cleanup Dockerfile

Dockerfile

@@ -24,7 +24,7 @@ RUN apt-get update \
 WORKDIR /tmp
 
 ARG abinit_version="9.4.0"
-COPY configs/abinit_config.ac9 /tmp/abinit-${abinit_version}/build/abinit_config.ac9
+COPY configs/abinit/abinit_config.ac9 /tmp/abinit-${abinit_version}/build/abinit_config.ac9
 
 RUN wget -k "https://www.abinit.org/sites/default/files/packages/abinit-${abinit_version}.tar.gz" \
  && tar xzf abinit-${abinit_version}.tar.gz \
@@ -38,11 +38,34 @@ RUN wget -k "https://www.abinit.org/sites/default/files/packages/abinit-${abinit
 FROM jupyter/scipy-notebook
 LABEL maintainer="Gian-Marco Rignanese <gian-marco.rignanese@uclouvain.be>"
 
+
+# Setup slurm
+# ===========
+
+USER root
+
+RUN apt-get update \
+ && apt install -y --no-install-recommends \
+    slurmd slurm-client slurmctld \
+ && rm -rf /var/lib/apt/lists/*
+
+COPY configs/slrum/slurm.conf /etc/slurm-llnl/slurm.conf
+COPY configs/slurm/start_slurm.sh  /usr/local/bin/before-notebook.d/
+
+# https://github.com/yuwata/slurm-fedora/blob/master/slurm-setuser.in
+RUN mkdir -p /run/munge \
+ && chown -R jovyan /run/munge /etc/munge /var/lib/munge /var/log/munge \
+ && mkdir -p /var/run/slurm-llnl \
+ && chown -R jovyan /var/run/slurm-llnl /var/lib/slurm-llnl /var/log/slurm-llnl
+
+USER $NB_UID
+
+
 # Abinit installation
 # ===================
-# # 1. MPI libraries - choice for Open MPI: mpi-default-bin openmpi-bin libopenmpi3
-# # 2. math libraries - choice for lapack and blas: liblapack3 libblas3
-# # 3. mandatory libraries: libhdf5-103 libnetcdf15 libnetcdff7 libpnetcdf0d libxc5 libfftw3-bin libxml2
+# - MPI libraries - choice for Open MPI: mpi-default-bin openmpi-bin libopenmpi3
+# - math libraries - choice for lapack and blas: liblapack3 libblas3
+# - mandatory libraries: libhdf5-103 libnetcdf15 libnetcdff7 libpnetcdf0d libxc5 libfftw3-bin libxml2
 
 USER root
 
@@ -62,64 +85,34 @@ ENV PATH=/opt/abinit/bin:$PATH
 
 # Install Python 3 packages
 # =========================
-# fireworks's depenecies: flask-paginate gunicorn pymongo
-# pseudo_dojo's depenecies: periodic-table-plotter atomicfile
+# Depenecies:
+# - fireworks: flask-paginate gunicorn pymongo
+# - pseudo_dojo: periodic-table-plotter atomicfile
 
 RUN conda install --quiet --yes \
     'abipy' \
     'jupyter-server-proxy' \
     'flask-paginate' 'gunicorn' 'pymongo' \
     'periodic-table-plotter' 'atomicfile' \
- && pip install --no-cache-dir jupyter-jsmol fireworks \
+ && pip install --no-cache-dir jupyter-jsmol \
+ && pip install --no-cache-dir git+https://github.com/modl-uclouvain/fireworks.git \
+ && pip install --no-cache-dir git+https://github.com/modl-uclouvain/jupyter-fireworks-proxy.git \
+ && pip install --no-cache-dir git+https://github.com/gpetretto/abiflows.git@develop \
  && conda clean --all -f -y \
  && fix-permissions "${CONDA_DIR}" \
  && fix-permissions "/home/${NB_USER}"
 
-# Pseudo-dojo
-# ===========
-
+# Install a "lightweight" version of Pseudo-dojo
 COPY --chown=$NB_UID:$NB_GID pseudo_dojo /opt/pseudo_dojo
 WORKDIR /opt/pseudo_dojo
 RUN pip install -e .
 
-# Setup slurm
-# ===========
-
-USER root
-
-RUN apt-get update \
- && apt install -y --no-install-recommends \
-    slurmd slurm-client slurmctld \
- && rm -rf /var/lib/apt/lists/*
-
-COPY configs/slurm.conf /etc/slurm-llnl/slurm.conf
-COPY configs/start_slurm.sh  /usr/local/bin/before-notebook.d/
-
-# https://github.com/yuwata/slurm-fedora/blob/master/slurm-setuser.in
-RUN mkdir -p /run/munge \
- && chown -R jovyan /run/munge /etc/munge /var/lib/munge /var/log/munge \
- && mkdir -p /var/run/slurm-llnl \
- && chown -R jovyan /var/run/slurm-llnl /var/lib/slurm-llnl /var/log/slurm-llnl
-
-USER $NB_UID
-
-COPY --chown=$NB_UID:$NB_GID fireworks /opt/fireworks
-WORKDIR /opt/fireworks
-RUN pip install -e .
-
-COPY --chown=$NB_UID:$NB_GID jupyter-fireworks-proxy /opt/jupyter-fireworks-proxy
-WORKDIR /opt/jupyter-fireworks-proxy
-RUN pip install -e .
-
-# RUN pip install git+https://github.com/fekad/jupyter-fireworks-proxy.git \
-#  && jupyter serverextension enable --sys-prefix jupyter_server_proxy
-
-# temporarily install abiflows from develop repository
-RUN pip install git+https://github.com/gpetretto/abiflows.git@develop
+# Setup home folder 
+# =================
 
 WORKDIR $HOME
 
-COPY --chown=$NB_UID:$NB_GID tutorials tutorials
-COPY --chown=$NB_UID:$NB_GID configs/FW_config.yaml configs/my_launchpad.yaml configs/my_fworker.yaml configs/my_qadapter.yaml configs/SLURM_template.txt .fireworks/
-COPY --chown=$NB_UID:$NB_GID configs/manager.yml configs/scheduler.yml configs/fw_manager.yaml .abinit/abipy/
+COPY --chown=$NB_UID:$NB_GID configs/abipy .abinit/abipy
+COPY --chown=$NB_UID:$NB_GID configs/fireworks .fireworks
 
+COPY --chown=$NB_UID:$NB_GID tutorials tutorials