FabMaMiCo Commands

FabMaMiCo offers the following tasks to set up and run MaMiCo simulations.

Verify FabMaMiCo Plugin Installation

mamico_test_plugin

fabsim <machine> mamico_test_plugin

This should output a message that the FabMaMiCo plugin is installed correctly. The parameters <machine> is irrelevant for this command.

Get System Information

The following commands make use of the remote lmod system to load modules.

mamico_mod_overview

fabsim <machine> mamico_mod_overview

This lists an overview of available modules that can be loaded via lmod on the remote machine.

mamico_mod_available

fabsim <machine> mamico_mod_available:<query>

This lists a more detailed overview of available modules that can be loaded via lmod on the remote machine. The optional parameter <query> can be used to filter the list of available modules.

mamico_mod_keyword

fabsim <machine> mamico_mod_keyword:<keyword>

This searches modules that can be loaded via lmod on the remote machine for a specific keyword.

Handle MaMiCo Installations

mamico_install

fabsim <machine> mamico_install:<config>

This downloads the source code of MaMiCo and optionally of ls1-mardyn and OpenFOAM, transfers it to the remote machine and compiles it according to the configuration specified in plugins/FabMaMiCo/config_files/<config>/settings.yml.

Note

The compilation process is submitted as a job. However, certain remote hosts like HSUper require compilation on the login node. The job script is thus executed via bash, and its completion might take a while as the local shell shows the progress of the remote compilation.

mamico_list_installations

fabsim <machine> mamico_list_installations:verbose

This lists all MaMiCo installations on the remote machine. The optional parameter verbose provides the settings of each installations.

mamico_installation_available

fabsim <machine> mamico_installation_available:<checksum>

This checks if a specific MaMiCo installation is available on the remote machine.

mamico_remove_installation

fabsim <machine> mamico_remove_installation:<checksum>

This removes a specific MaMiCo installation from the remote machine, if it exists.

mamico_remove_all_installations

fabsim <machine> mamico_remove_all_installations

This removes all MaMiCo installations from the remote machine.

Execute MaMiCo Simulations

mamico_run

fabsim <machine> mamico_run:<config>

This command internally calls the mamico_install-task to make sure the MaMiCo executable is available. It then transfers all config files to the remote machine, generates a batch script file and submits it to the scheduler.

Note

Here, the command returns after the job has been submitted to the job scheduler.

Note

You can append the parameter replicas=<number> to run multiple replicas of the simulation.

mamico_run_ensemble

fabsim <machine> mamico_run_ensemble:<config>

This internally calls the mamico_install-task to make sure the MaMiCo executable is available. It requires multiple folders inside a SWEEP-directory. If a generate_ensemble.py script is available in the config directory, the script is executed to populate the SWEEP/ directory. The task copies all config files to the remote machine and generates a batch script file for each simulation. Finally, it submits all jobs to the scheduler.

MaMiCo Post-Processing

Note

The remote postprocessing is still under development.

MaMiCo Monitoring

mamico_stat

fabsim <machine> mamico_stat

This shows the output of squeue on the remote machine for the user defined in machines_user.yml.

mamico_jobs_overview

fabsim <machine> mamico_jobs_overview

This shows the number of jobs in the queue (planned, running) on the remote machine for the user defined in machines_user.yml.

mamico_jobs_cancel_all

fabsim <machine> mamico_jobs_cancel_all

This cancels all jobs in the queue on the remote machine for the user defined in machines_user.yml.