.. _tutorials:

Tutorials
=========

All users need to have a basic knowledge of UNIX and a sufficient proficiency
with simple commands. Here we provide links to RCIC-authored presentations and
a few online tutorials.

.. _rcic presentations:

.. centered:: :section:`RCIC presentations`

`RCIC Overview </_static/2021-symposium-RCIC-overview.pdf>`_:
  presentation given during the June 4th, 2021 virtual symposium of UCI’s Research Cyberinfrastructure Center (RCIC)
  Please see symposium :ref:`agenda<symposium 2021>`.

`Introduction to HPC3 </_static/2020-tutorial-intro-hpc3.pdf>`_:
  December 2020 tutorial covers topics to help users move to HPC3 cluster:

  - What is HPC3?
  - Basics of Linux and Shell necessary for running jobs
  - How to search for modules/programs?  What are the differences between modules
    and programs?  How to download modules/programs?  How to set environment?
  - How to run jobs? What queues are available? What are the common problems?

.. _online tutorials:

.. centered:: :section:`Online tutorials`

**Basic skills**
  - `The Missing Semester of Your CS Education <https://missing.csail.mit.edu>`_
    has many topics as separate lectures, including Shell Tools and Scripting, Editors (Vim), Command-line Environment,
    Data Wrangling, Git, security and much more.
  - `The Software Carpentry <https://software-carpentry.org/lessons/index.html>`_
    teaches basic skills  via workshops and lessons. 
  - `The UNIX Shell <http://swcarpentry.github.io/shell-novice>`_,
    the fundamentals of UNIX Shell all users need to know.

.. _editors:

**File Editors**
  - `A beginners guide to vim <https://www.linux.com/training-tutorials/vim-101-beginners-guide-vim/>`_
  - `Absolute beginners guide to emacs <http://www.jesshamrick.com/2012/09/10/absolute-beginners-guide-to-emacs/>`_

.. _programming tutorials:

**Programming**:
  - `Introduction to Python <https://swcarpentry.github.io/python-novice-inflammation/>`_ - to
    the basics of Python programming language
  - `Introduction to R <http://swcarpentry.github.io/r-novice-inflammation/>`_ - to
    the basics of R programming language
  - `Python Scientific computing <https://pythonspeed.com/datascience/>`_

.. _ssh tutorials:

**SSH**:
  - `What is SSH? <https://www.ssh.com/academy/ssh>`_
  - `SSH Academy <https://www.ssh.com/academy/ssh/passphrase>`_ - learn about SSH passphrases
  -  `PAM module
     <https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/6/html/managing_smart_cards/pluggable_authentication_modules>`_
     DUO-supplied module design/implementation
  - `Troubleshoot ssh problems <https://www.linux.com/topic/networking/4-reasons-why-ssh-connection-fails>`_
  - `Set up authorized_keys <https://www.ssh.com/ssh/authorized_keys/>`_
  - `How to use ssh-agent <https://www.ssh.com/ssh/agent>`_
  - `Linux ssh-agent <https://www.ssh.com/academy/ssh/agent>`_
  - `macOS proper use of SSH client <https://www.getpagespeed.com/work/proper-use-of-ssh-client-in-mac-os-x>`_