HERA-Team/hera-singularity:hera1

$ singularity pull shub://HERA-Team/hera-singularity:hera1

Singularity Recipe

# =============================================================================
# Definition file for a singularity container for HERA
# This container is for general purpose work. It consists of
#   - a miniconda base on Ubuntu 20.04
#   - a `hera1` conda environment that has:
#     - python=3.8
#     - numpy, scipy, astropy, astroquery, matplotlib, and etc (see line 61)
#     - linsolve (https://github.com/HERA-Team/linsolve)
#     - uvtools (https://github.com/HERA-Team/uvtools)
#     - hera_cal (https://github.com/HERA-Team/hera_cal)
#     - hera_sim (https://github.com/HERA-Team/hera_sim)
#     - pyuvdata (https://github.com/RadioAstronomySoftwareGroup/pyuvdata/)
#     - pyuvsim (https://github.com/RadioAstronomySoftwareGroup/pyuvsim)
#     - pyradiosky (https://github.com/RadioAstronomySoftwareGroup/pyradiosky)
#     - pygdsm (https://github.com/telegraphic/pygdsm)
# =============================================================================
Bootstrap: docker
From: ubuntu:20.04


# -----------------------------------------------------------------------------
# - Pre-build environment variables -
# Define environment variables that will be set at runtime.
# -----------------------------------------------------------------------------
# %environment

# -----------------------------------------------------------------------------
# - Built commands -
# Commands to be executed at build time after the base OS has been installed.
# These commands are executed as root in /root inside the container.
# -----------------------------------------------------------------------------
%post
  # Update Ubuntu packages and install necessary packages
  apt-get update
  apt-get install -y git wget vim
  apt-get clean

  # Fix locale bugs see https://github.com/hpcng/singularity/issues/11
  apt-get install -y locales
  echo 'en_US.UTF-8 UTF-8' >> /etc/locale.gen
  locale-gen && update-locale LANG=en_US.UTF-8

  # DONE with OS install and update

  # Define environment variables for install paths
  ROOT_INSTALL_PATH="/usr/local"
  CONDA_INSTALL_PATH="/usr/local/miniconda3"
  CONDA_INIT_SCRIPT="$CONDA_INSTALL_PATH/etc/profile.d/conda.sh"

  # Download and install miniconda
  cd $ROOT_INSTALL_PATH
  wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  bash Miniconda3-latest-Linux-x86_64.sh -b -p $CONDA_INSTALL_PATH

  # Make conda executable available during build and update.
  # This does not make the executable available during runtime.
  . $CONDA_INIT_SCRIPT && conda update -n base conda

  # Create `hera1` enviroment and install dependencies for HEREA packages.
  # All dependencies are available in conda although the conda ephem
  # package seems to be too old for hera_cal.
  conda create -n hera1 -c conda-forge python=3.8 numpy scipy scikit-learn \
    matplotlib astropy astroquery pyuvdata h5py aipy pyyaml healpy \
    astropy-healpix click ipykernel pandas cartopy xarray netcdf4 h5netcdf \
    mpi4py dask jupyterlab ipympl

  # Install hera_packages. For debugging purpose, we will clone and pip install .

  # Activate `hera1`, make directory for the source codes, pip install ..
  conda activate hera1
  # Loop over and pip install.
  # linsolve is used in most hera software and should be installed first
  # hera_qm should be installed before hera_cal
  # pyuvsim and pyradiosky will be automatically installed by hera_sim
  for pkg in linsolve uvtools hera_qm hera_cal hera_sim
  do
    pip install git+https://github.com/HERA-Team/$pkg
  done
  # Install pygdsm
  pip install git+https://github.com/telegraphic/pygdsm

  # Export CONDA_INSTALL_PATH variables to the container
  echo "export CONDA_INSTALL_PATH=$CONDA_INSTALL_PATH" >> $SINGULARITY_ENVIRONMENT
  # This CONDA_INIT_SCRIPT variable will be useful for initializing conda
  echo "export CONDA_INIT_SCRIPT=$CONDA_INIT_SCRIPT" >> $SINGULARITY_ENVIRONMENT

  # List installed environments and check environment variables at start
  echo "miniconda installed path is $CONDA_INSTALL_PATH"
  conda env list
  echo "Done building HERA RTP singularity container"


# -----------------------------------------------------------------------------
# - run scripts -
# The contents of the %runscript section are written to a file within the
# container that is executed when the container image is run (either via the
# `singularity run` command or by executing the container directly as a command).
# -----------------------------------------------------------------------------
# %runscript


# -----------------------------------------------------------------------------
# - start scripts -
# The contents of the %startscript section are written to a file within
# the container at build time, and this file is executed when the instance
# start command is issued. The instance command run the container as a deamon.
# -----------------------------------------------------------------------------
# %startscript


# -----------------------------------------------------------------------------
# - test scripts -
# Commands in %test are run at the very end of the build process and can be
# turned off with --notest tag in singularity commands
# -----------------------------------------------------------------------------
# %test


%labels
  Author HERA Team
  Version v0.0.1


%help
  This is a container for general purpose work on HERA

Collection

• Name: HERA-Team/hera-singularity
• License: BSD 2-Clause “Simplified” License

Metrics

Feedback

Was this page helpful?

Glad to hear it! Please tell us how we can improve.

Sorry to hear that. Please tell us how we can improve.