gprMax/docs/source/hpc.rst

.. _hpc:

***
HPC
***

Using gprMax in an HPC environment is heavily dependent on the configuration of your specific HPC/cluster, e.g. the and compiler modules, programming environments, and job submission processes will vary between systems.

.. note::

    General details about the types of acceleration available in gprMax are shown in the :ref:`accelerators` section.


Installation
============

Full installation instructions for gprMax can be found in the :ref:`Getting Started guide <installation>`, however HPC systems programming environments can vary (and often have pre-installed software). For example, the following can be used to install gprMax on `ARCHER2, the UK National Supercomputing Service <https://www.archer2.ac.uk/>`_:

.. code-block:: console

    $ git clone https://github.com/gprMax/gprMax.git
    $ cd gprMax
    $ module load PrgEnv-gnu
    $ module load cray-python
    $ module load cray-fftw
    $ module load cray-hdf5-parallel
    $ export CC=cc
    $ export CXX=CC
    $ export FC=ftn
    $ python -m venv --system-site-packages --prompt gprMax .venv
    $ source .venv/bin/activate
    (gprMax)$ python -m pip install --upgrade pip
    (gprMax)$ HDF5_MPI='ON' python -m pip install --no-binary=h5py h5py
    (gprMax)$ python -m pip install -r requirements.txt
    (gprMax)$ python -m pip install -e .

.. tip::

    Consult your system's documentation for site specific information.

Job Submission examples
=======================

High-performance computing (HPC) environments usually require jobs to be submitted to a queue using a job script. The following are examples of job scripts for an HPC environment that uses `Open Grid Scheduler/Grid Engine <http://gridscheduler.sourceforge.net/index.html>`_, and are intended as general guidance to help you get started. The names of parallel environments (``-pe``) and compiler modules will depend on how they were defined by your system administrator.

OpenMP
^^^^^^

:download:`gprmax_omp.sh <../../toolboxes/Utilities/HPC/gprmax_omp.sh>`

Here is an example of a job script for running models, e.g. A-scans to make a B-scan, one after another on a single cluster node. This is not as beneficial as the OpenMP/MPI example, but it can be a helpful starting point when getting the software running in your HPC environment. The behaviour of most of the variables is explained in the comments in the script.

.. literalinclude:: ../../toolboxes/Utilities/HPC/gprmax_omp.sh
    :language: bash
    :linenos:

In this example 10 models will be run one after another on a single node of the cluster (on this particular cluster a single node has 16 cores/threads available). Each model will be parallelised using 16 OpenMP threads.

MPI domain decomposition
^^^^^^^^^^^^^^^^^^^^^^^^

Here is an example of a job script for running a model across multiple tasks in an HPC environment using MPI. The behaviour of most of the variables is explained in the comments in the script.

.. note::

    This example is based on the `ARCHER2 <https://www.archer2.ac.uk/>`_ system and uses the `SLURM <https://slurm.schedmd.com/>`_ scheduler.

.. literalinclude:: ../../toolboxes/Utilities/HPC/gprmax_omp_mpi.sh
    :language: bash
    :linenos:

In this example, the model will be divided across 8 MPI ranks in a 2 x 2 x 2 pattern:

.. figure:: ../../images_shared/mpi_domain_decomposition.png
    :width: 80%
    :align: center
    :alt: MPI domain decomposition diagram

    The full model (left) is evenly divided across MPI ranks (right).

The ``--mpi`` argument is passed to gprMax which takes three integers to define the number of MPI processes in the x, y, and z dimensions to form a cartesian grid.

Unlike the grid engine examples, here we specify the number of CPUs per task (16) and the number of tasks (8), rather than the total number of CPUs/slots.

.. note::

    Some restrictions apply to the domain decomposition when using fractal geometry as explained :ref:`here <fractal_domain_decomposition>`.

MPI task farm
^^^^^^^^^^^^^

:download:`gprmax_omp_taskfarm.sh <../../toolboxes/Utilities/HPC/gprmax_omp_taskfarm.sh>`

Here is an example of a job script for running models, e.g. A-scans to make a B-scan, distributed as independent tasks in an HPC environment using MPI. The behaviour of most of the variables is explained in the comments in the script.

.. literalinclude:: ../../toolboxes/Utilities/HPC/gprmax_omp_taskfarm.sh
    :language: bash
    :linenos:

In this example, 10 models will be distributed as independent tasks in an HPC environment using MPI.

The ``--taskfarm`` argument is passed to gprMax which takes the number of MPI tasks to run. This should be the number of models (worker tasks) plus one extra for the master task.

The ``NSLOTS`` variable which is required to set the total number of slots/cores for the parallel environment ``-pe mpi`` is usually the number of MPI tasks multiplied by the number of OpenMP threads per task. In this example the number of MPI tasks is 11 and the number of OpenMP threads per task is 16, so 176 slots are required.


Job array
^^^^^^^^^

:download:`gprmax_omp_jobarray.sh <../../toolboxes/Utilities/HPC/gprmax_omp_jobarray.sh>`

Here is an example of a job script for running models, e.g. A-scans to make a B-scan, using the job array functionality of Open Grid Scheduler/Grid Engine. A job array is a single submit script that is run multiple times. It has similar functionality, for gprMax, to using the aforementioned MPI task farm. The behaviour of most of the variables is explained in the comments in the script.

.. literalinclude:: ../../toolboxes/Utilities/HPC/gprmax_omp_jobarray.sh
    :language: bash
    :linenos:

The ``-t`` tells Grid Engine that we are using a job array followed by a range of integers which will be the IDs for each individual task (model). Task IDs must start from 1, and the total number of tasks in the range should correspond to the number of models you want to run, i.e. the integer with the ``-n`` flag passed to gprMax. The ``-i`` flag is passed to gprMax along with the specific number of the task (model) with the environment variable ``$SGE_TASK_ID``.

A job array means that exactly the same submit script is going to be run multiple times, the only difference between each run is the environment variable ``$SGE_TASK_ID``.