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