.. _tutorials:

Tutorials
=========

All users need to have a basic knowledge of UNIX and a basic but sufficient proficiency 
with simple commands. Here we provide links to RCIC-authored presentations and links to 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, here are direct links:
- `The UNIX Shell <http://swcarpentry.github.io/shell-novice>`_ -
  the fundamentals of UNIX Shell all users need to know

..  _editors:

**File Editors**

See the following links for beginners guides, many more are available online:

- `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
  learn the basics of Python programming language
- `Introduction to R <http://swcarpentry.github.io/r-novice-inflammation/>`_ - to
  learn the basics of R programming language
- `Python Articles <https://pythonspeed.com/datascience/>`_ - how to **Speedup your data science and scientific computing code in Python**.

..   _ssh tutorials:

**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
- `https://www.ssh.com <https://www.ssh.com>`_
- `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>`_