Installation and Requirements

Basic Installation

To install Abed only for the current user, run:

$ python2 setup.py install --user

Note, if you’re on LISA, you need to specify the Python version you wish to use by first running:

$ module load python/2.7.9

After installation, the executable will be placed in ~/.local/bin, which you should add to your PATH variable for convenience, by placing the following line in your ~/.bashrc:

export PATH=$PATH:~/.local/bin/

After this, either open a new terminal or run source ~/.bashrc.

Note: Installation of Abed and its dependencies must be done under the same Python version.

Requirements

Abed works with a single configuration file. It was designed for the Dutch LISA compute cluster, but can hopefully be generalized to other environments as well. Some functionality provided by LISA is used which may not be available in other environments:

• Scratch directories: tasks executed through the PBS server are executed on nodes which have a temporary local storage directory, called the “scratch” directory. The location of this storage is provided through the TMPDIR environment variable, which is used by Abed to place the result files. This reduces communication overhead to the users home directory, which is located outside the compute node.

• mpicopy is a command which copies data from the home directory of the user to the scratch directory on the node. The Abed setting ‘PBS_MPICOPY’ can be used to define folders or files which need to be copied to the nodes. In the skeleton configuration file the dataset, executable, abed task file are added to this list.

• pbzip2

• mail system, see here