.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/hello_world.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_hello_world.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_hello_world.py:


Hello World!
=================

Interface Tutorial

Requirements:
    - HPC cluster
    - Python 3.x

Author: DY

.. GENERATED FROM PYTHON SOURCE LINES 14-19

.. code-block:: Python


    from pathlib import Path
    import os
    import time








.. GENERATED FROM PYTHON SOURCE LINES 20-24

One of the motivations behind reForge was to provide a user- and beginner-friendly interface
for managing potentially hundreds or thousands of MD simulations without having to switch 
between multiple scripts and constantly rewriting them—all while staying within comfort of Python.
This is what the 'cli' module is for:

.. GENERATED FROM PYTHON SOURCE LINES 24-26

.. code-block:: Python

    from reforge.cli import run, sbatch, dojob








.. GENERATED FROM PYTHON SOURCE LINES 27-29

The idea is very simple: suppose you have "n" mutants and you need to perform "n" independent runs 
for each mutant to achieve sufficient sampling.

.. GENERATED FROM PYTHON SOURCE LINES 29-32

.. code-block:: Python

    systems = [f'mutant_{i}' for i in range(4)]
    mdruns = [f'mdrun_{i}' for i in range(4)]








.. GENERATED FROM PYTHON SOURCE LINES 33-34

The functions run, sbatch, and dojob allow you to execute the same script for all cases:

.. GENERATED FROM PYTHON SOURCE LINES 34-38

.. code-block:: Python

    for system in systems:
        for mdrun in mdruns:
            run(f'echo "Hello, I\'m run {mdrun} of {system}"')








.. GENERATED FROM PYTHON SOURCE LINES 39-40

Alternatively, you can call run like this:

.. GENERATED FROM PYTHON SOURCE LINES 40-44

.. code-block:: Python

    for system in systems:
        for mdrun in mdruns:
            run('echo', 'Hello, I\'m run', f'{mdrun} of {system}')     








.. GENERATED FROM PYTHON SOURCE LINES 45-47

Alternatively, you can sbatch a script. This command passes all positional arguments to the script 
and keyword arguments to the SLURM scheduler.

.. GENERATED FROM PYTHON SOURCE LINES 47-52

.. code-block:: Python

    if 0:  # Set to 1 to actually submit jobs.
        for system in systems:
            for mdrun in mdruns:
                sbatch('hello.sh', mdrun, system, mem='50M', t='00:00:01', partition='htc', qos='public')   








.. GENERATED FROM PYTHON SOURCE LINES 53-54

By default, output is written to "slurm_jobs/output_file" and "slurm_jobs/error_file".

.. GENERATED FROM PYTHON SOURCE LINES 54-60

.. code-block:: Python

    outfiles = [f for f in Path('slurm_jobs').glob('*output*')]
    for fpath in outfiles:
        with open(fpath, 'r') as file:
            # Print only the first line of each output file.
            print(file.readline(), end='')





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    Hello I am run mdrun_0 of system mutant_1
    Hello I am run mdrun_2 of system mutant_0
    Hello I am run mdrun_2 of system mutant_3
    Hello I am run mdrun_1 of system mutant_2
    Hello I am run mdrun_0 of system mutant_2
    Hello I am run mdrun_3 of system mutant_1
    Hello I am run mdrun_2 of system mutant_1
    Hello I am run mdrun_1 of system mutant_3
    Hello I am run mdrun_3 of system mutant_0
    Hello I am run mdrun_0 of system mutant_3
    Hello I am run mdrun_1 of system mutant_0
    Hello I am run mdrun_1 of system mutant_1
    Hello I am run mdrun_3 of system mutant_2
    Hello I am run mdrun_3 of system mutant_3
    Hello I am run mdrun_0 of system mutant_0
    Hello I am run mdrun_2 of system mutant_2




.. GENERATED FROM PYTHON SOURCE LINES 61-63

For convenience, dojob will either submit or run the script based on its first argument.
In this case, we do not want to sbatch the script.

.. GENERATED FROM PYTHON SOURCE LINES 63-67

.. code-block:: Python

    submit = False
    for system in systems:
        for mdrun in mdruns:
            dojob(submit, 'hello.sh', mdrun, system, mem='50M', t='00:00:01', partition='htc', qos='public')








.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 1.175 seconds)


.. _sphx_glr_download_auto_examples_hello_world.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: hello_world.ipynb <hello_world.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: hello_world.py <hello_world.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: hello_world.zip <hello_world.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_