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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>Arcetri | FAQ</title>
<link href="bootstrap-4/css/bootstrap.css" rel="stylesheet">
<link href="bootstrap-4/css/bootstrap-grid.css" rel="stylesheet">
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<link href="css/custom.css" rel="stylesheet">
<link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
</head>
<body>
<nav class="navbar navbar-expand-lg navbar-dark bg-dark fixed-top">
<div class="container">
<a class="navbar-brand" href="index.html">Arcetri Cluster</a>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarResponsive">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarResponsive">
<ul class="navbar-nav ml-auto">
<li class="nav-item ">
<a class="nav-link" href="index.html">Home</a>
</li>
<!--<li class="nav-item">-->
<!--<a class="nav-link " href="about.html">About</a>-->
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<!--<a class="nav-link " href="projects.html">Projects</a>-->
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<!--<a class="nav-link" href="help.html">Help</a>-->
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<li class="nav-item">
<a class="nav-link active " href="faq.html">FAQ</a>
</li>
<li class="nav-item">
<a class="nav-link " href="contacts.html">Contacts</a>
</li>
</ul>
</div>
</div>
</nav>
<div class="jumbotron jumbotron-fluid">
<h1 class="display-3">Frequently asked questions</h1>
<a name="top"></a>
<p class="lead">You didn't find appropriate answer? <a class="jumbotron-href" href="contacts.html">Contact us!</a></p>
</div>
<div class="container-fluid">
<div class="row">
<div class="col-1"></div>
<div class="col-10 content">
<h1 class="textheader">Master FAQ Index</h1>
<ul>
<li> <a href="#Arcetri-index">Arcetri FAQ</a>
<li> <a href="#Graphical-desktop-index">Graphical desktop FAQ</a>
<li> <a href="#Modules-index">Modules FAQ</a>
<li> <a href="#SLURM-index">SLURM FAQ</a>
<a name="Arcetri-index"></a>
<li> <a href="#Python-index">Python FAQ</a>
</ul>
<div class="textblock">
<h1 class="textheader">Arcetri FAQ</h1>
<p><a href="#top">(jump to top)</a></p>
<ul>
<li> <a href="#arcetri-account">How can I obtain an account on the Arcetri cluster?</a>
<li> <a href="#unix-arcetri-key">How do I use Unix/Linux/macOS to generate SSH keys?</a>
<li> <a href="#windows-arcetri-key">How do I use Windows to generate SSH keys?</a>
<li> <a href="#arcetri-login">How do I login to the pacini head node on Arcetri?</a>
<li> <a href="#arcetri-contact">Who do I contact if I need help with Arcetri?</a>
<li> <a href="#arcetri-names">What is the meaning behind the names, pacini, franco, hack, and Arcetri?</a>
<li> <a href="#arcetri-differences">What is the difference between pacini and Arcetri?</a>
<a name="Graphical-desktop-index"></a>
<li> <a href="#arcetri-structure">What is the structure of Arcetri?</a>
<li> <a href="#arcetri-filesystems">What should I know about filesystems on pacini?</a>
</ul>
<h1 class="textheader">Graphical desktop FAQ</h1>
<p><a href="#top">(jump to top)</a></p>
<ul>
<a name="Modules-index"></a>
<li> <a href="#graphical-X2Go">How do I open a graphical desktop on pacini?</a>
<li> <a href="#graphical-matlab">How do I use Matlab in graphical mode?</a>
</ul>
<h1 class="textheader">Modules FAQ</h1>
<p><a href="#top">(jump to top)</a></p>
<ul>
<li> <a href="#modules-what">What are modules?</a>
<li> <a href="#modules-available">What modules are available on the Arcetri cluster?</a>
<li> <a href="#modules-load">How can I load a module?</a>
<li> <a href="#modules-list">How can I see loaded modules?</a>
<li> <a href="#modules-purge">How can I get rid of loaded modules?</a>
<li> <a href="#modules-show">What commands can I use with modules?</a>
<a name="SLURM-index"></a>
<li> <a href="#modules-modulecmd">How can I use module command within a shell script?</a>
<li> <a href="#modules-request">I need a module that is not in a list, what should I do?</a>
</ul>
<h1 class="textheader">SLURM FAQ</h1>
<p><a href="#top">(jump to top)</a></p>
<ul>
<li> <a href="#slurm-launch">How do I launch jobs?</a>
<li> <a href="#slurm-monitor">How do I monitor my jobs?</a>
<li> <a href="#slurm-number">How can I check my job's number?</a>
<li> <a href="#slurm-specific">Why can’t I launch jobs on a specific node?</a>
<li> <a href="#slurm-ssh">What can't I ssh into a compute node?</a>
<li> <a href="#slurm-head">Why can’t I launch jobs on the head node?</a>
<li> <a href="#slurm-results">Where are the results of my job?</a>
<li> <a href="#slurm-queue">What if my job is still in the queue?</a>
<li> <a href="#slurm-cancel">How may I cancel my job?</a>
<li> <a href="#slurm-resources">What resources may I request for my job?</a>
<li> <a href="#slurm-msub">How may I use SLURM commands?</a>
<a name="Python-index"></a>
<li> <a href="#slurm-example">Where can I find an example of an Open MPI job run under SLURM?</a>
<li> <a href="#slurm-more">Where can I read more about SLURM?</a>
</ul>
<h1 class="textheader">Python FAQ</h1>
<p><a href="#top">(jump to top)</a></p>
<ul>
<li> <a href="#python-libraries">How to install new python libraries?</a>
<li> <a href="#python-new">How to create a new python virtual environment?</a>
<li> <a href="#python-activate">How to activate my python environment?</a>
<li> <a href="#python-deactivate">How to deactivate python virtual environment?</a>
<li> <a href="#python-version">How to specify Python version inside an environment?</a>
<li> <a href="#python-more">Where can I read more about python virtual environments?</a>
</ul>
</div>
<!-- -->
<h1 class="textheader">Full FAQ Follows</h1>
<div class="textblock">
<a name="arcetri-account"></a>
<h1 class="textheader">Arcetri</h1>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#arcetri-account">
How can I obtain an account on the Arcetri cluster?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
Write to our email address: <b>arcetri-admin-people@cisco.com</b><br>
To handle your request faster please provide information about:
<ul>
<li>Name</li>
<li>Preferred account name</li>
<li>Email address</li>
<li>Phone number</li>
<li>SSH RSA public key</li>
</ul>
<p>For information on how to generate and/or find your SSH RSA public key, see:</p>
<ul>
<li> <a href="#unix-arcetri-key">How do I use Unix/Linux/macOS to generate SSH keys?</a></li>
<li> <a href="#windows-arcetri-key">How do I use Windows to generate SSH keys?</a></li>
</ul>
<p>
Once we have created your account and notified you that it is ready,
you need to <A HREF="contacts.html">call us</A> so that we can give you
your VPN password over the phone.
</p>
<p>
<a name="unix-arcetri-key"></a>
After your account is created, see how to login to Arcetri.
</p>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#unix-arcetri-key">
How do I use Unix/Linux/macOS to generate SSH keys?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<h4>If you are a Unix/Linux/macOS user</h4>
<p>
<b>1. Check for existing SSH keys</b><br>
Open the terminal, and run<br>
<code>cd ~/.ssh</code>
<ul>
<li>If you see "No such file or directory", then there aren't any existing keys: go to step 2.</li>
<li>Check to see if you have a key already:</li>
<code>ls id_*</code><br>
If there are existing keys, you may want to use those. Go to step 3 to send us your public SSH key
</ul>
<b>2. If you don't have SSH key, generate a new SSH key</b>
If you don't have an existing SSH key that you wish to use, generate one as follows:<br>
<ul>
<li>Open a terminal on your local computer and enter the following:</li>
<code>ssh-keygen -t rsa -C "your_email@example.com"</code>
Associating the key with your email address helps you to identify the key later on.<br>
<li>
Just press Enter to accept the default location and file name.
If the .ssh directory doesn't exist, the system creates one for you.
</li>
<li>Enter, and re-enter, a passphrase when prompted.</li>
<li>You're done! Go to step 3 to send us your public SSH key</li>
</ul>
<b>3. Send us public SSH key</b>
Attach your <code>id_rsa.pub</code> file to your account request email.<br>
<a name="windows-arcetri-key"></a>
<b>WARNING:</b> send <code>id_rsa.pub</code>, not <code>id_rsa</code> file! <code>id_rsa</code> is your private confidential key, similar to your passwords!
</p>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#windows-arcetri-key">
How do I use Windows to generate SSH keys?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<p>
<h4>If you are a Windows user</h4>
<b>1. Check for existing SSH keys</b><br>
Open a command prompt, and run<br>
<code>cd %userprofile%/.ssh</code>
<ul>
<li>If you see "No such file or directory", then there aren't any existing keys: go to step 2.</li>
<li>Check to see if you have a key already:</li>
<code>dir id_*</code><br>
If there are existing keys, you may want to use those. Go to step 3 to send us your public SSH key
</ul>
<b>2. Use PuTTY's Key Generator generate SSH keys</b>
<ol type="A">
<li> If you don't have an existing SSH key that you wish to use,
you will need to use PuTTY generarte your SSH keys.</li>
<li> If you do not have PuTTY installed, you need to download and install the
<a href="https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html">latest
version of PuTTY</a></li>
<li>Once you have downloaded and installed PuTTY, you need to run the
PuTTY Key Generator: <code>puttygen.exe</code></li>
<li>
Launch the program and click on the Load button and select your id_rsa.ppk file.<br>
<img src="img/faq/graphical/putty-1.png">
<img src="img/faq/graphical/putty-2.png"><br>
</li><br>
<li>
Enter the key's passphrase if prompted.<br>
<img src="img/faq/graphical/putty-3.png">
</li><br>
<li>
Detail's of the imported key will be displayed.<br>
<img src="img/faq/graphical/putty-4.png">
</li><br>
<li>
Go to Conversions → Export OpenSSH key from the menu.<br>
<img src="img/faq/graphical/putty-5.png">
</li><br>
<li>
Save your converted key to a new file named "id_rsa"<br>
<img src="img/faq/graphical/putty-6.png">
</li><br>
</ol>
<b>3. Send us public SSH key</b>
<p>
You can attach your <code>id_rsa.pub</code> file to your account request email,
or you can copy and paste the public key that you is available in:
</p>
<p>
<b>Step 2: F. Detail's of the imported key will be displayed.</b> (see above)
</p>
<p>
<a name="arcetri-login"></a>
<b>WARNING:</b> Send <code>id_rsa.pub</code>, not <code>id_rsa</code> file!
<code>id_rsa</code> is your private confidential key, similar to your passwords!
</p>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#arcetri-login">
How do I login to the pacini head node on Arcetri?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<ul>
<li>First, you should install Cisco AnyConnect</li>
<ul>
<li>Login with username and password we provided you: <a href="https://arcetri-asa.cisco.com">https://arcetri-asa.cisco.com</a></li>
<img src="img/faq/arcetri/asa-1.png" width="50%">
<li>Press "Continue"</li>
<img src="img/faq/arcetri/asa-2.png" width="50%">
<li>Wait for Java detection and press on AnyConnect VPN download link</li>
<img src="img/faq/arcetri/asa-3.png" width="50%">
</ul>
<li>Open it and type arcetri-asa.cisco.com</li>
<img src="img/faq/arcetri/anyconnect-1.png" width="50%"><br><br>
<li>Press ‘Connect’ and enter your login detail</li>
<img src="img/faq/arcetri/anyconnect-2.png" width="50%"><br><br>
<li>Type in your arcetri user name and VPN password and press Enter</li>
<li>Now open a terminal and enter the following command:</li>
<code>$ ssh pacini.cisco.com</code><br><br>
<p>
<b>NOTE:</b> The ssh command should <B>NOT</B> ask for a password, instead ssh
will attempt to use your SSH private key to login to pacini.cisco.com.
</p>
<p>
<b>NOTE:</b> If ssh asks you for a password, it most likely means that the private
ssh key on the host where ssh is running is not matched with the
public ssh key that we installed when your account was created.
<a name="arcetri-contact"></a>
Please <A HREF="contacts.html">contact us</A> for help if ssh asks for a password.
</p>
</ul>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#arcetri-contact">
Who do I contact if I need help with Arcetri?
</a>
<a href="#top">(jump to top)</a>
</h5>
<a name="arcetri-names"></a>
</div>
<div class="card-block textcard">
Visit the <a href="contacts.html">contacts page</a>. We will be happy to assist you!
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#arcetri-names">
What is the meaning behind the names, pacini, franco hack, and Arcetri?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<img src="img/faq/arcetri/whats-is-in-a-name.png" width="70%"><br><br>
<p>
Arcetri is location in Florance Italy.
The Arcetri cluser named after Arcetri Astrophysical Observatory, Franco Pacini.
</p>
<img src="img/faq/arcetri/Franco-Pacini.jpg" width="70%"><br><br>
<p>
(<a href="https://en.wikipedia.org/wiki/Arcetri_Observatory">Osservatorio Astrofisico di Arcetri)</a>.
The hosts franco and pacini are named in honor of
<a href="https://en.wikipedia.org/wiki/Franco_Pacini">Franco Pacini</A>,
a famous astronomer who was also the director of the Arcetri Astrophysical Observatory.
</p>
<p>
The full formal name of the Arcetri cluster is:
</p>
<ul>
<li>
<b>Sistema condiviso in Cisco per calcoli ad alte prestazioni in onore di Franco Pacini,
direttore dell'osservatorio astrofisico di Arcetri</b>
</ul>
<p>
which, translated from Italian into English reads:
</p>
<p>
<ul>
<li>
<b><i>Shared system for High-Performance Computations at Cisco in honor of Franco Pacini,
director of the Arcetri Astrophysical Observatory</i></b>
</ul>
</p>
<p>
As an astronomer, <a href="https://en.wikipedia.org/wiki/Landon_Curt_Noll">Landon Curt Noll</a>
had the honor of observing the 2004 Transit of Venus, under Franco Pacini,
where Landon helped determine <a href="http://www.isthe.com/chongo/tech/astro/venus2004.html">the
distance to the Sun</a> is 149,596,765 km ± 3543 km (0.0237% uncertainty: 1 part in 42224).
</p>
<img src="img/faq/arcetri/au.png" width="70%"><br><br>
<p>NOTE: There are also special nodes known as hack nodes.
These nodes are named after <a href="https://en.wikipedia.org/wiki/Margherita_Hack">Margherita Hack</a>
an astronomer who also worked at the Arcetri observatory.</p>
<img src="img/faq/arcetri/Margherita-Hack.jpg" width="70%"><br><br>
<a name="arcetri-differences"></a>
<p>Hack nodes are not available for general use.
These nodes are used for special testing only.</p>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#arcetri-differences">
What is the difference between pacini and Arcetri?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
The term arcetri refers to the entire cluster whereas pacini refers to a head node inside arcetri.
<a name="arcetri-structure"></a>
There is also a head node named fracno that services as a backup and spare head node.
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#arcetri-structure">
What is the structure of Arcetri?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<img src="img/faq/arcetri/structure-1.png" width="100%"><br>
</div>
<ul>
<a name="arcetri-filesystems"></a>
<li>You may access to a pacini head node (pacini.cisco.com) via the ASA firewall (arcetri-asa.cisco.com).</li>
</ul>
</div>
<div class="card">
<div class="card-header" role="tab" id="arcetri-card-filesystems">
<h5 class="mb-0">
<a href="#arcetri-filesystems">
What should I know about filesystems on the Arcetri cluster?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<p>
<h4><code>/home/</code></h4>
<code>/username</code> - mode 0700 - no other user/group access
</p>
<p>
<h4><code>/usr/global/</code></h4>
<code>/{bin, sbin, lib, include, ...}</code> - common software for Arcetri cluster - mod by admin only<br>
<code>/_group_name_</code> - writable for group for software/libs<br>
<code>/src/{bin, sbin, lib, ...}</code> - source for common software - mod by admin only<br>
<code>/src/_group_name_</code> - writable for group for source code
</p>
<p>
<h4><code>/shared/</code></h4>
<a name="graphical-X2Go"></a>
<code>/_group_name_</code> - writable by group for source code
</p>
</div>
</div>
</div>
<!-- -->
<div class="textblock">
<h1 class="textheader">Graphical desktop</h1>
<div class="card">
<div class="card-header" role="tab" id="graphical-card-matlab">
<h5 class="mb-0">
<a href="#graphical-X2Go">
How do I open a graphical desktop on pacini?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<p>To start an graphical desktop on pacini, you need to use <b>X2Go</b>
and connect to pacini over ssh.</p>
<h4>OS Requirements</h4>
<ul>
<li>macOS 10.9 or later -
macOS 10.15 or later recommended</li>
<li>Linux with X Windows -
Red Hat Enterprise Linux (RHEL) 7.8 or later recommended<br>
If not RHEL7.8 then one of:
<ul>
<li> Fedora 20 or later
<li> CentOS 8 or later
</ul>
</li>
<li>Windows 7 or later -
Windows 10 or later recommended</li>
</ul>
<h4>Installation</h4>
<ul>
<li><B>macOS only:</B>
Xquartz 2.7.11 or later -
<a href="https://www.xquartz.org">Download Xquartz for macOS</a></li>
<li>X2Go Client 4.1.2.2 or later -
<a href="http://wiki.x2go.org/">Download X2Go</a></li>
</ul>
<p>
<h4>X2Go Client configuration</h4>
<p>Run <b>X2Go</b> and setup a pacini profile as follows:</p>
<img src="img/faq/graphical/osx-1.png" width="70%"><br>
<br><b>X2Go configuration steps:</b>
<ol>
<li>Name the session: <b>pacini</b></li>
<li>Enter the Host: <B>pacini.cisco.com</B></li>
<li>Enter your pacini username</li>
<li>Check [x] <B>Try auto login (via SSH Agent or default SSH key)</B></li>
<li>Set the session type to <B>KDE</B></li>
<li>Select <B>Media</B> tab for next settings</li>
</ol>
<p>
<h4>X2Go Client Media settings</h4>
<p>In addition to the above X2Go configuration, configure X2Go media as follows:</p>
<img src="img/faq/graphical/osx-3.png" width="70%"><br><br>
<p><b>X2Go Media setting steps:</b></p>
<ol>
<li>Check [x] <B>Enable sound support</B></li>
<li>Check (*) <B>esd</B></li>
<li>Uncheck [ ] <B>client side printing support</B></li>
<li>Check [x] <B>Use SSH port forwarding to tunnel ...</B></li>
<li>Save dialog settings by clicking the ((<B>OK</B>)) button</li>
</ol>
<p>
<h4>macOS only suggestion: pre-launch XQuartz</h4>
<p>While not strictly nessicary, it is helpful to have
XQuartz running before you attempt to use the X2Go client.
When the X2Go client makes, over ssh, a connection to pacini,
it will want to start a graphical window.
Pre-starting XQuartz helps avoid a connection timeout
should XQuartz take too long to initialize and start.</p>
<p>
<h4>Login to pacini using ssh over Cisco AnyConnect</h4>
<p>In order to be able to connect to pacini using the
X2Go client connection over ssh. one needs to
first establish a VPN connection to <b>arcetri-asa.cisco.com</b>.
</p>
<p> For more information, see:
<a href="#arcetri-login">
How do I login to the pacini head node on Arcetri?
</a>
</p>
<p>
<h4>X2Go client connection over ssh</h4>
<p>Run the X2Go client and select the pacini profile.</p>
<p>NOTE: The pacini profile was created in the
<b>X2Go Client configuration</b> step above.</p>
<p>NOTE: The X2Go client on macOS is called <b>x2goclient</b>.</p>
<img src="img/faq/graphical/osx-4.png" width="70%"><br><br>
<p>Double click the <b>pacini</b> session card to start the session</p>
<img src="img/faq/graphical/osx-5.png" width="70%"><br><br>
<p>Be <b>patient</b> as the X2Go client launches a KDE desktop
as a new X Window.
This can take longer to start then you might think,
and certainly takes longer then starting just a simple
ssh connection.</p>
<img src="img/faq/graphical/osx-6.png" width="70%"><br>
</p>
<p>
<h4>Open a Terminal window</h4>
<p>You may access a shell prompt via the Terminal desktop application.</p>
<img src="img/faq/graphical/osx-7.png" width="70%"><br><br>
<p>For example:</p>
<img src="img/faq/graphical/osx-8.png" width="70%"><br>
<p>
<h4>To end the X2Go session</h4>
<p>To end the X2Go client session, click on the stop buttion
(see below) obn the main X2Go client window:</p>
<img src="img/faq/graphical/osx-10.png" width="70%">
<p>click ((<b>Yes</b>))</p>
<p>After clicking ((<b>Yes</b>)) the X2Go client window will
show you a Login / Password field.</p>
<p>Because we do NOT use a password based ssh, this field will not work.
Just click ((<b>Cancel</b>)) to restore the pacini profile.</p>
<img src="img/faq/graphical/osx-11.png" width="70%"><br>
<a name="graphical-matlab"></a>
<p>This will make it slightly easier to reconnect next time.</p>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="graphical-card-matlab">
<h5 class="mb-0">
<a href="#graphical-matlab">
How do I use Matlab in graphical mode?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<h4>Important note</h4>
The matlab application should ONLY be run on <b>laplace000</b>.
<br><br>
<h4>Start a graphical session</h4>
First, access a graphical desktop on the pacini cluster.
<p>
<h4>Open a graphical terminal</h4>
<img src="img/faq/graphical/osx-7.png" width="70%"><br>
<p>
<h4>ssh -X laplace000</h4>
<img src="img/faq/graphical/osx-8a.png" width="70%"><br><br>
<p>The matlab applcation should only be run on laplace000.
Please do <b>NOT</b> run it on the head node.</p>
<p>In order to run matlab on laplace000, you need to <b>ssh</b>
over to the laplace000 while using the <b>-X</b> option
in order to enable X11 forwarding.</b>
<h4>module load matlab</h4>
<img src="img/faq/graphical/osx-8.png" width="70%"><br><br>
<p>You need to be sure the matlab module is loaded before you run matlab.</p>
<h4>start matlab</h4>
<img src="img/faq/graphical/osx-9.png" width="70%"><br>
<p>After you have <b>ssh -X laplace000</b> and performed the
<b>module laod matlab</b> you need to run matlab from the command line.</p>
<p>After a bit of tiem you should see a matlab logo:</p>
<img src="img/faq/graphical/osx-9a.png" width="70%"><br>
<p>The matlab window will appear soon afterwards.</p>
<a name="modules-what"></a>
<p><b>Important note:</b> We have only one matlab license, so when you
are finished, please <b>EXIT</b> matlab so that others may be able
to use it after you are finished.</p>
</div>
</div>
</div>
<!-- -->
<div class="textblock">
<h1 class="textheader">Modules</h1>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#modules-what">
What are modules?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<p>
In general, modules are designed to create user's environment. For example, if you need to use CUDA with version 8.0,
you can easily load appropriate module via command <code>module load mpi</code>
</p>
<p>
In some cases you may wish to load a specific version of a module.
For example: <code>module load openmpi3/3.1.3</code>.
Without the "/version", the default recommended module will be loaded.
Depending on specific specific version is not recommended
<a name="modules-available"></a>
as old versions are retired and purged from system from time to time.
</p>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#modules-available">
What modules are available on pacini?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<p>
You can check available modules via command <code>module avail</code>
</p>
<p>
The string <b>(default)</b> indicates that the particular module/version is
the default module that is loaded if only the module name is loaded.
</p>
<p>
For example, <b>CUDA/10.2(default)</b> indicates that <b>CUDA/10.2</b> is
currenrtly the default module that is loaded if one loads just <b>CUDA</b>.
Using just the module name without the <b>/version</b> is recommended
<a name="modules-load"></a>
to be sure you are using the best version that is available.
</p>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#modules-load">
How can I load a module?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
You can load a module via command <code>module add <i>MODULE_NAME</i></code>
<p>
We recommend ust the module name without the <b>/version</b>
to be sure you are using the best version that is available.
For example, using the default <code>module add CUDA</code> is recommended
<a name="modules-list"></a>
over a version specific <code>module add CUDA/10.2</code> command.
</p>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#modules-list">
How can I see loaded modules?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<a name="modules-purge"></a>
<div class="card-block textcard">
You can check loaded modules via command <code>module list</code>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#modules-purge">
How can I get rid of loaded modules?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<a name="modules-show"></a>
<code>module rm <i>MODULE_NAME</i></code> command unloads specific module<br>
<code>module purge</code> command unloads all loaded modulefiles
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#modules-show">
What commands can I use with modules?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
Most useful commands are:
<ul>
<li><code>module add <i>MODULE_NAME</i></code> - load a module</li>
<li><code>module list</code> - show loaded modules</li>
<li><code>module rm <i>MODULE_NAME</i></code> - unload a module</li>
<li><code>module purge</code> - unload all loaded modules</li>
<li><code>module show <i>MODULE_NAME</i></code> - show information about a module</li>
<li><code>module avail</code> - list all available modules</li>
<a name="modules-modulecmd"></a>
<li><code>module help</code> - give some helpful information about <code>module</code> command</li>
</ul>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#modules-modulecmd">
How can I use module command within a shell script?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<p>
The module command is a shell alias that is available from an interactive shell.
The alias causes a <b>eval</b> to be performed at the interactive shell level
that can display and/or modify shell environment variables of the interactive shell.
</p>
<p>
This shell script <b>WILL NOT</B> load a modules:
</p>
<ul><i>
#!/bin/bash<br>
#<br>
# DO NOT DO THIS -- This will NOT properly load the mpi and CUDA default modules<br>
<br>
..<br>
module load mpi CUDA # WRONG !!!<br>
mpirun ..<br>
..<br>
</i></ul>
<p>
In shell scripts, one must explicitly eval the output of <b>/usr/bin/modulecmd</b>.
Instead of using:
<ul>
<code>module cmd <i>arg ..</i></code>
</ul>
<p>
in a shell script one must use:
</p>
<ul>
<code>eval $(/usr/bin/modulecmd bash cmd <i>arg ..</i>)</code>
</ul>
<p>
where <b>bash</b> is the name of your shell.
</p>
<ul>
NOTE: The bash shell is the default and recommended shell.
</ul>
<p>
To be sure that a shell script is using only the modules you intent to use,
it is recommended that you first purge any previous modules that may have
been exported.
</p>
<p>
Under certain conditions the <b>MODULEPATH</b> environment variable is not set.
We recommend that you source <b>/etc/profile</b> if that happens:<br>
<ul><pre>if [[ -z $MODULEPATH ]]; then
source /etc/profile
fi</pre></ul></p>
<p>
This shell script <b>WILL</b> load modules:<br>
<ul><pre>#!/bin/bash
#
# How to use modules in a bash shell script
..
# setup modules very early in your shell script
#
if [[ -z $MODULEPATH ]]; then
source /etc/profile
fi
eval $(/usr/bin/modulecmd bash purge) # equivalent to: module purge
eval $(/usr/bin/modulecmd bash load mpi CUDA) # equivalent to: module load mpi CUDA
..
# then for example:
mpirun ..
<a name="modules-request"></a>..
</pre></ul></p>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="headingOne">
<h5 class="mb-0">
<a href="#modules-request">
I need a module that is not in a list, what should I do?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<a name="slurm-launch"></a>
<div class="card-block textcard">
Please, feel free to contact us and request a new module: <a href="contacts.html">our contact page</a>
</div>
</div>
</div>
<!-- -->
<div class="textblock">
<h1 class="textheader">SLURM</h1>
<div class="card">
<div class="card-header" role="tab" id="slurm-card-launch">
<h5 class="mb-0">
<a href="#slurm-launch">
How do I launch jobs?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<p>
<h4>Via batch script</h4>
<ul>
<li>Create a .slurm file with parameters for the job</li>
<li>Type in the command</li>
<code>$ sbatch <i>yourfilename</i>.slurm</code>
</ul>
<p>To learn more about SLURM parameters see the
<a href="https://slurm.schedmd.com/sbatch.html">SLURM sbatch</a> man page.
</p>
</p>
<p>
<h4>Via interactive ssh job</h4>
<ul>
<li>Submit your job using the following format:</li>
<a name="slurm-monitor"></a>
<code>$ sbatch --ntasks=1 --time=2:00:00 --mem-per-cpu=1G --job-name="JobName" --qos=normal --export=ALL</code>
</ul>
</p>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="slurm-card-monitor">
<h5 class="mb-0">
<a href="#slurm-monitor">
How do I monitor my jobs?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<p>
After you launch your job you could monitor its progress using the following command:<br>
<code>$ squeue --job JOB_ID</code><br>
</p>
<p>
This command will show your jobs' progress in the following format:<br>
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)<br>
<a name="slurm-number"></a>
34239 arcetri_c node-rie prime R 1:49:52 1 pacini063
</p>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="slurm-card-number">
<h5 class="mb-0">
<a href="#slurm-number">
How can I check my job's number?
</a>
<a href="#top">(jump to top)</a>
</h5>
</div>
<div class="card-block textcard">
<p>
<code>squeue</code> - list all job numbers
</p>
<p>
<code>sprio -j JobID</code> - show priorities for the current job
</p>
<p>
<a name="slurm-specific"></a>
<code>sinfo</code> - show detailed info about the nodes
</p>
</div>
</div>
<div class="card">
<div class="card-header" role="tab" id="slurm-card-specific">
<h5 class="mb-0">
<a href="#slurm-specific">
Why can’t I launch jobs on a specific node?
</a>
<a href="#top">(jump to top)</a>
</h5>