sunny 0.3.1-dev2

from savannah.ornl.gov/gravitas/jupyter-notebook:25.2.1

FROM savannah.ornl.gov/gravitas/jupyter-notebook:25.2.1

run apt-get update -y && \

RUN apt-get update -y && \

    apt-get upgrade -y && \

    apt-get install -y g++

    apt-get install -y g++ tini xorg-dev mesa-utils xvfb libgl1 freeglut3-dev

user jovyan

ENV XDG_RUNTIME_DIR=/run/user/0

RUN mkdir -p $XDG_RUNTIME_DIR

USER jovyan

ENV JULIA_CPU_TARGET="x86-64-v3"

run julia -e 'using Pkg; Pkg.Registry.update(); \

    Pkg.add([Pkg.PackageSpec(;name="JLLWrappers", version="1.7.0"), \

             Pkg.PackageSpec(;name="Sunny", version="0.7.5"), \

ENV DISPLAY=:0

RUN julia -e 'using Pkg; Pkg.Registry.update(); \

    Pkg.add([Pkg.PackageSpec(;name="Sunny", version="0.7.5"), \

             Pkg.PackageSpec(;name="MKL"), \

             Pkg.PackageSpec(;name="WGLMakie"), \

             Pkg.PackageSpec(;name="PackageCompiler"), \

             Pkg.PackageSpec(;url="https://github.com/quantumsteve/Bonito.jl",rev="jupyter_base_url")])'

RUN tini -v -- xvfb-run -s '-screen 0 1024x768x24' julia -e 'using Pkg; Pkg.add("GLMakie"); Pkg.precompile()'

ADD precompile ./precompile

run julia -e 'using PackageCompiler; \

    create_sysimage(["IJulia", "Sunny", "WGLMakie", "MKL"], \

                      sysimage_path="/home/jovyan/sys_flux_plots.so", \

                      precompile_execution_file=["precompile/01_LSWT_CoRh2O4.jl", "precompile/02_LLD_CoRh2O4.jl"], \

                      cpu_target=ENV["JULIA_CPU_TARGET"])'

run julia -e 'using IJulia; IJulia.installkernel("Julia Sunny WGLMakie", "--sysimage=/home/jovyan/sys_flux_plots.so")'

RUN tini -v -- xvfb-run -s '-screen 0 1024x768x24' --auto-servernum julia -e 'using PackageCompiler; create_sysimage(["IJulia", "Sunny", "WGLMakie", "MKL"], sysimage_path="/home/jovyan/sys_flux_plots.so", precompile_execution_file=["precompile/01_LSWT_CoRh2O4.jl", "precompile/02_LLD_CoRh2O4.jl"], cpu_target=ENV["JULIA_CPU_TARGET"])'

RUN julia -e 'using IJulia; IJulia.installkernel("Julia Sunny WGLMakie", "--sysimage=/home/jovyan/sys_flux_plots.so")'

# Move the kernelspec out of ${HOME} to the system share location.

# Avoids problems with runtime UID change not taking effect properly

# on the .local folder in the jovyan home dir.

run mv "${HOME}/.local/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/"

run chmod -R go+rx "${CONDA_DIR}/share/jupyter"

run rm -rf "${HOME}/.local"

run fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"

RUN mv "${HOME}/.local/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/"

RUN chmod -R go+rx "${CONDA_DIR}/share/jupyter"

RUN rm -rf "${HOME}/.local"

RUN fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"

run chmod -R 777 /opt/julia

RUN chmod -R 777 /opt/julia

user root

USER root

run rm -rf precompile

RUN rm -rf precompile

COPY examples ./examples

run chmod -R 777 examples

RUN chmod -R 777 examples

ADD ./startup.sh /startup.sh

CMD /startup.sh

#!/bin/bash

# The IPython image starts as privileged user.

# The parent Galaxy server is mounting data into /import with the same 

# permissions as the Galaxy server is running on.

# In case of 1450 as UID and GID we are fine, because our preconfigured ipython

# user owns this UID/GID. 

# (1450 is the user id the Galaxy-Docker Image is using)

# If /import is not owned by 1450 we need to create a new user with the same

# UID/GID as /import and make everything accessible to this new user.

#

# In the end the IPython Server is started as non-privileged user. Either

# with the UID 1450 (preconfigured jupyter user) or a newly created 'galaxy' user

# with the same UID/GID as /import.

export PATH=/home/jovyan/.local/bin:$PATH

python /get_notebook.py

#if [ ! -f /import/ipython_galaxy_notebook.ipynb ]; then

#    cp /home/$NB_USER/notebook.ipynb /import/ipython_galaxy_notebook.ipynb

#    chown $NB_USER /import/ipython_galaxy_notebook.ipynb

#fi

jupyter trust /import/ipython_galaxy_notebook.ipynb

##/monitor_traffic.sh &

export XDG_RUNTIME_DIR=/run/user/0

mkdir -p $XDG_RUNTIME_DIR

xvfb-run -s '-screen 0 1024x768x24' jupyter notebook --no-browser