mirror of
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138 lines
4.2 KiB
Markdown
138 lines
4.2 KiB
Markdown
```
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\ / / |-\ -----
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\ / | | \ |
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\ / / | | |--
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\ / | | / |
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\/ / |-/ -----
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*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
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```
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This is VIDE, the Void IDentification and Examination toolkit.
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For more information, see http://www.cosmicvoids.net
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Please cite arXiv:1406.1191 and arXiv:0712.0349 if you use this software,
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using the following suggested sentence:
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"This work uses voids identified with VIDE\footnote{\url{http:www.cosmicvoids.net}} (Sutter et al. 2014),
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which implements an enhanced version of ZOBOV (Neyrinck 2008) to construct
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voids with a watershed algorithm."
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License/Copyright information
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-----------------------------
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Copyright (C) 2010-2025 CNRS, Author: Guilhem Lavaux, 2011-2014 P.M. Sutter.
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This software is put under the GNU Public License.
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Please see LICENSE for further information.
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Mainline VIDE contributions from Ben Wandelt, Nico Hamaus, Alice Pisani,
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Paul Zivick, and Qingqing Mao.
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This toolkit includes ZOBOV, originally developed by Mark Neyrinck.
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See `zobov/zobov_readme.txt` for copyright/license information.
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SDF library provided by Michael S. Warren and John Salmon.
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HOD fitting code provided by Francisco Navarro.
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HOD halo population code provided by Jeremy Tinker.
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RAMSES module provided by Benjamin B. Thompson.
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Requirements
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------------
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The package swig needs to be installed and available in the PATH (http://www.swig.org/). It
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is required by scipy and we have not decided to bundle it with VIDE at the moment.
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Quick Start Guide
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-----------------
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It is generally advised to create a python3 virtual environment. This can be achieved as follows
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```
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python3 -m venv --system-site-packages $PLACE_OF_VENV
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source $PLACE_OF_VENV/bin/activate
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```
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where `$PLACE_OF_VENV` is where you decide to put your environment on your
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harddrive (e.g. `$HOME/my_venv`).
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Note: on OSX there are some difficulties to use the native clang compiler.
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Please use a brew installed compiler like GCC.
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```
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brew install gcc
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export CC=/usr/local/bin/gcc-10
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export CXX=/usr/local/bin/g++-10
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```
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The gcc-10 is of course dependent on the version that was installed by brew.
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After this step you may start the build process
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```
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python3 setup.py build
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```
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It will take a lot of time. It may also download python packages that you miss
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on your system. On BigSur some of them fail to compile by default.
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After installing the package with
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```python3 setup.py install
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```
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To test that the package is indeed installed you can execute
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```
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python3 -m void_pipeline
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```
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which will state
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```
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Usage: ./generateCatalog.py parameter_file.py
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```
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The VIDE tools are all packaged in the `vide` package.
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Running with simulation
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-----------------------
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Using simulation requires a preliminary step, consisting in using the script
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`vide_prepare_simulation` which is installed during the installation procedure.
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The script generates mock catalog and a default pipeline to handle simulations.
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An example of the complete procedure is given here-below:
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```
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mkdir $HOME/my_vide_test
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cp python_tools/void_pipeline/datasets/example_simulation.py $HOME/my_vide_test
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mkdir $HOME/my_vide_test/examples
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cp examples/example_simulation_z0.0.dat $HOME/my_vide_test/examples
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cd $HOME/my_vide_test
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vide_prepare_simulation --all --parm example_simulation.py
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python3 -m void_pipeline example_simulation/sim_ss1.0.py
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```
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The example copies the required data in a separate directory. Then, we execute
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the `vide_prepare_simulation` script to generate the auxiliary pipeline. The
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`void_pipeline` is finally executed on this generated script.
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Notes for CONDA
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---------------
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If you use a conda installation, you have to be sure to use all the building tools that
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are consistent. On linux that means for example installing the conda packages `gcc_linux-64`
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and `gxx_linux-64`. In addition to that it is recommended to define the environment variable
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`LIBRARY_PATH=the_path_of_your_conda_environment_with_/lib`. For example if your environment
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is in '/home/user/conda' you should define
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```
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export LIBRARY_PATH=/home/user/conda/lib
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```
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You can then initiate the construction with
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```
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python3 setup.py build
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```
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Version Summary
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-----------------
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v1.0 - Initial Release
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v2.0 - Ported to python3, revisited build system
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