Basic Execution

ShapePipe pipelines are launched and managed via the shapepipe_run script.

A list of command line arguments can be displayed using the --help option:

See also

The shapepipe environment will need to be built and activated in order to run this script (see Installation).

shapepipe_run --help

The options for defining a pipeline are managed via a configuration file.

Running ShapePipe with Joblib

By default ShapePipe is run using Joblib to manage parallel processes. The shapepipe_run script can run as follows


which will by default look for a file called config.ini in the current directory. To specify the path to a given configuration file (with any name) you would run

shapepipe_run -c <PATH TO CONFIG FILE>

Running the Pipeline with MPI

ShapePipe can also use mpi4py for managing parallel processes on clusters with multiple nodes. The shapepipe_run script can be run with MPI as follows

mpiexec -n <NUMBER OF CORES> shapepipe_run

where <NUMBER OF CORES> is the number of cores to allocate to the run.