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
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 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.
I built a Docker Image for an R Shiny App and ran the corresponding container with Docker Toolbox on Windows 10 Home. When trying to open the App with my web browser, only the index is shown. I don't know why the app isn't executed.
The log shows me this:
*** warning - no files are being watched ***
[2019-08-12T15:34:42.688] [INFO] shiny-server - Shiny Server v1.5.12.1 (Node.js v10.15.3)
[2019-08-12T15:34:42.704] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"
[2019-08-12T15:34:43.100] [INFO] shiny-server - Starting listener on http://[::]:3838
I already specified the app host-to-container path by executing the following command which refers to a docker hub image:
docker run --rm -p 3838:3838 -v /C/Docker/App/:/srv/shinyserver/ -v /C/Docker/shinylog:/var/log/shiny-server/ didsh123/ps_app:heatmap
My Docker File looks like the following:
# get shiny serves plus tidyverse packages image
FROM rocker/shiny-verse:latest
# system libraries of general use
RUN apt-get update && apt-get install -y \
sudo \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev \
libxt-dev \
libssl-dev \
libssh2-1-dev
##Install R packages that are required--> were already succesfull
RUN R -e "install.packages(c('shinydashboard','shiny', 'plotly', 'dplyr', 'magrittr'))"
#Heatmap related packages
RUN R -e "install.packages('gpclib', type='source')"
RUN R -e "install.packages('rgeos', type='source')"
RUN R -e "install.packages('rgdal', type='source')"
# copy app to image
COPY ./App /srv/shiny-server/App
# add .conf file to image/container to preserve log file
COPY ./shiny-server.conf /etc/shiny-server/shiny-server.conf
##When run image and create a container, this container will listen on port 3838
EXPOSE 3838
###Avoiding running as root --> run container as user instead
# allow permission
RUN sudo chown -R shiny:shiny /srv/shiny-server
# execute in the following as user --> imortant to give permission before that step
USER shiny
##run app
CMD ["/usr/bin/shiny-server.sh"]
So when I address the docker ip and the assessed port in the browser, the app should run there, but only the index is displayed. I use the following line:
http://192.168.99.100:3838/App/
I'm glad for every hint or advice. I'm new to Docker, so I'm also happy for detailed explanations.
To use shiny with docker, I suggest you use the golem package. golem provides a framework for builing shiny apps. If you have an app developed according to their framework, the function golem::add_dockerfile() can be used to create dockerfiles automatically.
If you are not interested in a framework, You can still have a look at the source for add_dockerfile() to see how they manage the deployment. Their strategy is to use shiny::runApp() with the port argument. Therefore, shiny-server is not necessary in this case.
The Dockerfile in golem looks roughly like this
FROM rocker/tidyverse:3.6.1
RUN R -e 'install.packages("shiny")'
COPY app.R /app.R
EXPOSE 3838
CMD R -e 'shiny::runApp("app.R", port = 3838, host = "0.0.0.0")'
This will make the app available on port 3838. Of course, you will have to install any other R packages and system dependencies.
Additional tips
To increase reproducibility, I would suggest you use remotes::install_version() instead of install.packages().
If you are going to deploy several applications with similar dependencies (for example shinydashboard), it makes sense to write your own base image that can be used in place of rocker/tidyverse:3.6.1. This way, your builds will be much quicker.
Minimal Reproducible Example
Create an empty directory (can be called anything you want)
Inside it, create two things:
i. A file called Dockerfile
ii. An empty directory called app
Place your shiny app inside the directory called app.
Your shiny app can be a single app.R file, or, for older shiny apps, ui.R and server.R. Either way is fine (see here for more on that).
If unsure about any of the above, just copy the files found here.
Place this in Dockerfile
FROM rocker/shiny:latest
COPY ./app/* /srv/shiny-server/
CMD ["/usr/bin/shiny-server"]
In the terminal, cd to the root of the empty directory you created in step 1, and build the image with
docker build -t shinyimage .
Run the container with
docker run -p 3838:3838 shinyimage
Finally, visit this url to see your shiny app: http://localhost:3838/
Here's a copy of all of the above in case anything's unclear.
Check the logs for any useful information? And exec into the container to verify if the App content is copied to the correct location.
Because the way /App content is copied looks incorrect
The content of /App is copied into the image to /srv/shiny-server/App during the build phase and you are trying to override /srv/shiny-server content using -v option when running the container.
Looks like during runtime the App data copied is being overwritten.
Try without -v /C/Docker/App/:/srv/shinyserver/ or use -v /C/Docker/App/:/srv/shinyserver/App/
docker run --rm -p 3838:3838 -v /C/Docker/shinylog:/var/log/shiny-server/ didsh123/ps_app:heatmap
There are a ton of little-upvoted questions about how to address local folders from inside a docker container, but I can't find one that quite matches mine, so here goes another one:
How can I run a docker container, and mount a local folder so that it's accessible by R/RStudio, inside the container?
That sounds kind of like: mounting local home directory in Rstudio docker? and using an approach similar to that, I can start a container and mount a volume:
docker run -d -p 8787:8787 -v $HOME/my_folder:/LOOKATMEEE -e ROOT=TRUE rocker/tidyverse:3.4
and if I run a bash shell in the container, I can see the folder:
docker exec -it 38b2d6ca427f bash
> ls
bin dev home lib LOOKATMEEE mnt proc run srv tmp var boot etc init lib64 media opt root sbin sys usr
# ^ there is is!
But if I go connect to RStudio server at localhost:8787, I don't see it in the files pane, nor does it show up when run list.files() in the R console:
I'm sure I'm missing something basic, but if someone can tell me what that is... thank you!
In this circumstance, R and RStudio have a default working directory of /home/rstudio, two levels down from /, where I was telling docker to mount the folder.
After the docker run command in the question, you can go list.files('/') to see the folder.
If you want your folder to show up in the default working directory for R, as I do, then modify docker run like this:
docker run -d -p 8787:8787 -v $HOME/my_folder:/home/rstudio/LOOKATMEEE -e ROOT=TRUE rocker/tidyverse:3.4
and there it shall be:
Thank you to user alistaire.
This answer is for future generations :)
The concept is a "match" of the resource from the host with the container:
:
The command structure should be like this:
docker run -d -e PASSWORD= -p 8787:8787 -v
: /home/rstudio/ rocker/rstudio
Check the explanation here
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.