I am trying to run a docker image, but it will not stay running.
cd /Users/emma/Documents/examples/question-1 .
docker build -t q1-model:v1 .
docker run \
-v $(pwd)/synthetic_data:/data:ro \
-v $(pwd)/output:/output:rw \
-v $(pwd)/scratch:/scratch:rw \
awesome-covid19-q1-model:v1 R /app/model-1.r
On docker desktop, I can see the image, but it says it has been "exited," and when I try to click the "start" arrow to run it, it only runs for a second and then goes back to "exited."
Does anyone know what I am doing wrong here?
Thank you
Try appending to the end of your command && sleep infinity.
If your container does not die, it means that your command is running for a couple of seconds and finishing,and after that the container is killed as well.
Try running the container in detached mode by using the -d flag.
Related
I'm trying to put my shiny app in docker container. My shiny app works totally fine on my local computer. But after dockerize my shiny app, I always have error message on my localhost like The application failed to start. The application exited during initialization..
I have no idea why that happens. I'm new to docker. How can I find the error logs when I run the docker image? I need the log to know what goes wrong.
Here is my dockfile:
# Install R version 3.6
FROM r-base:3.6.0
# Install Ubuntu packages
RUN apt-get update && apt-get install -y \
sudo \
gdebi-core \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev/unstable \
libxt-dev \
libssl-dev
# Download and install ShinyServer (latest version)
RUN wget --no-verbose https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/VERSION -O "version.txt" && \
VERSION=$(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)
I am new to docker (working on OSX) and am trying to run R scripts within it and came across a hurdle when tried to create plots in a loop with docker. The code recurrently calls a script like that:
pdf(plotname)
boxplot(X)
dev.off()
The routine seems to work and does not produce any error message, but the plots are not created.
Any suggestions as to how to overcome this?
Original docker run
#!/bin/bash
docker run -vpwd"/data":/data -ti jbms/fuzzycmeans $1
$1 is the datafilename
Thank you in advance
Edit: This answer require further information to get the container working on OSX.
Share your X11 display to the docker container:
docker run -it \
-v /tmp/.X11-unix:/tmp/.X11-unix \
-e DISPLAY=unix$DISPLAY \
# the rest of your docker run
So it is able to open graphics windows
I'm looking for how to install Graphicsmagick at Meteor Up Docker.
I found this solution (Access binaries inside docker) but I couldn't make work, where do I put those lines at start.sh?
meteorDockerId=docker ps | grep meteorhacks/meteord:base | awk '{print $1}'
docker exec $meteorDockerId apt-get install graphicsmagick -y
That's my start.sh:
#!/bin/bash
APPNAME=instagatas
APP_PATH=/opt/$APPNAME
BUNDLE_PATH=$APP_PATH/current
ENV_FILE=$APP_PATH/config/env.list
PORT=80
USE_LOCAL_MONGO=0
# remove previous version of the app, if exists
docker rm -f $APPNAME
# remove frontend container if exists
docker rm -f $APPNAME-frontend
set -e
docker pull meteorhacks/meteord:base
if [ "$USE_LOCAL_MONGO" == "1" ]; then
docker run \
-d \
--restart=always \
--publish=$PORT:80 \
--volume=$BUNDLE_PATH:/bundle \
--env-file=$ENV_FILE \
--link=mongodb:mongodb \
--hostname="$HOSTNAME-$APPNAME" \
--env=MONGO_URL=mongodb://mongodb:27017/$APPNAME \
--name=$APPNAME \
meteorhacks/meteord:base
else
docker run \
-d \
--restart=always \
--publish=$PORT:80 \
--volume=$BUNDLE_PATH:/bundle \
--hostname="$HOSTNAME-$APPNAME" \
--env-file=$ENV_FILE \
--name=$APPNAME \
meteorhacks/meteord:base
fi
docker pull meteorhacks/mup-frontend-server:latest
docker run \
-d \
--restart=always \
--volume=/opt/$APPNAME/config/bundle.crt:/bundle.crt \
--volume=/opt/$APPNAME/config/private.key:/private.key \
--link=$APPNAME:backend \
--publish=443:443 \
--name=$APPNAME-frontend \
meteorhacks/mup-frontend-server /start.sh
Re-installing the graphicsmagick package every time you re-start the containers seems like a hack I wouldn't want to do.
If you're modifying the start script already, might as well use a Dockerfile:
FROM meteorhacks/meteord:base
RUN apt-get install graphicsmagick -y
Then modify start.sh template to build a new docker image with graphicsmagick, tag it and use that image instead:
see: https://gist.github.com/so0k/7d4be21c5e2d9abd3743/revisions
EDIT: Where to put Dockerfile?
start.sh template is copied to /opt/<appName>/config/, currently the Dockerfile would need to be in that same directory (/opt/<appName>/config/Dockerfile)
see Linux init Task
Alternatively, you can specify specific Dockerfile with the -f flag for the docker build
Or your third option is to pipe Dockerfile to docker build using a here document
I've updated the start.sh gist, we no longer pull the meteord:base image and build it instead:
docker build -t meteorhacks/meteord:app - << EOF
FROM meteorhacks/meteord:base
RUN apt-get install graphicsmagick -y
EOF
The docker build will run every time, but as long as the requirements aren't changing, docker will use the docker images it cached.
The development Version of Meteor Up at Kadirahq allows specification of a custom Docker Image in the config file (mup.js).
MeteorD-Images with Graphicsmagick installed are available on Docker Hub.
This got me a working deployment (Meteor 1.3.2.4, Meter Up 309cefb, Node v5.4.1):
mup.js:
module.exports = {
…
meteor: {
dockerImage: 'ianmartorell/meteord-graphicsmagick',
…
},
};
I couldn't get the docker image that #bskp mentioned to work, so I figured out how to write one that uses abernix/meteord:base and then has graphicsmagick installed. Very simple, but it seems to be working for me on Meteor 1.4.1.1
I just did this in my mup.js file
docker: {
image: "joshjoe/meteor-graphicsmagick",
},
This was a huge pain to get working, so I'd be happy to help anyone who is struggling with this.
https://github.com/c316/meteor-graphicsmagick
If the if statement successes, you should be able to see a running container corresponding to the image you are grepping. In my opinion you can add the two lines after the fi to obtain the environment variable.
Build an image for get things right, but you can do temporary:
docker exec -it MeteorAppName apt-get install imagemagick -y
docker restart MeteorAppName
Check imagemagick: docker exec -it MeteorAppName convert -version
Why don't you add the following package meteor add cfs:graphicsmagick
https://atmospherejs.com/cfs/graphicsmagick
It tries to make sure Graphicsmagick is available. It worked for my use case i think it will work with docker too.
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
I'm setting up a simple image: one that holds Riak (a NoSQL database). The image starts the Riak service with riak start as a CMD. Now, if I run it as a daemon with docker run -d quintenk/riak-dev, it does start the Riak process (I can see that in the logs). However, it closes automatically after a few seconds. If I run it using docker run -i -t quintenk/riak-dev /bin/bash the riak process is not started (UPDATE: see answers for an explanation for this). In fact, no services are running at all. I can start it manually using the terminal, but I would like Riak to start automatically. I figure this behavior would occur for other services as well, Riak is just an example.
So, running/restarting the container should automatically start Riak. What is the correct approach of setting this up?
For reference, here is the Dockerfile with which the image can be created (UPDATE: altered using the chosen answer):
FROM ubuntu:12.04
RUN apt-get update
RUN apt-get install -y openssh-server curl
RUN curl http://apt.basho.com/gpg/basho.apt.key | apt-key add -
RUN bash -c "echo deb http://apt.basho.com precise main > /etc/apt/sources.list.d/basho.list"
RUN apt-get update
RUN apt-get -y install riak
RUN perl -p -i -e 's/(?<=\{http,\s\[\s\{")127\.0\.0\.1/0.0.0.0/g' /etc/riak/app.config
EXPOSE 8098
CMD /bin/riak start && tail -F /var/log/riak/erlang.log.1
EDIT: -f changed to -F in CMD in accordance to sesm his remark
MY OWN ANSWER
After working with Docker for some time I picked up the habit of using supervisord to tun my processes. If you would like example code for that, check out https://github.com/Krijger/docker-cookbooks. I use my supervisor image as a base for all my other images. I blogged on using supervisor here.
To keep docker containers running, you need to keep a process active in the foreground.
So you could probably replace that last line in your Dockerfile with
CMD /bin/riak console
Or even
CMD /bin/riak start && tail -F /var/log/riak/erlang.log.1
Note that you can't have multiple lines of CMD statements, only the last one gets run.
Using tail to keep container alive is a hack. Also, note, that with -f option container will terminate when log rotation happens (this can be avoided by using -F instead).
A better solution is to use supervisor. Take a look at this tutorial about running Riak in a Docker container.
The explanation for:
If I run it using docker run -i -t quintenk/riak-dev /bin/bash the riak process is not started
is as follows. Using CMD in the Dockerfile is actually the same functionality as starting the container using docker run {image} {command}. As Gigablah remarked only the last CMD is used, so the one written in the Dockerfile is overwritten in this case.
By using CMD /bin/riak start && tail -f /var/log/riak/erlang.log.1 in the Buildfile, you can start the container as a background process using docker run -d {image}, which works like a charm.
"If I run it using docker run -i -t quintenk/riak-dev /bin/bash the riak process is not started"
It sounds like you only want to be able to monitor the log when you attach to the container. My use case is a little different in that I want commands started automatically, but I want to be able to attach to the container and be in a bash shell. I was able to solve both of our problems as follows:
In the image/container, add the commands you want automatically started to the end of the /etc/bash.bashrc file.
In your case just add the line /bin/riak start && tail -F /var/log/riak/erlang.log.1, or put /bin/riak start and tail -F /var/log/riak/erlang.log.1 on separate lines depending on the functionality desired.
Now commit your changes to your container, and run it again with: docker run -i -t quintenk/riak-dev /bin/bash. You'll find the commands you put in the bashrc are already running as you attach.
Because I want a clean way to have the process exit later I make the last command a call to the shell's read which causes that process to block until I later attach to it and hit enter.
arthur#macro:~/docker$ sudo docker run -d -t -i -v /raid:/raid -p 4040:4040 subsonic /bin/bash -c 'service subsonic start && read -p "waiting"'
WARNING: Docker detected local DNS server on resolv.conf. Using default external servers: [8.8.8.8 8.8.4.4]
f27229a260c9
arthur#macro:~/docker$ sudo docker ps
[sudo] password for arthur:
ID IMAGE COMMAND CREATED STATUS PORTS
35f253bdf45a subsonic:latest /bin/bash -c service 2 days ago Up 2 days 4040->4040
arthur#macro:~/docker$ sudo docker attach 35f253bdf45a
arthur#macro:~/docker$ sudo docker ps
ID IMAGE COMMAND CREATED STATUS PORTS
as you can see the container exits after you attach to it and unblock the read.
You can of course use a more sophisticated script than read -p if you need to do other clean up, such as stopping services and saving logs etc.
I use a simple trick whenever I start building a new docker container. To keep it alive, I use a ping in the entrypoint script.
So in the Dockerfile, when using debian, for instance, I make sure I can ping.
This is btw, always nice, to check what is accessible from within the container.
...
RUN DEBIAN_FRONTEND=noninteractive apt-get update \
&& apt-get install -y iputils-ping
...
ENTRYPOINT ["entrypoint.sh"]
And in the entrypoint.sh file
#!/bin/bash
...
ping 10.10.0.1 >/dev/null 2>/dev/null
I use this instead of CMD bash, as I always wind up using a startup file.