Desktop Setup - Ubuntu 12.04

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Currently still testing the distribution, so please report any problems to Ehsan and Jose!!

  • 0 - Install Ubuntu 12.04 x86_64

NOTE: ONLY if you have trouble with Step 4 of the installation process, the partition selection, open a terminal in the trial mode and run: 

sudo dmraid -r -E /dev/sda

NOTE: When prompted for a username, choose one that is NOT your SOE login! For example "ian_local" rather than my SOE login of "ianlee1521". Otherwise you will not be able to login to your computer after you setup LDAP.

NOTE: When prompted for a machine name, enter the name that machine is supposed to be (mascd1, omelette, quiche, etc)

Installation should complete as normal.

Plain Ubuntu Installation

  • 1 - Enable root account

Login to the GUI with your local login, then open a terminal (Applications -> Accessories -> Terminal): 

sudo su - 
passwd

Enter your new root password for the machine.

Add your local and SOE logins to the sudoers list: 

vi /etc/sudoers
  • 2 - Install NVIDIA Drivers

Blacklist some kernel modules 

vi /etc/modprobe.d/blacklist.conf

Add the following lines to the file 

blacklist vga16fb
blacklist nouveau
blacklist rivafb
blacklist nvidiafb
blacklist rivatv

Get rid of any installed NVIDIA drivers (you are already root, if not use with sudo): 

apt-get --purge remove nvidia-* 

apt-get update
apt-get install nvidia-current


Reboot the machine and X should start normally. Login at the GUI login as root and open a terminal.

  • 3 - Setup the new repo
scp <username>@mascd12:/etc/apt/sources.list /etc/apt/source.list
apt-get update -y
apt-get dist-upgrade -y


  • 4 - Adjust sysctl options

mmap problem for qemu 

vi /etc/sysctl.d/10-zeropage.conf

Edit the following value: 

vm.mmap_min_addr = 4096

increase (add) the inotify watches in /etc/sysctl.conf 

echo -e "\nfs.inotify.max_user_watches = 65535 \nkernel.randomize_va_space = 0" | tee -a /etc/sysctl.conf
  • 5 - Replicate the installation on Master machine (mascd12, dhcp-63-154.cse.ucsc.edu)
ssh <username>@mascd12 dpkg --get-selections | grep -v deinstall > mypackages.txt
dpkg –clear-selections (?)
dpkg --set-selections < mypackages.txt

"apt-get dselect-upgrade -y" Will give many options and take a long time for the upgrade (about an hour for me).

Select all default options EXCEPT! for ion3: acknowledge the lack of support (non-default option) 

apt-get dselect-upgrade -y

MADA Related Stuff

  • 6 - Install autofs

Create mada directory 

mkdir /mada

Get autofs files from another machine 

scp <username>@mascd12:/etc/auto.* /etc/
ln -s /mada/users /soe
initctl reload autofs
  • 7 - awk for cadence
apt-get install -y ksh csh original-awk
ln -s /usr/bin/awk /bin/awk
  • 8 - Set the firewall
ufw enable
ufw default deny
ufw reject auth
ufw limit ssh/tcp
  • 9 - Get tempcap from another ubuntu machine (mascd1, mascd12, ...), and some lib preparation:
scp <username>@mascd12:/usr/lib64/libtermcap.so.2.0.8 /usr/lib64/
ln -s /usr/lib64/libtermcap.so.2.0.8 /usr/lib64/libtermcap.so.2

ln -s /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3
  • 10 - LDAP

Install 

apt-get install -y ldap-auth-client libpam-krb5 krb5-user libsasl2-modules-gssapi-mit

Leave the kerberos config entry blank. You will copy it in the next step.

Create /ect/krb5.conf 

scp <username>@mascd1:/etc/krb5.conf /etc/

Copy the ldap certificate 

scp <username>@mascd1:/etc/ssl/certs/* /etc/ssl/certs/

Create "/etc/auth-client-config/profile.d/krb-ldap-config" 

scp <username>@mascd1:/etc/auth-client-config/profile.d/krb-ldap-config /etc/auth-client-config/profile.d/krb-ldap-config
auth-client-config -a -p krb_ldap

Update ldap.conf 

scp <username>@mascd1:/etc/ldap.conf /etc/ldap.conf
scp <username>@mascd1:/etc/ldap/ldap.conf /etc/ldap/ldap.conf

Now you should be able to execute: 

ldapsearch -x LLL
  • 11 - Lock SOE people out of your machine :)
scp <username>@mascd12:/etc/security/access.conf /etc/security/access.conf

You will need to add your local login to the machine, or you will lock yourself out: 

vim /etc/security/access.conf

Go to very bottom of file and add your local user account to the list below root Example of the last lines of my file (Replace "ian_local" with your local login): 

+ : root : ALL
+ : nx   : ALL
+ : ian_local : ALL
+ : (masc) : ALL
+ : (vlsi) : ALL
-:ALL :ALL

Now, you should see people with "getent passwd" but, calling "su - cormac" should say "permission denied", but, calling "su - renau" should work.

  • 12 - Since the LDAP has timeouts, setup the local backup
apt-get install nss-updatedb
nss_updatedb ldap
cd /etc/cron.hourly/
scp mada1:/etc/cron.hourly/nss_updatedb-ldap.sh .
scp mada1:/etc/nsswitch.conf /etc
  • 13 - Edit lines passwd and group in /etc/nsswitch.conf so that they are as follows (involves adding db before ldap)

sudo vi /etc/nsswitch.conf passwd: files db ldap group: files db ldap

  • 14 - Allow other accounts to be shown at the login screen, and disable Guest user.
 sudo vi /etc/lightdm/lightdm.conf

add the following lines to lightdm.conf 

greeter-show-manual-login=true
allow-guest=false


  • 15 - Restart your computer:
shutdown -r now
  • 16 - Login to the GUI with your SOE login information. If you get a prompt asking for an "LDAP Password" this means that you typed your password incorrectly.
  • 17 - Remove old desktop configuration files (KDE / GNOME / browser)

NOTE: Removing ".config" will delete any saved passwords in your browser, but will fix other problems. NOTE: You can use kubuntu(KDE), gnome, unity, or awesome as desktop/windows manager.

Logout of / kill any open X sessions. Switch to tty1 (CTRL + ALT + F1), and login with your SOE account. 

rm -rf .config .kde* .gconf* .gnome* .awesome*
  • 18 - Some Minor Patches for things that don't work properly

Disable apparmor 

sudo invoke-rc.d apparmor stop
sudo update-rc.d -f apparmor remove
  • 19 - Add bash as default shell
cd /bin
sudo ln -sf bash sh
  • 20 - Using QEMU and ARM in 32 bit mode. We need to install 32 bit libraries for this (as root). 
sudo apt-get install g++-multilib lib32z1 lib32z1-dev lib32ncurses5 lib32ncurses5-dev -y
  • 21 - Ruby Gems
 sudo apt-get install rubygem
 gem install --remote builder colored cucumber diff-lcs gherkim nanoc2 polyglot rake rgl rspec stream treetop 
 gem install cri --version 1.0.1
  • 22 - Install some fonts
 sudo apt-get install t1-xfree86-nonfree ttf-xfree86-nonfree ttf-xfree86-nonfree-syriac xfonts-75dpi xfonts-100dpi


  • 23 - Make sure that there is no file indexing (beagle)
sudo apt-get purge beagle
  • 24 - Add to /etc/crontab to maintain same time (13:13 use any other random time)
echo -e "13 13   * * *   root    /usr/sbin/ntpdate ntp.ucsc.edu" | sudo tee -a /etc/crontab
  • 25 - Add a freenx server to your desktop
sudo add-apt-repository ppa:freenx-team
sudo apt-get update
sudo apt-get install freenx-server
  • 26 - Add sendmail (no external forwarding)
sudo apt-get purge exim4
sudo apt-get install sendmail
cd /etc/mail/
sudo scp <username>@mada0:/etc/mail/alias* .
sudo scp <username>@mada0:/etc/mail/sendmail.* .
sudo scp <username>@mada0:/etc/mail/generi* .
sudo chmod 777 /var/spool/mqueue
sudo /etc/init.d/sendmail restart


  • 27- Install extra tools (should have been installed through dpkg --set-selection)
 sudo apt-get install -y git-core
 sudo apt-get install -y libglib2.0-dev
 sudo apt-get install -y bison flex
 sudo apt-get install -y libboost-dev
 sudo apt-get install -y ack-grep
 sudo apt-get install -y cmake
 sudo apt-get install -y texlive-latex-base texlive-latex-extra texlive-latex-recommended preview-latex-style latex-xcolor latex-beamer texlive-science texlive-fonts-recommended

 sudo apt-get install -y okular
  • 28 - Copy libtermcap needed by some synopsys aps
 sudo scp <username>@mada0:/usr/lib/libtermcap.so.2.0.8 /usr/lib/.
 sudo ln -s libtermcap.so.2.0.8 libtermcap.so.2


Upgrade from Ubuntu 10.04

  • 1- sudo apt-get dist-upgrade -y
  • 2- Upgrade to Ubuntu 1.10:
 https://help.ubuntu.com/community/MaverickUpgrades


Upgrade from Ubuntu 10.04 LTS

  • 1 - Upgrade the distribution:
 sudo apt-get dist-upgrade -y


  • 2- Follow the instructions here:
 https://help.ubuntu.com/community/PreciseUpgrades


  • 3 - install nvidia driver
sudo apt-get --purge remove nvidia-* 
sudo apt-get update
sudo apt-get install nvidia-current
sudo shutdown -r now

Installing CUDA 3.2

(Not validated yet!!!)

You will need sudo access to install CUDA 3.2. It can only be installed on machines with NVIDIA GPUS.

Move these files to your home directory.


  • Make sure the following kernel modules are blacklisted
sudo vim /etc/modprobe.d/blacklist.conf

If not already present, add the following lines to the file 

blacklist vga16fb
blacklist nouveau
blacklist rivafb
blacklist nvidiafb
blacklist rivatv


  • Get rid of any installed NVIDIA drivers:
sudo apt-get --purge remove nvidia-*


  • Reboot the machine. X11 will not start. Switch to a terminal (CTRL + ALT + F1), and login.


  • Stop X11
sudo service gdm stop


  • Install the downloaded device driver first. 
sudo devdriver_3.2_linux_64_260.24.run
  • Accept the license agreement.
  • Install NVIDIA's 32-bit compatibility OpenGL libraries? Answer: YES
  • Would you like to run the nvidia-xconfig utility to automatically update your X configuration file so that the NVIDIA X driver will be used when you restart X? Answer: YES


  • Install the CUDA toolkit (nvcc etc. ) 
sudo cudatoolkit_3.2.9_linux_64_ubuntu10.04.run

Choose default options. CUDA will be installed in the /usr/local/cuda directory. When the installation is complete, you will be asked to make changes to your INCLUDE and LD_LIBRARY_PATH env. variables.


  • Reboot and login.



Installing grid-engine (server)

  • Firewall
ufw allow in 6444
ufw allow in 6445
  • packages
apt-get purge gridengine-exec
apt-get install gridengine-exec gridengine-client
  • Set SGE master
echo "mada0.cse.ucsc.edu" >/var/lib/gridengine/default/common/act_qmaster
  • Start daemon (do not wait for the next reboot)
/etc/init.d/gridengine-exec restart
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