Installation¶

Dependencies¶

Modern C++ compiler
cmake
sqlite3
Python3
Jupyter Notebook
Open MPI and mpi4py (optional)

Installation on macOS¶

Install Modern C++:

xcode-select --install    # Then click "install" button on dialog

Install Homebrew https://brew.sh, an open source package manager

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

To install cmake:

brew install cmake

You will also want python3; both homebrew’s python and Anaconda3 have been tested.

Experience seems to indicate Anaconda3 is the most fool-proof setup for most people.

Another option is to use homebrew python:

brew install python

To use the Signatures tool, which uses MPI <https://en.wikipedia.org/wiki/Message_Passing_Interface> you also need:

brew install openmpi
pip install mpi4py

Finally,

# Install DSGRN
git clone https://github.com/shaunharker/DSGRN.git
cd DSGRN
./install.sh

Installation on Linux¶

On an HPC cluster it is likely modern compilers, python, and a suitable version of MPI are already installed. However, you cannot pip install due to permissions issues. In this case one solution is to pass the --user flag:

pip install mpi4py --user
# Install DSGRN
git clone https://github.com/shaunharker/DSGRN.git
cd DSGRN
./install.sh --user

This would put the Signatures script in ~/.local/bin, so you may consider putting that on your PATH.

On your own system you may use the package manager to install dependencies, e.g.

sudo apt install libopenmpi-dev

on Ubuntu.

Uninstalling¶

pip uninstall DSGRN

Troubleshooting¶

Python issues:¶

If python won’t stop giving you trouble, I recommend trying Anaconda3.

This will install into a folder named anaconda3 and add a line in ~/.bash_profile:

#added by Anaconda3 5.0.1 installer
export PATH="/PATH/TO/anaconda3/bin:$PATH"

This will redirect command line python and pip. Note you may have to start a new bash session for the path changes to take effect (i.e. close and reopen the terminal program). This has the effect of plastering over any problems you might be having with multiple installations/permissions problems/jupyter not seeing the package/etc.

Permissions issues on macOS:¶

If the installation gives permissions issues, oftentimes the culprit is broken permissions on the subfolders of the homebrew folder /usr/local.

First, see what

brew doctor

says. A common fix is:

sudo chown -R $(whoami) $(brew --prefix)/*

If it still doesn’t work after this, then you might try uninstalling and reinstalling homebrew.

To uninstall homebrew:

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

Or sudo if it gives issues:

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

To install homebrew (don’t use sudo here!):

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

Linux permissions issues:¶

For missing dependencies, you’ll need to contact your system admin.

For python modules, you can pass the --user flag:

# Install DSGRN
git clone https://github.com/shaunharker/DSGRN.git
cd DSGRN
./install.sh --user

Python/Jupyter Integration issues:¶

If the package installs but it is not visible in jupyter, the likely problem is that the jupyter python kernel is not the same python for which pychomp was installed. That is, you may have multiple pythons on your system.

You can try to confirm this by typing

which python
which pip
which jupyter

Possible fixes include steps such as

Checking/changing your environmental variable PATH in ~/.bash_profile or .bashrc
Uninstalling python and jupyter, then reinstalling python then jupyter
Plastering over with anaconda3
Googling for answers until 3AM

You suspect you have an old install of DSGRN conflicting:¶

In python, type

import DSGRN
print(DSGRN.__name__)

This will tell you the path to the DSGRN the python module loader used, and you can check if it correct.