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Initial configuration for Storrs HPC workshop
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pan14001 committed Apr 11, 2017
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4 changes: 2 additions & 2 deletions _config.yml
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Expand Up @@ -37,8 +37,8 @@ training_site: "https://swcarpentry.github.io/instructor-training"
swc_installer: "https://github.com/swcarpentry/windows-installer/releases/download/v0.3/SWCarpentryInstaller.exe"

# Surveys.
pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id="
post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id="
pre_survey: "https://uconn.co1.qualtrics.com/jfe/form/SV_2rC3DedvVoYORrT"
post_survey: "https://uconn.co1.qualtrics.com/SE/?SID=SV_cAc15sbUMlafLOB"

# Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am)
start_time: 0
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177 changes: 61 additions & 116 deletions index.html
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@@ -1,21 +1,21 @@
---
layout: workshop # DON'T CHANGE THIS.
root: . # DON'T CHANGE THIS EITHER. (THANK YOU.)
carpentry: "FIXME" # what kind of Carpentry (must be either "dc" or "swc")
venue: "FIXME" # brief name of host site without address (e.g., "Euphoric State University")
address: "FIXME" # full street address of workshop (e.g., "Room A, 123 Forth Street, Blimingen, Euphoria")
country: "FIXME" # lowercase two-letter ISO country code such as "fr" (see https://en.wikipedia.org/wiki/ISO_3166-1)
language: "FIXME" # lowercase two-letter ISO language code such as "fr" (see https://en.wikipedia.org/wiki/ISO_639-1)
latlng: "FIXME" # decimal latitude and longitude of workshop venue (e.g., "41.7901128,-87.6007318" - use http://www.latlong.net/)
humandate: "FIXME" # human-readable dates for the workshop (e.g., "Feb 17-18, 2020")
humantime: "FIXME" # human-readable times for the workshop (e.g., "9:00 am - 4:30 pm")
startdate: FIXME # machine-readable start date for the workshop in YYYY-MM-DD format like 2015-01-01
enddate: FIXME # machine-readable end date for the workshop in YYYY-MM-DD format like 2015-01-02
instructor: ["FIXME"] # boxed, comma-separated list of instructors' names as strings, like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["FIXME"] # boxed, comma-separated list of helpers' names, like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: ["fixme@example.org"] # boxed, comma-separated list of contact email addresses for the host, lead instructor, or whoever else is handling questions, like ["marlyn.wescoff@example.org", "fran.bilas@example.org", "ruth.lichterman@example.org"]
carpentry: "dc" # what kind of Carpentry (must be either "dc" or "swc")
venue: "University of Connecticut, Storrs" # brief name of host site without address (e.g., "Euphoric State University")
address: "Laurel Hall 306, Storrs, CT 06269" # full street address of workshop (e.g., "Room A, 123 Forth Street, Blimingen, Euphoria")
country: "us" # lowercase two-letter ISO country code such as "fr" (see https://en.wikipedia.org/wiki/ISO_3166-1)
language: "en" # lowercase two-letter ISO language code such as "fr" (see https://en.wikipedia.org/wiki/ISO_639-1)
latlng: "41.807232, -72.253436" # decimal latitude and longitude of workshop venue (e.g., "41.7901128,-87.6007318" - use http://www.latlong.net/)
humandate: "Apr 17, 2017" # human-readable dates for the workshop (e.g., "Feb 17-18, 2020")
humantime: "10:00 am - 12:00 pm" # human-readable times for the workshop (e.g., "9:00 am - 4:30 pm")
startdate: 2017-04-17 # machine-readable start date for the workshop in YYYY-MM-DD format like 2015-01-01
enddate: 2017-04-17 # machine-readable end date for the workshop in YYYY-MM-DD format like 2015-01-02
instructor: ["Pariksheet Nanda"] # boxed, comma-separated list of instructors' names as strings, like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["Jingwen Pei", "Xin Li", "Tingyang Xu", "Christian Kuntz", "Luke Malinowski", "Dave Christianson", "Ed Swindelles"] # boxed, comma-separated list of helpers' names, like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: ["hpc@uconn.edu"] # boxed, comma-separated list of contact email addresses for the host, lead instructor, or whoever else is handling questions, like ["marlyn.wescoff@example.org", "fran.bilas@example.org", "ruth.lichterman@example.org"]
collaborative_notes: # optional: URL for the workshop collaborative notes, e.g. an Etherpad or Google Docs document
eventbrite: # optional: alphanumeric key for Eventbrite registration, e.g., "1234567890AB" (if Eventbrite is being used)
eventbrite: 33643014161 # optional: alphanumeric key for Eventbrite registration, e.g., "1234567890AB" (if Eventbrite is being used)
---

<!-- See instructions in the comments below for how to edit specific sections of this workshop template. -->
Expand Down Expand Up @@ -47,10 +47,12 @@ eventbrite: # optional: alphanumeric key for Eventbrite registration,
</iframe>
{% endif %}

<!--
<h4>This is the workshop template. Use it to create your own website.
Delete these lines and please fill in
<a href="{{site.amy_site}}/submit">this self-organized workshop form</a>
and the administrator will contact you if we need any extra information.</h4>
-->

<h2 id="general">General Information</h2>

Expand All @@ -61,15 +63,12 @@ and the administrator will contact you if we need any extra information.</h4>
the pitch.
-->
<p>
<a href="{{site.swc_site}}">Software Carpentry</a>
aims to help researchers get their work done
in less time and with less pain
by teaching them basic research computing skills.
This hands-on workshop will cover basic concepts and tools,
including program design, version control, data management,
and task automation.
Participants will be encouraged to help one another
and to apply what they have learned to their own research problems.
The HPC Essentials workshop is for any researcher
to use UConn's computer cluster
with no prior experience of the command-line or programming.
We will cover what the cluster can do for you,
how to navigate the command-line interface to run your programs
and transfer data.
</p>
<p align="center">
<em>
Expand Down Expand Up @@ -132,7 +131,7 @@ and the administrator will contact you if we need any extra information.</h4>
<p id="requirements">
<strong>Requirements:</strong> Participants must bring a laptop with a
Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges
on. They should have a few specific software packages installed (listed
on. They should have a few specific software packages installed and an account on the HPC cluster (listed
<a href="#setup">below</a>). They are also required to abide by
Software Carpentry's
<a href="{{site.swc_site}}/conduct.html">Code of Conduct</a>.
Expand Down Expand Up @@ -206,25 +205,12 @@ and the administrator will contact you if we need any extra information.</h4>

<div class="row">
<div class="col-md-6">
<h3>Day 1</h3>
<table class="table table-striped">
<tr> <td>09:00</td> <td>Automating tasks with the Unix shell</td> </tr>
<tr> <td>10:30</td> <td>Coffee</td> </tr>
<tr> <td>12:00</td> <td>Lunch break</td> </tr>
<tr> <td>13:00</td> <td>Building programs with Python</td> </tr>
<tr> <td>14:30</td> <td>Coffee</td> </tr>
<tr> <td>16:00</td> <td>Wrap-up</td> </tr>
</table>
</div>
<div class="col-md-6">
<h3>Day 2</h3>
<table class="table table-striped">
<tr> <td>09:00</td> <td>Version control with Git</td> </tr>
<tr> <td>10:30</td> <td>Coffee</td> </tr>
<tr> <td>12:00</td> <td>Lunch break</td> </tr>
<tr> <td>13:00</td> <td>Managing data with SQL</td> </tr>
<tr> <td>14:30</td> <td>Coffee</td> </tr>
<tr> <td>16:00</td> <td>Wrap-up</td> </tr>
<tr> <td>10:00</td> <td>What is a modern supercomputer?</td> </tr>
<tr> <td>10:10</td> <td>Using the UNIX shell</td> </tr>
<tr> <td>11:00</td> <td>Loading modules and submitting jobs to the cluster</td> </tr>
<tr> <td>11:45</td> <td>Saving results with Globus</td> </tr>
<tr> <td>12:00</td> <td>Wrap-up</td> </tr>
</table>
</div>
</div>
Expand Down Expand Up @@ -272,13 +258,11 @@ and the administrator will contact you if we need any extra information.</h4>
<ul>
<li>Files and directories</li>
<li>History and tab completion</li>
<li>Pipes and redirection</li>
<li>Looping over files</li>
<li>Creating and running shell scripts</li>
<li>Finding things</li>
<li><a href="{{site.swc_pages}}/shell-novice/reference/">Reference...</a></li>
</ul>
</div>
<!--
<div class="col-md-6">
<h3 id="syllabus-python">Programming in Python</h3>
<ul>
Expand All @@ -292,6 +276,7 @@ and the administrator will contact you if we need any extra information.</h4>
<li><a href="{{site.swc_pages}}/python-novice-inflammation/reference/">Reference...</a></li>
</ul>
</div>
-->
<!--
<div class="col-md-6">
<h3 id="syllabus-r">Programming in R</h3>
Expand Down Expand Up @@ -319,7 +304,7 @@ and the administrator will contact you if we need any extra information.</h4>
</div>
-->
</div>

<!--
<div class="row">
<div class="col-md-6">
<h3 id="syllabus-git">Version Control with Git</h3>
Expand Down Expand Up @@ -350,7 +335,7 @@ and the administrator will contact you if we need any extra information.</h4>
</ul>
</div>
</div>

-->
<hr/>

<!--
Expand All @@ -368,7 +353,7 @@ and the administrator will contact you if we need any extra information.</h4>
<h2 id="setup">Setup</h2>

<p>
To participate in a Software Carpentry workshop, you will need
To participate in the workshop, you will need
access to the software described below. In addition, you will
need an up-to-date web browser.
</p>
Expand All @@ -389,59 +374,13 @@ and the administrator will contact you if we need any extra information.</h4>
<div class="row">
<div class="col-md-4">
<h4 id="shell-windows">Windows</h4>
<a href="https://www.youtube.com/watch?v=339AEqk9c-8">Video Tutorial</a>
<p>You will need a terminal program to access the HPC cluster.</p>
<ol>
<li>Download the Git for Windows <a href="https://git-for-windows.github.io/">installer</a>.</li>
<li>Run the installer and follow the steps bellow:
<ol>
<!-- Git 2.8.2 Setup -->
<!-- Information -->
<li>Click on "Next".</li>
<!-- Select Components -->
<li>Click on "Next".</li>
<!-- Adjusting your PATH environment -->
<li>
<strong>
Keep "Use Git from the Windows Command Prompt" selected and click on "Next".
</strong>
If you forgot to do this programs that you need for the workshop will not work properly.
If this happens rerun the installer and select the appropriate option.
</li>
<!-- Choosing the SSH executable -->
<li>Click on "Next".</li>
<!-- Configuring the line ending conversions -->
<li>
<strong>
Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
</strong>
</li>
<!-- Configuring the terminal emulator to use with Git Bash -->
<li>
<strong>
Keep "Use Windows' default console window" selected and click on "Next".
</strong>
</li>
<!-- Configuring experimental performance tweaks -->
<li>Click on "Install".</li>
<!-- Installing -->
<!-- Completing the Git Setup Wizard -->
<li>Click on "Finish".</li>
</ol>
</li>
<li>
If your "HOME" environment variable is not set (or you don't know what this is):
<ol>
<li>Open command prompt (Open Start Menu then type <code>cmd</code> and press [Enter])</li>
<li>
Type the following line into the command prompt window exactly as shown:
<p><code>setx HOME "%USERPROFILE%"</code></p>
</li>
<li>Press [Enter], you should see <code>SUCCESS: Specified value was saved.</code></li>
<li>Quit command prompt by typing <code>exit</code> then pressing [Enter]</li>
</ol>
</li>
<li>Go to the Putty <a href="http://www.chiark.greenend.org.uk/%7Esgtatham/putty/download.html">download
page</a></li>
<li>Click on <i>putty.exe</i> link under <strong>Alternative binary files</strong> to download putty</li>
<li>To use it, double-click on the downloaded file</li>
</ol>
<p>This will provide you with both Git and Bash in the Git Bash program.</p>
</div>
<div class="col-md-4">
<h4 id="shell-macosx">Mac OS X</h4>
Expand All @@ -450,8 +389,6 @@ and the administrator will contact you if we need any extra information.</h4>
need to install anything. You access Bash from the Terminal
(found in
<code>/Applications/Utilities</code>).
See the Git installation <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">video tutorial</a>
for an example on how to open the Terminal.
You may want to keep
Terminal in your dock for this workshop.
</p>
Expand All @@ -468,8 +405,19 @@ and the administrator will contact you if we need any extra information.</h4>
</div>
</div> <!-- End of 'shell' section. -->

<div id="git"> <!-- Start of 'Git' section. GitHub browser compatability
is given at https://help.github.com/articles/supported-browsers/-->
<div id="cluster">
<h3>HPC cluster account</h3>
<p>
You will need to be able to access the HPC cluster via <code>login.storrs.hpc.uconn.edu</code>
as described on our <a href="https://wiki.hpc.uconn.edu/index.php/HPC_Getting_Started">HPC wiki</a>.
Otherwise, you will need an account on our HPC cluster.
You can request an account from
<a href="http://hpc.uconn.edu/storrs/account-application">hpc.uconn.edu</a>.
</p>
</div>

<!--
<div id="git">
<h3>Git</h3>
<p>
Git is a version control system that lets you track who made changes
Expand Down Expand Up @@ -522,9 +470,9 @@ and the administrator will contact you if we need any extra information.</h4>
</p>
</div>
</div>
</div> <!-- End of 'Git' section. -->
</div>
<div id="editor"> <!-- Start of 'editor' section. -->
<div id="editor">
<h3>Text Editor</h3>
<p>
Expand Down Expand Up @@ -585,12 +533,9 @@ and the administrator will contact you if we need any extra information.</h4>
</p>
</div>
</div>
</div> <!-- End of 'editor' section. -->
</div>
<div id="python"> <!-- Start of 'Python' section. Remove the third paragraph if
the workshop will teach Python using something other than
the IPython notebook.
Details at http://ipython.org/ipython-doc/2/install/install.html#browser-compatibility -->
<div id="python">
<h3>Python</h3>
<p>
Expand Down Expand Up @@ -670,16 +615,16 @@ and the administrator will contact you if we need any extra information.</h4>
</ol>
</div>
</div>
<!--
<p>
Once you are done installing the software listed above,
please go to <a href="setup/index.html">this page</a>,
which has instructions on how to test that everything was installed correctly.
</p>
-->
</div> <!-- End of 'Python' section. -->
<div id="r"> <!-- Start of 'R' section. -->
</div>
<div id="r">
<h3>R</h3>
<p>
Expand Down Expand Up @@ -728,9 +673,9 @@ and the administrator will contact you if we need any extra information.</h4>
</p>
</div>
</div>
</div> <!-- End of 'R' section. -->
</div>
<div id="sql"> <!-- Start of 'SQLite' section. -->
<div id="sql">
<h3>SQLite</h3>
<p>
Expand Down

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