multi-stage build

Dockerfile

 # https://github.com/jupyter/docker-stacks
 # https://jupyter-docker-stacks.readthedocs.io/en/latest/index.html
-FROM jupyter/scipy-notebook
-LABEL maintainer="Gian-Marco Rignanese <gian-marco.rignanese@uclouvain.be>"
-
 
-# # Fix DL4006
-# SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+FROM jupyter/scipy-notebook AS builder
 
 # Abinit installation
 # ===================
@@ -23,24 +19,46 @@ RUN apt-get update \
     liblapack-dev libblas-dev \
     libhdf5-dev libnetcdf-dev libnetcdff-dev libpnetcdf-dev libxc-dev \
     libfftw3-dev libxml2-dev \
-    slurmd slurm-client slurmctld \
  && rm -rf /var/lib/apt/lists/*
 
-WORKDIR /opt
+WORKDIR /tmp
 
 ARG abinit_version="9.4.0"
-COPY configs/abinit_config.ac9 /opt/abinit-${abinit_version}/build/abinit_config.ac9
+COPY configs/abinit_config.ac9 /tmp/abinit-${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 \
  && cd abinit-${abinit_version} \
  && cd build \
- && ../configure --with-config-file='abinit_config.ac9'   \
+ && ../configure --with-config-file='abinit_config.ac9'  --prefix=/opt/abinit \
  && make -j4 \
- && make install \
- && rm /opt/abinit-${abinit_version}.tar.gz \
- # && rm -rf /opt/abinit-${abinit_version}
- && fix-permissions "/opt/abinit-${abinit_version}"
+ && make install
+
+
+FROM jupyter/scipy-notebook
+LABEL maintainer="Gian-Marco Rignanese <gian-marco.rignanese@uclouvain.be>"
+
+# Abinit installation
+# ===================
+# # 1. MPI libraries - choice for Open MPI: mpi-default libopenmpi
+# # 2. math libraries - choice for lapack and blas: liblapack libblas
+# # 3. mandatory libraries: libhdf5 libnetcdf libnetcdff libpnetcdf libxc libfftw3 libxml2
+
+USER root
+WORKDIR /opt/abinit
+
+RUN apt-get update \
+ && apt install -y --no-install-recommends \
+    mpi-default-bin openmpi-bin libopenmpi3 \
+    liblapack3 libblas3 \
+    libhdf5-103 libnetcdf15 libnetcdff7 libpnetcdf0d libxc5 \
+    libfftw3-bin libxml2 \
+   #  slurmd slurm-client slurmctld \
+ && rm -rf /var/lib/apt/lists/*
+
+
+COPY --from=builder /opt/abinit .
+RUN fix-permissions "/opt/abinit"
 
 USER $NB_UID
 
@@ -62,17 +80,20 @@ RUN conda install --quiet --yes \
  && fix-permissions "${CONDA_DIR}" \
  && fix-permissions "/home/${NB_USER}"
 
-# Pseudo-dojo
-USER root
-WORKDIR /opt
+# # Pseudo-dojo
+# USER root
+# WORKDIR /opt
 
-RUN git clone --depth 1 https://github.com/abinit/pseudo_dojo.git \
- && cd pseudo_dojo \
- && fix-permissions "/opt/pseudo_dojo"
+# RUN git clone --depth 1 https://github.com/abinit/pseudo_dojo.git \
+#  && cd pseudo_dojo \
+#  && fix-permissions "/opt/pseudo_dojo"
+
+# USER $NB_UID
+
+# RUN pip install -e pseudo_dojo
 
-USER $NB_UID
 
-RUN pip install -e pseudo_dojo
+ENV PATH=/opt/abinit/bin:$PATH
 
 USER $NB_UID
 WORKDIR $HOME