On a previous post I discussed that I created a dockerfile for greta, and one of top of that for rstudio to use with nvidia-docker. Rstudio and greta work as expected. Alas, i cannot change the password for rstudio using -e PASSWORD='MYSUPERSECRETPASSWORD!!'.
This is the dockerfile for r and greta:
## Based on work by https://github.com/earthlab/dockerfiles/blob/master/r-greta/Dockerfile
## https://github.com/rocker-org/ml
## rocker
##
FROM nvidia/cuda:9.0-cudnn7-runtime
MAINTAINER "Ignacio Martinez" ignacio@protonmail.com
RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections
## Prepare R installation from
RUN sh -c 'echo "deb https://cloud.r-project.org/bin/linux/ubuntu xenial/" >> /etc/apt/sources.list' \
&& apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
RUN apt-get update \
&& apt-get upgrade -y -q \
&& apt-get install -y --no-install-recommends \
libapparmor1 \
r-base \
r-base-dev \
littler \
r-cran-littler \
libxml2-dev \
libxt-dev \
libssl-dev \
libcurl4-openssl-dev \
imagemagick \
python-pip \
libpython2.7 \
build-essential \
curl \
libfreetype6-dev \
libzmq3-dev \
pkg-config \
python \
python-dev \
rsync \
software-properties-common \
unzip \
htop \
&& Rscript -e "install.packages(c('littler', 'docopt'), repo = 'https://cloud.r-project.org')" \
&& ln -s /usr/local/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
&& ln -s /usr/local/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
&& ln -s /usr/local/lib/R/site-library/littler/bin/r /usr/local/bin/r \
&& \
apt-get clean && \
rm -rf /var/lib/apt/lists/* \
&& echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' >> /etc/R/Rprofile.site
RUN curl -O https://bootstrap.pypa.io/get-pip.py && \
python get-pip.py && \
rm get-pip.py
RUN pip --no-cache-dir install \
ipykernel \
jupyter \
matplotlib \
numpy \
scipy \
&& \
python -m ipykernel.kernelspec
RUN install2.r --error \
devtools
RUN R -e "devtools::install_github('rstudio/tensorflow')"
RUN R -e "devtools::install_github('rstudio/keras')"
RUN install2.r --error \
devtools \
rstan \
tictoc \
bayesplot \
DiagrammeR \
greta \
rgexf \
XML \
tidyverse
RUN pip install virtualenv
## Need to configure non-root user for RStudio
RUN useradd rstudio \
&& echo "rstudio:rstudio" | chpasswd \
&& mkdir /home/rstudio \
&& chown rstudio:rstudio /home/rstudio \
&& addgroup rstudio staff
USER rstudio
RUN R -e "tensorflow::install_tensorflow(version = 'gpu')"
USER root
and this is the dockerfile for rstudio:
FROM r-gpu
ARG RSTUDIO_VERSION
## Comment the next line to use the latest RStudio Server version by default
#ENV RSTUDIO_VERSION=${RSTUDIO_VERSION:-1.1.447}
ENV PATH=/usr/lib/rstudio-server/bin:$PATH
## Download and install RStudio server & dependencies
## Attempts to get detect latest version, otherwise falls back to version given in $VER
## Symlink pandoc, pandoc-citeproc so they are available system-wide
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
git \
libedit2 \
psmisc \
python-setuptools \
sudo \
wget \
&& RSTUDIO_LATEST=$(wget --no-check-certificate -qO- https://s3.amazonaws.com/rstudio-server/current.ver) \
&& [ -z "$RSTUDIO_VERSION" ] && RSTUDIO_VERSION=$RSTUDIO_LATEST || true \
&& wget -q http://download2.rstudio.org/rstudio-server-${RSTUDIO_VERSION}-amd64.deb \
&& dpkg -i rstudio-server-${RSTUDIO_VERSION}-amd64.deb \
&& rm rstudio-server-*-amd64.deb \
## Symlink pandoc & standard pandoc templates for use system-wide
&& ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc /usr/local/bin \
&& ln -s /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc /usr/local/bin \
&& git clone https://github.com/jgm/pandoc-templates \
&& mkdir -p /opt/pandoc/templates \
&& cp -r pandoc-templates*/* /opt/pandoc/templates && rm -rf pandoc-templates* \
&& mkdir /root/.pandoc && ln -s /opt/pandoc/templates /root/.pandoc/templates \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/ \
&& mkdir -p /usr/local/lib/R/etc \
## RStudio wants an /etc/R, will populate from $R_HOME/etc
&& mkdir -p /etc/R \
## Write config files in $R_HOME/etc
&& echo '\n\
\n# Configure httr to perform out-of-band authentication if HTTR_LOCALHOST \
\n# is not set since a redirect to localhost may not work depending upon \
\n# where this Docker container is running. \
\nif(is.na(Sys.getenv("HTTR_LOCALHOST", unset=NA))) { \
\n options(httr_oob_default = TRUE) \
\n}' >> /usr/local/lib/R/etc/Rprofile.site \
&& echo "PATH=${PATH}" >> /usr/local/lib/R/etc/Renviron \
## Prevent rstudio from deciding to use /usr/bin/R if a user apt-get installs a package
&& echo 'rsession-which-r=/usr/local/bin/R' >> /etc/rstudio/rserver.conf \
## use more robust file locking to avoid errors when using shared volumes:
&& echo 'lock-type=advisory' >> /etc/rstudio/file-locks \
## configure git not to request password each time
&& git config --system credential.helper 'cache --timeout=3600' \
&& git config --system push.default simple \
## Set up S6 init system
&& wget -P /tmp/ https://github.com/just-containers/s6-overlay/releases/download/v1.11.0.1/s6-overlay-amd64.tar.gz \
&& tar xzf /tmp/s6-overlay-amd64.tar.gz -C / \
&& mkdir -p /etc/services.d/rstudio \
&& echo '#!/usr/bin/with-contenv bash \
\n exec /usr/lib/rstudio-server/bin/rserver --server-daemonize 0' \
> /etc/services.d/rstudio/run \
&& echo '#!/bin/bash \
\n rstudio-server stop' \
> /etc/services.d/rstudio/finish
COPY userconf.sh /etc/cont-init.d/userconf
## running with "-e ADD=shiny" adds shiny server
COPY add_shiny.sh /etc/cont-init.d/add
COPY pam-helper.sh /usr/lib/rstudio-server/bin/pam-helper
RUN ln /usr/bin/R /usr/local/bin/R
EXPOSE 8787
CMD ["/usr/lib/rstudio-server/bin/rserver", "--server-daemonize=0", "--server-app-armor-enabled=0"]
From looking at the rockerdockerfile, my understanding is that userconf.sh should be doing the magic of changing the password. This are the commands that I run:
nvidia-docker build -t r-gpu .
nvidia-docker build -t rstudio-gpu .
nvidia-docker run -d --restart=always -p 8787:8787 --name="rstudio-gpu" -e PASSWORD='MYSUPERSECRETPASSWORD!!' rstudio-gpu
Alas, the password still rstudio. What am I missing?
Thanks!