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This is VIDE, the Void IDentification and Examination toolkit.

For more information, see http://www.cosmicvoids.net

Please cite arXiv:1406.1191 and arXiv:0712.0349 if you use this software, using the following suggested sentence:

"This work uses voids identified with VIDE\footnote{\url{http:www.cosmicvoids.net}} (Sutter et al. 2014), which implements an enhanced version of ZOBOV (Neyrinck 2008) to construct voids with a watershed algorithm."

License/Copyright information

Copyright (C) 2010-2020 Guilhem Lavaux, 2011-2014 P.M. Sutter. This software is put under the GNU Public License. Please see LICENSE for further information.

Mainline VIDE contributions from Ben Wandelt, Nico Hamaus, Alice Pisani, Paul Zivick, and Qingqing Mao. This toolkit includes ZOBOV, originally developed by Mark Neyrinck. See zobov/zobov_readme.txt for copyright/license information. SDF library provided by Michael S. Warren and John Salmon. HOD fitting code provided by Francisco Navarro. HOD halo population code provided by Jeremy Tinker. RAMSES module provided by Benjamin B. Thompson.

Requirements

The package swig needs to be installed and available in the PATH (http://www.swig.org/). It is required by scipy and we have not decided to bundle it with VIDE at the moment.

Quick Start Guide

It is generally advised to create a python3 virtual environment. This can be achieved as follows

python3 -m venv --system-site-packages $PLACE_OF_VENV
source $PLACE_OF_VENV/bin/activate

where $PLACE_OF_VENV is where you decide to put your environment on your harddrive (e.g. $HOME/my_venv).

Note: on OSX there are some difficulties to use the native clang compiler. Please use a brew installed compiler like GCC.

brew install gcc
export CC=/usr/local/bin/gcc-10
export CXX=/usr/local/bin/g++-10

The gcc-10 is of course dependent on the version that was installed by brew.

After this step you may start the build process

python3 setup.py build

It will take a lot of time. It may also download python packages that you miss on your system. On BigSur some of them fail to compile by default.

After installing the package with

To test that the package is indeed installed you can execute

python3 -m void_pipeline

which will state

Usage: ./generateCatalog.py parameter_file.py

The VIDE tools are all packaged in the vide package.

Running with simulation

Using simulation requires a preliminary step, consisting in using the script vide_prepare_simulation which is installed during the installation procedure. The script generates mock catalog and a default pipeline to handle simulations. An example of the complete procedure is given here-below:

mkdir $HOME/my_vide_test
cp python_tools/void_pipeline/datasets/example_simulation.py $HOME/my_vide_test
mkdir $HOME/my_vide_test/examples
cp examples/example_simulation_z0.0.dat $HOME/my_vide_test/examples
cd $HOME/my_vide_test
vide_prepare_simulation   --all --parm example_simulation.py
python3 -m void_pipeline example_simulation/sim_ss1.0.py

The example copies the required data in a separate directory. Then, we execute the vide_prepare_simulation script to generate the auxiliary pipeline. The void_pipeline is finally executed on this generated script.

Notes for CONDA

If you use a conda installation, you have to be sure to use all the building tools that are consistent. On linux that means for example installing the conda packages gcc_linux-64 and gxx_linux-64. In addition to that it is recommended to define the environment variable LIBRARY_PATH=the_path_of_your_conda_environment_with_/lib. For example if your environment is in '/home/user/conda' you should define

export LIBRARY_PATH=/home/user/conda/lib

You can then initiate the construction with

python3 setup.py build

Version Summary

v1.0 - Initial Release v2.0 - Ported to python3, revisited build system