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Doc updates (#202)
Co-authored-by: Roberto Pastor Muela <[email protected]>
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‎.gitignore‎

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# Ignore rendered examples
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doc/source/examples/
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doc/source/API/_autosummary/
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doc/source/autoapi

‎doc/source/conf.py‎

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# Intersphinx mapping
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intersphinx_mapping = {
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"python": ("https://docs.python.org/dev", None),
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"python": ("https://docs.python.org/3", None),
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"numpy": ("https://numpy.org/devdocs", None),
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"matplotlib": ("https://matplotlib.org/stable", None),
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"imageio": ("https://imageio.readthedocs.io/en/stable", None),
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# general
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"GL06", # Found unknown section
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"GL07", # Sections are in the wrong order.
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"GL08", # The object does not have a docstring
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# "GL08", # The object does not have a docstring
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"GL09", # Deprecation warning should precede extended summary
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"GL10", # reST directives {directives} must be followed by two colons
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# Summary

‎doc/source/getting-started/index.rst‎

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Getting started
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===============
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************
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Installation
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~~~~~~~~~~~~
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************
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This package is not yet available on the public PyPI, but you can still install
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it using ``pip`` from the private PyPI repository.
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Python module
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~~~~~~~~~~~~~
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The following on Windows:
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The ``ansys.dyna.core`` package currently supports Python 3.8 through
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Python 3.10 on Windows, Mac OS, and Linux.
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.. code::
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Install the latest release from
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`PyPI <pydyna_pypi_>`_ with:
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set PYANSYS_PYPI_PRIVATE_PAT=<REDACTED>
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set INDEX_URL=https://%PYANSYS_PYPI_PRIVATE_PAT%@pkgs.dev.azure.com/pyansys/_packaging/pyansys/pypi/simple/
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python -m pip install ansys-dyna-core --index-url %INDEX_URL%
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.. code:: console
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And if you are running Linux:
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pip install ansys-dyna-core
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.. code::
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Alternatively, install the latest from
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`PyDyna GitHub <pydyna_issues_>`_ via:
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PYANSYS_PYPI_PRIVATE_PAT=<REDACTED>
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export INDEX_URL='https://[email protected]/pyansys/_packaging/pyansys/pypi/simple/'
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python -m pip install ansys-dyna-core --index-url $INDEX_URL
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.. code:: console
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pip install git+https://github.com/pyansys/pydyna.git
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Email your friendly PyAnsys team member for the ``PYANSYS_PYPI_PRIVATE_PAT``
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at `[email protected] <mailto:[email protected]>`_ or send a message via Teams.
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For a local *development* version, install with:
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**Installing from git**
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.. code:: console
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If you have ``git`` installed and want the bleeding edge version:
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git clone https://github.com/pyansys/pydyna.git
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cd pydyna
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pip install -e .
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.. code::
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This allows you to install the ``ansys-dyna-core`` module
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and modify it locally and have the changes reflected in your setup
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after restarting the Python kernel.
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pip install -U git+https://github.com/pyansys/pyDyna@main
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Offline installation
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~~~~~~~~~~~~~~~~~~~~
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If you lack an internet connection on your install machine, the recommended way
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of installing PyDyna is downloading the wheelhouse archive from the
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`Releases Page <pydyna_releases_>`_ for your corresponding
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machine architecture.
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You need to be logged into GitHub locally and be a member of the `PyAnsys Organization <https://github.com/pyansys>`_.
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Each wheelhouse archive contains all the Python wheels necessary to install
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PyDyna from scratch on Windows and Linux for Python 3.8 through 3.11. You can install
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this on an isolated system with a fresh Python or on a virtual environment.
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Alternatively, if you need to modify the repository locally (or want to
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do local development), you can clone it and install it in "development" mode with:
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For example, on Linux with Python 3.8, unzip it and install it with the following:
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.. code::
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.. code:: console
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git clone https://github.com/pyansys/pyDyna
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cd pyDyna
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pip install -e .
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unzip ansys-dyna-core-v0.3.1-wheelhouse-ubuntu-latest-3.8.zip wheelhouse
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pip install ansys-dyna-core -f wheelhouse --no-index --upgrade --ignore-installed
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If you're on Windows with Python 3.8, unzip to a ``wheelhouse`` directory and
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install using the preceding command.
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Consider installing using a `virtual environment <using_venv_>`_.
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.. include:: ../../../docker/pre/README.rst
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.. include:: ../../../docker/solver/README.rst
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Note the ``-e`` flag, which denotes that you are in development mode.
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You can make changes in the local ``pyDyna`` and have them reflected
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in your local install of PyDyna.
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.. LINKS
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.. _pydyna_pypi: https://pypi.org/projects/ansys-dyna-core/
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.. _pydyna_releases: https://github.com/ansys/pydyna/releases
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.. _pydyna_issues: https://github.com/ansys/pydyna/issues
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.. _using_venv: https://docs.python.org/3/library/venv.html

‎doc/source/user-guide/index.rst‎

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Visit the `DPF-Post Documentation <https://post.docs.pyansys.com>`_ for a
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detailed description of the package
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.. toctree::
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:hidden:
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pydyna_pre
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pydyna_solver
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pydyna_post
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‎docker/pre/README.rst‎

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Create your own pydyna-pre service docker container
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===================================================
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Build pydyna-pre service docker container
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:::::::::::::::::::::::::::::::::::::::::
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The pydyna-pre service Docker containers can be easily built by following
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these steps.
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Inside this folder, the instructions (i.e. ``Dockerfile`` files) for
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building the pydyna-pre service Docker containers are made available.
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To build the docker image you will need to clone pydyna repo locally:
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* ``Dockerfile``: this file builds the Linux-based Docker image.
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.. code:: console
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git clone https://github.com/pyansys/pydyna.git
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cd pydyna
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* ``docker/pre/Dockerfile``: this file builds the Linux-based Docker image.
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Prerequisites
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^^^^^^^^^^^^^
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* Ensure that ``docker`` is installed in your machine.
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If you do not have ``docker`` available, please refer to the
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`official Docker site <https://www.docker.com>`_.
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Note that the container can also be started on Windows if the Docker Desktop has been installed.
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How to install the Docker Desktop: https://docs.docker.com/desktop/install/windows-install/
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* Download the latest release artifacts. You can do this as follows:
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* Download the latest release artifacts for the Linux
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Docker container. You can do this as follows:
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* Latest Linux artifacts: `linux-binaries.zip <https://github.com/ansys/pydyna/releases/download/v0.2.1/linux-binaries.zip>`_
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* Move these ``.zip`` files to the current location (i.e. ``<repository-root-folder>/docker/pre``).
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Starting the docker container
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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There are two ways to start docker container.
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1.bulid image and run container
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>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
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* Move these ``.zip`` files to the current location (i.e. ``<repository-root-folder>/docker``).
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Building the Docker images
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::::::::::::::::::::::::::
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^^^^^^^^^^^^^^^^^^^^^^^^^^
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In order to build your images, follow the next instructions:
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* Locate yourself at ``<repository-root-folder>/docker/pre`` in your terminal.
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* Locate yourself at ``<repository-root-folder>/docker`` in your terminal.
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* Run the following Docker command:
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.. code:: bash
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>>> ...... ...... ............ .............. ......
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Run the image as a container
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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* Run the following Docker command:
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docker run -d -p 50051:50051 ghcr.io/ansys/ls-pre
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docker run -d -p 50051:50051 ghcr.io/ansys/ls-pre .
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* Check that the image has been created successfully.
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>>> CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
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>>> c77ffd67f9fa ghcr.io/ansys/ls-pre "python3 ./linux-bin…" 7 seconds ago Up 7 seconds 0.0.0.0:50051->50051/tcp, :::50051->50051/tcp hardcore_margulis
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2.Start the container from docker-compose.yml file
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>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
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Make sure the docker compose have been installed on your computer.
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For more information: https://docs.docker.com/compose/install/
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* Locate yourself at ``<repository-root-folder>/docker/pre`` in your terminal.
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* Run the following Docker command:
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docker compose up -d
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>>> c77ffd67f9fa ghcr.io/ansys/ls-pre "python3 ./linux-bin…" 7 seconds ago Up 7 seconds 0.0.0.0:50051->50051/tcp, :::50051->50051/tcp hardcore_margulis

‎docker/solver/Dockerfile‎

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FROM centos:7
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#
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# The order of the lines in here should be (as much as possible) in
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# an order that will create the same series of intermediate images
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# no mater what version of dyna we are using. This will speed up
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# experiments when creating containers over and over. Ordering the
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# commands this way makes the Dockerfile a bit more confusing, because
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# for example we make all the directories up top, but don't put things
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# in them until further down. And some environment variables are near
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# the top, but others near the bottom
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LABEL "com.ansys.description"="Ansys MPPDYNA with gRPC server"
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# install some missing stuff we want/need
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RUN yum -y install openssh-clients openssh-server bind-utils sudo python3
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RUN python3 -m pip install --upgrade pip
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RUN python3 -m pip install grpcio
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RUN python3 -m pip install grpcio-tools
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#
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ENV USER mpirun
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ENV HOME /home/mpirun
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ENV LD_LIBRARY_PATH /ansys_inc/lib
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ENV LSTC_LICENSE network
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ENV LSTC_LICENSE_SERVER license
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ENV SSHDIR ${HOME}/.ssh/
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RUN groupadd ${USER}
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RUN useradd -g ${USER} -d ${HOME} ${USER} && \
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echo "${USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
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#
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RUN mkdir -p /ansys_inc/lib
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RUN mkdir -p /rundir
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RUN mkdir /var/run/sshd
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RUN mkdir -p ${SSHDIR}
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RUN chown -R ${USER}:${USER} /rundir
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RUN chmod -R 755 /rundir
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WORKDIR /rundir
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# set up the runtime environment variables for
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# dyna
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RUN echo "export LD_LIBRARY_PATH=/ansys_inc/lib:/opt/openmpi/lib" > ${HOME}/.bashrc
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# Adding these causes problems because they can't be overridden
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# via the "environment" attribute in a docker-compose file.
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# The ENV commands above come through as defaults, but can be
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# overridden (to use the ANSYS license, or a different license server)
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#
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# RUN echo "export LSTC_LICENSE=network" >> ${HOME}/.bashrc
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# RUN echo "export LSTC_LICENSE_SERVER=license" >> ${HOME}/.bashrc
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#
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# Get ssh properly set up
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#
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RUN sed -i 's/PermitRootLogin without-password/PermitRootLogin yes/' /etc/ssh/sshd_config
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# SSH login fix. Otherwise user is kicked off after login
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RUN sed 's@session\s*required\s*pam_loginuid.so@session optional pam_loginuid.so@g' -i /etc/pam.d/sshd
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#
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EXPOSE 22
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CMD ["/usr/sbin/sshd", "-D"]
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#
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# Everything above here should not depend on the version of DYNA or the MPI we are using
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# and so should behave nicely as regards the Docker image cache. Below here not so much
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#
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ENV PATH /opt/openmpi/bin:${PATH}
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RUN echo "export PATH=/opt/openmpi/bin:\${PATH}" >> ${HOME}/.bashrc
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ADD ssh/config ${SSHDIR}/config
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ADD ssh/id_rsa ${SSHDIR}/id_rsa
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ADD ssh/id_rsa.pub ${SSHDIR}/id_rsa.pub
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ADD ssh/id_rsa.pub ${SSHDIR}/authorized_keys
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RUN ssh-keygen -A
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RUN chmod -R 600 ${SSHDIR}* && \
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chown -R ${USER}:${USER} ${SSHDIR}
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RUN chown -R ${USER}:${USER} ${HOME}
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# Copy the openmpi libraries
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RUN mkdir -p /opt
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COPY mpi /opt/openmpi
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# The executable will go in /ansys_inc, and the
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# ifort runtime libraries in /ansys_inc/lib
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COPY docker_dir /ansys_inc

‎docker/solver/README.rst‎

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Build pydyna-solver service docker container
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::::::::::::::::::::::::::::::::::::::::::::
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The pydyna-solver service Docker containers can be easily built by following
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these steps.
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* ``docker/solver/Dockerfile``: this file builds the Linux-based Docker image.
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Prerequisites
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^^^^^^^^^^^^^
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* Ensure that ``docker`` is installed in your machine.
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If you do not have ``docker`` available, please refer to the
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`official Docker site <https://www.docker.com>`_.
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* If you are building the image on Windows, you will need to have
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Windows Subsystem for Linux (WSL) installed. The instructions for that can be found `here <https://learn.microsoft.com/en-us/windows/wsl/install>`
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* Download the latest release artifacts for the Linux
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Docker container. You can do this as follows:
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* Latest Linux artifacts: `mppdyna_docker_centos7.zip <https://github.com/ansys/pydyna/releases/download/v0.2.1/mppdyna_docker_centos7.zip>`_
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* Move these ``.zip`` files to a local directory ``local_image_build_dir``.
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Building the Docker images
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^^^^^^^^^^^^^^^^^^^^^^^^^^
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In order to build your images, follow the next instructions:
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* cd to ``local_image_build_dir``.
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* Run the following Docker command:
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.. code:: bash
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./do_build
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* Check that the image has been created successfully. You should see an output similar
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to this one when running the following command:
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.. code:: bash
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docker images
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>>> REPOSITORY TAG IMAGE ID CREATED SIZE
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>>> dyna_solver_v04 latest defbadbeee8e 16 minutes ago 730MB
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>>> ...... ...... ............ .............. ......
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Run the image as a container
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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* Edit the docker-compose.yml file and replace ``<license_server_name>`` with the correct license server hosting the DYNA license.
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If you are using Ansy Flexlm license
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* Run the following Docker command:
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.. code:: bash
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docker-compose up
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* Check that the image has been created successfully.
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.. code:: bash
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>>> CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
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>>> be84c95db31d dyna_solver_v04 "/ansys_inc/server.p…" 18 minutes ago Up 8 seconds 22/tcp, 0.0.0.0:5000->5000/tcp mppdyna_docker_centos7_dyna_1

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