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Alexsavio en 17:41 9 sep 2010
2010-09-09T17:41:50Z
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Alexsavio
https://ehu.eus/ccwintco/index.php?title=Setting_up_Ubuntu_Cluster&diff=6681&oldid=prev
Alexsavio en 17:41 9 sep 2010
2010-09-09T17:41:00Z
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<title>Technical report of the procedure of setup of a Ubuntu Server computer cluster</title><br />
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<body><br />
<div id="globalWrapper"><br />
<br />
<h1 class="title"><br />
Technical report of the procedure of setup of a Ubuntu Server computer cluster<br />
</h1><br />
<h2 class="author"><br />
Alexandre Manhães Savio<br />
</h2><br />
<h2 class="Date"><br />
September 24th, 2010<br />
</h2><br />
<h1 class="Section"><br />
<a class="toc" name="toc-Section-1">1</a> Master Node - Giclus1<br />
</h1><br />
<h2 class="Subsection"><br />
<a class="toc" name="toc-Subsection-1.1">1.1</a> Operating system and network configuration<br />
</h2><br />
<ul><br />
<br />
<li><br />
Install Ubuntu Server 10.04.1 amd64<br />
</li><br />
<li><br />
Partitions<br />
<ul><br />
<br />
<li><br />
<tt>/dev/sda1</tt>: 20GB on <tt>/</tt> <br />
</li><br />
<li><br />
<tt>/dev/sda2</tt>: 20GB on <tt>/usr/local</tt><br />
</li><br />
<li><br />
<tt>/dev/sda3</tt>: 130GB on <tt>/home </tt><br />
</li><br />
<li><br />
<tt>/dev/sda5</tt>: 280GB on <tt>/opt</tt><br />
</li><br />
<li><br />
<tt>/dev/sda6:</tt>20GB of swap area<br />
</li><br />
</ul><br />
</li><br />
<li><br />
Add gic group:<br />
<ul><br />
<br />
<li><br />
<tt>sudo addgroup gic </tt><br />
</li><br />
<li><br />
<tt>sudo addgroup alexandre gic</tt><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Add more users: <br />
<ul><br />
<br />
<li><br />
<tt>sudo adduser &lt;user_name&gt; --ingroup gic --disabled-password</tt><br />
</li><br />
<li><br />
<tt>ssh-keygen -b 4096 -t rsa -C user_name </tt><br />
</li><br />
<li><br />
<tt>chown -R user_name:root /home/user_name/.ssh</tt><br />
</li><br />
<li><br />
<tt>chmod 700 /home/user_name/.ssh </tt><br />
</li><br />
<li><br />
<tt>chmod 400 /home/user_name/.ssh/authorized_keys</tt><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Edit <tt>/etc/network/interfaces</tt><br />
<div class="Unindented"><br />
<br />
<div class="left"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing"><br />
auto lo<br/><br />
iface lo inet loopback<br/><br />
<br/><br />
auto eth1<br/><br />
iface eth1 inet static<br/><br />
address 192.168.1.81<br/><br />
netmask 255.255.255.0<br/><br />
gateway 192.168.1.1<br/><br />
<br/><br />
auto eth0 <br/><br />
iface eth0 inet dhcp <br/><br />
#for more information about this email me<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
Edit <tt>/etc/resolv.conf</tt><br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">nameserver 10.20.13.6<br/><br />
nameserver 10.10.13.6<br/><br />
nameserver 10.30.13.6<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
<tt>sudo /etc/init.d/networking restart</tt><br />
</li><br />
<li><br />
Install packages: <br />
<ul><br />
<br />
<li><br />
Add "partner" repository, editing <tt>/etc/apt/sources.list</tt> <br />
</li><br />
<li><br />
<tt>sudo apt-get update </tt><br />
</li><br />
<li><br />
<tt>sudo apt-get install ssh molly-guard openssh-blacklist openssh-blacklist-extra ssh-askpass binutils unzip sun-java6-jre</tt><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Edit <tt>/etc/ssh/sshd_conf</tt>: disable <tt>root</tt> access and password auth<br />
</li><br />
<li><br />
Edit <tt>/etc/hosts</tt><br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">127.0.0.1 localhost giclus1<br/><br />
192.168.1.81 giclus1<br/><br />
192.168.1.82 giclus2<br/><br />
192.168.1.83 giclus3<br/><br />
192.168.1.84 giclus4<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
Edit <tt>/etc/hosts.allow</tt><br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<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<br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
</ul><br />
<h2 class="Subsection"><br />
<a class="toc" name="toc-Subsection-1.2">1.2</a> NIS Server <br />
</h2><br />
<ul><br />
<br />
<li><br />
<tt>sudo apt-get install portmap nis</tt> <br />
</li><br />
<li><br />
NIS domain name: <tt>giclus</tt> <br />
</li><br />
<li><br />
For more details: <a class="URL" href="https://help.ubuntu.com/community/SettingUpNISHowTo">https://help.ubuntu.com/community/SettingUpNISHowTo</a> <br />
</li><br />
<li><br />
Edit <tt>/etc/default/portmap</tt> and comment out the <tt>ARGS="-i 127.0.0.1"</tt> line <br />
</li><br />
<li><br />
Edit <tt>/etc/default/nis</tt> and set the <tt>NISSERVER</tt> line to <tt>NISSERVER=master</tt> <br />
</li><br />
<li><br />
Edit <tt>/etc/yp.conf</tt>: <tt>domain giclus server giclus1</tt> <br />
</li><br />
<li><br />
Edit <tt>/etc/ypserv.securenets</tt><br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">host 192.168.1.81<br/><br />
host 192.168.1.82<br/><br />
host 192.168.1.83<br/><br />
host 192.168.1.84<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
Build the DB for the first time, run: <tt>sudo /usr/lib/yp/ypinit -m</tt><br />
</li><br />
<li><br />
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)<br />
</li><br />
<li><br />
Restart:<br />
<ul><br />
<br />
<li><br />
<tt>sudo /etc/init.d/portmap restart </tt><br />
</li><br />
<li><br />
<tt>sudo /etc/init.d/nis restart</tt><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
<h2 class="Subsection"><br />
<a class="toc" name="toc-Subsection-1.3">1.3</a> NFS Kernel Server <br />
</h2><br />
<ul><br />
<br />
<li><br />
<a class="URL" href="https://help.ubuntu.com/community/SettingUpNFSHowTo">https://help.ubuntu.com/community/SettingUpNFSHowTo</a><br />
</li><br />
<li><br />
<tt>sudo apt-get install nfswatch nfs-kernel-server</tt> <br />
</li><br />
<li><br />
Edit <tt>/etc/exports</tt> and add the shares: <br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<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/><br />
/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/><br />
/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/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
<tt>sudo exportfs -ra</tt><br />
</li><br />
</ul><br />
<h2 class="Subsection"><br />
<a class="toc" name="toc-Subsection-1.4">1.4</a> MSMTP:<br />
</h2><br />
<ul><br />
<br />
<li><br />
Create a Gmail account for monitoring. I do this because I don’t want my gmail password floating around in plaintext on various machines. <br />
</li><br />
<li><br />
Install the <tt>ca-certificates</tt> package<br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">sudo aptitude install ca-certificates<br/><br />
sudo update-ca-certificates<br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
<tt>sudo apt-get install msmtp </tt><br />
</li><br />
<li><br />
Edit <tt>/etc/msmtprc </tt><br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">account gmail<br/><br />
host smtp.gmail.com<br/><br />
from giclus1@gmail.com<br/><br />
auth on<br/><br />
tls on<br/><br />
tls_trust_file /etc/ssl/certs/ca-certificates.crt<br/><br />
user giclus1@gmail.com<br/><br />
password *******<br/><br />
port 587<br/><br />
<br/><br />
account default : gmail<br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
Create a sendmail simlink:<br />
<ul><br />
<br />
<li><br />
<tt>sudo ln -s /usr/bin/msmtp /usr/sbin/sendmail</tt><br />
</li><br />
</ul><br />
</li><br />
<li><br />
-Run a test<br />
<ul><br />
<br />
<li><br />
<tt>echo “This is a an awesome test email” | msmtp youremail@domain.com </tt><br />
</li><br />
</ul><br />
</li><br />
<li><br />
- If you want mdadm to mail you when something goes wrong<br />
<ul><br />
<br />
<li><br />
Edit <tt>/etc/mdadm/mdadm.conf</tt>: <tt>MAILADDR giclus1@gmail.com</tt><br />
</li><br />
</ul><br />
</li><br />
<li><br />
And then run a mdadm test by running<br />
<ul><br />
<br />
<li><br />
<tt>sudo mdadm --monitor --scan --test --oneshot</tt><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
<h2 class="Subsection"><br />
<a class="toc" name="toc-Subsection-1.5">1.5</a> Share internet connection with the others in the cluster:<br />
</h2><br />
<h3 class="Subsubsection"><br />
<a class="toc" name="toc-Subsubsection-1.5.1">1.5.1</a> UFW Version<br />
</h3><br />
<ul><br />
<br />
<li><br />
Enable <a class="URL" href="https://help.ubuntu.com/community/UFW">UFW</a><br />
<div class="Unindented"><br />
<br />
<div class="left"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">sudo ufw enable<br/><br />
sudo ufw allow 22/tcp<br/><br />
sudo ufw allow 22/udp<br/><br />
sudo ufw allow in on eth1<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
Edit file <tt>/etc/ufw/before.rules</tt>:<br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing"># nat Table rules<br/><br />
*nat :POSTROUTING ACCEPT [0:0]<br/><br />
# .<br/><br />
-A POSTROUTING -s 192.168.0.0/24 -o eth1 -j MASQUERADE<br/><br />
COMMIT<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
Edit <tt>/etc/default/ufw</tt><br />
<ul><br />
<br />
<li><br />
Change <tt>DEFAULT_FORWARD_POLICY</tt> to “<tt>ACCEPT</tt>”<br />
</li><br />
<li><br />
Uncomment:<br />
<ul><br />
<br />
<li><br />
<tt>net/ipv4/ip_forward=1</tt><br />
</li><br />
<li><br />
<tt>net/ipv6/conf/default/forwarding=1</tt><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Restart ufw:<br />
<ul><br />
<br />
<li><br />
<tt>sudo ufw disable</tt><br />
</li><br />
<li><br />
<tt>sudo ufw enable</tt><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
<h3 class="Subsubsection"><br />
<a class="toc" name="toc-Subsubsection-1.5.2">1.5.2</a> IPTABLES Version<br />
</h3><br />
<ul><br />
<br />
<li><br />
<tt>sudo iptables -A FORWARD -i eth0 -o eth1 -s 192.168.1.0/24 -m conntrack --ctstate NEW -j ACCEPT</tt><br />
</li><br />
<li><br />
<tt>sudo iptables -A FORWARD -m conntrack --ctstate ESTABLISHED,RELATED -j ACCEPT</tt><br />
</li><br />
<li><br />
<tt>sudo iptables -A POSTROUTING -t nat -j MASQUERADE</tt><br />
</li><br />
<li><br />
<tt>sudo iptables-save | sudo tee /etc/iptables.sav</tt><br />
</li><br />
<li><br />
Add to /etc/rc.local<br />
<ul><br />
<br />
<li><br />
<tt>iptables-restore &lt; /etc/iptables.sav</tt><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Add to <tt>/etc/sysctl.conf</tt><br />
<ul><br />
<br />
<li><br />
<tt>net.ipv4.conf.default.forwarding=1</tt><br />
</li><br />
<li><br />
<tt>net.ipv4.conf.all.forwarding=1</tt><br />
</li><br />
</ul><br />
</li><br />
<li><br />
<tt>sudo sh -c "echo 1 &gt; /proc/sys/net/ipv4/ip_forward"</tt><br />
</li><br />
</ul><br />
<h2 class="Subsection"><br />
<a class="toc" name="toc-Subsection-1.6">1.6</a> Sun Grid Engine Master<br />
</h2><br />
<ul><br />
<br />
<li><br />
<a class="URL" href="http://biowiki.org/HowToAdministerSunGridEngine">http://biowiki.org/HowToAdministerSunGridEngine</a><br />
</li><br />
<li><br />
<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><br />
</li><br />
<li><br />
<tt>sudo apt-get install libmotif3 libxpm4</tt><br />
</li><br />
<li><br />
Download SGE from: http://www.oracle.com<br />
</li><br />
<li><br />
Install SGE (check this):<br />
<div class="Unindented"><br />
<br />
<div class="left"><br />
<tt><br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">mkdir /opt/soft/sge<br/><br />
mv ge-6.1u6-* ../../soft/sge<br/><br />
cd ../../soft/sge<br/><br />
tar xvzf ge-6.1u6-common.tar.gz<br/><br />
tar xvzf ge-6.1u6-arco.tar.gz<br/><br />
tar xvzf ge-6.1u6-bin-lx24-amd64.tar.gz<br/><br />
cd ..\\ sudo cp -rdvfa sge /<br/><br />
cd /sge<br/><br />
scp -rdv giclus1:/sge/* .<br/><br />
sudo ./inst_sge -m -x<br/><br />
</code><br />
</div><br />
</div></tt><br />
</div><br />
</div><br />
</li><br />
<li><br />
Now go through the interactive install process<br />
</li><br />
<li><br />
Add to <tt>/etc/bash.bashrc</tt><br />
<div class="Unindented"><br />
<br />
<div class="left"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">#SGE settings export<br/><br />
SGE_ROOT=/sge<br/><br />
export SGE_CELL=default<br/><br />
if [ -e $SGE_ROOT/$SGE_CELL ]<br/><br />
then<br/><br />
. $SGE_ROOT/$SGE_CELL/common/settings.sh<br/><br />
fi<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
<b>ERROR “<tt>[: 359: 11: unexpected operator</tt>”</b><br />
<ul><br />
<br />
<li><br />
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>: <br />
<div class="Unindented"><br />
<br />
<div class="left"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">libc_version=‘echo $libc_string | tr ’ ,’ ’\n’ | grep "2\." | cut -f 2 -d "." | uniq‘<br />
</code><br />
</div><br />
</div><br />
</div><br />
</div><br />
</li><br />
</ul><br />
</li><br />
<li><br />
<b>ERROR sgemaster and sgeexecd won’t start on boot</b><br />
<div class="Unindented"><br />
<br />
<div class="left"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">cd /etc/init.d/<br/><br />
sudo update-rc.d sgeexecd.giclus defaults<br/><br />
sudo update-rc.d sgemaster.giclus defaults<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</div><br />
</li><br />
</ul><br />
<h1 class="Section"><br />
<a class="toc" name="toc-Section-2">2</a> The other nodes: GICLUS{2-3-4}<br />
</h1><br />
<h2 class="Subsection"><br />
<a class="toc" name="toc-Subsection-2.1">2.1</a> Operating system and network configuration<br />
</h2><br />
<ul><br />
<br />
<li><br />
Install Ubuntu Server 10.04.1 amd64<br />
</li><br />
<li><br />
Partitions<br />
<ul><br />
<br />
<li><br />
<tt>/dev/sda1</tt>: 30GB on <tt>/</tt> <br />
</li><br />
<li><br />
<tt>/dev/sda2</tt>: 450GB on <tt>/local_opt</tt><br />
</li><br />
<li><br />
<tt>/dev/sda3: 20GB of swap area</tt><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Add gic group:<br />
<ul><br />
<br />
<li><br />
<tt>sudo addgroup gic </tt><br />
</li><br />
<li><br />
<tt>sudo addgroup alexandre gic</tt><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Add more users: <br />
<ul><br />
<br />
<li><br />
<tt>sudo adduser &lt;user_name&gt; --ingroup gic --disabled-password</tt><br />
</li><br />
<li><br />
<tt>ssh-keygen -b 4096 -t rsa -C user_name </tt><br />
</li><br />
<li><br />
<tt>chown -R user_name:root /home/user_name/.ssh</tt><br />
</li><br />
<li><br />
<tt>chmod 700 /home/user_name/.ssh </tt><br />
</li><br />
<li><br />
<tt>chmod 400 /home/user_name/.ssh/authorized_keys</tt><br />
</li><br />
</ul><br />
</li><br />
<li><br />
Edit <tt>/etc/network/interfaces</tt><br />
<div class="Unindented"><br />
<br />
<div class="left"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">auto lo<br/><br />
iface lo inet loopback<br/><br />
<br/><br />
auto eth1<br/><br />
iface eth1 inet static<br/><br />
address 192.168.1.8{2,3,4}<br/><br />
netmask 255.255.255.0<br/><br />
gateway 192.168.1.81<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
Edit <tt>/etc/resolv.conf</tt><br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">nameserver 10.20.13.6<br/><br />
nameserver 10.10.13.6<br/><br />
nameserver 10.30.13.6<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
<tt>sudo /etc/init.d/networking restart</tt><br />
</li><br />
<li><br />
Install packages: <br />
<ul><br />
<br />
<li><br />
Add "partner" repository, editing <tt>/etc/apt/sources.list</tt> <br />
</li><br />
<li><br />
<tt>sudo apt-get update </tt><br />
</li><br />
<li><br />
<tt>sudo apt-get install ssh molly-guard openssh-blacklist openssh-blacklist-extra ssh-askpass binutils unzip sun-java6-jre</tt><br />
</li><br />
<li><br />
Edit <tt>/etc/ssh/sshd_conf</tt>: disable <tt>root</tt> access and password authentication<br />
</li><br />
</ul><br />
</li><br />
<li><br />
Edit <tt>/etc/ssh/sshd_conf</tt>: disable <tt>root</tt> access and password auth<br />
</li><br />
<li><br />
Edit <tt>/etc/hosts</tt><br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">127.0.0.1 localhost giclus{2,3,4}<br/><br />
192.168.1.81 giclus1<br/><br />
192.168.1.82 giclus2<br/><br />
192.168.1.83 giclus3<br/><br />
192.168.1.84 giclus4<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
<tt>sudo /etc/init.d/networking restart</tt><br />
</li><br />
<li><br />
Install packages: <br />
<ul><br />
<br />
<li><br />
Add "partner" repository, editing <tt>/etc/apt/sources.list</tt> <br />
</li><br />
<li><br />
<tt>sudo apt-get update</tt><br />
</li><br />
<li><br />
<tt>sudo apt-get upgrade</tt><br />
</li><br />
<li><br />
<tt>sudo apt-get install ssh molly-guard openssh-blacklist openssh-blacklist-extra ssh-askpass binutils unzip sun-java6-jre</tt><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
<h2 class="Subsection"><br />
<a class="toc" name="toc-Subsection-2.2">2.2</a> NIS Client <br />
</h2><br />
<ul><br />
<br />
<li><br />
<a class="URL" href="https://help.ubuntu.com/community/SettingUpNISHowTo">https://help.ubuntu.com/community/SettingUpNISHowTo</a><br />
</li><br />
<li><br />
<tt>sudo apt-get install nis </tt><br />
</li><br />
<li><br />
NIS domain name: <tt>giclus</tt> <br />
</li><br />
<li><br />
Edit <tt>/etc/hosts.allow</tt>: <tt>portmap : 192.168.1.81</tt> <br />
</li><br />
<li><br />
Add to <tt>/etc/passwd (+6x’:’)</tt><br />
<ul><br />
<br />
<li><br />
+::::::<br />
</li><br />
</ul><br />
</li><br />
<li><br />
Add to <tt>/etc/group (+3x’:’)</tt><br />
<ul><br />
<br />
<li><br />
+:::<br />
</li><br />
</ul><br />
</li><br />
<li><br />
Add to <tt>/etc/shadow (+8x’:’)</tt><br />
<ul><br />
<br />
<li><br />
+::::::::<br />
</li><br />
</ul><br />
</li><br />
<li><br />
Edit <tt>/etc/yp.conf</tt> and add the line: <tt>ypserver giclus1</tt><br />
</li><br />
<li><br />
<tt>/etc/init.d/nis restart </tt><br />
</li><br />
<li><br />
<tt>/etc/init.d/ssh restart </tt><br />
</li><br />
<li><br />
or <tt>sudo reboot</tt><br />
</li><br />
</ul><br />
<h2 class="Subsection"><br />
<a class="toc" name="toc-Subsection-2.3">2.3</a> NFS Client <br />
</h2><br />
<ul><br />
<br />
<li><br />
<tt>sudo apt-get install nfs-common</tt><br />
</li><br />
<li><br />
Add to /etc/fstab<br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">#NFS Cluster mount<br/><br />
giclus1:/home /home nfs rsize=8192,wsize=8192,timeo=14,intr,rw<br/><br />
giclus1:/opt /opt nfs rsize=8192,wsize=8192,timeo=14,intr,rw<br/><br />
giclus1:/usr/local /usr/local nfs rsize=8192,wsize=8192,timeo=14,intr,rw<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
</ul><br />
<h2 class="Subsection"><br />
<a class="toc" name="toc-Subsection-2.4">2.4</a> Sun Grid Engine Exec Daemon<br />
</h2><br />
<ul><br />
<br />
<li><br />
<a class="URL" href="http://biowiki.org/HowToAdministerSunGridEngine">http://biowiki.org/HowToAdministerSunGridEngine</a><br />
</li><br />
<li><br />
<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><br />
</li><br />
<li><br />
<tt>sudo apt-get install libmotif3 libxpm4</tt><br />
</li><br />
<li><br />
Download SGE from: http://www.oracle.com<br />
</li><br />
<li><br />
Install SGE (check this):<br />
<div class="Unindented"><br />
<tt><br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">mkdir /opt/soft/sge<br/><br />
mv ge-6.1u6-* ../../soft/sge<br/><br />
cd ../../soft/sge<br/><br />
tar xvzf ge-6.1u6-common.tar.gz<br/><br />
tar xvzf ge-6.1u6-arco.tar.gz<br/><br />
tar xvzf ge-6.1u6-bin-lx24-amd64.tar.gz<br/><br />
cd ..\\ sudo cp -rdvfa sge /<br/><br />
cd /sge<br/><br />
scp -rdv giclus1:/sge/* .<br/><br />
sudo ./install_execd<br/><br />
</code><br />
</div><br />
</div></tt><br />
</div><br />
</li><br />
<li><br />
Now go through the interactive install process<br />
</li><br />
<li><br />
Add to <tt>/etc/bash.bashrc</tt><br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">#SGE settings export<br/><br />
SGE_ROOT=/sge<br/><br />
export SGE_CELL=default<br/><br />
if [ -e $SGE_ROOT/$SGE_CELL ]<br/><br />
then<br/><br />
. $SGE_ROOT/$SGE_CELL/common/settings.sh<br/><br />
fi<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
<b>ERROR “<tt>[: 359: 11: unexpected operator</tt>”</b><br />
<ul><br />
<br />
<li><br />
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>: <br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">libc_version=‘echo $libc_string | tr ’ ,’ ’\n’ | grep "2\." | cut -f 2 -d "." | uniq‘<br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
</ul><br />
</li><br />
<li><br />
<b>ERROR sgemaster and sgeexecd won’t start on boot</b><br />
<div class="Unindented"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">cd /etc/init.d/<br/><br />
sudo update-rc.d sgeexecd.giclus defaults<br />
</code><br />
</div><br />
</div><br />
</div><br />
</li><br />
</ul><br />
<h1 class="Section"><br />
<a class="toc" name="toc-Section-3">3</a> Execute in all nodes<br />
</h1><br />
<h2 class="Subsection"><br />
<a class="toc" name="toc-Subsection-3.1">3.1</a> Install NeuroDebian Repository ( http://neuro.debian.net/ )<br />
</h2><br />
<ul><br />
<br />
<li><br />
Installation:<br />
<div class="Unindented"><br />
<br />
<div class="left"><br />
<br />
<div class="float"><br />
<br />
<div class="listing"><br />
<code class="listing">wget -c http://neuro.debian.net/_static/neurodebian.lucid.de.sources.list<br/><br />
wget -c http://neuro.debian.net/_static/neuro.debian.net.asc<br/><br />
sudo apt-key add neuro.debian.net.asc<br/><br />
sudo cp neurodebian.lucid.de.sources.list /etc/apt/sources.list.d<br/><br />
sudo apt-get update<br/><br />
sudo apt-get upgrade<br/><br />
sudo apt-get install fsl fsl-atlases fsl-first-data nifti-bin<br/><br />
</code><br />
</div><br />
</div><br />
</div><br />
</div><br />
</li><br />
<li><br />
Add to <tt>/etc/bash.bashrc</tt>: <br />
<ul><br />
<br />
<li><br />
<tt>. /etc/fsl/fsl.sh</tt><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
<h2 class="Subsection"><br />
<a class="toc" name="toc-Subsection-3.2">3.2</a> Other configuration details<br />
</h2><br />
<ul><br />
<br />
<li><br />
Local temporary work directory <br />
<ul><br />
<br />
<li><br />
Add to <tt>/etc/environment</tt><br />
<ul><br />
<br />
<li><br />
<tt>LOCAL_TEMP="/local"</tt><br />
</li><br />
<li><br />
(for <tt>giclus1</tt>) this has been set to <tt>“/opt/temp”</tt><br />
</li><br />
</ul><br />
</li><br />
<li><br />
<tt>sudo chown -R alexandre:gic /local</tt><br />
</li><br />
<li><br />
<tt>sudo chmod -R 770 /local </tt><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
<hr/><br />
<p>Copyright (C) 2010 Alexandre Manhães Savio</p><br />
</div><br />
</body><br />
</html></div>
Alexsavio