Bottom line: output from container is not appearing in mounted local directory
I have read the documentation for bind mounts and on another project had success with this.
My docker file:
FROM ubuntu:18.04
RUN apt-get update && apt-get install -yq build-essential autoconf libnetcdf-dev libxml2-dev libproj-dev valgrind wget unzip git nano
# pulls ADBM from github and unzips in folder ADMBcode
RUN mkdir /ADMBcode
RUN wget https://github.com/admb-project/admb/releases/download/admb-12.2/admb-12.2-linux.zip
RUN mv admb-12.2-linux.zip /ADMBcode
RUN unzip ADMBcode/admb-12.2-linux.zip -d /ADMBcode
# pulls hydra repo from github into folder HYDRA
RUN mkdir /HYDRA
RUN git clone https://github.com/NOAA-EDAB/hydra_sim.git /HYDRA
# compiles and runs model
WORKDIR /HYDRA
RUN /ADMBcode/admb-12.2/admb hydra_sim.tpl
RUN ./hydra_sim
# create dir for output and move output
#RUN mkdir -p /HYDRA/output/diagnostics
#RUN mkdir /HYDRA/output/indices
# moves output to folder to be mounted
RUN mv *.out /HYDRA/output/diagnostics
RUN mv *.txt /HYDRA/output/indices
I build the image
podman build -t hydra .
and run the container using the following :
podman run --rm --name hydra --mount "type=bind,src=/path_on_local_machine/test,dst=/HYDRA/output" hydra
I have test folder on my local machine but the output is not mounted.
I have entered the container
podman run -it hydra
and checked that the output is there
I have done this before for another model and everything behaved. Not sure why this is not.
Any ideas what i am doing wrong?
Thanks
However
I am trying to run a shiny application on an open port on my server. I usually run docker images using command docker run -p 4000:3838 tag_name, assuming that docker container has exposed port, and shiny app is running at this port.
This all works completely fine for any shiny application that is using http. But I need https.
So the Dockerfile I use consists of:
FROM rocker/r-ver:4.0.1
# System libs:
RUN apt-get update
RUN apt-get install -y libcurl4-openssl-dev
RUN apt-get install -y libssl-dev
RUN apt-get install -y zlib1g-dev
RUN apt-get install -y libxml2-dev
# R packages installed
RUN R -e "install.packages('remotes')"
RUN R -e "remotes::install_version('searchConsoleR')"
RUN R -e "remotes::install_version('googleAuthR')"
# [...] more R libraries are installed
# Copy application files to a dir
RUN mkdir /root/app
COPY . /root/app
# Expose and set run command from dir above
EXPOSE 3838
CMD ["R", "-e", "shiny::runApp('/root/app', port = 3838, host = '0.0.0.0')"]
Then I execute docker build -t tag_name . and docker run -p 4000:3838 tag_name.
The page is available at http://server.host:4000
However, since I am using Google Login, I need to use https. But when I visit server's https://server.host:4000 I see an error of page not existing.
Can someone please help?
I have a Docker container running a shiny app (Dockerfile here).
Shiny server logs are output to stdout and application logs are written to /var/log/shiny-server. I'm deploying this container to AWS Fargate and logging applications only display stdout which makes debugging an application when deployed challenging. I'd like to write the application logs to stdout.
I've tried a number of potential solutions:
I've tried the solution provided here, but have had no luck.. I added the exec xtail /var/log/shiny-server/ to my shiny-server.sh as the last line in the file. App logs are not written to stdout
I noticed that writing application logs to stdout is now the default behavior in rocker/shiny, but as I'm using rocker/verse:3.6.2 (upgraded from 3.6.0 today) along with RUN export ADD=shiny, I don't think this is standard behavior for the rocker/verse:3.6.2 container with Shiny add-on. As a result, I don't get the default behavior out of the box.
This issue on github suggests an alternative method of forcing application logging to stdout by way of an environment variable SHINY_LOG_STDERR=1 set at runtime but I'm not Linux-savvy enough to know where that env variable needs to be set to be effective. I found this documentation from Shiny Server v1.5.13 which gave suggestions in which file to set the environment variable depending on Linux distro; however, the output from my container when I run cat /etc/os-release is:
which doesn't really line up with any of the distributions in the Shiny Server documentation, thus making the documentation unhelpful.
I tried adding adding the environment variable from the github issue above in the docker run command, i.e.,
docker run --rm -e SHINY_LOG_STDERR=1 -p 3838:3838 [my image]
as well as
docker run --rm -e APPLICATION_LOGS_TO_STDOUT=true -p 3838:3838 [my image]
and am still not getting the logs to stdout.
I must be missing something here. Can someone help me identify how to successfully get application logs to stdout successfully?
You can add the line ENV SHINY_LOG_STDERR=1 to your Dockerfile (at least, this works with rocker/shiny, not sure about rocker/verse), such as with your Dockerfile:
FROM rocker/verse:3.6.2
## Add shiny capabilities to container
RUN export ADD=shiny && bash /etc/cont-init.d/add
## Install curl and xtail
RUN apt-get update && apt-get install -y \
curl \
xtail
## Add pip3 and other Python packages
RUN sudo apt-get update -y && apt-get install -y python3-pip
RUN pip3 install boto3
## Add R packages
RUN R -e "install.packages(c('shiny', 'tidyverse', 'tidyselect', 'knitr', 'rmarkdown', 'jsonlite', 'odbc', 'dbplyr', 'RMySQL', 'DBI', 'pander', 'sciplot', 'lubridate', 'zoo', 'stringr', 'stringi', 'openxlsx', 'promises', 'future', 'scales', 'ggplot2', 'zip', 'Cairo', 'tinytex', 'reticulate'), repos = 'https://cran.rstudio.com/')"
## Update and install
RUN tlmgr update --self --all
RUN tlmgr install ms
RUN tlmgr install beamer
RUN tlmgr install pgf
#Copy app dir and theme dirs to their respective locations
COPY iarr /srv/shiny-server/iarr
COPY iarr/reports/interim_annual_report/theme/SwCustom /opt/TinyTeX/texmf-dist/tex/latex/beamer/
#Force texlive to find my custom beamer theme
RUN texhash
EXPOSE 3838
## Add shiny-server information
COPY shiny-server.sh /usr/bin/shiny-server.sh
COPY shiny-customized.config /etc/shiny-server/shiny-server.conf
## Add dos2unix to eliminate Win-style line-endings and run
RUN apt-get update -y && apt-get install -y dos2unix
RUN dos2unix /usr/bin/shiny-server.sh && apt-get --purge remove -y dos2unix && rm -rf /var/lib/apt/lists/*
# Enable Logging from stdout
ENV SHINY_LOG_STDERR=1
RUN ["chmod", "+x", "/usr/bin/shiny-server.sh"]
CMD ["/usr/bin/shiny-server.sh"]
I want to mount a Cloud Filestore instance in a GCP AI Platform Jupyter notebook instance so that I don't have to upload all of my data into the notebook.
I followed the instructions at https://cloud.google.com/filestore/docs/mounting-fileshares, but get these error messages:
root#0084329abd1b:/home# mount <IP_ADDRESS>:/streams cfs
mount.nfs: rpc.statd is not running but is required for remote locking.
mount.nfs: Either use '-o nolock' to keep locks local, or start statd.
root#0084329abd1b:/home# mount -o nolock <IP_ADDRESS>:/streams cfs
mount.nfs: Operation not permitted
From your terminal, you can do something like this.
mkdir des_bucket
gcsfuse --debug_gcs --implicit-dirs src_bucket des_bucket
Create a Filestore instance link
Crerate a Google VM instance link
Create a Notebook AI instance link
On the VM instance run the commands:
sudo apt-get -y update
sudo apt-get -y install nfs-common
sudo mkdir test
# fileshare remote target
sudo mount 111.11.111.11:/fileshare test
sudo chmod go+rw test
echo 'This is a test' > test/testfile
ls test
#testfile
On the Notebook AI instance run the commands link:
sudo apt-get -y update
sudo apt-get -y install nfs-common
sudo mkdir test
# fileshare remote target
sudo mount 111.11.111.11:/fileshare /test
ls test
#testfile
You can also check link
i have a ubuntu machine that hosts a docker container.
and in the docker container i am running a web service which must validate
the user's password with the docker host's /etc/password.
my view is to ssh into docker host from the docker container.
so when i run command ssh in the docker container its saying ssh not found.
so,basically ssh is not installed in the container.
how can i install ssh in the container.
is there any way to accomplish this scenario?.
Well, as part of the image file you'll simply have to install openssh-server:
sudo apt-get install openssh-server
The problem then is that traditionally, a running docker container will only run a single command. You can get around this problem by using something like supervisord. There's an example in the docker docs: https://docs.docker.com/engine/admin/using_supervisord/
Your dockerfile might look like this:
FROM ubuntu:16.04
MAINTAINER examples#docker.com
RUN apt-get update && apt-get install -y openssh-server apache2 supervisor
RUN mkdir -p /var/lock/apache2 /var/run/apache2 /var/run/sshd /var/log/supervisor
COPY supervisord.conf /etc/supervisor/conf.d/supervisord.conf
EXPOSE 22 80
CMD ["/usr/bin/supervisord"]
Your supervisord.conf might look something like this:
[supervisord]
nodaemon=true
[program:sshd]
command=/usr/sbin/sshd -D
[program:apache2]
command=/bin/bash -c "source /etc/apache2/envvars && exec /usr/sbin/apache2 -DFOREGROUND"