Introduction to Sockeye

.title[
# Introduction to Sockeye
]
.subtitle[
## <br/>Adapted from UBC ARC Sockeye Workshop
]
.author[
### Tony Liang
]
.institute[
### University of British Columbia
]
.date[
### Last modified - 2023-05-26
]

---

# Land acknowledgement

.pull-left[
**I would like to acknowledge that I work on the traditional, ancestral, and unceded territory of the Coast Salish Peoples, including the territories of the xwməθkwəy̓əm (Musqueam), Skwxwú7mesh (Squamish), Stó:lō and Səl̓ílwətaʔ/Selilwitulh (Tsleil- Waututh) Nations.**

*Traditional*: Traditionally used and/or occupied by Musqueam people

*Ancestral*: Recognizes land that is handed down from generation to generation

*Unceded*: Refers to land that was not turned over to the Crown (government) by a treaty or other agreement

]

.pull-right[
.center[<img src ="materials/img/land_acknowledgement.gif" alt="matrix", width="80%"/>]
]

---

## Topics

I'm being very extra to show what we are doing today **hopefully?**

it's gonna be a heavy session.
]

- VS Code Setup

- Basic information of Sockeye

- Sockeye Login
]

- Linux and CLI

- Bashrc

- Job Submission
]

<br>

.secondary[About to start, make sure to follow along!]
.center[
<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#0a8754;overflow:visible;position:relative;"><path d="M323.8 34.8c-38.2-10.9-78.1 11.2-89 49.4l-5.7 20c-3.7 13-10.4 25-19.5 35l-51.3 56.4c-8.9 9.8-8.2 25 1.6 33.9s25 8.2 33.9-1.6l51.3-56.4c14.1-15.5 24.4-34 30.1-54.1l5.7-20c3.6-12.7 16.9-20.1 29.7-16.5s20.1 16.9 16.5 29.7l-5.7 20c-5.7 19.9-14.7 38.7-26.6 55.5c-5.2 7.3-5.8 16.9-1.7 24.9s12.3 13 21.3 13L448 224c8.8 0 16 7.2 16 16c0 6.8-4.3 12.7-10.4 15c-7.4 2.8-13 9-14.9 16.7s.1 15.8 5.3 21.7c2.5 2.8 4 6.5 4 10.6c0 7.8-5.6 14.3-13 15.7c-8.2 1.6-15.1 7.3-18 15.1s-1.6 16.7 3.6 23.3c2.1 2.7 3.4 6.1 3.4 9.9c0 6.7-4.2 12.6-10.2 14.9c-11.5 4.5-17.7 16.9-14.4 28.8c.4 1.3 .6 2.8 .6 4.3c0 8.8-7.2 16-16 16H286.5c-12.6 0-25-3.7-35.5-10.7l-61.7-41.1c-11-7.4-25.9-4.4-33.3 6.7s-4.4 25.9 6.7 33.3l61.7 41.1c18.4 12.3 40 18.8 62.1 18.8H384c34.7 0 62.9-27.6 64-62c14.6-11.7 24-29.7 24-50c0-4.5-.5-8.8-1.3-13c15.4-11.7 25.3-30.2 25.3-51c0-6.5-1-12.8-2.8-18.7C504.8 273.7 512 257.7 512 240c0-35.3-28.6-64-64-64l-92.3 0c4.7-10.4 8.7-21.2 11.8-32.2l5.7-20c10.9-38.2-11.2-78.1-49.4-89zM32 192c-17.7 0-32 14.3-32 32V448c0 17.7 14.3 32 32 32H96c17.7 0 32-14.3 32-32V224c0-17.7-14.3-32-32-32H32z"/></svg>  .hand[FOLLOW ME]
<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#e98a15;overflow:visible;position:relative;"><path d="M459.1 52.4L442.6 6.5C440.7 2.6 436.5 0 432.1 0s-8.5 2.6-10.4 6.5L405.2 52.4l-46 16.8c-4.3 1.6-7.3 5.9-7.2 10.4c0 4.5 3 8.7 7.2 10.2l45.7 16.8 16.8 45.8c1.5 4.4 5.8 7.5 10.4 7.5s8.9-3.1 10.4-7.5l16.5-45.8 45.7-16.8c4.2-1.5 7.2-5.7 7.2-10.2c0-4.6-3-8.9-7.2-10.4L459.1 52.4zm-132.4 53c-12.5-12.5-32.8-12.5-45.3 0l-2.9 2.9C256.5 100.3 232.7 96 208 96C93.1 96 0 189.1 0 304S93.1 512 208 512s208-93.1 208-208c0-24.7-4.3-48.5-12.2-70.5l2.9-2.9c12.5-12.5 12.5-32.8 0-45.3l-80-80zM200 192c-57.4 0-104 46.6-104 104v8c0 8.8-7.2 16-16 16s-16-7.2-16-16v-8c0-75.1 60.9-136 136-136h8c8.8 0 16 7.2 16 16s-7.2 16-16 16h-8z"/></svg>  .hand[FOLLOW ME]
]

---

---

## VS Code

Visual Studio Code (VS Code) is a code/text editor, IDE made by Microsoft.

.secondary[VS code]
<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#0a8754;overflow:visible;position:relative;"><path d="M323.8 34.8c-38.2-10.9-78.1 11.2-89 49.4l-5.7 20c-3.7 13-10.4 25-19.5 35l-51.3 56.4c-8.9 9.8-8.2 25 1.6 33.9s25 8.2 33.9-1.6l51.3-56.4c14.1-15.5 24.4-34 30.1-54.1l5.7-20c3.6-12.7 16.9-20.1 29.7-16.5s20.1 16.9 16.5 29.7l-5.7 20c-5.7 19.9-14.7 38.7-26.6 55.5c-5.2 7.3-5.8 16.9-1.7 24.9s12.3 13 21.3 13L448 224c8.8 0 16 7.2 16 16c0 6.8-4.3 12.7-10.4 15c-7.4 2.8-13 9-14.9 16.7s.1 15.8 5.3 21.7c2.5 2.8 4 6.5 4 10.6c0 7.8-5.6 14.3-13 15.7c-8.2 1.6-15.1 7.3-18 15.1s-1.6 16.7 3.6 23.3c2.1 2.7 3.4 6.1 3.4 9.9c0 6.7-4.2 12.6-10.2 14.9c-11.5 4.5-17.7 16.9-14.4 28.8c.4 1.3 .6 2.8 .6 4.3c0 8.8-7.2 16-16 16H286.5c-12.6 0-25-3.7-35.5-10.7l-61.7-41.1c-11-7.4-25.9-4.4-33.3 6.7s-4.4 25.9 6.7 33.3l61.7 41.1c18.4 12.3 40 18.8 62.1 18.8H384c34.7 0 62.9-27.6 64-62c14.6-11.7 24-29.7 24-50c0-4.5-.5-8.8-1.3-13c15.4-11.7 25.3-30.2 25.3-51c0-6.5-1-12.8-2.8-18.7C504.8 273.7 512 257.7 512 240c0-35.3-28.6-64-64-64l-92.3 0c4.7-10.4 8.7-21.2 11.8-32.2l5.7-20c10.9-38.2-11.2-78.1-49.4-89zM32 192c-17.7 0-32 14.3-32 32V448c0 17.7 14.3 32 32 32H96c17.7 0 32-14.3 32-32V224c0-17.7-14.3-32-32-32H32z"/></svg> Plugins for many programming languages
<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#0a8754;overflow:visible;position:relative;"><path d="M323.8 34.8c-38.2-10.9-78.1 11.2-89 49.4l-5.7 20c-3.7 13-10.4 25-19.5 35l-51.3 56.4c-8.9 9.8-8.2 25 1.6 33.9s25 8.2 33.9-1.6l51.3-56.4c14.1-15.5 24.4-34 30.1-54.1l5.7-20c3.6-12.7 16.9-20.1 29.7-16.5s20.1 16.9 16.5 29.7l-5.7 20c-5.7 19.9-14.7 38.7-26.6 55.5c-5.2 7.3-5.8 16.9-1.7 24.9s12.3 13 21.3 13L448 224c8.8 0 16 7.2 16 16c0 6.8-4.3 12.7-10.4 15c-7.4 2.8-13 9-14.9 16.7s.1 15.8 5.3 21.7c2.5 2.8 4 6.5 4 10.6c0 7.8-5.6 14.3-13 15.7c-8.2 1.6-15.1 7.3-18 15.1s-1.6 16.7 3.6 23.3c2.1 2.7 3.4 6.1 3.4 9.9c0 6.7-4.2 12.6-10.2 14.9c-11.5 4.5-17.7 16.9-14.4 28.8c.4 1.3 .6 2.8 .6 4.3c0 8.8-7.2 16-16 16H286.5c-12.6 0-25-3.7-35.5-10.7l-61.7-41.1c-11-7.4-25.9-4.4-33.3 6.7s-4.4 25.9 6.7 33.3l61.7 41.1c18.4 12.3 40 18.8 62.1 18.8H384c34.7 0 62.9-27.6 64-62c14.6-11.7 24-29.7 24-50c0-4.5-.5-8.8-1.3-13c15.4-11.7 25.3-30.2 25.3-51c0-6.5-1-12.8-2.8-18.7C504.8 273.7 512 257.7 512 240c0-35.3-28.6-64-64-64l-92.3 0c4.7-10.4 8.7-21.2 11.8-32.2l5.7-20c10.9-38.2-11.2-78.1-49.4-89zM32 192c-17.7 0-32 14.3-32 32V448c0 17.7 14.3 32 32 32H96c17.7 0 32-14.3 32-32V224c0-17.7-14.3-32-32-32H32z"/></svg> Easy learning curve
<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#0a8754;overflow:visible;position:relative;"><path d="M323.8 34.8c-38.2-10.9-78.1 11.2-89 49.4l-5.7 20c-3.7 13-10.4 25-19.5 35l-51.3 56.4c-8.9 9.8-8.2 25 1.6 33.9s25 8.2 33.9-1.6l51.3-56.4c14.1-15.5 24.4-34 30.1-54.1l5.7-20c3.6-12.7 16.9-20.1 29.7-16.5s20.1 16.9 16.5 29.7l-5.7 20c-5.7 19.9-14.7 38.7-26.6 55.5c-5.2 7.3-5.8 16.9-1.7 24.9s12.3 13 21.3 13L448 224c8.8 0 16 7.2 16 16c0 6.8-4.3 12.7-10.4 15c-7.4 2.8-13 9-14.9 16.7s.1 15.8 5.3 21.7c2.5 2.8 4 6.5 4 10.6c0 7.8-5.6 14.3-13 15.7c-8.2 1.6-15.1 7.3-18 15.1s-1.6 16.7 3.6 23.3c2.1 2.7 3.4 6.1 3.4 9.9c0 6.7-4.2 12.6-10.2 14.9c-11.5 4.5-17.7 16.9-14.4 28.8c.4 1.3 .6 2.8 .6 4.3c0 8.8-7.2 16-16 16H286.5c-12.6 0-25-3.7-35.5-10.7l-61.7-41.1c-11-7.4-25.9-4.4-33.3 6.7s-4.4 25.9 6.7 33.3l61.7 41.1c18.4 12.3 40 18.8 62.1 18.8H384c34.7 0 62.9-27.6 64-62c14.6-11.7 24-29.7 24-50c0-4.5-.5-8.8-1.3-13c15.4-11.7 25.3-30.2 25.3-51c0-6.5-1-12.8-2.8-18.7C504.8 273.7 512 257.7 512 240c0-35.3-28.6-64-64-64l-92.3 0c4.7-10.4 8.7-21.2 11.8-32.2l5.7-20c10.9-38.2-11.2-78.1-49.4-89zM32 192c-17.7 0-32 14.3-32 32V448c0 17.7 14.3 32 32 32H96c17.7 0 32-14.3 32-32V224c0-17.7-14.3-32-32-32H32z"/></svg> Has a GUI (clickable)
<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#0a8754;overflow:visible;position:relative;"><path d="M323.8 34.8c-38.2-10.9-78.1 11.2-89 49.4l-5.7 20c-3.7 13-10.4 25-19.5 35l-51.3 56.4c-8.9 9.8-8.2 25 1.6 33.9s25 8.2 33.9-1.6l51.3-56.4c14.1-15.5 24.4-34 30.1-54.1l5.7-20c3.6-12.7 16.9-20.1 29.7-16.5s20.1 16.9 16.5 29.7l-5.7 20c-5.7 19.9-14.7 38.7-26.6 55.5c-5.2 7.3-5.8 16.9-1.7 24.9s12.3 13 21.3 13L448 224c8.8 0 16 7.2 16 16c0 6.8-4.3 12.7-10.4 15c-7.4 2.8-13 9-14.9 16.7s.1 15.8 5.3 21.7c2.5 2.8 4 6.5 4 10.6c0 7.8-5.6 14.3-13 15.7c-8.2 1.6-15.1 7.3-18 15.1s-1.6 16.7 3.6 23.3c2.1 2.7 3.4 6.1 3.4 9.9c0 6.7-4.2 12.6-10.2 14.9c-11.5 4.5-17.7 16.9-14.4 28.8c.4 1.3 .6 2.8 .6 4.3c0 8.8-7.2 16-16 16H286.5c-12.6 0-25-3.7-35.5-10.7l-61.7-41.1c-11-7.4-25.9-4.4-33.3 6.7s-4.4 25.9 6.7 33.3l61.7 41.1c18.4 12.3 40 18.8 62.1 18.8H384c34.7 0 62.9-27.6 64-62c14.6-11.7 24-29.7 24-50c0-4.5-.5-8.8-1.3-13c15.4-11.7 25.3-30.2 25.3-51c0-6.5-1-12.8-2.8-18.7C504.8 273.7 512 257.7 512 240c0-35.3-28.6-64-64-64l-92.3 0c4.7-10.4 8.7-21.2 11.8-32.2l5.7-20c10.9-38.2-11.2-78.1-49.4-89zM32 192c-17.7 0-32 14.3-32 32V448c0 17.7 14.3 32 32 32H96c17.7 0 32-14.3 32-32V224c0-17.7-14.3-32-32-32H32z"/></svg> <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#0a8754;overflow:visible;position:relative;"><path d="M323.8 34.8c-38.2-10.9-78.1 11.2-89 49.4l-5.7 20c-3.7 13-10.4 25-19.5 35l-51.3 56.4c-8.9 9.8-8.2 25 1.6 33.9s25 8.2 33.9-1.6l51.3-56.4c14.1-15.5 24.4-34 30.1-54.1l5.7-20c3.6-12.7 16.9-20.1 29.7-16.5s20.1 16.9 16.5 29.7l-5.7 20c-5.7 19.9-14.7 38.7-26.6 55.5c-5.2 7.3-5.8 16.9-1.7 24.9s12.3 13 21.3 13L448 224c8.8 0 16 7.2 16 16c0 6.8-4.3 12.7-10.4 15c-7.4 2.8-13 9-14.9 16.7s.1 15.8 5.3 21.7c2.5 2.8 4 6.5 4 10.6c0 7.8-5.6 14.3-13 15.7c-8.2 1.6-15.1 7.3-18 15.1s-1.6 16.7 3.6 23.3c2.1 2.7 3.4 6.1 3.4 9.9c0 6.7-4.2 12.6-10.2 14.9c-11.5 4.5-17.7 16.9-14.4 28.8c.4 1.3 .6 2.8 .6 4.3c0 8.8-7.2 16-16 16H286.5c-12.6 0-25-3.7-35.5-10.7l-61.7-41.1c-11-7.4-25.9-4.4-33.3 6.7s-4.4 25.9 6.7 33.3l61.7 41.1c18.4 12.3 40 18.8 62.1 18.8H384c34.7 0 62.9-27.6 64-62c14.6-11.7 24-29.7 24-50c0-4.5-.5-8.8-1.3-13c15.4-11.7 25.3-30.2 25.3-51c0-6.5-1-12.8-2.8-18.7C504.8 273.7 512 257.7 512 240c0-35.3-28.6-64-64-64l-92.3 0c4.7-10.4 8.7-21.2 11.8-32.2l5.7-20c10.9-38.2-11.2-78.1-49.4-89zM32 192c-17.7 0-32 14.3-32 32V448c0 17.7 14.3 32 32 32H96c17.7 0 32-14.3 32-32V224c0-17.7-14.3-32-32-32H32z"/></svg> <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#0a8754;overflow:visible;position:relative;"><path d="M323.8 34.8c-38.2-10.9-78.1 11.2-89 49.4l-5.7 20c-3.7 13-10.4 25-19.5 35l-51.3 56.4c-8.9 9.8-8.2 25 1.6 33.9s25 8.2 33.9-1.6l51.3-56.4c14.1-15.5 24.4-34 30.1-54.1l5.7-20c3.6-12.7 16.9-20.1 29.7-16.5s20.1 16.9 16.5 29.7l-5.7 20c-5.7 19.9-14.7 38.7-26.6 55.5c-5.2 7.3-5.8 16.9-1.7 24.9s12.3 13 21.3 13L448 224c8.8 0 16 7.2 16 16c0 6.8-4.3 12.7-10.4 15c-7.4 2.8-13 9-14.9 16.7s.1 15.8 5.3 21.7c2.5 2.8 4 6.5 4 10.6c0 7.8-5.6 14.3-13 15.7c-8.2 1.6-15.1 7.3-18 15.1s-1.6 16.7 3.6 23.3c2.1 2.7 3.4 6.1 3.4 9.9c0 6.7-4.2 12.6-10.2 14.9c-11.5 4.5-17.7 16.9-14.4 28.8c.4 1.3 .6 2.8 .6 4.3c0 8.8-7.2 16-16 16H286.5c-12.6 0-25-3.7-35.5-10.7l-61.7-41.1c-11-7.4-25.9-4.4-33.3 6.7s-4.4 25.9 6.7 33.3l61.7 41.1c18.4 12.3 40 18.8 62.1 18.8H384c34.7 0 62.9-27.6 64-62c14.6-11.7 24-29.7 24-50c0-4.5-.5-8.8-1.3-13c15.4-11.7 25.3-30.2 25.3-51c0-6.5-1-12.8-2.8-18.7C504.8 273.7 512 257.7 512 240c0-35.3-28.6-64-64-64l-92.3 0c4.7-10.4 8.7-21.2 11.8-32.2l5.7-20c10.9-38.2-11.2-78.1-49.4-89zM32 192c-17.7 0-32 14.3-32 32V448c0 17.7 14.3 32 32 32H96c17.7 0 32-14.3 32-32V224c0-17.7-14.3-32-32-32H32z"/></svg> You could `ssh` and transmit files through it
<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#e98a15;overflow:visible;position:relative;"><path d="M459.1 52.4L442.6 6.5C440.7 2.6 436.5 0 432.1 0s-8.5 2.6-10.4 6.5L405.2 52.4l-46 16.8c-4.3 1.6-7.3 5.9-7.2 10.4c0 4.5 3 8.7 7.2 10.2l45.7 16.8 16.8 45.8c1.5 4.4 5.8 7.5 10.4 7.5s8.9-3.1 10.4-7.5l16.5-45.8 45.7-16.8c4.2-1.5 7.2-5.7 7.2-10.2c0-4.6-3-8.9-7.2-10.4L459.1 52.4zm-132.4 53c-12.5-12.5-32.8-12.5-45.3 0l-2.9 2.9C256.5 100.3 232.7 96 208 96C93.1 96 0 189.1 0 304S93.1 512 208 512s208-93.1 208-208c0-24.7-4.3-48.5-12.2-70.5l2.9-2.9c12.5-12.5 12.5-32.8 0-45.3l-80-80zM200 192c-57.4 0-104 46.6-104 104v8c0 8.8-7.2 16-16 16s-16-7.2-16-16v-8c0-75.1 60.9-136 136-136h8c8.8 0 16 7.2 16 16s-7.2 16-16 16h-8z"/></svg> Not available in all device, requires installation
]

.pull-right[
.secondary[Other editors like Nano/Emacs/Vi]
<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#0a8754;overflow:visible;position:relative;"><path d="M323.8 34.8c-38.2-10.9-78.1 11.2-89 49.4l-5.7 20c-3.7 13-10.4 25-19.5 35l-51.3 56.4c-8.9 9.8-8.2 25 1.6 33.9s25 8.2 33.9-1.6l51.3-56.4c14.1-15.5 24.4-34 30.1-54.1l5.7-20c3.6-12.7 16.9-20.1 29.7-16.5s20.1 16.9 16.5 29.7l-5.7 20c-5.7 19.9-14.7 38.7-26.6 55.5c-5.2 7.3-5.8 16.9-1.7 24.9s12.3 13 21.3 13L448 224c8.8 0 16 7.2 16 16c0 6.8-4.3 12.7-10.4 15c-7.4 2.8-13 9-14.9 16.7s.1 15.8 5.3 21.7c2.5 2.8 4 6.5 4 10.6c0 7.8-5.6 14.3-13 15.7c-8.2 1.6-15.1 7.3-18 15.1s-1.6 16.7 3.6 23.3c2.1 2.7 3.4 6.1 3.4 9.9c0 6.7-4.2 12.6-10.2 14.9c-11.5 4.5-17.7 16.9-14.4 28.8c.4 1.3 .6 2.8 .6 4.3c0 8.8-7.2 16-16 16H286.5c-12.6 0-25-3.7-35.5-10.7l-61.7-41.1c-11-7.4-25.9-4.4-33.3 6.7s-4.4 25.9 6.7 33.3l61.7 41.1c18.4 12.3 40 18.8 62.1 18.8H384c34.7 0 62.9-27.6 64-62c14.6-11.7 24-29.7 24-50c0-4.5-.5-8.8-1.3-13c15.4-11.7 25.3-30.2 25.3-51c0-6.5-1-12.8-2.8-18.7C504.8 273.7 512 257.7 512 240c0-35.3-28.6-64-64-64l-92.3 0c4.7-10.4 8.7-21.2 11.8-32.2l5.7-20c10.9-38.2-11.2-78.1-49.4-89zM32 192c-17.7 0-32 14.3-32 32V448c0 17.7 14.3 32 32 32H96c17.7 0 32-14.3 32-32V224c0-17.7-14.3-32-32-32H32z"/></svg> Available in every Unix-liked sytem 
<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#0a8754;overflow:visible;position:relative;"><path d="M323.8 34.8c-38.2-10.9-78.1 11.2-89 49.4l-5.7 20c-3.7 13-10.4 25-19.5 35l-51.3 56.4c-8.9 9.8-8.2 25 1.6 33.9s25 8.2 33.9-1.6l51.3-56.4c14.1-15.5 24.4-34 30.1-54.1l5.7-20c3.6-12.7 16.9-20.1 29.7-16.5s20.1 16.9 16.5 29.7l-5.7 20c-5.7 19.9-14.7 38.7-26.6 55.5c-5.2 7.3-5.8 16.9-1.7 24.9s12.3 13 21.3 13L448 224c8.8 0 16 7.2 16 16c0 6.8-4.3 12.7-10.4 15c-7.4 2.8-13 9-14.9 16.7s.1 15.8 5.3 21.7c2.5 2.8 4 6.5 4 10.6c0 7.8-5.6 14.3-13 15.7c-8.2 1.6-15.1 7.3-18 15.1s-1.6 16.7 3.6 23.3c2.1 2.7 3.4 6.1 3.4 9.9c0 6.7-4.2 12.6-10.2 14.9c-11.5 4.5-17.7 16.9-14.4 28.8c.4 1.3 .6 2.8 .6 4.3c0 8.8-7.2 16-16 16H286.5c-12.6 0-25-3.7-35.5-10.7l-61.7-41.1c-11-7.4-25.9-4.4-33.3 6.7s-4.4 25.9 6.7 33.3l61.7 41.1c18.4 12.3 40 18.8 62.1 18.8H384c34.7 0 62.9-27.6 64-62c14.6-11.7 24-29.7 24-50c0-4.5-.5-8.8-1.3-13c15.4-11.7 25.3-30.2 25.3-51c0-6.5-1-12.8-2.8-18.7C504.8 273.7 512 257.7 512 240c0-35.3-28.6-64-64-64l-92.3 0c4.7-10.4 8.7-21.2 11.8-32.2l5.7-20c10.9-38.2-11.2-78.1-49.4-89zM32 192c-17.7 0-32 14.3-32 32V448c0 17.7 14.3 32 32 32H96c17.7 0 32-14.3 32-32V224c0-17.7-14.3-32-32-32H32z"/></svg> Highly customizable
<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#e98a15;overflow:visible;position:relative;"><path d="M459.1 52.4L442.6 6.5C440.7 2.6 436.5 0 432.1 0s-8.5 2.6-10.4 6.5L405.2 52.4l-46 16.8c-4.3 1.6-7.3 5.9-7.2 10.4c0 4.5 3 8.7 7.2 10.2l45.7 16.8 16.8 45.8c1.5 4.4 5.8 7.5 10.4 7.5s8.9-3.1 10.4-7.5l16.5-45.8 45.7-16.8c4.2-1.5 7.2-5.7 7.2-10.2c0-4.6-3-8.9-7.2-10.4L459.1 52.4zm-132.4 53c-12.5-12.5-32.8-12.5-45.3 0l-2.9 2.9C256.5 100.3 232.7 96 208 96C93.1 96 0 189.1 0 304S93.1 512 208 512s208-93.1 208-208c0-24.7-4.3-48.5-12.2-70.5l2.9-2.9c12.5-12.5 12.5-32.8 0-45.3l-80-80zM200 192c-57.4 0-104 46.6-104 104v8c0 8.8-7.2 16-16 16s-16-7.2-16-16v-8c0-75.1 60.9-136 136-136h8c8.8 0 16 7.2 16 16s-7.2 16-16 16h-8z"/></svg> Almost to no language supports
<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#e98a15;overflow:visible;position:relative;"><path d="M459.1 52.4L442.6 6.5C440.7 2.6 436.5 0 432.1 0s-8.5 2.6-10.4 6.5L405.2 52.4l-46 16.8c-4.3 1.6-7.3 5.9-7.2 10.4c0 4.5 3 8.7 7.2 10.2l45.7 16.8 16.8 45.8c1.5 4.4 5.8 7.5 10.4 7.5s8.9-3.1 10.4-7.5l16.5-45.8 45.7-16.8c4.2-1.5 7.2-5.7 7.2-10.2c0-4.6-3-8.9-7.2-10.4L459.1 52.4zm-132.4 53c-12.5-12.5-32.8-12.5-45.3 0l-2.9 2.9C256.5 100.3 232.7 96 208 96C93.1 96 0 189.1 0 304S93.1 512 208 512s208-93.1 208-208c0-24.7-4.3-48.5-12.2-70.5l2.9-2.9c12.5-12.5 12.5-32.8 0-45.3l-80-80zM200 192c-57.4 0-104 46.6-104 104v8c0 8.8-7.2 16-16 16s-16-7.2-16-16v-8c0-75.1 60.9-136 136-136h8c8.8 0 16 7.2 16 16s-7.2 16-16 16h-8z"/></svg> Steep learning curve
<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#e98a15;overflow:visible;position:relative;"><path d="M459.1 52.4L442.6 6.5C440.7 2.6 436.5 0 432.1 0s-8.5 2.6-10.4 6.5L405.2 52.4l-46 16.8c-4.3 1.6-7.3 5.9-7.2 10.4c0 4.5 3 8.7 7.2 10.2l45.7 16.8 16.8 45.8c1.5 4.4 5.8 7.5 10.4 7.5s8.9-3.1 10.4-7.5l16.5-45.8 45.7-16.8c4.2-1.5 7.2-5.7 7.2-10.2c0-4.6-3-8.9-7.2-10.4L459.1 52.4zm-132.4 53c-12.5-12.5-32.8-12.5-45.3 0l-2.9 2.9C256.5 100.3 232.7 96 208 96C93.1 96 0 189.1 0 304S93.1 512 208 512s208-93.1 208-208c0-24.7-4.3-48.5-12.2-70.5l2.9-2.9c12.5-12.5 12.5-32.8 0-45.3l-80-80zM200 192c-57.4 0-104 46.6-104 104v8c0 8.8-7.2 16-16 16s-16-7.2-16-16v-8c0-75.1 60.9-136 136-136h8c8.8 0 16 7.2 16 16s-7.2 16-16 16h-8z"/></svg> No GUI (master your keyboard usage)
]

Use whatever is provided to you, unless you have permission to make more from what's available.
]

---

### Installation Mac

Open this **[link](https://code.visualstudio.com/sha/download?build=stable&os=darwin-universal)** and download.

Once download is finished: 
1. Open the downloaded `zip`

1. Move the extracted VS Code app from `Downloads` to `Applications` (Located to your left under `Favorites`)

1. Launch VS Code and open the `Command Palette` by `Cmd + Shift + P`

1. Type `shell command`

1. Select the option: **Install `code` command in PATH**

1. Restart your terminal and try entering: `code --version` to confirm successful installation

<hr>

Your output should be something like:
  ```
  1.74.3
  97dec172d3256f8ca4bfb2143f3f76b503ca0534
  arm64 # or x64 if you are intel chip
  ```
--

.secondary[If you were lost or it did not work for you, checkout this [site](https://ubc-dsci.github.io/dsci-310-student/install_stack_mac_arm.html) or this [site](https://code.visualstudio.com/docs/setup/mac)]

---

### Installation Windows

Open this **[link](https://code.visualstudio.com/sha/download?build=stable&os=win32-x64-user)** and download.

.pull-left[
Once download is finished, run the installer and accept all default configuration except:
 - **On Select Additional Tasks**
    + Add 'Open with Code action to Windows file context menu'
    
    + Add ‘Open with Code’ action to Windows directory context menu”
    
    + Register Code as an editor for supported file types
    
    + Add to PATH (should be selected by default)
]

<br>
.secondary[If you were lost or it did not work for you, checkout this [site](https://ubc-dsci.github.io/dsci-310-student/install_stack_windows.html#visual-studio-code)]

---

### Installation Linux

Open this **[link](https://code.visualstudio.com/download)** and find the right installer upon your platform Linux Debian based or Red-hat based.

Test that VS code is installed and can be opened from Terminal by restarting terminal and typing the following command:
`code --version`

.secondary[If you were lost or it did not work for you, checkout this [site](https://ubc-dsci.github.io/dsci-310-student/install_stack_ubuntu.html)]

---

---

# Linux and CLI
.pull-left[
We will be using the .hand[famous] Linux system, where everything is going to be blacked out.

It is very cool once you are familiar at this.

.pull-right[
.secondary[Useful CL commands]
```bash
cd ~/path/to/dir/
cp ~/file/to/copy.md file/to/paste.md
cp -r ~/dir/to/copy/ dir/to/paste
ls -a # list all files (including hidden)
rm ~/file/to/delete.txt
```
]

The `-r` flag means to be done recursively. Many linux commands have this flag, in the case of `rm`, it remove directories and their contents recursively.

---

# Linux and CLI

Note, there are cases that you want to delete directories where files are protected (like those of **git**)

Use the following with **CAUTION**:

The `-f` flag tells to delete .hand[force] without confirmation. Be very careful on what are you deleting.

You likely don't want to contact admin:
> You: Hey, I think I have deleted my $HOME directory
>
> Admin: .......
>

Don't .secondary[panic] either, you rarely can delete those directories.

---

# Linux and CLI

Most Linux commands have a built-in manual (man page) that serves as a quick guide to tell you what a command does. You could almost always type `command --help`.

Let's see an example
--

Seems scary right? I agree! <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#0a8754;overflow:visible;position:relative;"><path d="M323.8 34.8c-38.2-10.9-78.1 11.2-89 49.4l-5.7 20c-3.7 13-10.4 25-19.5 35l-51.3 56.4c-8.9 9.8-8.2 25 1.6 33.9s25 8.2 33.9-1.6l51.3-56.4c14.1-15.5 24.4-34 30.1-54.1l5.7-20c3.6-12.7 16.9-20.1 29.7-16.5s20.1 16.9 16.5 29.7l-5.7 20c-5.7 19.9-14.7 38.7-26.6 55.5c-5.2 7.3-5.8 16.9-1.7 24.9s12.3 13 21.3 13L448 224c8.8 0 16 7.2 16 16c0 6.8-4.3 12.7-10.4 15c-7.4 2.8-13 9-14.9 16.7s.1 15.8 5.3 21.7c2.5 2.8 4 6.5 4 10.6c0 7.8-5.6 14.3-13 15.7c-8.2 1.6-15.1 7.3-18 15.1s-1.6 16.7 3.6 23.3c2.1 2.7 3.4 6.1 3.4 9.9c0 6.7-4.2 12.6-10.2 14.9c-11.5 4.5-17.7 16.9-14.4 28.8c.4 1.3 .6 2.8 .6 4.3c0 8.8-7.2 16-16 16H286.5c-12.6 0-25-3.7-35.5-10.7l-61.7-41.1c-11-7.4-25.9-4.4-33.3 6.7s-4.4 25.9 6.7 33.3l61.7 41.1c18.4 12.3 40 18.8 62.1 18.8H384c34.7 0 62.9-27.6 64-62c14.6-11.7 24-29.7 24-50c0-4.5-.5-8.8-1.3-13c15.4-11.7 25.3-30.2 25.3-51c0-6.5-1-12.8-2.8-18.7C504.8 273.7 512 257.7 512 240c0-35.3-28.6-64-64-64l-92.3 0c4.7-10.4 8.7-21.2 11.8-32.2l5.7-20c10.9-38.2-11.2-78.1-49.4-89zM32 192c-17.7 0-32 14.3-32 32V448c0 17.7 14.3 32 32 32H96c17.7 0 32-14.3 32-32V224c0-17.7-14.3-32-32-32H32z"/></svg>

But it gets better later, and let's dig more into its details. Look at the following:
.emphasis[
Usage: ls [OPTION] ... [FILE] ...
]

This part is where it tells you how you should use a command, what **possible** options it accepts

The [...] are .secondary[optional argument/s] and could be specified with the **flag** it takes. For example: `ls -a` or `ls --all` list **ALL** files of a directory.

]
.pull-right[
![](materials/img/help_usage.jpg)
]

---

Try on any commands of your interest and look at its doc with `--help`

]

--
You could combine flags as well

```bash
ls -alh
```
Single letter flags **can** be combined together, BUT whole words .secondary[cannot]

```bash
ls --all --human-readable -l
```
--

---

# How to connect

Login to sockeye with:
```bash
# replace cwl with your actual cwl
# sockeye dynamically select one of three possible "login" nodes
ssh cwl@sockeye.arc.ubc.ca
```
.pull-left[
- Upon login, you're on a `login` node
- You can run **short** interactive jobs there
- We will have an alias to do this later
- But requires some configuration on your laptop/PC
]
--
.pull-right[
.your-turn[
- Try `ssh --help` and see what it says?
]]

<hr>

You could also login to specific login node:
```bash
# one of login01, login02, login03
ssh cwl@login03.sockeye.arc.ubc.ca
```
--

I rarely use this one ^

You need to have an IP address from UBC, either by connected to UBC Wifi or VPN

]

---

class: middle, center
background-image: url(materials/img/ssh-keys.png)
background-size: contain

???

Explain difference of private and public keys, and its usage

---

## Faster way to connect
.pull-left[
Configure ssh keys, store it in your local and arc.

]

.pull-right[
Prompt the following to check existing `ssh` keys with `id_*` format:
```bash
ls -a ~/.ssh/
```
]
--

<hr>

.pull-left[
Generate a new ssh key pair (`Bash`/`Zsh`/`Powershell`)
```bash
ssh-keygen -t rsa
```
- Follow the defaults by prompting `Enter`
- Passphrase not required, personal flavor

]

.pull-right[
Two keys generated:
- one .tertiary[public] (`id_*.pub`)
- one .secondary[private] (`id_*`)

<hr>
Add it to Sockeye

```bash
# Note we are using the public key
ssh-copy-id -i ~/.ssh/id_rsa.pub cwl@sockeye.arc.ubc.ca # replace cwl
```
```bash
# For Powershell
type $env:USERPROFILE\.ssh\id_rsa.pub | ssh cwl@sockeye.arc.ubc.ca "cat >> .ssh/authorized_keys"
```

???

This is the last time entering password to sockeye

---

.pull-left[
Only fixed not having to enter password, but still have to type the full `username@host`.
- Looking into **alias**

- Need .secondary[configuration]

<br>
Use VScode or any text editor to create `~/.ssh/config`:
```bash
Host alias-you-like # I use arc
    HostName sockeye.arc.ubc.ca
    User cwl
```
- `Host` = `User@Hostname`

- Multiple configuration (multiple servers)

- More options available , look at [here](https://www.ssh.com/academy/ssh/config)
]

![:scale 97%](materials/img/config-ssh.png)
]

Try now with your newly created alias
```bash
ssh arc # Again I used arc as the alias 
```

---

### Use SSH with GitHub

1. Go to this **[GitHub site](https://github.com/settings/ssh/new)**

1. Add a suitable .tertiary[title/name] for the key

1. Copy the content of your .secondary[public] key, `id_*.pub` created early into the textbox

1. Leave everything as it is and click `Add SSH key`
]

<br>

---

#### SSH with VSCode

1. Open you VScode by prompting `code `in terminal

1. Press `Ctrl + Shift + X `

1. Type `Remote - SSH` in the search bar

1. Open the first option and click `install`

- It should be installed in a few seconds
]

![](materials/img/ssh-install.png)
]

---

#### Optional: Scp files

To copy files around sockeye and your local, use the `scp` command

```bash
scp FROM:~/path/from TO:~/path/to
```
- The `FROM` and `TO` need to be specified, such that it represents IP address
- `WHERE`**:**`WHAT`, **Note** the **:** is required
- The **sockeye** server is fixed

```bash
# This means to download some_file from your $HOME
# in sockeye to your local desktop
scp cwl@sockeye.arc.ubc.ca:/home/cwl/some_file ~/Desktop
```

```bash
# This means to upload some_file from your local Desktop
# to your project dir on sockeye 
scp ~/Desktop/some_file cwl@sockeye.arc.ubca:/arc/project/cwl/some_file
```

Remember the alias earlier?
```bash
# This works as well, if you have configure the ssh properly
scp arc:/home/cwl/some_file ~/Desktop
```

---

---

# Basic Information of Sockeye

**Sockeye** is a High Performance Computing (HPC) platform, use it to run .secondary[large] computational analysis or works here.

- Although requires knowledge to **Linux and CLI**

- You have different **nodes** on Sockeye
]

]

- Where you land after `ssh`
- Has internet access
- You spend **MOST** time here
]

- "You don't do much on here"
- Do **not** have internet access
- There's an interactive type of this

]

.footnote[For more information, visit its official [documentation](https://confluence.it.ubc.ca/display/UARC/Quickstart+Guide#QuickstartGuide-SettingupyourComputer)]

---

class: middle, center
background-image: url(materials/img/arc-structure.jpg)
background-size: contain

???

Explain what each node is, and the workflow

---

<div class="datatables html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-3ddf61f37a3b681f1823" style="width:100%;height:auto;"></div>
<script type="application/json" data-for="htmlwidget-3ddf61f37a3b681f1823">{"x":{"filter":"none","vertical":false,"fillContainer":false,"data":[["1","2","3","4","5","6","7","8","9","10"],[210,8,8,6,170,8,8,44,3,2],["Base","Medium","Large","GPU16","Base","Medium","Large","GPU32","Login","Data Transfer"],["2 x Intel Xeon Gold 6130 (2.1GHz)","2 x Intel Xeon Gold 6130 (2.1GHz)","2 x Intel Xeon Gold 6130 (2.1GHz)","2 x Intel Xeon Silver 4116 (2.1GHz)","2 x Intel Xeon Gold 6230 (2.1GHz)","2 x Intel Xeon Gold 6230 (2.1GHz)","2 x Intel Xeon Gold 6230 (2.1GHz)","2 x Intel Xeon Silver 4216 (2.1GHz)","2 x Intel Xeon Silver 4110 (2.1GHz)","2 x Intel Xeon Silver 4110 (2.1GHz)"],[32,32,32,24,40,40,40,24,16,16],["Skylake","Skylake","Skylake","Skylake","Cascade Lake","Cascade Lake","Cascade Lake","Cascade Lake","Skylake","Skylake"],["192GB DDR4-2666 ECC","384GB DDR4-2666 ECC","768GB DDR4-2666 ECC","192GB DDR4-2666 ECC","192GB DDR4-2666 ECC","384GB DDR4-2666 ECC","768GB DDR4-2666 ECC","192GB DDR4-2666 ECC","192GB DDR4-2666 ECC","192GB DDR4-2666 ECC"],["6GB","12GB","24GB","8GB","4.8GB","9.6GB","19.2GB","8GB","8GB","8GB"],["2TB SATA HDD","2TB SATA HDD","2TB SATA HDD","1.9TB NVMe SSD","2TB SATA HDD","2TB SATA HDD","2TB SATA HDD","1.9TB NVMe SSD","2TB SATA HDD","2TB SATA HDD"],["N/A","N/A","N/A","4 x NVIDIA Tesla V100 16GB NVLink","N/A","N/A","N/A","4 x NVIDIA Tesla V100 32GB NVLink","N/A","N/A"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Nodes<\/th>\n      <th>Type<\/th>\n      <th>CPU<\/th>\n      <th>Total.Cores<\/th>\n      <th>Architecture<\/th>\n      <th>System.Memory<\/th>\n      <th>Mem.per.Core<\/th>\n      <th>Local.Storage<\/th>\n      <th>General.Purpose.GPU<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":2,"scrollX":true,"columnDefs":[{"className":"dt-right","targets":[1,4]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false,"lengthMenu":[2,10,25,50,100]}},"evals":[],"jsHooks":[]}</script>

.footnote[For more information, visit [here](https://confluence.it.ubc.ca/display/UARC/About+Sockeye)]

???

Explain nodes difference here, add footnote

---

## Directories on Sockeye
.pull-left[
![:scale 100%](materials/img/arc-dir.png)
]
.pull-right[
![:scale 90%](materials/img/ro-dir.png)
]
--

#### /home
- The place you land after `ssh`, equivalent to `~`
- Only the **$USER** has access

]

.pull-right[
#### **/project**
- Store your data, containers here
- Do not store intermediate results here

#### **/scratch**
- Playground space, widely used in compute node
- Your intermediate results should be written here
- .secondary[Try not storing huge stuff here]

]

???

These are soft links of directories, its actual path is different, demo it

1. Copy/transfer input data to /arc/project/<alloc-code> 
2. Login to Sockeye and create/modify job script(s) in /scratch/<alloc-code>
3. Submit jobs that read input data from /arc/project/<alloc-code> and writes output to /scratch/<alloc-code>  (or $TMDIR)
4. Job completes successfully
5. Copy/transfer job output from /scratch/<alloc-code> to /arc/projects/<alloc-code> 
6. Interactively post-process and/or analyze results in /arc/project/<alloc-code>

---

Try on it and explore through actual coding!

First setup `ENV` variables .alert[This is only valid for current bash session, need to configure .secondary[.bashrc] to work all time]

.pull-left[
  
- **KEY=value**, .secondary[Upper] case by convention 
- Case sensitive
- Retrieve the value by `$KEY`
]

.pull-right[
  ```bash
  export ALLOC=st-singha53-1
  export SCRATCH_PATH=/scratch/$ALLOC/$USER
  export PROJECT_PATH=/arc/project/$ALLOC/$USER
  ```
]

Print these `*_PATH` variables out to get its path, and `cd` into them

```bash
  echo $SCRATCH_PATH && echo $PROJECT_PATH
  ```
  ```bash
  cd $SCRATCH_PATH && ls -a
  ```
  ```bash
  cd $PROJECT_PATH && ls -a
  ```
  - The `&&` is the .secondary[AND] operator in **shell**

This one is more sockeye-specific to check spaces allocated to you
  ```bash
  print_quota
  ```

---

---

# Bashrc

- We mentioned earlier, that the `export ...` is only valid for the current bash session
- once you log-out, it's gone

<hr>

- You need to add this to the `.bashrc` or `.bash_profile` located in the root path `~`
- These are places where you store configurations
]

- <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#0a8754;overflow:visible;position:relative;"><path d="M323.8 34.8c-38.2-10.9-78.1 11.2-89 49.4l-5.7 20c-3.7 13-10.4 25-19.5 35l-51.3 56.4c-8.9 9.8-8.2 25 1.6 33.9s25 8.2 33.9-1.6l51.3-56.4c14.1-15.5 24.4-34 30.1-54.1l5.7-20c3.6-12.7 16.9-20.1 29.7-16.5s20.1 16.9 16.5 29.7l-5.7 20c-5.7 19.9-14.7 38.7-26.6 55.5c-5.2 7.3-5.8 16.9-1.7 24.9s12.3 13 21.3 13L448 224c8.8 0 16 7.2 16 16c0 6.8-4.3 12.7-10.4 15c-7.4 2.8-13 9-14.9 16.7s.1 15.8 5.3 21.7c2.5 2.8 4 6.5 4 10.6c0 7.8-5.6 14.3-13 15.7c-8.2 1.6-15.1 7.3-18 15.1s-1.6 16.7 3.6 23.3c2.1 2.7 3.4 6.1 3.4 9.9c0 6.7-4.2 12.6-10.2 14.9c-11.5 4.5-17.7 16.9-14.4 28.8c.4 1.3 .6 2.8 .6 4.3c0 8.8-7.2 16-16 16H286.5c-12.6 0-25-3.7-35.5-10.7l-61.7-41.1c-11-7.4-25.9-4.4-33.3 6.7s-4.4 25.9 6.7 33.3l61.7 41.1c18.4 12.3 40 18.8 62.1 18.8H384c34.7 0 62.9-27.6 64-62c14.6-11.7 24-29.7 24-50c0-4.5-.5-8.8-1.3-13c15.4-11.7 25.3-30.2 25.3-51c0-6.5-1-12.8-2.8-18.7C504.8 273.7 512 257.7 512 240c0-35.3-28.6-64-64-64l-92.3 0c4.7-10.4 8.7-21.2 11.8-32.2l5.7-20c10.9-38.2-11.2-78.1-49.4-89zM32 192c-17.7 0-32 14.3-32 32V448c0 17.7 14.3 32 32 32H96c17.7 0 32-14.3 32-32V224c0-17.7-14.3-32-32-32H32z"/></svg> .primary[With suitable configs, Linux >> Mac >> Windows]
- <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#e98a15;overflow:visible;position:relative;"><path d="M459.1 52.4L442.6 6.5C440.7 2.6 436.5 0 432.1 0s-8.5 2.6-10.4 6.5L405.2 52.4l-46 16.8c-4.3 1.6-7.3 5.9-7.2 10.4c0 4.5 3 8.7 7.2 10.2l45.7 16.8 16.8 45.8c1.5 4.4 5.8 7.5 10.4 7.5s8.9-3.1 10.4-7.5l16.5-45.8 45.7-16.8c4.2-1.5 7.2-5.7 7.2-10.2c0-4.6-3-8.9-7.2-10.4L459.1 52.4zm-132.4 53c-12.5-12.5-32.8-12.5-45.3 0l-2.9 2.9C256.5 100.3 232.7 96 208 96C93.1 96 0 189.1 0 304S93.1 512 208 512s208-93.1 208-208c0-24.7-4.3-48.5-12.2-70.5l2.9-2.9c12.5-12.5 12.5-32.8 0-45.3l-80-80zM200 192c-57.4 0-104 46.6-104 104v8c0 8.8-7.2 16-16 16s-16-7.2-16-16v-8c0-75.1 60.9-136 136-136h8c8.8 0 16 7.2 16 16s-7.2 16-16 16h-8z"/></svg> .secondary[Without configs, Linux sucks]
- <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#e98a15;overflow:visible;position:relative;"><path d="M459.1 52.4L442.6 6.5C440.7 2.6 436.5 0 432.1 0s-8.5 2.6-10.4 6.5L405.2 52.4l-46 16.8c-4.3 1.6-7.3 5.9-7.2 10.4c0 4.5 3 8.7 7.2 10.2l45.7 16.8 16.8 45.8c1.5 4.4 5.8 7.5 10.4 7.5s8.9-3.1 10.4-7.5l16.5-45.8 45.7-16.8c4.2-1.5 7.2-5.7 7.2-10.2c0-4.6-3-8.9-7.2-10.4L459.1 52.4zm-132.4 53c-12.5-12.5-32.8-12.5-45.3 0l-2.9 2.9C256.5 100.3 232.7 96 208 96C93.1 96 0 189.1 0 304S93.1 512 208 512s208-93.1 208-208c0-24.7-4.3-48.5-12.2-70.5l2.9-2.9c12.5-12.5 12.5-32.8 0-45.3l-80-80zM200 192c-57.4 0-104 46.6-104 104v8c0 8.8-7.2 16-16 16s-16-7.2-16-16v-8c0-75.1 60.9-136 136-136h8c8.8 0 16 7.2 16 16s-7.2 16-16 16h-8z"/></svg> .secondary[It's HARD to setup the configs, it will get better]
]

--
.center[.pull-left[
  ![](materials/img/bashrc.png)
]]
.center[.pull-right[
  ![](materials/img/bash_profile.png)
]]

---
class:top
.pull-left[
Append the following to your `.bashrc` or `bash_profile`

```bash
export ALLOC=st-singha53-1
export SCRATCH_PATH=/scratch/$ALLOC/$USER
export PROJECT_PATH=/arc/project/$ALLOC/$USER
```

- You could also load modules here
- I mostly use `git`, `gcc`

```bash
module load gcc
module load git
```
]
.pull-right[
To make it work you need either of:
- `source ~/.bashrc`
- `source ~/.bash_profile`
- .secondary[It'r required to "reactivate" the configs]
- It's what it does behind the scenes when you login

.emphasis[
The `source` is only required when you want update right away. Bash auto source everytime you start it. 
]
]

--
<hr>
**More advanced usage**
- You could make `alias` for long commands, or hard to remember ones
```bash
alias la='ls -a'
alias h='history' # Prints list of commands you entered
# do not delete / or prompt if deleting more than 3 files at a time 
alias rm='rm -I --preserve-root'
# confirmation 
alias mv='mv -i'
alias cp='cp -i'
```
--

---

## Acessing softwares in Sockeye

.pull-left-narrow[
- Load pre-downloaded modules
- Limited option, if not provided use `virtual environment` or `container`
- Download, compile and install (Last option)
- Sockeye prefer `conda` over `virtualenv`
]

```bash
module load bin1/x.y.z bin2/x.y.z # load two modules and their versions
module purge # unload all modules
module list # what you have loaded
module save name_col # save loaded modules to "name_col"
module savelist # list saved collections (name col this case)
module restore name_col # load saved collection
module avail # show all available modules
module spider mod_name # check available `mod_name` in sockeye
```
]

<br>

I.e. `Python` is the programming language, `python` is the binary exe 
]

Compare the difference of these two:

```bash
module purge && python --version
```

```bash
module load gcc/7.5.0 python/3.7.10 && python --version
```

---

# Job Submission

**Sockeye** is a High Performance Computing (HPC) platform, use it to run .secondary[large] computational analysis or works here.

- System manage it through queue and runs it for you

- No internet access at all
]

.pull-right[
- .secondary[batch job]
  - Most cases, advanced usage see [`here`](https://confluence.it.ubc.ca/display/UARC/Running+Jobs)
- .secondary[interactive job]
  - Test small to intermediate analysis
- Launch in `$SCRATCH_PATH`
]

```bash
#!/bin/bash
 
#PBS -l walltime=02:00:00,select=2:ncpus=2:mem=2gb
#PBS -N job_name
#PBS -A alloc-code
#PBS -m abe
#PBS -M your.name@ubc.ca
#PBS -o output.txt
#PBS -e error.txt
 
#####################################################
 
module load software_package_1
module load software_package_2
 
cd $PBS_O_WORKDIR
 
<executing commands here>
```
]

.pull-right[
- These are `pbs headers` to specify resources
- It could be specified in `CLI` as well
- `walltime=DD:HH:MM:SS`, time expected for job
- `select=2:ncpus=4:mem=2gb` means to select 2 node, each with 4 cpus and 2gb of memory
- `alloc-code` is fixed to `st-singha53-1` or `st-singha53-1-gpu` for gpu usage

---

## Submitting your first job!

```bash
#!/bin/bash
 
#PBS -l walltime=02:00:00,select=1:ncpus=1:mem=2gb
#PBS -N hello-world
#PBS -A st-singha53-1
#PBS -m abe
#PBS -M cwl@ubc.ca
#PBS -o output.txt
#PBS -e error.txt
 
#####################################################
 
module load gcc/7.5.0
module load python/3.7.10
 
cd $PBS_O_WORKDIR # required by Sockeye
 
python hello_world.py
```
]

```bash
print("hello world")
```

To submit it:
```bash
qsub sample.sh
```

To check status:
```bash
qstat -u $USER
```

]

---

class: middle, center
background-image: url(materials/img/website_bkg.png)
background-position: top
background-size: contain

<br><br>
.secondary[.center[.larger[Thanks!]]]

Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan).

Credits to:

[Stat 406 Lecture Slides @DJM](https://ubc-stat.github.io/stat-406/)