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Commit 57ade5b8 authored by Guido Sterbini's avatar Guido Sterbini
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Some changes

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......@@ -42,60 +42,47 @@ RUN echo "deb [arch=$(dpkg --print-architecture)] \
&& apt-get -yqq clean \
&& chmod 0755 /root/create_eos_folders.sh \
&& /root/create_eos_folders.sh
# we can prepare the files and then ADD them directly
#&& echo '{"name":"home-a","hostport":"eoshome-a.cern.ch",\
# "remotemountdir":"/eos/user/a/","localmountdir":"/eos/user/a/"}' > \
# /etc/eos/fuse.home-a.conf \
#&& echo '{"name":"home-e","hostport":"eoshome-e.cern.ch", \
# "remotemountdir":"/eos/user/e/","localmountdir":"/eos/user/e/"}' > \
# /etc/eos/fuse.home-e.conf \
#&& echo '{"name":"home-s","hostport":"eoshome-s.cern.ch", \
# "remotemountdir":"/eos/user/s/","localmountdir":"/eos/user/s/"}' > \
# /etc/eos/fuse.home-s.conf \
#&& mkdir -p /eos/user/a \
#&& mkdir -p /eos/user/e \
#& mkdir -p /eos/user/s \
#&& echo '{"name":"project-l","hostport":"eosproject-l.cern.ch",\
# "remotemountdir":"/eos/project/l/","localmountdir":"/eos/project/l/"}' > \
# /etc/eos/fuse.project-l.conf \
#&& mkdir -p /eos/project/l
###############################################################################
# Installing AFS in the docker (not working)
# the main problem is related I think to docker
# https://stackoverflow.com/questions/53383431/how-to-enable-systemd-on-dockerfile-with-ubuntu18-04
# the present policy is to install it on the host_machine and share the volume with the docker
# e.g., http://abpcomputing.web.cern.ch/guides/openafs/
# ideally also for eos
#RUN apt-get install -y software-properties-common \
#&& apt-get update \
#&& add-apt-repository ppa:openafs/stable \
#&& apt-get update \
#&& apt-get upgrade \
#&& apt install -y openafs-client openafs-modules-dkms openafs-krb5 krb5-config
###############################################################################
# RUN apt-get install -y software-properties-common \
# && apt-get update \
# && add-apt-repository ppa:openafs/stable \
# && apt-get update \
# && apt-get upgrade \
# && apt install -y openafs-client openafs-modules-dkms openafs-krb5 krb5-config
###############################################################################
# Some minimal packages
###############################################################################
RUN apt-get -qq update \
&& apt-get -yqq install x11-apps sudo wget git tmux vim meld openssh-server\
build-essential cmake python-dev python3-dev \
&& apt-get -yqq clean
# COPY start.sh /root/start.sh
# RUN chmod 0755 /root/start.sh \
# && /root/start.sh
###############################################################################
# MAD-X installation (last releases)
###############################################################################
RUN wget http://madx.web.cern.ch/madx/releases/last-rel/madx-linux64-gnu \
&& mv madx-linux64-gnu /usr/bin/madx \
&& chmod +x /usr/bin/madx
###############################################################################
# Install miniconda
# https://hub.docker.com/r/continuumio/miniconda/dockerfile
###############################################################################
# from https://towardsdatascience.com/conda-pip-and-docker-ftw-d64fe638dc45
###############################################################################
SHELL [ "/bin/bash", "--login", "-c" ]
# Create a non-root user
ARG username=abpuser
ARG username=jovyan
ARG uid=1000
ARG gid=100
ENV USER $username
......@@ -111,89 +98,78 @@ RUN adduser --disabled-password \
$USER
COPY environment.yml requirements.txt /tmp/
RUN chown $UID:$GID /tmp/environment.yml /tmp/requirements.txt
COPY postBuild.sh /usr/local/bin/postBuild.sh
RUN chown $UID:$GID /usr/local/bin/postBuild.sh && \
chmod u+x /usr/local/bin/postBuild.sh
COPY entrypoint.sh /usr/local/bin/
RUN chown $UID:$GID /usr/local/bin/entrypoint.sh && \
chmod u+x /usr/local/bin/entrypoint.sh
RUN chown $UID:$GID /tmp/environment.yml /tmp/requirements.txt \
&& chown $UID:$GID /usr/local/bin/postBuild.sh \
&& chmod u+x /usr/local/bin/postBuild.sh \
&& chown $UID:$GID /usr/local/bin/entrypoint.sh \
&& chmod u+x /usr/local/bin/entrypoint.sh
USER $USER
# install miniconda
ENV MINICONDA_VERSION 4.7.12
ENV CONDA_DIR $HOME/miniconda3
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-$MINICONDA_VERSION-Linux-x86_64.sh -O ~/miniconda.sh && \
chmod +x ~/miniconda.sh && \
~/miniconda.sh -b -p $CONDA_DIR && \
rm ~/miniconda.sh
# make non-activate conda commands available
ENV PATH=$CONDA_DIR/bin:$PATH
# make conda activate command available from /bin/bash --login shells
RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> ~/.profile
# make conda activate command available from /bin/bash --interative shells
RUN conda init bash
# create a project directory inside user home
ENV PROJECT_DIR $HOME/app
RUN mkdir $PROJECT_DIR \
&& mkdir $HOME/local_host_folder
WORKDIR $PROJECT_DIR
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-$MINICONDA_VERSION-Linux-x86_64.sh -O ~/miniconda.sh \
&& chmod +x ~/miniconda.sh \
&& ~/miniconda.sh -b -p $CONDA_DIR \
&& rm ~/miniconda.sh \
# make conda activate command available from /bin/bash --login shells
&& echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> ~/.profile \
# make conda activate command available from /bin/bash --interative shells
&& conda init bash \
# create a project directory inside user home
&& mkdir $HOME/local_host_home
WORKDIR $HOME
# build the conda environment
ENV ENV_PREFIX $HOME/env
RUN conda update --name base --channel defaults conda && \
conda env create --prefix $ENV_PREFIX --file /tmp/environment.yml --force && \
conda clean --all --yes
# run the postBuild script to install any JupyterLab extensions
RUN conda activate $ENV_PREFIX && \
/usr/local/bin/postBuild.sh && \
conda deactivate
#ENTRYPOINT [ "/usr/local/bin/entrypoint.sh" ]
###############################3
#ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
#ENV PATH /opt/conda/bin:$PATH
#RUN apt-get update --fix-missing \
# && apt-get install -y wget bzip2 ca-certificates \
# && apt-get clean \
# && rm -rf /var/lib/apt/lists/*
#RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh -O ~/miniconda.sh \
# && /bin/bash ~/miniconda.sh -b -p /opt/conda \
# && rm ~/miniconda.sh \
# && /opt/conda/bin/conda clean -tipsy \
# && ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \
# && echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
# && echo "conda activate base" >> ~/.bashrc
#CMD /bin/bash -c "source root/bin/thisroot.sh":q
#CMD eosxd -ofsname=home-s
#USER jovyan
###########
#RUN pip install \
# ipython \
# cpymad \
# pandarallel \
# pyarrow \
# sphinx
###########
#RUN mkdir abp
#ENV HOME=/abp
#VOLUME /abp
#WORKDIR /abp
# Configure access to Jupyter
# CMD jupyter lab --no-browser --ip=0.0.0.0 --allow-root
RUN conda update --name base --channel defaults conda \
&& conda env create --prefix $ENV_PREFIX --file /tmp/environment.yml --force \
&& conda clean --all --yes \
# run the postBuild script to install any JupyterLab extensions
&& conda activate $ENV_PREFIX \
&& /usr/local/bin/postBuild.sh \
&& conda deactivate
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
ENV PATH /opt/conda/bin:$PATH
RUN conda activate $ENV_PREFIX \
&& pip install -r /tmp/requirements.txt \
&& pip install pyNAFF \
&& git clone https://github.com/SixTrack/pysixtrack.git \
&& cd pysixtrack \
&& pip install -e . \
&& cd .. \
&& git clone https://github.com/SixTrack/sixtracktools.git \
&& cd sixtracktools \
&& pip install -e . \
&& cd .. \
&& git clone https://github.com/SixTrack/sixtracklib.git \
&& cd sixtracklib \
&& mkdir build \
&& cd build \
&& cmake .. \
&& make \
&& cd ../python \
&& pip install -e . \
&& cd .. \
&& conda deactivate
COPY start.sh $HOME/start.sh
RUN echo "source /home/"$USER"/local_host_home/docker_start.sh" >> ~/.bashrc
USER $USER
CMD ["/bin/bash" ]
#docker build . -t sterbini/test
#docker run -it -u 0 -v /afs:/afs -v $PWD:/home/abpuser/local_host_folder --rm --cap-add SYS_ADMIN --device /dev/fuse sterbini/test
# FOR BUILDING
# docker build . --build-arg username=jovyan -t sterbini/test
# FOR RUNNING
# docker run -it -u 0 -v /afs:/afs -v ~:/home/jovyan/local_host_home -p 8889:8888 --rm --cap-add SYS_ADMIN --device /dev/fuse sterbini/test
# TO LAUNCH jupyterlab
# jupyter lab --no-browser --ip=0.0.0.0 --allow-root
requirements.txt
+ 12
− 4
View file @ 57ade5b8
# Installs
# A version of numpy no older than 1.14.0
# Exactly the version 0.23.4 of Pandas
numpy>=1.14.0
pandas>=0.23.4
ipython
jupyterlab
numpy
scipy
matplotlib
pandas
pyarrow
cpymad
pandarallel
sphinx
pdoc3
dask
start.sh
+ 21
− 4
View file @ 57ade5b8
#!/bin/bash
eosxd -ofsname=home-a
eosxd -ofsname=home-e
eosxd -ofsname=home-s
eosxd -ofsname=project-l
# Mounting EOS
if [ `whoami` == 'root' ]
then
if mountpoint -q /eos/user/s
then
:
else
eosxd -ofsname=home-s
fi
if mountpoint -q /eos/project/l
then
:
else
eosxd -ofsname=project-l
fi
fi
# activating conda
conda activate env/
alias jupy='jupyter lab --no-browser --ip=0.0.0.0 --allow-root'
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