GENESIS: Documentation

Related Documentation:

Developer Installation From Source On Mac OSX – Lion

The procedure for the installation of GENESIS on a Mac OSX is similar to that for a Linux build on a regular PC. The major difference is that it requires build tools for the Mac. These are somewhat hidden on disk 2 of the Mac OS installation disks. Installation requires administrator privileges. (Note: Some installation must be done from the Terminal). If you do not have administrator privileges you should contact your system administrator for help. The Terminal can be found in the Applications –> Utilities folder. For regular use of GENESIS it is convenient to place a Terminal in the dock for easy access. Installation requires executing the following major steps:

Prepare and upgrade the system software

Install the following packages:

WARNING: The compilers available from MacPorts should NOT be used for installation (see below). Prior to installing the DeveloperPackage you should check which Perl libraries OSX uses with “which perl”. This should return /usr/bin/perl. If the response is /opt/local/bin/perl, there is a MacPorts installation of Perl. This is most easily corrected by removing the MacPorts path /opt/local/bin from your path in the .profile file (or the .bash_profile) in your home directory. To do this open the .profile file in an editor and convert the line (or similar):


by removing /opt/local/bin to give:


Note: Only remove the MacPorts path and leave all others alone. If you do not make this change, running GENESIS may result in a bus error as the correct Perl libraries will not be found. It may also call MacPorts versions of build tools, which can result in some undesirable behavior.

Download and Install the DeveloperPackage

Download the latest version of the DeveloperPackage, available from the GENESIS package archive. It is called developer-release-label.tar.gz, where release-label is the current release identifier. (Note: If downloading via your browser, do not unpack the package during the download as it will be placed into its own subdirectory).

Install software packages

Download the and install the developer package. Once that is done source code can be pulled from the GENESIS repository and a build performed with the following commands:

  1. neurospaces_create_directories
  2. neurospaces_pull
  3. neurospaces_update
  4. neurospaces_configure
  5. neurospaces_install (requires admin password)

If there are any mixed architectures on some of the programs on the machine then you must use the –universal flag. For instance if the current version of python in your path is 32-bit and the host machine is 64-bit, then you should use the universal flag. Easy way to tell what a programs architecture is is to use the lipo command on the executable file:

lipo -info ‘which python‘  
Architectures in the fat file: /usr/bin/python are: x86_64 i386 ppc7400

The architectures can be read as follows.

If you are using all pure apple programs for perl and python with no macports, then it is safe to use –universal for any calls to neurospaces_install and neurospaces_upgrade. However it should be noted that this will increase the compile time three fold.

Check if installation was successful

Once these have completed the installation can be tested with the following command:

This will perform a series of regression tests and save the output to file. The output can be checked by typing “less /tmp/check.out”. Importantly, search for lines containing the string error_count that will indicate any inconsistencies with the installation.

Note: The running of tests is optional, but strongly advised.