server socket
-w: Working directory
Here is a docker-compose.yml version of it:
# docker-compose.yml
version: '3'
services:
unciv:
build: .
container_name: unciv
devices:
- /dev/dri:/dev/dri # * Either this
entrypoint: java -jar /App/Unciv.jar
environment:
- DISPLAY=$DISPLAY
- PULSE_SERVER=unix:/run/user/1000/pulse/native
privileged: true # * or this
user: 1000:1000
volumes:
- /path/to/game/:/App
- /run/user/1000/pulse:/run/user/1000/pulse
- /tmp/.X11-unix:/tmp/.X11-unix
working_dir: /App
FROM ubuntu:20.04
RUN apt-get update
RUN apt-get install openjdk-11-jre -y
RUN apt-get install -y xserver-xorg-video-all
RUN apt-get install -y libgl1-mesa-glx libgl1-mesa-dri
RUN apt-get install -y pulseaudio
USER unciv
Notes:
*Only required for a game or anything that uses openGL. Either passing the devices explicitly or running it as privileged, but I think it's enough to pass the device, making it privileged may be overkill.
**This math may be bundled with the docker image, but for a demo.
For the audio, it's required to pass env variable PULSE_SERVER and mounting the pulseaudio socket