CHomP -- Computation Homology Project software
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README.md

CHomP -- Computational Homology Project software

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Overview

This software is a tool for computational homology for both cellular complexes and induced homology on maps. It is based on discrete Morse theory. It is used to compute Conley indices in the Conley-Morse-Database project.

See "LICENSE" for license details. See "INSTALL" for more installation notes.

Installation

Dependencies

  • cmake
  • boost
  • GMP
  • CImg
  • X11

General Instructions

  • First install dependencies.
  • Then, either:

Option 1. Install in default location.

To install into the system, i.e. /usr/local install with

./install.sh

In the event of an error (e.g. the installer says Run with admin privileges or choose a non-system install path with —prefix) then see the troubleshooting steps below.

Option 2. Install in a custom location.

Install via

./install.sh --prefix=/path/to/install/folder

Specific instructions for macOS:

For macOS the easiest way to install dependencies is with "homebrew" http://brew.sh.

Install homebrew via

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Install dependencies via

brew install cmake
brew install gmp
brew install boost
brew install cimg

To install X11, follow the instructions on https://www.xquartz.org

To install CHomP:

git clone https://github.com/shaunharker/CHomP.git
cd CHomP
./install.sh

To test an example:

chomp-simplicial ./examples/simplex.simp

Examples

Cubical complexes

Example:

chomp-cubical ./examples/square.cub

File format: a list of new-line separated d-tuples, where d is the dimension of the cubical complex, and the tuples represent d-dimensional cubes which will be added to the complex (along with all of their faces):

Example: (Annulus-like shape made out of squares)

(0, 1)
(0, 2)
(1, 0)
(1, 2)
(2, 0)
(2, 1)
(2, 2)

Simplicial complexes

chomp-simplicial ./examples/simplex.simp

File format: each line represents a simplex in the complex given by its vertices. For each simplex encountered, the simplex and all of its faces are generated. For instance 0 1 2 constructs a 2-cell, 3 1-cells, and 3 0-cells. The line 4 would create a single 0-cell corresponding to the vertex 4. Because subfaces are automatically created, it is sufficient to include maximal simplices (though allowed to include all)

Example: (Tetrahedron along with an isolated vertex)

0 1 2
0 1 3
0 2 3
1 2 3
4

General chain complexes (given by matrices for boundary map)

chomp-matrix ./examples/torus.mat

File format: The format is in terms of a sparse matrix representation of the boundary maps $d_n : C_{n+1} \to C_{n}$ for $n = 0 \cdots D-1$. The file has $D$ sections, corresponding to each map $d_0$, $d_1$, in turn. Each section begins with a line n, where $n$ is the index of the boundary map. Then follow lines indicating the non-zero entries for the incidence matrix for $d_n$. In particular each line is a triple i j k indicating that $d_{n}{i,j} = k$, i.e. the jth cell in $C{n+1}$ has in its boundary $k$ times the cell $i$ in $C_{n}$. It is allowed to include zero entries in the matrix explicitly, and it necessary for the software to learn of any cells which are not in the image of a boundary operator.

Example: (Torus; 1 2d-cell, 2 1d-cells, and 1 1d cell)

0
0 0 0
0 1 0
1
0 0 0
1 0 0

Troubleshooting

Question. The installer fails with the message

Run with admin privileges or choose a non-system install path with —prefix

What do I do?

Answer. The default install location is /usr/local and typing ./install.sh is equivalent to typing ./install.sh --prefix=/usr/local. The error indicates that /usr/local is owned by the system and is not writable. Thus it doesn't do the install unless you give it a different location to install or otherwise change the situation.

Three explicit solutions are given below. The first two are for macOS users.

Solution 1. Install homebrew.

On macOS the package manager homebrew is widely used and sets the permissions on /usr/local to be writable. CHomP expects this is installed (as it is the simplest way to install the dependencies) and has made /usr/local writable. Therefore, if homebrew is not installed then installing it will likely solve the problem as it will fix the permissions on /usr/local.

To check if homebrew is installed, type

brew help

If this says command not found then homebrew is not installed. Instructions for installing homebrew can be found on http://brew.sh. Currently, it is as simple as running the following line on the terminal and following instructions:

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Solution 2. Change the permissions on /usr/local

On macOS permissions on /usr/local are typically made writable by user (thus preventing the above problem) when homebrew is installed.

It is possible that an OS update has mucked up the permissions on /usr/local subsequent to homebrew being installed. In particular the El Capitan update was known to do this.

Thus, the permissions on /usr/local are not suitable and need to be fixed. A known solution to this problem (http://stackoverflow.com/questions/16432071/how-to-fix-homebrew-permissions) is to type the following lines on the command line:

sudo chown -R "$USER":admin /usr/local
sudo chown -R "$USER":admin /Library/Caches/Homebrew

Solution 3. Make a custom installation which is not to /usr/local

Note. This solution is not recommended to macOS users, but it IS recommended for Linux users who do not have the privileges to change the permissions on /usr/local or otherwise want a custom install location.

To install to a custom location, use

./install.sh --prefix=/path/to/where/you/want/it/installed

This will install the executables to

/path/to/where/you/want/it/installed/bin

Now update ~/.bashrc to add this location to the PATH environmental variable, so that the command line can find the executables (e.g. chomp-simplicial). That is, add the line

export PATH=/path/to/where/you/want/it/installed/bin/:$PATH

to the end of your ~/.bashrc file (create one if it does not exist).

More information

Documentation can be found here.

Please e-mail Shaun Harker sharker81@gmail.com about problems or feature requests.