AiiDA-ICON Recipes

Run ICON via a wrapper script

Warning

None of the following will work if you opt out of running with MPI.

On some HPC facilities it is common to run ICON using the following pattern

mpirun --<options> wrapper_script.sh </path/to/icon/binary>

srun --<options> wrapper_script.sh </path/to/icon/binary>

etc, where the job of the wrapper_script.sh is to prepare environment variables and other things specific to the machine being used to obtain the best possible performance.

Here is an example how to do this with AiiDA-ICON:

from aiida import orm
from aiida_icon.calculations import IconCalculation

builder = IconCalculation.get_builder()
builder.wrapper_script = orm.SinglefileData("/path/to/my/wrapper_script.sh")
...

Currently you have to have a copy of this wrapper script locally, which AiiDA will upload for you. Alternatively you can create a SinglefileData instance from a string with the script contents.

This is so that the AiiDA graph after the fact can record exactly how you ran ICON at the time.

Note

Adding the .wrapper_script input will automatically add a line to the builder.metadata.options.prepend_text. Take care not to delete it or you will get an error at run time that the wrapper script is not executable.

Note

Adding the .wrapper_script input will automatically add the wrapper script to builder.metadata.options.mpirun_extra_params. Take care to keep it as the last entry of that list (unless it takes additional arguments itself, those have to go afterwards).

Since this affects also the prepend text as well as the parameters sent to the "mpirun equivalent" on your system, here is a continuation of the above example that shows how to manipulate those in the presence of a wrapper script.

builder.wrapper_script = orm.SinglefileData("/path/to/my/wrapper_script.sh")
...
options = builder.metadata.options
# load a module before making the wrapper script executable
# and print a message afterwards
options.prepend_text = f"module load somemodule\n{options.prepend_text}\necho 'everything ready'"
# add an mpirun/srun/etc option
options.mpirun_extra_params.insert(-1, "--myoption")

Note

AiiDA-ICON will rename the uploaded copy of your wrapper script to run_icon.sh for simplicity and

universal readability.