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setup.html
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<li><a href="#terminal" id="toc-terminal" class="nav-link" data-scroll-target="#terminal">Terminal</a></li>
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<li><a href="#mac-logon-to-artemis" id="toc-mac-logon-to-artemis" class="nav-link" data-scroll-target="#mac-logon-to-artemis">Mac Logon to Artemis</a></li>
<li><a href="#windows-logon-to-artemis" id="toc-windows-logon-to-artemis" class="nav-link" data-scroll-target="#windows-logon-to-artemis">Windows Logon to Artemis</a></li>
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<li><a href="#x11-forwarding" id="toc-x11-forwarding" class="nav-link" data-scroll-target="#x11-forwarding">X11 FORWARDING</a></li>
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<h1 class="title">Setup</h1>
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<div class="quarto-title-meta">
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<section id="essential-software" class="level2">
<h2 class="anchored" data-anchor-id="essential-software">Essential Software</h2>
<section id="terminal" class="level3">
<h3 class="anchored" data-anchor-id="terminal">Terminal</h3>
<p>To connect to Artemis HPC, and follow this lesson, you will need a ‘terminal emulator with SSH (secure shell). SSH provides encrypted communication between the your computer and a remote server, in this case Artemis. The SSH client will be invoked by the command ‘ssh’.</p>
<p>If you are a <strong>Windows</strong> users please have one of either apps below installed:</p>
<ol type="1">
<li><p><a href="https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html">Putty</a> (recommended)</p></li>
<li><p><a href="https://mobaxterm.mobatek.net/download.html">MobaXterm</a></p></li>
<li><p><a href="https://ubuntu.com/tutorials/tutorial-ubuntu-on-windows#1-overview">WSL and Ubuntu</a> (advanced)</p></li>
</ol>
<p>If you are a <strong>Mac</strong> user we will be using the Terminal which comes pre-installed on your device.</p>
</section>
<section id="vpn" class="level3">
<h3 class="anchored" data-anchor-id="vpn">VPN</h3>
<p>For all users, if you are not on campus install and/or have your <a href="https://sydneyuni.service-now.com/sm?id=kb_article_view&sysparm_article=KB0011049&sys_kb_id=9e86e1a3dbdf0c50e35b89e4059619b9">Cisco Anyconnect VPN</a> up and running.</p>
</section>
</section>
<section id="credentials-to-access-artemis" class="level2">
<h2 class="anchored" data-anchor-id="credentials-to-access-artemis">Credentials to Access Artemis</h2>
<p>You would normally use your unikey and unikey password to access Artemis. For the course you will be using training credentials. which will give access to the <code>Training</code> project:</p>
<p><strong>Username:</strong> <code>ict_hpctrain<N></code>, with N from 1-20 (replace <n> with your assigned number)</n></p>
<p><strong>Password</strong>: to be provided.</p>
<section id="mac-logon-to-artemis" class="level3">
<h3 class="anchored" data-anchor-id="mac-logon-to-artemis">Mac Logon to Artemis</h3>
<p>Use the <em>Terminal App</em>. Found in your Applications folder, or hit <code>Command-Space</code> and type <code>terminal</code>. Then in the terminal enter:</p>
<p><code>ssh <unikey>@hpc.sydney.edu.au</code></p>
</section>
<section id="windows-logon-to-artemis" class="level3">
<h3 class="anchored" data-anchor-id="windows-logon-to-artemis">Windows Logon to Artemis</h3>
<ol type="1">
<li><p>Open Putty.</p></li>
<li><p>Fill in the connection details:</p>
<p><em>Host Name</em>: <code>hpc.sydney.edu.au</code></p>
<p><em>Port</em>: <code>22</code></p>
<p><em>Connection type</em>: <code>SSH</code></p></li>
<li><p>Name this session “Artemis” and click ‘Save’</p></li>
</ol>
</section>
</section>
<section id="working-on-artemis-with-graphical-applications" class="level2">
<h2 class="anchored" data-anchor-id="working-on-artemis-with-graphical-applications">Working on Artemis with Graphical Applications</h2>
<section id="x11-forwarding" class="level3">
<h3 class="anchored" data-anchor-id="x11-forwarding">X11 FORWARDING</h3>
<p>X11 forwarding allows you to run graphical applications on a remote server and have their Graphical User Interfaces (GUIs) displayed on your local machine. This is particularly useful when you are working on a remote server or computer and need to run graphical applications, such as graphical text editors, web browsers, or any other GUI-based tools.</p>
<p>To use X11 forwarding you need to install additional tools and tweak the way you connect. Recommendtions are as follows.</p>
<section id="mac-users" class="level4">
<h4 class="anchored" data-anchor-id="mac-users">Mac Users</h4>
<p>You will need to install and start <a href="https://www.xquartz.org/">Xquartz</a>. Then log in to Artemis by providing the extra <code>-X</code> flag. That is:</p>
<p><code>ssh -X <unikey>@hpc.sydney.edu.au</code></p>
</section>
<section id="windows-users" class="level4">
<h4 class="anchored" data-anchor-id="windows-users">Windows Users</h4>
<p>You will need to install and start <a href="https://sourceforge.net/projects/xming/">Xming</a>. Then in <em>PuTTY</em>, you can enable X11 forwarding in a new or saved SSH sessions by selecting <em>Enable X11 forwarding</em> in the <em>PuTTY Configuration</em> window (Connection > SSH > X11).</p>
<p>Alternatively, <a href="https://mobaxterm.mobatek.net/download.html">MobaXterm</a> offers a rich experience as a full-featured X-server and terminal emulator for SSH connections, the free version is more than adequate.</p>
</section>
</section>
<section id="nomachine" class="level3">
<h3 class="anchored" data-anchor-id="nomachine">NOMACHINE</h3>
<p>An alternative to X11 forwarding is to use our graphical login nodes via the NoMachine App. These special are graphics-enabled login servers which host <em>NoMachine</em>, a kind of remote desktop service.</p>
<p>Our experience is that no-machine is preferrable when using visualisation software that rely on computation done on the HPC.</p>
<p>To use the graphical login nodes:</p>
<p>Download and install the <a href="https://pages.github.sydney.edu.au/rc/Artemis-HPC-glogin/">NoMachine Enterprise Client</a> for your operating system. Please don’t download the client from NoMachine directly, as their current version may not work with Artemis.</p>
<p>If you’re using MacOS, you need to install <a href="https://www.xquartz.org">XQuartz</a>.</p>
<p>Download the <a href="https://pages.github.sydney.edu.au/rc/Artemis-HPC-glogin/glogin.nxs">glogin.nxs</a> session configuration file to your computer.</p>
<p>To connect:</p>
<p>Double-click or run the <code>glogin.nxs</code> shortcut you downloaded (it will open NoMachine Client). A NoMachine window should start, asking for a username and password. Replace <code>YOUR_UNIKEY</code> with your UniKey, then enter your UniKey password in the password field, then click <em>OK</em>. A short while later, an Artemis terminal window should open.</p>
</section>
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const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
const lineIds = lines.map((line) => {
return targetCell + "-" + line;
})
let top = null;
let height = null;
let parent = null;
if (lineIds.length > 0) {
//compute the position of the single el (top and bottom and make a div)
const el = window.document.getElementById(lineIds[0]);
top = el.offsetTop;
height = el.offsetHeight;
parent = el.parentElement.parentElement;
if (lineIds.length > 1) {
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
height = bottom - top;
}
if (top !== null && height !== null && parent !== null) {
// cook up a div (if necessary) and position it
let div = window.document.getElementById("code-annotation-line-highlight");
if (div === null) {
div = window.document.createElement("div");
div.setAttribute("id", "code-annotation-line-highlight");
div.style.position = 'absolute';
parent.appendChild(div);
}
div.style.top = top - 2 + "px";
div.style.height = height + 4 + "px";
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
if (gutterDiv === null) {
gutterDiv = window.document.createElement("div");
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
gutterDiv.style.position = 'absolute';
const codeCell = window.document.getElementById(targetCell);
const gutter = codeCell.querySelector('.code-annotation-gutter');
gutter.appendChild(gutterDiv);
}
gutterDiv.style.top = top - 2 + "px";
gutterDiv.style.height = height + 4 + "px";
}
selectedAnnoteEl = annoteEl;
}
};
const unselectCodeLines = () => {
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
elementsIds.forEach((elId) => {
const div = window.document.getElementById(elId);
if (div) {
div.remove();
}
});
selectedAnnoteEl = undefined;
};
// Attach click handler to the DT
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
for (const annoteDlNode of annoteDls) {
annoteDlNode.addEventListener('click', (event) => {
const clickedEl = event.target;
if (clickedEl !== selectedAnnoteEl) {
unselectCodeLines();
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
if (activeEl) {
activeEl.classList.remove('code-annotation-active');
}
selectCodeLines(clickedEl);
clickedEl.classList.add('code-annotation-active');
} else {
// Unselect the line
unselectCodeLines();
clickedEl.classList.remove('code-annotation-active');
}
});
}
const findCites = (el) => {
const parentEl = el.parentElement;
if (parentEl) {
const cites = parentEl.dataset.cites;
if (cites) {
return {
el,
cites: cites.split(' ')
};
} else {
return findCites(el.parentElement)
}
} else {
return undefined;
}
};
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
const ref = bibliorefs[i];
const citeInfo = findCites(ref);
if (citeInfo) {
tippyHover(citeInfo.el, function() {
var popup = window.document.createElement('div');
citeInfo.cites.forEach(function(cite) {
var citeDiv = window.document.createElement('div');
citeDiv.classList.add('hanging-indent');
citeDiv.classList.add('csl-entry');
var biblioDiv = window.document.getElementById('ref-' + cite);
if (biblioDiv) {
citeDiv.innerHTML = biblioDiv.innerHTML;
}
popup.appendChild(citeDiv);
});
return popup.innerHTML;
});
}
}
});
</script>
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