.. _`thpc-deprecated-quickstart`:

=============================
THPC Quick Start - Deprecated
=============================

.. contents::
   :depth: 1
   :local:

.. note::
    This page contains a quick start guide for earlier version(s) of THPC that are still available but no longer
    directly supported. Please refer to the :ref:`latest version <ris-thpc-quickstart>` for direct support.

.. admonition:: Compute Resources

    - Have questions or need help with compute, including activation or issues? Follow `this link. <https://washu.atlassian.net/servicedesk/customer/portal/2/group/6/create/43>`__
    - :ref:`User Agreement <compute-user-agreement>`

.. admonition:: Docker Usage

    - The information contained on this page assumes that you have a knowledge base of using Docker to create images and push them to a repository for use. If you need to review that information, please see the links below.
    - :ref:`Docker and the RIS Compute Service <docker-on-compute>`
    - :ref:`Docker Basics: Building, Tagging, & Pushing A Custom Docker Image <ris-docker-basics>`

.. _`thpc-quickstart-video`:

Video
-----

.. raw:: confluence

    <ac:structured-macro ac:name="html">
        <ac:plain-text-body><![CDATA[

.. raw:: confluence html

    <iframe width="560" height="315" src="https://www.youtube.com/embed/3mK8o5Ukh98" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

.. raw:: confluence

    ]]></ac:plain-text-body>
        </ac:structured-macro>

.. _`thpc-quickstart-cli`:

Interactive Command-Line
------------------------

Starting a Session
~~~~~~~~~~~~~~~~~~

- Connect to compute client.

.. code::

    ssh wustlkey@compute1-client-1.ris.wustl.edu

- Start up a session.

.. code::

    compute1-terminal /bin/bash

.. Note::

    - If you are a member of more than one compute group, you will be prompted to specify an LSF User Group with ``-G group_name`` or by setting the ``LSB_SUB_USER_GROUP`` variable.

Using the Command-Line
~~~~~~~~~~~~~~~~~~~~~~

- View available modules.

.. code::

    # view all available modules
    module avail

    # filter module search (case specific)
    module avail <search_criteria>

- Load a specific module for use.

.. code::

    module load <software_module>

- Unload module when finished.

.. code::

    module unload <software_module>

.. _`thpc-quickstart-gui`:

Interactive GUI
---------------

Starting a Session
~~~~~~~~~~~~~~~~~~

- Connect to compute client.

.. code::

    ssh wustlkey@compute1-client-1.ris.wustl.edu

- Start up a session.

.. code::

    compute1-gui-desktop

.. Note::

    A password for the GUI will automatically generate on the initial run and be
    output in the terminal. To choose your own password, prepend the job command
    with VNC_PW=password, replacing “password” with that of your choosing.

.. Note::

    If you are a member of more than one compute group, you will be prompted to
    specify an LSF User Group with ``-G group_name`` or by setting the
    ``LSB_SUB_USER_GROUP`` variable.

- Open a browser and insert the URL received in the terminal as output.

.. Note::

    Given the large size of the THPC environment, it may take up to a minute for
    the session to be fully loaded and viewable in the browser.

- The below page should now be displayed. Select ‘Connect’ and submit your
  password. Select the ‘Terminal Emulator’ icon at the bottom of the browser page
  or from the ‘Applications’ dropdown to open a terminal.

.. image:: ./images/noVNC_opening_screen.png

.. image:: ./images/noVNC_select_terminal.png

Using the GUI
~~~~~~~~~~~~~

- View available software modules.

.. code::

    # view all available modules
    module avail

    # filter module search (case specific)
    module avail <search_criteria>

- Load a specific module for use (the generic listed first will always run the
  latest version available).

.. code::

    module load <software_module>

- Unload module when finished.

.. code::

    module unload <software_module>

Extra Features
~~~~~~~~~~~~~~

- Settings, clipboard and extra features are available by clicking to extend the
  minimized tab on the left.

.. image:: ./images/noVNC_settings_extras.png

Non-Interactive Batch Job
-------------------------

Job Submission
~~~~~~~~~~~~~~~~~~

- Connect to compute client.

.. code::

    ssh wustlkey@compute1-client-1.ris.wustl.edu

- Submit a non-interactive batch job, replacing ``script.sh`` with your submission script.

.. code::

    compute1-batch /bin/zsh script.sh

.. _`thpc-quickstart-batch`:

Example Gaussian Batch Job
~~~~~~~~~~~~~~~~~~~~~~~~~~

.. Note::

    Replace ``${COMPUTE_ALLOCATION}`` with the name of the compute allocation
    you are a member of when running the code blocks below.

- Create a folder in your scratch folder named ``gaussian``.

.. code::

    mkdir -p /scratch1/fs1/${COMPUTE_ALLOCATION}/gaussian

- Create a submission script named ``gaussian_job.sh`` in your home folder.

.. code::

    cat <<EOF > $HOME/gaussian_job.sh
        #!/bin/bash

        cd /scratch1/fs1/${COMPUTE_ALLOCATION}/gaussian
        module load gaussian09
        export GAUSS_SCRDIR=/scratch1/fs1/${COMPUTE_ALLOCATION}
        g09 < test.inp >& test.out
    EOF

- Create sample Gaussian input data (the empty line at the end is important).

.. code::

    cat <<EOF > /scratch1/fs1/${COMPUTE_ALLOCATION}/gaussian/test.inp
        $ RunGauss

        #n test rohf/sto-3g pop=full GFINPUT

        O sto-3g triplet

        0 3
        O

    EOF

- Submit the non-interactive Gaussian batch job

.. code::

    LSF_DOCKER_VOLUMES="/scratch1/fs1/${COMPUTE_ALLOCATION}:/scratch1/fs1/${COMPUTE_ALLOCATION}" compute1-batch /bin/zsh $HOME/gaussian_job.sh

- Once the job is complete, you can access the output file at
  ``/scratch1/fs1/${COMPUTE_ALLOCATION}/gaussian/test.out``.

.. code::

    cat /scratch1/fs1/${COMPUTE_ALLOCATION}/gaussian/test.out