HERA-Team/hera-singularity:rtp
$ singularity pull shub://HERA-Team/hera-singularity:rtp
Singularity Recipe
# =============================================================================
# Definition file for a singularity container for HERA RTP
# This containe consists of a miniconda base on Ubuntu 18.04 with
# the following Python packages:
# pyuvdata (https://github.com/RadioAstronomySoftwareGroup/pyuvdata/)
# linsolve (https://github.com/HERA-Team/linsolve)
# uvtools (https://github.com/HERA-Team/uvtools)
# hera_cal (https://github.com/HERA-Team/hera_cal)
# hera_qm (https://github.com/HERA-Team/hera_qm)
# hera_opm (https://github.com/HERA-Team/hera_opm)
# hera_pipelines (https://github.com/HERA-Team/hera_pipelines)
# hera_notebook_templates (https://github.com/HERA-Team/hera_notebook_templates)
# hera_mc (https://github.com/HERA-Team/hera_mc; required by hera_notebook_templates)
#
# Empty sections are commented out to avoid unexpcted builder bugs.
# =============================================================================
Bootstrap: docker
From: ubuntu:20.04
# Commands to be executed on the host system outside of the container after the base OS has been installed.
# %setup
# Copy files from the host system to the container
# %files
# Define environment variables that will be set at runtime.
# %environment
# 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 neccesary 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"
HERA_INSTALL_PATH="/usr/local/hera"
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 an RTP enviroment and install dependencies for HEREA packages.
# All dependencies are available in conda although the conda epheem
# package seems to be too old for hera_cal.
conda create -n RTP -c conda-forge ipython numpy scipy scikit-learn h5py \
astropy aipy pyyaml matplotlib ephem pandas cartopy sqlalchemy psycopg2 \
alembic python-dateutil tabulate psutil redis-py setuptools_scm mako \
pyuvdata
# Install hera_packages. For debugging purpose, we will clone and pip install. .
# Activate rtp to pip install to the environment and ake directory for the source codes.
conda activate RTP && mkdir $HERA_INSTALL_PATH && cd $HERA_INSTALL_PATH
# Loop over, clone and pip install.
# linsolve is used in most hera software packages and should be installed first
# hera_qm should be installed before hera_cal as the latter requires the former
# hera_mc installation has a step that sets up database configuration file,
# which is not currently done and not sure if it will be needed ...
for pkg in linsolve uvtools hera_qm hera_cal hera_opm hera_mc hera_notebook_templates
do
git clone https://github.com/HERA-Team/$pkg && cd $pkg && pip install . && cd ..
done
# Only need to clone hera_pipelines
git clone https://github.com/HERA-Team/hera_pipelines
# Export HERA_INSTALL_PATH and CONDA_INSTALL_PATH variables to the container
echo "export HERA_INSTALL_PATH=$HERA_INSTALL_PATH" >> $SINGULARITY_ENVIRONMENT
echo "export CONDA_INSTALL_PATH=$CONDA_INSTALL_PATH" >> $SINGULARITY_ENVIRONMENT
# This environment avariable will be useful when needing to initialize conda
echo "export CONDA_INIT_SCRIPT=$CONDA_INIT_SCRIPT" >> $SINGULARITY_ENVIRONMENT
# List installed environments and check environment variables at start
echo "miniconda installed path is $CONDA_INSTALL_PATH"
echo "HERA packages path is $HERA_INSTALL_PATH"
conda env list
echo "Done building HERA RTP singularity container"
# 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
# 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
# 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 The HERRA Collaboration
Version v0.0.1
%help
This is a container for HERA RTP
Collection
- Name: HERA-Team/hera-singularity
- License: BSD 2-Clause “Simplified” License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/HERA-Team-hera-singularity-rtp |
collection name | HERA-Team/hera-singularity |
branch | master |
tag | rtp |
commit | 75ac73a58e2d6069cea4953a692ce944a96a2300 |
version (container hash) | 6f16987018eae136da1ddb24311c7b2ac5178ce666d73cc1141851e5cf735337 |
build date | 2020-12-16T19:14:32.787Z |
size (MB) | 1719.2578125 |
size (bytes) | 1802772480 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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