Running Excalibur

Before running Excalibur in a new shell session, the file scripts/ini_excalibur.sh must be sourced:

cd Excalibur
source scripts/ini_excalibur.sh

Running locally

The main executable for running Excalibur is excalibur.py. This is a Python wrapper around the executable generated from the C++ code which provides a flexible way of configuring Excalibur by supplying a configuration file written in Python.

Excalibur can be run locally by providing the full path to a Python configuration file:

excalibur.py /path/to/config.py

The preferred location of configuration files is the cfg/excalibur subdirectory. For convenience, a relative path starting from this directory can be given instead of a full path, and the extension .py can be omitted. The following commands are equivalent:

excalibur.py /path/to/Excalibur/cfg/excalibur/example_subdirectory/example_config.py
excalibur.py cfg/excalibur/example_subdirectory/example_config.py
excalibur.py example_subdirectory/example_config.py
excalibur.py example_subdirectory/example_config

TAB-autocompletion is also implemented for excalibur.py and assumes the configuration file is located in a subdirectory of cfg/excalibur.

To see a list of command line arguments and their description, run:

excalibur.py --help

Some useful arguments are:

• -b: run in batch mode. This parameter takes an optional argument specifying the computing resource use. See -h
• -c: only create config and exit
• -f <n>: only process the first <n> input files

Running on a batch system

For the batch functionality of Excalibur, you need grid-control (see above). Note that the directory containing the go.py executable should be in your $PATH.

Additionally, the $EXCALIBUR_WORK variable has to be set to an existing directory. By default, it is set to /storage/a/$USER/zjet by ini_excalibur.sh if this directory exists. Make sure it exists or set $EXCALIBUR_WORK to a different folder. Note that the batch system worker nodes must have write access to this directory!

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