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| <head>
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| <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
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| <meta name="generator" content="http://www.nongnu.org/elyxer/"/>
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| <meta name="create-date" content="2010-09-09"/>
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| <link rel="stylesheet" href="http://www.nongnu.org/elyxer/lyx.css" type="text/css" media="screen"/>
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| <title>Technical report of the procedure of setup of a Ubuntu Server computer cluster</title>
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| </head>
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| <body>
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| <div id="globalWrapper">
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|
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| <h1 class="title">
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| Technical report of the procedure of setup of a Ubuntu Server computer cluster
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| </h1>
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| <h2 class="author">
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| Alexandre Manhães Savio
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| </h2>
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| <h2 class="Date">
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| September 24th, 2010
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| </h2>
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| <h1 class="Section">
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| <a class="toc" name="toc-Section-1">1</a> Master Node - Giclus1
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| </h1>
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| <h2 class="Subsection">
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| <a class="toc" name="toc-Subsection-1.1">1.1</a> Operating system and network configuration
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| </h2>
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| <ul>
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|
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| <li>
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| Install Ubuntu Server 10.04.1 amd64
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| </li>
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| <li>
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| Partitions
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| <ul>
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|
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| <li>
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| <tt>/dev/sda1</tt>: 20GB on <tt>/</tt>
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| </li>
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| <li>
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| <tt>/dev/sda2</tt>: 20GB on <tt>/usr/local</tt>
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| </li>
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| <li>
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| <tt>/dev/sda3</tt>: 130GB on <tt>/home </tt>
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| </li>
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| <li>
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| <tt>/dev/sda5</tt>: 280GB on <tt>/opt</tt>
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| </li>
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| <li>
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| <tt>/dev/sda6:</tt>20GB of swap area
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| </li>
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| </ul>
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| </li>
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| <li>
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| Add gic group:
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| <ul>
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|
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| <li>
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| <tt>sudo addgroup gic </tt>
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| </li>
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| <li>
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| <tt>sudo addgroup alexandre gic</tt>
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| </li>
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| </ul>
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| </li>
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| <li>
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| Add more users:
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| <ul>
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|
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| <li>
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| <tt>sudo adduser <user_name> --ingroup gic --disabled-password</tt>
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| </li>
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| <li>
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| <tt>ssh-keygen -b 4096 -t rsa -C user_name </tt>
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| </li>
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| <li>
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| <tt>chown -R user_name:root /home/user_name/.ssh</tt>
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| </li>
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| <li>
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| <tt>chmod 700 /home/user_name/.ssh </tt>
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| </li>
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| <li>
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| <tt>chmod 400 /home/user_name/.ssh/authorized_keys</tt>
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| </li>
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| </ul>
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| </li>
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| <li>
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| Edit <tt>/etc/network/interfaces</tt>
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| <div class="Unindented">
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|
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| <div class="left">
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|
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| <div class="float">
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|
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| <div class="listing">
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| <code class="listing">
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| auto lo<br/>
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| iface lo inet loopback<br/>
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| <br/>
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| auto eth1<br/>
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| iface eth1 inet static<br/>
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| address 192.168.1.81<br/>
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| netmask 255.255.255.0<br/>
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| gateway 192.168.1.1<br/>
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| <br/>
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| auto eth0 <br/>
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| iface eth0 inet dhcp <br/>
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| #for more information about this email me<br/>
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| </code>
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| </div>
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| </div>
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| </div>
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| </div>
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| </li>
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| <li>
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| Edit <tt>/etc/resolv.conf</tt>
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| <div class="Unindented">
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|
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| <div class="float">
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|
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| <div class="listing">
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| <code class="listing">nameserver 10.20.13.6<br/>
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| nameserver 10.10.13.6<br/>
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| nameserver 10.30.13.6<br/>
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| </code>
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| </div>
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| </div>
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| </div>
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| </li>
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| <li>
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| <tt>sudo /etc/init.d/networking restart</tt>
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| </li>
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| <li>
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| Install packages:
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| <ul>
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|
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| <li>
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| Add "partner" repository, editing <tt>/etc/apt/sources.list</tt>
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| </li>
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| <li>
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| <tt>sudo apt-get update </tt>
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| </li>
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| <li>
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| <tt>sudo apt-get install ssh molly-guard openssh-blacklist openssh-blacklist-extra ssh-askpass binutils unzip sun-java6-jre</tt>
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| </li>
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| </ul>
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| </li>
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| <li>
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| Edit <tt>/etc/ssh/sshd_conf</tt>: disable <tt>root</tt> access and password auth
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| </li>
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| <li>
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| Edit <tt>/etc/hosts</tt>
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| <div class="Unindented">
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|
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| <div class="float">
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|
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| <div class="listing">
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| <code class="listing">127.0.0.1 localhost giclus1<br/>
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| 192.168.1.81 giclus1<br/>
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| 192.168.1.82 giclus2<br/>
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| 192.168.1.83 giclus3<br/>
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| 192.168.1.84 giclus4<br/>
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| </code>
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| </div>
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| </div>
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| </div>
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| </li>
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| <li>
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| Edit <tt>/etc/hosts.allow</tt>
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| <div class="Unindented">
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|
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| <div class="float">
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|
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| <div class="listing">
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| <code class="listing">portmap ypserv ypbind sge_qmaster sge_execd : 192.168.1.81 192.168.1.82 192.168.1.83 192.168.1.84
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| </code>
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| </div>
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| </div>
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| </div>
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| </li>
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| </ul>
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| <h2 class="Subsection">
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| <a class="toc" name="toc-Subsection-1.2">1.2</a> NIS Server
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| </h2>
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| <ul>
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|
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| <li>
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| <tt>sudo apt-get install portmap nis</tt>
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| </li>
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| <li>
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| NIS domain name: <tt>giclus</tt>
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| </li>
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| <li>
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| For more details: <a class="URL" href="https://help.ubuntu.com/community/SettingUpNISHowTo">https://help.ubuntu.com/community/SettingUpNISHowTo</a>
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| </li>
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| <li>
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| Edit <tt>/etc/default/portmap</tt> and comment out the <tt>ARGS="-i 127.0.0.1"</tt> line
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| </li>
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| <li>
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| Edit <tt>/etc/default/nis</tt> and set the <tt>NISSERVER</tt> line to <tt>NISSERVER=master</tt>
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| </li>
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| <li>
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| Edit <tt>/etc/yp.conf</tt>: <tt>domain giclus server giclus1</tt>
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| </li>
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| <li>
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| Edit <tt>/etc/ypserv.securenets</tt>
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| <div class="Unindented">
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|
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| <div class="float">
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|
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| <div class="listing">
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| <code class="listing">host 192.168.1.81<br/>
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| host 192.168.1.82<br/>
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| host 192.168.1.83<br/>
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| host 192.168.1.84<br/>
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| </code>
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| </div>
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| </div>
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| </div>
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| </li>
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| <li>
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| Build the DB for the first time, run: <tt>sudo /usr/lib/yp/ypinit -m</tt>
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| </li>
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| <li>
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| Read the web page (<a class="URL" href="https://help.ubuntu.com/community/SettingUpNISHowTo">https://help.ubuntu.com/community/SettingUpNISHowTo</a>) for more information on security and the client config (see next section)
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| </li>
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| <li>
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| Restart:
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| <ul>
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|
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| <li>
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| <tt>sudo /etc/init.d/portmap restart </tt>
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| </li>
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| <li>
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| <tt>sudo /etc/init.d/nis restart</tt>
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| </li>
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| </ul>
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| </li>
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| </ul>
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| <h2 class="Subsection">
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| <a class="toc" name="toc-Subsection-1.3">1.3</a> NFS Kernel Server
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| </h2>
| |
| <ul>
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|
| |
| <li>
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| <a class="URL" href="https://help.ubuntu.com/community/SettingUpNFSHowTo">https://help.ubuntu.com/community/SettingUpNFSHowTo</a>
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| </li>
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| <li>
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| <tt>sudo apt-get install nfswatch nfs-kernel-server</tt>
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| </li>
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| <li>
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| Edit <tt>/etc/exports</tt> and add the shares:
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| <div class="Unindented">
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|
| |
| <div class="float">
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|
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| <div class="listing">
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| <code class="listing">/home giclus1(rw,sync,no_subtree_check) giclus2(rw,sync,no_subtree_check) giclus3(rw,sync,no_subtree_check) giclus4(rw,sync,no_subtree_check)<br/>
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| /usr/local giclus1(rw,sync,no_subtree_check) giclus2(rw,sync,no_subtree_check) giclus3(rw,sync,no_subtree_check) giclus4(rw,sync,no_subtree_check)<br/>
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| /opt giclus1(rw,sync,no_subtree_check) giclus2(rw,sync,no_subtree_check) giclus3(rw,sync,no_subtree_check) giclus4(rw,sync,no_subtree_check)<br/>
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| </code>
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| </div>
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| </div>
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| </div>
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| </li>
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| <li>
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| <tt>sudo exportfs -ra</tt>
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| </li>
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| </ul>
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| <h2 class="Subsection">
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| <a class="toc" name="toc-Subsection-1.4">1.4</a> MSMTP:
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| </h2>
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| <ul>
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|
| |
| <li>
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| Create a Gmail account for monitoring. I do this because I don’t want my gmail password floating around in plaintext on various machines.
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| </li>
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| <li>
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| Install the <tt>ca-certificates</tt> package
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| <div class="Unindented">
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|
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| <div class="float">
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|
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| <div class="listing">
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| <code class="listing">sudo aptitude install ca-certificates<br/>
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| sudo update-ca-certificates
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| </code>
| |
| </div>
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| </div>
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| </div>
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| </li>
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| <li>
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| <tt>sudo apt-get install msmtp </tt>
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| </li>
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| <li>
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| Edit <tt>/etc/msmtprc </tt>
| |
| <div class="Unindented">
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|
| |
| <div class="float">
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|
| |
| <div class="listing">
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| <code class="listing">account gmail<br/>
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| host smtp.gmail.com<br/>
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| from giclus1@gmail.com<br/>
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| auth on<br/>
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| tls on<br/>
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| tls_trust_file /etc/ssl/certs/ca-certificates.crt<br/>
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| user giclus1@gmail.com<br/>
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| password *******<br/>
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| port 587<br/>
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| <br/>
| |
| account default : gmail
| |
| </code>
| |
| </div>
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| </div>
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| </div>
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| </li>
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| <li>
| |
| Create a sendmail simlink:
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| <ul>
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|
| |
| <li>
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| <tt>sudo ln -s /usr/bin/msmtp /usr/sbin/sendmail</tt>
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| </li>
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| </ul>
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| </li>
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| <li>
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| -Run a test
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| <ul>
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|
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| <li>
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| <tt>echo “This is a an awesome test email” | msmtp youremail@domain.com </tt>
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| </li>
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| </ul>
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| </li>
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| <li>
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| - If you want mdadm to mail you when something goes wrong
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| <ul>
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|
| |
| <li>
| |
| Edit <tt>/etc/mdadm/mdadm.conf</tt>: <tt>MAILADDR giclus1@gmail.com</tt>
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| </li>
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| </ul>
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| </li>
| |
| <li>
| |
| And then run a mdadm test by running
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| <ul>
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|
| |
| <li>
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| <tt>sudo mdadm --monitor --scan --test --oneshot</tt>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| </ul>
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| <h2 class="Subsection">
| |
| <a class="toc" name="toc-Subsection-1.5">1.5</a> Share internet connection with the others in the cluster:
| |
| </h2>
| |
| <h3 class="Subsubsection">
| |
| <a class="toc" name="toc-Subsubsection-1.5.1">1.5.1</a> UFW Version
| |
| </h3>
| |
| <ul>
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|
| |
| <li>
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| Enable <a class="URL" href="https://help.ubuntu.com/community/UFW">UFW</a>
| |
| <div class="Unindented">
| |
|
| |
| <div class="left">
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|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">sudo ufw enable<br/>
| |
| sudo ufw allow 22/tcp<br/>
| |
| sudo ufw allow 22/udp<br/>
| |
| sudo ufw allow in on eth1<br/>
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| <li>
| |
| Edit file <tt>/etc/ufw/before.rules</tt>:
| |
| <div class="Unindented">
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|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing"># nat Table rules<br/>
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| *nat :POSTROUTING ACCEPT [0:0]<br/>
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| # .<br/>
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| -A POSTROUTING -s 192.168.0.0/24 -o eth1 -j MASQUERADE<br/>
| |
| COMMIT<br/>
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| <li>
| |
| Edit <tt>/etc/default/ufw</tt>
| |
| <ul>
| |
|
| |
| <li>
| |
| Change <tt>DEFAULT_FORWARD_POLICY</tt> to “<tt>ACCEPT</tt>”
| |
| </li>
| |
| <li>
| |
| Uncomment:
| |
| <ul>
| |
|
| |
| <li>
| |
| <tt>net/ipv4/ip_forward=1</tt>
| |
| </li>
| |
| <li>
| |
| <tt>net/ipv6/conf/default/forwarding=1</tt>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| Restart ufw:
| |
| <ul>
| |
|
| |
| <li>
| |
| <tt>sudo ufw disable</tt>
| |
| </li>
| |
| <li>
| |
| <tt>sudo ufw enable</tt>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| </ul>
| |
| <h3 class="Subsubsection">
| |
| <a class="toc" name="toc-Subsubsection-1.5.2">1.5.2</a> IPTABLES Version
| |
| </h3>
| |
| <ul>
| |
|
| |
| <li>
| |
| <tt>sudo iptables -A FORWARD -i eth0 -o eth1 -s 192.168.1.0/24 -m conntrack --ctstate NEW -j ACCEPT</tt>
| |
| </li>
| |
| <li>
| |
| <tt>sudo iptables -A FORWARD -m conntrack --ctstate ESTABLISHED,RELATED -j ACCEPT</tt>
| |
| </li>
| |
| <li>
| |
| <tt>sudo iptables -A POSTROUTING -t nat -j MASQUERADE</tt>
| |
| </li>
| |
| <li>
| |
| <tt>sudo iptables-save | sudo tee /etc/iptables.sav</tt>
| |
| </li>
| |
| <li>
| |
| Add to /etc/rc.local
| |
| <ul>
| |
|
| |
| <li>
| |
| <tt>iptables-restore < /etc/iptables.sav</tt>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| Add to <tt>/etc/sysctl.conf</tt>
| |
| <ul>
| |
|
| |
| <li>
| |
| <tt>net.ipv4.conf.default.forwarding=1</tt>
| |
| </li>
| |
| <li>
| |
| <tt>net.ipv4.conf.all.forwarding=1</tt>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| <tt>sudo sh -c "echo 1 > /proc/sys/net/ipv4/ip_forward"</tt>
| |
| </li>
| |
| </ul>
| |
| <h2 class="Subsection">
| |
| <a class="toc" name="toc-Subsection-1.6">1.6</a> Sun Grid Engine Master
| |
| </h2>
| |
| <ul>
| |
|
| |
| <li>
| |
| <a class="URL" href="http://biowiki.org/HowToAdministerSunGridEngine">http://biowiki.org/HowToAdministerSunGridEngine</a>
| |
| </li>
| |
| <li>
| |
| <a class="URL" href="https://www.fmrib.ox.ac.uk/phpwiki/index.php/FslSge">https://www.fmrib.ox.ac.uk/phpwiki/index.php/FslSge</a>
| |
| </li>
| |
| <li>
| |
| <tt>sudo apt-get install libmotif3 libxpm4</tt>
| |
| </li>
| |
| <li>
| |
| Download SGE from: http://www.oracle.com
| |
| </li>
| |
| <li>
| |
| Install SGE (check this):
| |
| <div class="Unindented">
| |
|
| |
| <div class="left">
| |
| <tt>
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">mkdir /opt/soft/sge<br/>
| |
| mv ge-6.1u6-* ../../soft/sge<br/>
| |
| cd ../../soft/sge<br/>
| |
| tar xvzf ge-6.1u6-common.tar.gz<br/>
| |
| tar xvzf ge-6.1u6-arco.tar.gz<br/>
| |
| tar xvzf ge-6.1u6-bin-lx24-amd64.tar.gz<br/>
| |
| cd ..\\ sudo cp -rdvfa sge /<br/>
| |
| cd /sge<br/>
| |
| scp -rdv giclus1:/sge/* .<br/>
| |
| sudo ./inst_sge -m -x<br/>
| |
| </code>
| |
| </div>
| |
| </div></tt>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| <li>
| |
| Now go through the interactive install process
| |
| </li>
| |
| <li>
| |
| Add to <tt>/etc/bash.bashrc</tt>
| |
| <div class="Unindented">
| |
|
| |
| <div class="left">
| |
|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">#SGE settings export<br/>
| |
| SGE_ROOT=/sge<br/>
| |
| export SGE_CELL=default<br/>
| |
| if [ -e $SGE_ROOT/$SGE_CELL ]<br/>
| |
| then<br/>
| |
| . $SGE_ROOT/$SGE_CELL/common/settings.sh<br/>
| |
| fi<br/>
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| <li>
| |
| <b>ERROR “<tt>[: 359: 11: unexpected operator</tt>”</b>
| |
| <ul>
| |
|
| |
| <li>
| |
| On Ubuntu 10.04 LTS libc version detection fails in util/arch. The reason is that now (around line 244) <tt>strings libc.so.6</tt> returns <tt>GNU C Library (Ubuntu EGLIBC 2.11.1-0ubuntu7) stable release version 2.11.1, by Roland McGrath et al.</tt> where the version number appears twice. The subsequent tests get a string like "<tt>11\n11</tt>" instead of just "<tt>11</tt>" and the shell complains that the syntax of the if conditions is wrong. I fixed it by adding uniq to this line to the file <tt>/sge/util/arch</tt>:
| |
| <div class="Unindented">
| |
|
| |
| <div class="left">
| |
|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">libc_version=‘echo $libc_string | tr ’ ,’ ’\n’ | grep "2\." | cut -f 2 -d "." | uniq‘
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| <b>ERROR sgemaster and sgeexecd won’t start on boot</b>
| |
| <div class="Unindented">
| |
|
| |
| <div class="left">
| |
|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">cd /etc/init.d/<br/>
| |
| sudo update-rc.d sgeexecd.giclus defaults<br/>
| |
| sudo update-rc.d sgemaster.giclus defaults<br/>
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| </ul>
| |
| <h1 class="Section">
| |
| <a class="toc" name="toc-Section-2">2</a> The other nodes: GICLUS{2-3-4}
| |
| </h1>
| |
| <h2 class="Subsection">
| |
| <a class="toc" name="toc-Subsection-2.1">2.1</a> Operating system and network configuration
| |
| </h2>
| |
| <ul>
| |
|
| |
| <li>
| |
| Install Ubuntu Server 10.04.1 amd64
| |
| </li>
| |
| <li>
| |
| Partitions
| |
| <ul>
| |
|
| |
| <li>
| |
| <tt>/dev/sda1</tt>: 30GB on <tt>/</tt>
| |
| </li>
| |
| <li>
| |
| <tt>/dev/sda2</tt>: 450GB on <tt>/local_opt</tt>
| |
| </li>
| |
| <li>
| |
| <tt>/dev/sda3: 20GB of swap area</tt>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| Add gic group:
| |
| <ul>
| |
|
| |
| <li>
| |
| <tt>sudo addgroup gic </tt>
| |
| </li>
| |
| <li>
| |
| <tt>sudo addgroup alexandre gic</tt>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| Add more users:
| |
| <ul>
| |
|
| |
| <li>
| |
| <tt>sudo adduser <user_name> --ingroup gic --disabled-password</tt>
| |
| </li>
| |
| <li>
| |
| <tt>ssh-keygen -b 4096 -t rsa -C user_name </tt>
| |
| </li>
| |
| <li>
| |
| <tt>chown -R user_name:root /home/user_name/.ssh</tt>
| |
| </li>
| |
| <li>
| |
| <tt>chmod 700 /home/user_name/.ssh </tt>
| |
| </li>
| |
| <li>
| |
| <tt>chmod 400 /home/user_name/.ssh/authorized_keys</tt>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| Edit <tt>/etc/network/interfaces</tt>
| |
| <div class="Unindented">
| |
|
| |
| <div class="left">
| |
|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">auto lo<br/>
| |
| iface lo inet loopback<br/>
| |
| <br/>
| |
| auto eth1<br/>
| |
| iface eth1 inet static<br/>
| |
| address 192.168.1.8{2,3,4}<br/>
| |
| netmask 255.255.255.0<br/>
| |
| gateway 192.168.1.81<br/>
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| <li>
| |
| Edit <tt>/etc/resolv.conf</tt>
| |
| <div class="Unindented">
| |
|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">nameserver 10.20.13.6<br/>
| |
| nameserver 10.10.13.6<br/>
| |
| nameserver 10.30.13.6<br/>
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| <li>
| |
| <tt>sudo /etc/init.d/networking restart</tt>
| |
| </li>
| |
| <li>
| |
| Install packages:
| |
| <ul>
| |
|
| |
| <li>
| |
| Add "partner" repository, editing <tt>/etc/apt/sources.list</tt>
| |
| </li>
| |
| <li>
| |
| <tt>sudo apt-get update </tt>
| |
| </li>
| |
| <li>
| |
| <tt>sudo apt-get install ssh molly-guard openssh-blacklist openssh-blacklist-extra ssh-askpass binutils unzip sun-java6-jre</tt>
| |
| </li>
| |
| <li>
| |
| Edit <tt>/etc/ssh/sshd_conf</tt>: disable <tt>root</tt> access and password authentication
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| Edit <tt>/etc/ssh/sshd_conf</tt>: disable <tt>root</tt> access and password auth
| |
| </li>
| |
| <li>
| |
| Edit <tt>/etc/hosts</tt>
| |
| <div class="Unindented">
| |
|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">127.0.0.1 localhost giclus{2,3,4}<br/>
| |
| 192.168.1.81 giclus1<br/>
| |
| 192.168.1.82 giclus2<br/>
| |
| 192.168.1.83 giclus3<br/>
| |
| 192.168.1.84 giclus4<br/>
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| <li>
| |
| <tt>sudo /etc/init.d/networking restart</tt>
| |
| </li>
| |
| <li>
| |
| Install packages:
| |
| <ul>
| |
|
| |
| <li>
| |
| Add "partner" repository, editing <tt>/etc/apt/sources.list</tt>
| |
| </li>
| |
| <li>
| |
| <tt>sudo apt-get update</tt>
| |
| </li>
| |
| <li>
| |
| <tt>sudo apt-get upgrade</tt>
| |
| </li>
| |
| <li>
| |
| <tt>sudo apt-get install ssh molly-guard openssh-blacklist openssh-blacklist-extra ssh-askpass binutils unzip sun-java6-jre</tt>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| </ul>
| |
| <h2 class="Subsection">
| |
| <a class="toc" name="toc-Subsection-2.2">2.2</a> NIS Client
| |
| </h2>
| |
| <ul>
| |
|
| |
| <li>
| |
| <a class="URL" href="https://help.ubuntu.com/community/SettingUpNISHowTo">https://help.ubuntu.com/community/SettingUpNISHowTo</a>
| |
| </li>
| |
| <li>
| |
| <tt>sudo apt-get install nis </tt>
| |
| </li>
| |
| <li>
| |
| NIS domain name: <tt>giclus</tt>
| |
| </li>
| |
| <li>
| |
| Edit <tt>/etc/hosts.allow</tt>: <tt>portmap : 192.168.1.81</tt>
| |
| </li>
| |
| <li>
| |
| Add to <tt>/etc/passwd (+6x’:’)</tt>
| |
| <ul>
| |
|
| |
| <li>
| |
| +::::::
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| Add to <tt>/etc/group (+3x’:’)</tt>
| |
| <ul>
| |
|
| |
| <li>
| |
| +:::
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| Add to <tt>/etc/shadow (+8x’:’)</tt>
| |
| <ul>
| |
|
| |
| <li>
| |
| +::::::::
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| Edit <tt>/etc/yp.conf</tt> and add the line: <tt>ypserver giclus1</tt>
| |
| </li>
| |
| <li>
| |
| <tt>/etc/init.d/nis restart </tt>
| |
| </li>
| |
| <li>
| |
| <tt>/etc/init.d/ssh restart </tt>
| |
| </li>
| |
| <li>
| |
| or <tt>sudo reboot</tt>
| |
| </li>
| |
| </ul>
| |
| <h2 class="Subsection">
| |
| <a class="toc" name="toc-Subsection-2.3">2.3</a> NFS Client
| |
| </h2>
| |
| <ul>
| |
|
| |
| <li>
| |
| <tt>sudo apt-get install nfs-common</tt>
| |
| </li>
| |
| <li>
| |
| Add to /etc/fstab
| |
| <div class="Unindented">
| |
|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">#NFS Cluster mount<br/>
| |
| giclus1:/home /home nfs rsize=8192,wsize=8192,timeo=14,intr,rw<br/>
| |
| giclus1:/opt /opt nfs rsize=8192,wsize=8192,timeo=14,intr,rw<br/>
| |
| giclus1:/usr/local /usr/local nfs rsize=8192,wsize=8192,timeo=14,intr,rw<br/>
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| </ul>
| |
| <h2 class="Subsection">
| |
| <a class="toc" name="toc-Subsection-2.4">2.4</a> Sun Grid Engine Exec Daemon
| |
| </h2>
| |
| <ul>
| |
|
| |
| <li>
| |
| <a class="URL" href="http://biowiki.org/HowToAdministerSunGridEngine">http://biowiki.org/HowToAdministerSunGridEngine</a>
| |
| </li>
| |
| <li>
| |
| <a class="URL" href="https://www.fmrib.ox.ac.uk/phpwiki/index.php/FslSge">https://www.fmrib.ox.ac.uk/phpwiki/index.php/FslSge</a>
| |
| </li>
| |
| <li>
| |
| <tt>sudo apt-get install libmotif3 libxpm4</tt>
| |
| </li>
| |
| <li>
| |
| Download SGE from: http://www.oracle.com
| |
| </li>
| |
| <li>
| |
| Install SGE (check this):
| |
| <div class="Unindented">
| |
| <tt>
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">mkdir /opt/soft/sge<br/>
| |
| mv ge-6.1u6-* ../../soft/sge<br/>
| |
| cd ../../soft/sge<br/>
| |
| tar xvzf ge-6.1u6-common.tar.gz<br/>
| |
| tar xvzf ge-6.1u6-arco.tar.gz<br/>
| |
| tar xvzf ge-6.1u6-bin-lx24-amd64.tar.gz<br/>
| |
| cd ..\\ sudo cp -rdvfa sge /<br/>
| |
| cd /sge<br/>
| |
| scp -rdv giclus1:/sge/* .<br/>
| |
| sudo ./install_execd<br/>
| |
| </code>
| |
| </div>
| |
| </div></tt>
| |
| </div>
| |
| </li>
| |
| <li>
| |
| Now go through the interactive install process
| |
| </li>
| |
| <li>
| |
| Add to <tt>/etc/bash.bashrc</tt>
| |
| <div class="Unindented">
| |
|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">#SGE settings export<br/>
| |
| SGE_ROOT=/sge<br/>
| |
| export SGE_CELL=default<br/>
| |
| if [ -e $SGE_ROOT/$SGE_CELL ]<br/>
| |
| then<br/>
| |
| . $SGE_ROOT/$SGE_CELL/common/settings.sh<br/>
| |
| fi<br/>
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| <li>
| |
| <b>ERROR “<tt>[: 359: 11: unexpected operator</tt>”</b>
| |
| <ul>
| |
|
| |
| <li>
| |
| On Ubuntu 10.04 LTS libc version detection fails in util/arch. The reason is that now (around line 244) <tt>strings libc.so.6</tt> returns <tt>GNU C Library (Ubuntu EGLIBC 2.11.1-0ubuntu7) stable release version 2.11.1, by Roland McGrath et al.</tt> where the version number appears twice. The subsequent tests get a string like "<tt>11\n11</tt>" instead of just "<tt>11</tt>" and the shell complains that the syntax of the if conditions is wrong. I fixed it by adding uniq to this line to the file <tt>/sge/util/arch</tt>:
| |
| <div class="Unindented">
| |
|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">libc_version=‘echo $libc_string | tr ’ ,’ ’\n’ | grep "2\." | cut -f 2 -d "." | uniq‘
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| <b>ERROR sgemaster and sgeexecd won’t start on boot</b>
| |
| <div class="Unindented">
| |
|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">cd /etc/init.d/<br/>
| |
| sudo update-rc.d sgeexecd.giclus defaults
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| </ul>
| |
| <h1 class="Section">
| |
| <a class="toc" name="toc-Section-3">3</a> Execute in all nodes
| |
| </h1>
| |
| <h2 class="Subsection">
| |
| <a class="toc" name="toc-Subsection-3.1">3.1</a> Install NeuroDebian Repository ( http://neuro.debian.net/ )
| |
| </h2>
| |
| <ul>
| |
|
| |
| <li>
| |
| Installation:
| |
| <div class="Unindented">
| |
|
| |
| <div class="left">
| |
|
| |
| <div class="float">
| |
|
| |
| <div class="listing">
| |
| <code class="listing">wget -c http://neuro.debian.net/_static/neurodebian.lucid.de.sources.list<br/>
| |
| wget -c http://neuro.debian.net/_static/neuro.debian.net.asc<br/>
| |
| sudo apt-key add neuro.debian.net.asc<br/>
| |
| sudo cp neurodebian.lucid.de.sources.list /etc/apt/sources.list.d<br/>
| |
| sudo apt-get update<br/>
| |
| sudo apt-get upgrade<br/>
| |
| sudo apt-get install fsl fsl-atlases fsl-first-data nifti-bin<br/>
| |
| </code>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </div>
| |
| </li>
| |
| <li>
| |
| Add to <tt>/etc/bash.bashrc</tt>:
| |
| <ul>
| |
|
| |
| <li>
| |
| <tt>. /etc/fsl/fsl.sh</tt>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| </ul>
| |
| <h2 class="Subsection">
| |
| <a class="toc" name="toc-Subsection-3.2">3.2</a> Other configuration details
| |
| </h2>
| |
| <ul>
| |
|
| |
| <li>
| |
| Local temporary work directory
| |
| <ul>
| |
|
| |
| <li>
| |
| Add to <tt>/etc/environment</tt>
| |
| <ul>
| |
|
| |
| <li>
| |
| <tt>LOCAL_TEMP="/local"</tt>
| |
| </li>
| |
| <li>
| |
| (for <tt>giclus1</tt>) this has been set to <tt>“/opt/temp”</tt>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| <li>
| |
| <tt>sudo chown -R alexandre:gic /local</tt>
| |
| </li>
| |
| <li>
| |
| <tt>sudo chmod -R 770 /local </tt>
| |
| </li>
| |
| </ul>
| |
| </li>
| |
| </ul>
| |
|
| |
| <hr/>
| |
| <p>Copyright (C) 2010 Alexandre Manhães Savio</p>
| |
| </div>
| |
| </body>
| |
| </html>
| |
