davecwright3 / bart-singularity

Bayesian Atmospheric Radiative Transfer (BART) packaged in a Singularity container https://github.com/davecwright3/bart-singularity

BART Singularity Guide

The Singularity image has BART installed at /bart_dir. The $topdir environment variable is set to this directory inside the image. This means that the instructions for the demo listed here https://github.com/exosports/BART/tree/master/examples/demo still work, but we need to mount a directory for outputs into the container for two reasons:

1. The demo expects your output directory to be parallel to the BART directory
2. The container file system is read-only (this is only a problem because of (1); being read-only is actually preferred because it helps ensure reproducible results)

• If the output directory wasn't required to be parallel to BART, you could run the container anywhere in $HOME because Singularity mounts $HOME of the current user into the container by default

The image has a directory parallel to BART that is meant for output at /bart_dir/run. Make a directory on your host system where you want to store results. For the sake of this guide, let's say it's under your current directory at demo/run and you have pulled the singularity image

singularity pull --name bart.sif shub://davecwright3/bart-singularity

to your current directory as well. Then start a shell in the singularity container with the bind mount specified

singularity shell -B demo/run:/bart_dir/run bart.sif

The BART conda environment will be automatically activated. Now just cd $topdir/run and follow the instructions here https://github.com/exosports/BART/tree/master/examples/demo if you would like to do a demo run. You can exit the container whenever you are done, and your results will remain in your demo/run directory.

License

Bayesian Atmospheric Radiative Transfer (BART), a code to infer properties of planetary atmospheres based on observed spectroscopic information.

This project was completed with the support of the NASA Planetary Atmospheres Program, grant NNX12AI69G, held by Principal Investigator Joseph Harrington. Principal developers included graduate students Patricio E. Cubillos and Jasmina Blecic, programmer Madison Stemm, and undergraduates M. Oliver Bowman and Andrew S. D. Foster. The included 'transit' radiative transfer code is based on an earlier program of the same name written by Patricio Rojo (Univ. de Chile, Santiago) when he was a graduate student at Cornell University under Joseph Harrington. Statistical advice came from Thomas J. Loredo and Nate B. Lust.

Copyright (C) 2015-2016 University of Central Florida. All rights reserved.

This is a test version only, and may not be redistributed to any third party. Please refer such requests to us. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Our intent is to release this software under an open-source, reproducible-research license, once the code is mature and the first research paper describing the code has been accepted for publication in a peer-reviewed journal. We are committed to development in the open, and have posted this code on github.com so that others can test it and give us feedback. However, until its first publication and first stable release, we do not permit others to redistribute the code in either original or modified form, nor to publish work based in whole or in part on the output of this code. By downloading, running, or modifying this code, you agree to these conditions. We do encourage sharing any modifications with us and discussing them openly.

We welcome your feedback, but do not guarantee support. Please send feedback or inquiries to: Patricio Cubillos [email protected] Jasmina Blecic [email protected] Joseph Harrington [email protected]

or alternatively, Joseph Harrington, Patricio Cubillos, and Jasmina Blecic UCF PSB 441 4111 Libra Drive Orlando, FL 32816-2385 USA

Thank you for testing BART!