Shiny app (leafviz) in docker container not loading in browser - docker

I am building a docker container to use the Leafcutter and Leafviz analysis tools. The final visualization commanded from an R file uses shiny app, it works fine on my machine but when ran in the container I can't connect to it.
I run the container with the following line of code:
docker run -dit --name leaf --rm -p 1234:1234 leafcutter
All is in order when I check with docker ps:
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
783f550df965 leafcutter "bash" 2 minutes ago Up 2 minutes 0.0.0.0:1234->1234/tcp, :::1234->1234/tcp leaf
Executing the pipeline in the container calls several snakefiles, and the last rule of the last one calls the R file:
Rscript /path/to/run_leafviz.R -i {input}
That script calls several functions before calling leafviz() which basically just runs the shiny app, I've modified the options like so:
shiny::runApp(launch.browser=FALSE, appDir = system.file("application", package = "leafviz"), host = "0.0.0.0", port = 1234)
All the shiny files and packages are installed with the R leafviz package. When I execute my container all goes fine, the output shows "Listening on http://0.0.0.0:1234", but when I try to connect I get the "connexion failed" page.
My Dockerfile is fairly large but here are the most relevant parts:
FROM ubuntu:22.04
ENV DEBIAN_FRONTEND noninteractive
#Install Ubuntu packages
RUN apt-get update && apt-get install \
-y cmake -y curl \
-y default-jre \
-y gdebi-core \
-y less -y libarchive13 -y libbz2-dev -y libcairo2-dev -y libcurl4-openssl-dev -y libgsl-dev \
-y liblzma-dev -y libncurses5-dev -y libncursesw5-dev -y libssl-dev -y libxml2-dev -y libxt-dev \
-y pandoc -y pandoc-citeproc -y python-pip \
-y tabix \
-y unzip \
-y wget \
-y zlib1g-dev \
&& rm -rf /var/lib/apt/lists/*
#Install conda, snakemake, samtools, regtools...
#[...]
#Install R
LABEL org.label-schema.license="GPL-2.0" \
org.label-schema.vcs-url="https://github.com/rocker-org/r-apt" \
org.label-schema.vendor="Rocker Project" \
maintainer="Dirk Eddelbuettel <edd#debian.org>"
RUN useradd docker \
&& mkdir /home/docker \
&& chown docker:docker /home/docker \
&& addgroup docker staff
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
littler r-base r-base-dev r-recommended r-cran-docopt
RUN ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
&& ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
&& ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
&& ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
&& rm -rf /var/lib/apt/lists/*
#Install shiny server (I have tried with and without this RUN command)
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
EXPOSE 1234
#Install R packages
COPY install_packages.R /tmp/install_packages.R
RUN Rscript /tmp/install_packages.R
CMD ["bash"]
I've been learning docker quite chaotically so I don't know if some elements are clashing, but I have exposed the container port and published it to the host and no error message seems to indicate there is a problem coming from somewhere else. I would really appreciate some help.

Related

Kartoza Geoserver on Heroku

I am new to docker and not an IT-specialist. I try to install Kartoza Geoserver in Docker on Heroku, but so far no success. Does anyone has experience with this and can explain me the settings in the dockerfile and the steps specifically for a Heroku install?
So far I tried a build with a modified dockerfile but I always get the same error (in the log trail) when opening/launching geoserver on Heroku:
"Error: groupadd: cannot open /etc/group".
I guess it is an permission/privileges issue.
Any sharing of experience on modifying the docker file so that the image is read by Heroku would be helpfull.
Modifying the settings in the dockerfile:
Removed the port forwarding from dockerfile
Add RUN adduser -D myuser USER myuser to dockerfile
Result dockerfile:
#--------- Generic stuff all our Dockerfiles should start with so we get caching ------------
ARG IMAGE_VERSION=9.0.65-jdk11-openjdk-slim-buster
ARG JAVA_HOME=/usr/local/openjdk-11
FROM tomcat:$IMAGE_VERSION
LABEL maintainer="Tim Sutton<tim#linfiniti.com>"
ARG GS_VERSION=2.22.0
ARG WAR_URL=https://downloads.sourceforge.net/project/geoserver/GeoServer/${GS_VERSION}/geoserver-${GS_VERSION}-war.zip
ARG STABLE_PLUGIN_BASE_URL=https://sourceforge.net/projects/geoserver/files/GeoServer
ARG DOWNLOAD_ALL_STABLE_EXTENSIONS=1
ARG DOWNLOAD_ALL_COMMUNITY_EXTENSIONS=1
ARG HTTPS_PORT=8443
ENV DEBIAN_FRONTEND=noninteractive
#Install extra fonts to use with sld font markers
RUN adduser -D myuser
USER myuser
RUN set -eux; \
apt-get update; \
apt-get -y --no-install-recommends install \
locales gnupg2 wget ca-certificates rpl pwgen software-properties-common iputils-ping \
apt-transport-https curl gettext fonts-cantarell lmodern ttf-aenigma \
ttf-bitstream-vera ttf-sjfonts tv-fonts libapr1-dev libssl-dev \
wget zip unzip curl xsltproc certbot cabextract gettext postgresql-client figlet gosu gdal-bin; \
# Install gdal3 - bullseye doesn't build libgdal-java anymore so we can't upgrade
curl https://deb.meteo.guru/velivole-keyring.asc | apt-key add - \
&& echo "deb https://deb.meteo.guru/debian buster main" > /etc/apt/sources.list.d/meteo.guru.list \
&& apt-get update \
&& apt-get -y --no-install-recommends install gdal-bin libgdal-java; \
dpkg-divert --local --rename --add /sbin/initctl \
&& (echo "Yes, do as I say!" | apt-get remove --force-yes login) \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*; \
# verify that the binary works
gosu nobody true
ENV \
JAVA_HOME=${JAVA_HOME} \
DEBIAN_FRONTEND=noninteractive \
GEOSERVER_DATA_DIR=/opt/geoserver/data_dir \
GDAL_DATA=/usr/share/gdal \
LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/tomcat/native-jni-lib:/usr/lib/jni:/usr/local/apr/lib:/opt/libjpeg-turbo/lib64:/usr/lib:/usr/lib/x86_64-linux-gnu" \
FOOTPRINTS_DATA_DIR=/opt/footprints_dir \
GEOWEBCACHE_CACHE_DIR=/opt/geoserver/data_dir/gwc \
CERT_DIR=/etc/certs \
RANDFILE=/etc/certs/.rnd \
FONTS_DIR=/opt/fonts \
GEOSERVER_HOME=/geoserver \
EXTRA_CONFIG_DIR=/settings \
COMMUNITY_PLUGINS_DIR=/community_plugins \
STABLE_PLUGINS_DIR=/stable_plugins
WORKDIR /scripts
ADD resources /tmp/resources
ADD build_data /build_data
ADD scripts /scripts
RUN echo $GS_VERSION > /scripts/geoserver_version.txt ;\
chmod +x /scripts/*.sh;/scripts/setup.sh \
&& apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN echo 'figlet -t "Kartoza Docker GeoServer"' >> ~/.bashrc
WORKDIR ${GEOSERVER_HOME}
ENTRYPOINT ["/bin/bash", "/scripts/entrypoint.sh"]
Then build it with argument --platform linux/amd64 (I use arm64 architecture). Then pushed it to Heroku. All the time I get the same error.

GCC compilation within docker with "-j"

I got strange errors while compiling my project within the docker container when I am using -j option of make.
The errors look like this:
/root/projects/obj/linux_debug/src/myos_make/libmyos.a: error adding symbols: Cannot allocate memory
/usr/protobuf-3.9.2/lib/libprotobuf.a: error adding symbols: Bad address
Compiling the same project inside the container without -j and outside the container with -j passes ok.
The Dockerfile :
#
# This docker must be built from projects/src folder as context
#
FROM ubuntu:18.04 as base
# copy the dockerfile to make it possible to keep track of the cntent of the image
COPY ./docker_build/docker_files/Dockerfile.ubuntu18.04-builder $HOME/.
# Disable Prompt During Packages Installation
ARG DEBIAN_FRONTEND=noninteractive
# Update Ubuntu Software repository
RUN apt update -y && apt upgrade -y
# Install base utils
RUN apt install -y \
nano \
wget \
sudo \
curl \
&& apt clean -y
# Install additional packages needed for build.
RUN apt install -y \
nasm \
pkg-config \
bc \
python \
python3 \
python3-pip \
sshpass \
libapr1 \
libapr1-dev \
&& apt clean -y
RUN apt install -y \
rpm \
libaio-dev \
libnuma-dev \
numactl \
valgrind \
openssl \
libssl-dev \
ldap-utils \
libldap2-dev \
libncurses5-dev \
libncursesw5-dev \
uuid-dev \
ncurses-base \
expat \
libfuse-dev \
cmake \
build-essential \
autotools-dev \
autoconf \
automake \
doxygen \
linux-headers-4.15.0-173-generic \
g++-multilib \
lib32z1-dev \
libasan4 \
software-properties-common \
libtool \
unzip \
xsltproc \
&& apt clean -y
RUN ln -s /usr/bin/doxygen /bin/doxygen
# install GCC compiler
RUN add-apt-repository ppa:ubuntu-toolchain-r/test -y \
&& apt update -y\
&& apt install gcc-10 -y \
&& apt install g++-10 -y \
&& apt clean -y && \
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-10 60 --slave /usr/bin/g++ g++ /usr/bin/g++-10 && \
update-alternatives --config gcc
RUN curl https://bootstrap.pypa.io/pip/2.7/get-pip.py --output get-pip.py && \
python get-pip.py
RUN ln -sf /usr/local/bin/pip2 /usr/bin/pip
RUN pip install \
pyyaml \
jinja2 \
gcovr
FROM base as env-prepare
COPY external/protobuf /protobuf
RUN cd protobuf && ./build_proto.sh
FROM base as builder
COPY --from=env-prepare /usr/protobuf-3.9.2/ /usr/protobuf-3.9.2/
COPY --from=env-prepare /usr/protobuf-c-1.3.2/ /usr/protobuf-c-1.3.2/
COPY docker_build/docker-image-release /etc/docker-image-release
ARG UID=1000
USER ${UID}
# This entrypoint is to make everything run inside bash, so the devtools script will alway run before the command
ENTRYPOINT [ "/bin/bash", "-c" ]

Install libjpeg.so.8 Debian 11 inside Docker

I tried to integrate an application - QCPump - inside an existing Docker, with an other application - QAtrack+. The goal is to use QCPump inside QAtrack+.
The application code seems to be integrated but when I launch it, I have an error :
ImportError: libjpeg.so.8: cannot open shared object file: No such file or directory
The error is raised by the wxPython package.
Okay, so I have to install it. Unfortunately, my Docker linux is Debian 11, and Debian seems to grab this package several years ago. So, after some reseach, I found that this package is "replaced" - for Debian - by libjpeg-dev. So, I did it. And same result ...
I found the code of the librairy (wxPython) and a docker part has done for Debian 10 : https://github.com/wxWidgets/Phoenix/blob/master/docker/build/debian-10/Dockerfile
I took this part and integrated it in my DockerFile :
RUN apt-get install -y \
freeglut3 \
freeglut3-dev \
libgl1-mesa-dev \
libglu1-mesa-dev \
libgstreamer-plugins-base1.0-dev \
libgtk-3-dev \
libjpeg-dev \
libnotify-dev \
libsdl2-dev \
libsm-dev \
libtiff-dev \
libwebkit2gtk-4.0-dev \
libxtst-dev; \
apt-get clean;
But same ...
In some forum, people mentionned the LD have to be update. I tried this way but I am not pretty sure :
RUN export LD_LIBRARY_PATH=/usr/local/lib
And to be honest, I am not sure this is the problem and so the solution here...
Any idea about this problem ?
Following, my complete DockerFile if you need it ;)
FROM python:3.6
RUN echo 'deb http://apt.postgresql.org/pub/repos/apt/ stretch-pgdg main' > /etc/apt/sources.list.d/pgdg.list
RUN wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add -
RUN apt-get update && apt-get install -y \
cron postgresql-client-10 cifs-utils dos2unix \
&& rm -rf /var/lib/apt/lists/*
RUN apt-get install tzdata
ENV TZ 'Europe/Paris'
RUN dpkg-reconfigure -f noninteractive tzdata
RUN touch /root/.is_inside_docker
RUN pip install virtualenv
RUN date "+%H:%M:%S %d/%m/%y"
RUN apt-get -q update && \
apt-get install -yq chromium && \
rm -rf /var/lib/apt/lists/*
RUN apt-get update -y && apt-get install -y libsdl2-ttf-2.0-0 && \
apt-get update -y && apt-get install -y libjpeg-dev libaio1 libaio-dev && \
wget -q -O /tmp/libpng12.deb http://mirrors.kernel.org/ubuntu/pool/main/libp/libpng/libpng12- 0_1.2.54-1ubuntu1_amd64.deb \
&& dpkg -i /tmp/libpng12.deb \
&& rm /tmp/libpng12.deb \
&& apt-get install -y \
freeglut3 \
freeglut3-dev \
libgl1-mesa-dev \
libglu1-mesa-dev \
libgstreamer-plugins-base1.0-dev \
libgtk-3-dev \
libjpeg-dev \
libnotify-dev \
libsdl2-dev \
libsm-dev \
libtiff-dev \
libwebkit2gtk-4.0-dev \
libxtst-dev; \
apt-get clean;
RUN export LD_LIBRARY_PATH=/usr/local/lib
WORKDIR /usr/src/qatrackplus

Running headless Chrome with webgl and Nvidia GPU inside a container

I'm trying to run headless chrome inside a docker container with the webgl support and the hardware acceleration.
I have a Nvidia graphic card and if I test of the drivers with the command suggested by Nvidia, it is successful
docker run --gpus all nvidia/opengl:base nvidia-smi
This is my dockerfile :
FROM nvidia/opengl:1.0-glvnd-runtime-ubuntu18.04
# Env vars for the nvidia-container-runtime.
ENV NVIDIA_VISIBLE_DEVICES all
ENV NVIDIA_DRIVER_CAPABILITIES all
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get install -y --no-install-recommends \
git \
ca-certificates \
build-essential \
g++ \
libxinerama-dev \
libxext-dev \
libxrandr-dev \
libxi-dev \
libxcursor-dev \
libxxf86vm-dev \
libvulkan-dev && \
rm -rf /var/lib/apt/lists/*
RUN apt-get update && apt-get install -y apt-utils && apt-get install -y curl
RUN apt-get update \
&& apt-get install -y wget gnupg ca-certificates \
&& wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add - \
&& sh -c 'echo "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google.list' \
&& apt-get update \
# We install Chrome to get all the OS level dependencies, but Chrome itself
# is not actually used as it's packaged in the node puppeteer library.
# Alternatively, we could could include the entire dep list ourselves
# (https://github.com/puppeteer/puppeteer/blob/master/docs/troubleshooting.md#chrome-headless-doesnt-launch-on-unix)
# but that seems too easy to get out of date.
&& apt-get install -y google-chrome-stable \
&& rm -rf /var/lib/apt/lists/* \
&& wget --quiet https://raw.githubusercontent.com/vishnubob/wait-for-it/master/wait-for-it.sh -O /usr/sbin/wait-for-it.sh \
&& chmod +x /usr/sbin/wait-for-it.sh
# Install GTK, pulseaudio and fonts
RUN apt-get update && \
apt-get -y --no-install-recommends install ca-certificates tzdata \
libcanberra-gtk-module libexif12 pulseaudio attr \
fonts-dejavu-core fonts-freefont-ttf fonts-guru-extra \
fonts-kacst fonts-kacst-one fonts-khmeros-core fonts-lao \
fonts-liberation fonts-lklug-sinhala fonts-lohit-guru \
fonts-nanum fonts-opensymbol fonts-sil-abyssinica \
fonts-sil-padauk fonts-symbola fonts-takao-pgothic \
fonts-tibetan-machine fonts-tlwg-garuda-ttf \
fonts-tlwg-kinnari-ttf fonts-tlwg-laksaman-ttf \
fonts-tlwg-loma-ttf fonts-tlwg-mono-ttf \
fonts-tlwg-norasi-ttf fonts-tlwg-purisa-ttf \
fonts-tlwg-sawasdee-ttf fonts-tlwg-typewriter-ttf \
fonts-tlwg-typist-ttf fonts-tlwg-typo-ttf \
fonts-tlwg-umpush-ttf fonts-tlwg-waree-ttf \
ttf-bitstream-vera ttf-dejavu-core ttf-ubuntu-font-family \
fonts-arphic-ukai fonts-arphic-uming \
fonts-ipafont-mincho fonts-ipafont-gothic \
fonts-unfonts-core && \
rm -rf -- /var/lib/apt/lists /tmp/*.deb
however when I run the container with :
docker run -it --gpus all mytest
and I try to capture a screenshot inside the container with:
google-chrome --no-sandbox --headless --screenshot=ss.png chrome://gpu/
I get the error : Segmentation fault (core dumped)
Any idea ?
GPU chome headless options are still problematic, especially when You try that in containers. Just update image to current nvidia/opengl:1.2-glvnd-runtime-ubuntu20.04 and You will get output without any memory dump. I had same issues about year ago on some chrome options with vulkan support (now same thing works ok).

the command ... returned a non-zero code 100 docker

I'm trying to install OpenVino on my Raspberry using Docker.
I have this Dockerfile:
FROM raspbian/stretch
ARG INSTALL_DIR="/opt/intel/inference_engine_vpu_arm"
RUN apt-get -y update \
&& DEBIAN_FRONTEND=noninteractive && apt-get -y upgrade && apt-get autoremove && \
apt-get install -y \
apt-transport-https \
build-essential \
cmake \
cpio \
lsb-release \
pciutils \
python3.5 \
python3.5-dev \
python3-pip \
python3-setuptools \
ffmpeg \
libjpeg-dev \
libtiff5-dev \
libjasper-dev \
libpng12-dev \
libavcodec-dev \
libavformat-dev \
libswscale-dev \
libv4l-dev \
libxvidcore-dev \
libx264-dev \
libgtk2.0-dev \
libgtk-3-dev \
libatlas-base-dev \
gfortran \
libgstreamer1.0-0 \
libgstreamer-plugins-base1.0-0
RUN usermod -a -G users "$(whoami)"
COPY inference_engine_vpu_arm $INSTALL_DIR
RUN sed -i "s|<INSTALLDIR>|$INSTALL_DIR|" $INSTALL_DIR/bin/setupvars.sh && \
echo "source $INSTALL_DIR/bin/setupvars.sh" >> $HOME/.bashrc
RUN ["/bin/bash", "-c", "source $INSTALL_DIR/bin/setupvars.sh && /bin/bash $INSTALL_DIR/install_dependencies/install_NCS_udev_rules.sh"]
RUN pip3 install numpy
RUN apt autoremove -y && \
rm -rf /var/lib/apt/lists/*
CMD ["/bin/bash"]
But I have this error when I try to build:
E: Unable to correct problems, you have held broken packages.
The command '/bin/sh -c apt-get -y update..... returned a non-zero code: 100
Do you have any idea?
Thanks
After a some google search it seems the error happens because the apt daemon is not able to connect to the configured repositories. This is likely since the base image was not updated for a while as i can see on docker hub.
If you not familiar with the available repositories you can generate them easily with online tools such as: https://debgen.simplylinux.ch/index.php?generate
You can put them into the docker image with a simple COPY command like
COPY sources.list /etc/apt/sources.list
where the first argument refers to a local file, the second to the docker image

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