updated dockerfile

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"]
+
+# Abinit installation
+# ===================
+# # 1. compiler: gfortran
+# # 2. MPI libraries - choice for Open MPI: mpi-default-dev libopenmpi-dev
+# # 3. math libraries - choice for lapack and blas: liblapack-dev libblas-dev
+# # 4. mandatory libraries:libhdf5-dev libnetcdf-dev libnetcdff-dev libpnetcdf-dev libxc-dev libfftw3-dev libxml2-dev
+
+USER root
+
+RUN apt-get update \
+ && apt install -y --no-install-recommends \
+    gfortran \
+    mpi-default-dev libopenmpi-dev \
+    liblapack-dev libblas-dev \
+    libhdf5-dev libnetcdf-dev libnetcdff-dev libpnetcdf-dev libxc-dev \
+    libfftw3-dev libxml2-dev \
+    mongodb \
+    slurmd slurm-client slurmctld \
+ && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /opt
+
+ARG abinit_version="9.4.0"
+COPY configs/abinit_config.ac9 /opt/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'   \
+ && make -j4 \
+ && make install \
+ && rm /opt/abinit-${abinit_version}.tar.gz \
+ # && rm -rf /opt/abinit-${abinit_version}
+ && fix-permissions "/opt/abinit-${abinit_version}"
+
+USER $NB_UID
+
+# Install Python 3 packages
+# =========================
+
+RUN conda install --quiet --yes \
+    # 'ase' \
+    # 'pymatgen' \
+    # 'atomate' \
+    # 'matminer' \
+    # 'jupyterlab-git' \
+    'abipy' \
+    'jupyter_contrib_nbextensions' \
+    'jupyter_nbextensions_configurator' \
+ && pip install --no-cache-dir jupyter-jsmol fireworks \
+ && conda clean --all -f -y \
+ && fix-permissions "${CONDA_DIR}" \
+ && fix-permissions "/home/${NB_USER}"
+
+# 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"
+
+USER $NB_UID
+
+RUN pip install -e pseudo_dojo
+
+
+WORKDIR $HOME
+

configs/abinit_config.ac9

+# MPI settings
+with_mpi="yes"
+enable_mpi_io="yes"
+
+# linear algebra settings
+with_linalg_flavor="netlib"
+LINALG_LIBS="-L/usr/lib/x86_64-linux-gnu -llapack -lblas"
+
+# mandatory libraries
+with_libxc="yes"
+with_hdf5="yes"
+with_netcdf="yes"
+with_netcdf_fortran="yes"
+
+# fast fourier settings
+with_fft_flavor="fftw3"
+FFTW3_CPPFLAGS="-I/usr/include"
+FFTW3_FCFLAGS="-I/usr/include"
+FFTW3_LIBS="-L/usr/lib/x86_64-linux-gnu -lfftw3 -lfftw3f"
+
+# XML2 library (used by multibinit)
+with_libxml2="yes"
+LIBXML2_FCFLAGS="-I/usr/lib/x86_64-linux-gnu/"
+LIBXML2_LIBS="-L/usr/include/libxml2/libxml/ -lxmlf90"
+

configs/manager.yml

+
+## Local runner ##############
+
+# policy:
+#   autoparal: 0
+
+qadapters: # List of `qadapters` objects  (just one in this simplified example)
+- priority: 1
+  queue:
+    qtype: shell        # "Submit" jobs via the shell.
+    qname: localhost    # "Submit" to the localhost queue
+                        # (it's a fake queue in this case)
+
+  job:
+    mpi_runner: "mpirun"
+    # pre_run: "export PATH=$HOME/git_repos/abinit/build_gcc/src/98_main:$PATH"
+
+  limits:
+    timelimit: 24:00:00   #  Time-limit for each task.
+    max_cores: 64          #  Max number of cores that can be used by a single task.
+    hint_cores:  8
+
+  hardware:
+    num_nodes: 1
+    sockets_per_node: 2
+    cores_per_socket: 64
+    mem_per_node: 256 Gb
+
+##############################

configs/scheduler.yml

+seconds: 30   # number of seconds to wait.
+#minutes: 0  # number of minutes to wait.
+#hours: 0    # number of hours to wait.
+
+
+# Limit on the number of jobs that can be present in the queue. (DEFAULT: 200)
+max_njobs_inqueue: 8
+
+# Maximum number of cores that can be used by the scheduler.
+max_ncores_used: 128