FabAlya is a FabSim3 plugin for automated Alya simulation code.

This plugin provides functionality to extend FabSim3's workflow and remote submission capabilities to Alya tasks.

To install FabSim3 toolkit, please follow the installation instruction.

In case of having any issue, please look at to the Known Issues page.

before submit a Alya simulation job, you should install FabAlya which provides functionality to extend FabSim3's workflow and remote submission capabilities to Alya tasks. Please got to your local FabSim3 folder , and install it by typing:

fab localhost install_plugin:FabMD

Once you have installed The FabAlya plugin, which will appear in FabSim3/plugins/FabAlya directory, , you need to take a few small configuration steps before submitting a job to remote machine.

Modify FabSim3/plugins/FabAlya/machines_FabAlya_user.yml file, and update the username and home_path_template variables with your username on MarenoStrum4 cluster.

...
marenostrum4:
    username: "pr1emk01"
    home_path_template: "/home/pr1emk00/pr1emk01"
    ...

Also, make sure the other required parameters for Alya job are filled correctly, variables such as :

1. ALYA_EXE_PATH : PATH to Alya code
2. MPIO_BIN_PATH : PATH to .mpio.bin files
3. ALYA_DAT_PATH : PATH to Alya input dat files
4. PYTHON_CODES_PATH: PATH to pre and post processing python codes
5. SH_SCRIPTS_PATH : PATH to pre and post processing sh scripts

Alya_simulation_config: &Alya_sim_config
  # ALYA_EXE_PATH: "/home/bsc21/bsc21717/Software/Alya_versions/777-hvad-pump-function_kpp_nobovel/Executables/unix_nastin_temper_fastest_ipo_onlyfiltAP/Alya.x"
  ALYA_EXE_PATH: "<PATH to Alya code>"

  MPIO_BIN_PATH: "<PATH to .mpio.bin files>"
  ALYA_DAT_PATH: "<PATH to Alya input dat files>"

  PYTHON_CODES_PATH: "<PATH to python pre/pos processing files>"
  PY_FILE_NAMES: ["field-ensi2mpio.py", "modifyHR.py", 
                  "remote_postpro.py", "remote_prepro.py"]

  SH_SCRIPTS_PATH: "<PATH to pre and post processing sh scripts>"
  SH_FILE_NAME: ["remote.sh", "remotepre.sh"]
 

To submit a Alya job, you can follow this structure:

fab <remote_machine_name> <Alya_task>:<Alya_config_name>

for example,

fab marenostrum4 alya:fluid

In case of testing to make sure that the job scripts is created correctly or file/folder structure is correct, you can add TestOnly=True option at the end of you command which do the same process but ignore the job_submission step.

fab marenostrum4 alya:fluid,TestOnly=True

To perform sensitivity analysis on input parameters, there are two sampler examples, namely (a) SCSampler (Stochastic Collocation sampler) and (b) PCESampler (Polynomial Chaos Expansion sampler). Both approach are implemented in Alya_SA.py python script.

• Alya_init_SA allows to run SA for parameter exploration.
• Alya_analyse_SA provides analysis of obtained results.

For the sensitivity analysis scripts, all input parameters are listed in FabSim3 Home)/plugins/FabAlya/templates/params.json file.

The configuration for a SA can be found in (FabSim3 Home)/plugins/FabAlya/SA/Alya_SA_config.yml as follows:

vary_parameters_range:
    # <parameter_name:>
    #   range: [<lower value>,<upper value>] 
    LAP:
        range: [5000, 50000]
    DENSI:
        range: [1.0, 1.1]
    VISCO:
        range: [0.03, 0.037]
    HR:
        range: [60.0, 80.0]
    EF:
        range: [0.1, 0.2]
    AORP:
        range: [1500.0, 2000.0]
    AOC:
        range: [0.0001, 0.001]
    AORS:
        range: [100.0, 500.0]

selected_vary_parameters: ["HR",
                          ]
distribution_type: "Uniform" # Uniform, DiscreteUniform
polynomial_order: 2
...
# available sampler: [SCSampler,PCESampler]
sampler_name: "SCSampler"
...
...
...

To vary input parameters and their corresponding distributions using stochastic collocation or polynomial chaos expansion samplers for sensitivity analysis, simply modify the selected_vary_parameters parameter in Alya_SA_config.yml file:

selected_vary_parameters: ["HR",
                          "DENSI",
                          "AORS"
                          ]

To change the number of polynomial order, modify the polynomial_order parameter in Alya_SA_config.yml file

polynomial_order: 2

And, by changing sampler_name parameter, you can select one of available SCSampler or PCESamplersampler for a SA run.

# available sampler: [SCSampler,PCESampler]
sampler_name: "SCSampler"

1. To execute sensitivy analysis on a remote machine, simply run:

fab marenostrum4 Alya_init_SA:fluid

2. Run the following command to copy back results from the remote machine and perform analysis. The results will then be in a directory inside (FabSim Home)/results.

fab marenostrum4 Alya_analyse_SA:fluid