Installation Issues

Fortran Compiler

1. Missing Fortran compiler

pymc requires a fortran compiler in order to work. Please ensure pymc can be imported.

>>> import pymc

During installation, MPAthic will look for existing fortran compilers on the user’s machine. If none are present, the following error will be thrown:

_images/install_issues_1.png

Fix

We recommend installing GCC, as this satisfies both Non-Python MPAthic dependencies (i.e. Cython and pymc). In addition to official instructions, GCC can be obtained easily on macOS via homebrew:

brew install gcc

2. Updating gcc

Updates to gcc does not seem to update the paths required by pymc. An example is shown below where the user initially installed gcc 4 but then updated to version 5:

_images/install_issues_gcc_version.png

Fix

Re-installing the version of gcc required by pymc (hence, mpathic) fixes this issue. In the case above, gcc version 4 was re-installed.

Cython

Ensure the correct version of Cython is installed.

$ pip freeze | grep 'Cython'
$ Cython==0.28.1

1. Existing Cython versions

_images/install_issues_2.png

2 Cython environment error

_images/install_issues_3.png

Fix

Run the anaconda command:

conda install -c anaconda cython

Or pip install directly:

pip install Cython==0.28.1

Permissions

The user might not have access to install to the global site-packages directory.

_images/install_issues_permission.png

Fix

pip install mpathic --user