Difference between revisions of "Desktop Setup - Ubuntu 12.04"

Latest revision as of 20:21, 14 January 2015

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>@mada0:/etc/apt/sources.list /etc/apt/sources.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 (mascd3)

The current apt-get/dpkg releases have problem. So we need to work around the problems that is going to happen in this process. Make sure the machine you are copying from is an Ubuntu 12.04 machine.

ssh <username>@mascd3 dpkg --get-selections > dpkg.list.full
grep -v i386 dpkg.list.full >dpkg.list.x64
grep i386 dpkg.list.full >dpkg.list.i386

dpkg --set-selections < dpkg.list.x64
apt-get update -y

dpkg --set-selections < dpkg.list.i386
apt-get update -y

then remove the problematic packages from the package selecting list, and run the apt-get dselect-upgrade again :

echo "libdb5.1-java:i386    deinstall" | dpkg --set-selections
echo "libsensors4:i386    deinstall" | dpkg --set-selections
echo "libapt-pkg4.12:i386    deinstall" | dpkg --set-selections

"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.

apt-get dselect-upgrade -y

It most likely will fail, complaining unable to install libapt-pkg4.12:i386, etc. You might need to repeat this until the apt-get dselect-upgrade finished gracefully. Pay attention to the error message. If it asks you to do 'apt-get install -f', then do so!

Finalized the installed packages so far:

dpkg --configure -a

Ruby Related Stuff

We use RVM to support multiple ruby versions

Install the base versions shared by all the users

 sudo apt-get install curl

Log as user (foo) and install the latest rvm

Do not use sudo when installing RVM

RVM only needs to be installed once per use

 curl -L https://get.rvm.io | sudo bash -s stable

Add yourself (foo) to to the rvm group (vi /etc/group)

Install the following ruby options

 rvm install ruby-1.8.7
 rvm install rbx
 rvm install rbx-2.0.0-rc1 # This may be better in the future, but rbx 2 has several advantages
 rvm install ruby-1.9.3
 rvm install jruby

Install the packages needed. These should work across ruby versions:

rvm use 1.9.3 
gem install rspec parslet treetop trollop rgl json gherkin cucumber

rvm use 1.8.7
rvm rubygems 1.3.5
gem install rspec-expectations
gem install rspec parslet treetop trollop rgl json gherkin cucumber
gem install reek flay flog

rvm use rbx
gem install rspec parslet treetop trollop rgl json gherkin cucumber

... # any ruby version that you may want to use

This are version specific

rvm use 1.8.7
gem install

rvm use 1.9.3
gem install

rvm use rbx-2.0.0-rc1
gem install

MADA Related Stuff

6 - Install autofs

Create mada directory

mkdir /mada

Get autofs files from another machine

apt-get install -y autofs 
scp <username>@mada7:/etc/auto.* /etc/
ln -s /mada/users /soe
initctl reload autofs

/etc/auto.mada should use nfs4. Something like this:

users               -rw,intr,soft,noquota,noatime,fstype=nfs4 mada0.cse.ucsc.edu:/mada/users 
software            -ro,intr,soft,noquota,noatime,fstype=nfs4 mada0.cse.ucsc.edu:/mada/software

edit /etc/default/nfs-common. If you have a NEED_IDMAPD variable, it must be set to true

NEED_IDMAPD=yes

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
ufw logging off

9 - Get tempcap from another ubuntu machine (mascd3, mascd9, ...), and some lib preparation:

scp <username>@mada0:/usr/lib/libtermcap.so.2.0.8 /usr/lib/
ln -s /usr/lib/libtermcap.so.2.0.8 /usr/lib/libtermcap.so.2

ln -sf /usr/lib/x86_64-linux-gnu/libtiff.so.4.3.4 /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>@mascd12:/etc/krb5.conf /etc/

Copy the ldap certificate

scp <username>@mascd12:/etc/ssl/certs/* /etc/ssl/certs/
scp -r <username>@mada4:/etc/openldap/cacerts /etc/openldap/.

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

scp <username>@mascd12:/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>@mascd12:/etc/pam_ldap.conf /etc/ldap.conf
scp <username>@mada7:/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>@mada7:/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
+ : (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. If it doesn't work, run

getent passwd renau
getent passwd | grep renau

If the result is empty for the first line, but not empty for the second one, restart nscd:

service nscd restart

12 - Since the LDAP has timeouts, setup the local backup

apt-get install nss-updatedb
nss_updatedb ldap
cd /etc/cron.hourly/
scp <username>@mada7:/etc/cron.hourly/nss_updatedb_ldap .
scp <username>@mada7:/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 [NOTFOUND=return] ldap 
 group:          files db [NOTFOUND=return] 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

16 - Edit the /etc/idmapd.conf and make sure that you use the correct idmapd for nfs4. It should

set:

Domain = localdomain

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 libxext-dev:i386 -y

21 - Install some fonts

 sudo apt-get install libtiff4 t1-xfree86-nonfree ttf-xfree86-nonfree ttf-xfree86-nonfree-syriac xfonts-75dpi xfonts-100dpi

22 - Make sure that there is no file indexing (beagle)

sudo apt-get purge beagle

23 - Add/create to /etc/cron.daily/ntpdate for keep time adjusted (chmod 755 ntpdate)

#!/bin/sh
ntpdate-debian

24 - Add a freenx server to your desktop

sudo apt-get install python-software-properties
sudo add-apt-repository ppa:freenx-team
sudo apt-get update
sudo apt-get install freenx-server

25 - 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

26- Install extra tools (should have been installed through dpkg --set-selection)

 sudo apt-get install -y git-core libjpeg62 
 sudo apt-get install -y libglib2.0-dev zlib1g-dev build-essential
 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 gridengine-client libtool mutrace
 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

27 - Copy libtermcap needed by some synopsys aps

 sudo scp <username>@mada0:/usr/lib/libtermcap.so.2.0.8 /usr/lib/.
 sudo ln -s /usr/lib/libtermcap.so.2.0.8 /usr/lib/libtermcap.so.2

28 - Manually install glib for i386, and get some more 32 bit libs.

 scp mascd9:/lib/i386-linux-gnu/libg.tar /tmp/
 cd /lib/i386-linux-gnu
 sudo tar zxvf /tmp/libg.tar

Upgrade from Ubuntu 10.04

1- sudo apt-get dist-upgrade -y
2- Upgrade to Ubuntu 1.10:

 https://help.ubuntu.com/community/MaverickUpgrades

Installing PBS Torque (server)

mada0 will be the headnode (pbsserver). Install the following packages on mada0:

apt-get install torque-server torque-scheduler torque-client

on other mada machines

apt-get install torque-client torque-mom

Torque will use TCP ports 15000-15004. Either open the ports or allow them for mada machines based on their IP address.

ufw allow proto tcp from EACH_MADA_IP to any port 15000:15004

Make sure server_name is properly set

vi /var/spool/torque/server_name

mada0

on mada0, add the other mada machines as compute node:

vi /var/spool/torque/server_priv/nodes

and add the following

mada8 np=16
mada1 np=48
mada2 np=4
mada3 np=4
mada4 np=4
mada5 np=4
mada6 np=4
mada7 np=4
mada0 np=10

on the all mada machines, set the pbsserver

vi /var/spool/torque/mom_priv/config

add the following lines:

$pbsserver mada0
$logevent  255

Now create a queue and run the server on mada0

qmgr -c "set server scheduling=true"
qmgr -c "create queue batch queue_type=execution"
qmgr -c "set queue batch started=true"
qmgr -c "set queue batch enabled=true"
qmgr -c "set queue batch resources_default.walltime=240:00:00"
qmgr -c "set server default_queue=batch"
qmgr -c "set server operators = root@mada0"
qmgr -c "set server keep_completed = 0"
qmgr -c "set queue batch resources_default.neednodes = 1:ppn=1"

restart the pbs_server, pbs_client and pbs_sched on mada0, and pbs_mom and pbs_client on others

pbsnode -a should show the status of all nodes. If nodes are down, check the firewall log to make sure it does not block the requests.

check the queue

echo "sleep 10" | qsub -l nodes=1:ppn=1
qstat

Configuring mdadm RAID (servers)

For mada0, we use mdadm raid 5.

To assemble the hard drives in a raid array:

mdadm --assemble /dev/md0 /dev/disk/by-id/ID-OF-DISK /dev/disk/by-id/ID-OF-DISK2 ...

You can preserve the same alphabetic order in which the list of disk IDs appear.

Note that this assembles the raid /dev/md0 from the devices already prepared for raid. You might need to stop the raid if it is already running to be able to reassemble it:

mdadm --stop /dev/md0

If the disk have not been prepared for raid before, then you need to create the raid partition tables first. We use the whole disk for raids.

mdadm --create --verbose /dev/md0 --level=5 --raid-devices=6 /dev/disk/by-id/ID-OF-DISK1 /dev/disk/by-id/ID-OF-DISK2 ...

You can preserve the same alphabetic order in which the list of disk IDs appear.

To see the preparation that will happen in the background:

watch cat /proc/mdstat

To see the details of the array:

mdadm --detail /dev/md0

Then you need to format the disks:

mkfs.ext4 /dev/md0

update the /etc/fstab.

Lets say we want to mount the raid at /mirror

mkdir /mirror
vi /etc/fstab

and make sure you specify the mount point for the raind.

/dev/md0        /mirror            ext4        rw,intr,soft,noquota,relatime     0        0

then mount the raid:

mount -a

Configuring zfs RAID (servers)

Install the zfs kernel module (not fuse)

sudo add-apt-repository ppa:zfs-native/stable

Format the SDDs to have the following partitions:

1 /boot : 4GB 2 cache : 80GB 3 log: 4GB 4 root : 32GB 5 swap : 4GB

create the radz1 zpool

 zpool create tank raidz1 sdc sdd sde sdf sdg sdh
 zpool status tank

 zpool iostat -v

add read and write caches. To make sure you add the right partition, use "lsblk" to ensure the right partition.

 zppol add tank cache /dev/disk/by-id/ata-FOO_disk1_part2  /dev/disk/by-id/ata-FOO_disk2_part2 log mirror /dev/disk/by-id/ata-FOO_disk1_part3 /dev/disk/by-id/ata-FOO_disk2_part3

 zpool iostat -v

Now prepare the folders

zfs create tank/users zfs create tank/software zfs create tank/servers

Setting up CUPS for Printing

1. Make sure cups and cups-bsd are installed:

 sudo apt-get install cups

2. Go to /etc/cups directory:

 cd /etc/cups

3. Add file called "client.conf" with this in it (you may need sudo access to create new file):

 ServerName cups-01.cse.ucsc.edu
 ServerName spooler4.cse.ucsc.edu
 spooler4.cse.ucsc.edu

4. Save the client.conf file and restart the cups server:

 /etc/init.d/cups restart

You should now be able to print. If you are not seeing a list of printer or are getting an error saying something like "client error: forbidden", then your machine does not have access to the VLAN printer network. Contact the IT tech staff and this issue should be resolved (Eric Shell helped with this).

Setting up Cadence Virtuoso on your Ubuntu 12.04 Desktop

1. cd /tmp

2. sudo apt-get update

3. sudo apt-get install nscd csh ksh gawk libelf1 libelf-dev ia32-libs libelf1:i386

This installs the library dependencies.

4. sudo apt-get update

5. sudo ln -s /usr/bin/awk /bin/awk

This ensures the awk utility is also available at the locations typically found on Solaris, CentOS, SuSE flavors.

6. For Hspice simulation, you may need to install libtiff4

 apt-get install libtiff4

If it won't work due to version difference, create a soft link using following command

 sudo ln -s /usr/lib/x86_64-linux-gnu/libtiff.so.4 /usr/lib/libtiff.so.3

Difference between revisions of "Desktop Setup - Ubuntu 12.04"

Latest revision as of 20:21, 14 January 2015

Contents

Plain Ubuntu Installation

Ruby Related Stuff

MADA Related Stuff

Upgrade from Ubuntu 10.04

Installing PBS Torque (server)

Configuring mdadm RAID (servers)

Configuring zfs RAID (servers)

Setting up CUPS for Printing

Setting up Cadence Virtuoso on your Ubuntu 12.04 Desktop

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@@ Line 24: / Line 24: @@
 Add your local and SOE logins to the sudoers list:
-  vim /etc/sudoers
+  vi /etc/sudoers
 * 2 - Install NVIDIA Drivers
 Blacklist some kernel modules
-  vim /etc/modprobe.d/blacklist.conf
+  vi /etc/modprobe.d/blacklist.conf
 Add the following lines to the file
@@ Line 37: / Line 37: @@
   blacklist rivatv
-Get rid of any installed NVIDIA drivers:
+Get rid of any installed NVIDIA drivers (you are already root, if not use with sudo):
-  sudo apt-get --purge remove nvidia-*
+  apt-get --purge remove nvidia-*
-  sudo apt-get update
+  apt-get update
-  sudo apt-get install nvidia-current
+  apt-get install nvidia-current
@@ Line 48: / Line 48: @@
 * 3 - Setup the new repo
-  scp <username>@mascd12:/etc/apt/sources.list /etc/apt/source.list
+  scp <username>@mada0:/etc/apt/sources.list /etc/apt/sources.list
   apt-get update -y
   apt-get dist-upgrade -y
@@ Line 55: / Line 55: @@
 * 4 - Adjust sysctl options
 mmap problem for qemu
-  vim /etc/sysctl.d/10-zeropage.conf
+  vi /etc/sysctl.d/10-zeropage.conf
 Edit the following value:
   vm.mmap_min_addr = 4096
@@ Line 62: / Line 62: @@
   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)
+* 5 - Replicate the installation on Master machine (mascd3)
-  ssh <username>@mascd12 dpkg --get-selections | grep -v deinstall > mypackages.txt
+The current apt-get/dpkg releases have problem. So we need to work around the problems that is going to happen in this process.
-  dpkg –clear-selections (?)
+Make sure the machine you are copying from is an Ubuntu 12.04 machine.
-  dpkg --set-selections < mypackages.txt
+  ssh <username>@mascd3 dpkg --get-selections > dpkg.list.full
+ grep -v i386 dpkg.list.full >dpkg.list.x64
+ grep i386 dpkg.list.full >dpkg.list.i386
+  dpkg --set-selections < dpkg.list.x64
+ apt-get update -y
+  dpkg --set-selections < dpkg.list.i386
+ apt-get update -y
+then remove the problematic packages from the package selecting list, and run the apt-get dselect-upgrade again :
+ echo "libdb5.1-java:i386    deinstall" | dpkg --set-selections
+ echo "libsensors4:i386    deinstall" | dpkg --set-selections
+ echo "libapt-pkg4.12:i386    deinstall" | dpkg --set-selections
 "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.
-Select all default options EXCEPT! for ion3: acknowledge the lack of support (non-default option)
   apt-get dselect-upgrade -y
+It most likely will fail, complaining unable to install libapt-pkg4.12:i386, etc. You might need to repeat this until the apt-get dselect-upgrade finished gracefully. Pay attention to the error message. If it asks you to do 'apt-get install -f', then do so!
+Finalized the installed packages so far:
+ dpkg --configure -a
+==Ruby Related Stuff==
+We use RVM to support multiple ruby versions
+* Install the base versions shared by all the users
+  sudo apt-get install curl
+Log as user (foo) and install the latest rvm
+* Do '''not use sudo''' when installing RVM
+* RVM only needs to be installed once per use
+  curl -L https://get.rvm.io | sudo bash -s stable
+Add yourself (foo) to to the rvm group (vi /etc/group)
+Install the following ruby options
+  rvm install ruby-1.8.7
+  rvm install rbx
+  rvm install rbx-2.0.0-rc1 # This may be better in the future, but rbx 2 has several advantages
+  rvm install ruby-1.9.3
+  rvm install jruby
+* Install the packages needed. These should work across ruby versions:
+ rvm use 1.9.3
+ gem install rspec parslet treetop trollop rgl json gherkin cucumber
+ rvm use 1.8.7
+ rvm rubygems 1.3.5
+ gem install rspec-expectations
+ gem install rspec parslet treetop trollop rgl json gherkin cucumber
+ gem install reek flay flog
+ rvm use rbx
+ gem install rspec parslet treetop trollop rgl json gherkin cucumber
+ ... # any ruby version that you may want to use
+* This are version specific
+ rvm use 1.8.7
+ gem install
+ rvm use 1.9.3
+ gem install
+ rvm use rbx-2.0.0-rc1
+ gem install
 ==MADA Related Stuff==
@@ Line 79: / Line 153: @@
 Get autofs files from another machine
-  scp <username>@mascd12:/etc/auto.* /etc/
+ apt-get install -y autofs
+  scp <username>@mada7:/etc/auto.* /etc/
   ln -s /mada/users /soe
   initctl reload autofs
+/etc/auto.mada should use nfs4. Something like this:
+ users               -rw,intr,soft,noquota,noatime,fstype=nfs4 mada0.cse.ucsc.edu:/mada/users
+ software            -ro,intr,soft,noquota,noatime,fstype=nfs4 mada0.cse.ucsc.edu:/mada/software
+edit /etc/default/nfs-common. If you have a NEED_IDMAPD variable, it must be set to true
+NEED_IDMAPD=yes
 * 7 - awk for cadence
@@ Line 92: / Line 175: @@
   ufw reject auth
   ufw limit ssh/tcp
+ ufw logging off
-* 9 - Get tempcap from another ubuntu machine (mascd1, mascd12, ...), and some lib preparation:
+* 9 - Get tempcap from another ubuntu machine (mascd3, mascd9, ...), 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
+  scp <username>@mada0:/usr/lib/libtermcap.so.2.0.8 /usr/lib/
+  ln -s /usr/lib/libtermcap.so.2.0.8 /usr/lib/libtermcap.so.2
-  ln -s /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3
+  ln -sf /usr/lib/x86_64-linux-gnu/libtiff.so.4.3.4 /usr/lib/libtiff.so.3
 * 10 - LDAP
@@ Line 106: / Line 191: @@
 Create /ect/krb5.conf
-  scp <username>@mascd1:/etc/krb5.conf /etc/
+  scp <username>@mascd12:/etc/krb5.conf /etc/
 Copy the ldap certificate
-  scp <username>@mascd1:/etc/ssl/certs/* /etc/ssl/certs/
+  scp <username>@mascd12:/etc/ssl/certs/* /etc/ssl/certs/
+ scp -r <username>@mada4:/etc/openldap/cacerts /etc/openldap/.
 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
+  scp <username>@mascd12:/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>@mascd12:/etc/pam_ldap.conf /etc/ldap.conf
-  scp <username>@mascd1:/etc/ldap/ldap.conf /etc/ldap/ldap.conf
+  scp <username>@mada7:/etc/ldap/ldap.conf /etc/ldap/ldap.conf
 Now you should be able to execute:
@@ Line 123: / Line 209: @@
 * 11 - Lock SOE people out of your machine :)
-  scp <username>@mascd12:/etc/security/access.conf /etc/security/access.conf
+  scp <username>@mada7:/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:
@@ Line 132: / Line 218: @@
   + : root : ALL
   + : nx   : ALL
- + : ian_local : ALL
   + : (masc) : ALL
   + : (vlsi) : ALL
@@ Line 138: / Line 223: @@
 Now, you should see people with "getent passwd" but, calling "su - cormac" should say "permission denied", but, calling "su - renau" should work.
+If it doesn't work, run
+ getent passwd renau
+ getent passwd | grep renau
+If the result is empty for the first line, but not empty for the second one, restart nscd:
+ service nscd restart
 * 12 - Since the LDAP has timeouts, setup the local backup
@@ Line 144: / Line 237: @@
   nss_updatedb ldap
   cd /etc/cron.hourly/
-  scp mada1:/etc/cron.hourly/nss_updatedb-ldap.sh .
+  scp <username>@mada7:/etc/cron.hourly/nss_updatedb_ldap .
-  scp mada1:/etc/nsswitch.conf /etc
+  scp <username>@mada7:/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
+  sudo vi /etc/nsswitch.conf
-passwd:         files db ldap
+  passwd:         files db [NOTFOUND=return] ldap
-group:          files db ldap
+  group:          files db [NOTFOUND=return] ldap
 * 14 - Allow other accounts to be shown at the login screen, and disable Guest user.
@@ Line 162: / Line 255: @@
   allow-guest=false
+* 16 - Edit the /etc/idmapd.conf and make sure that you use the correct idmapd for nfs4. It should
+set:
+ Domain = localdomain
 * 15 - Restart your computer:
@@ Line 170: / Line 267: @@
 * 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*
+  rm -rf .config .kde* .gconf* .gnome* .awesome*
 * 18 - Some Minor Patches for things that don't work properly
@@ Line 186: / Line 284: @@
 * 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
+  sudo apt-get install g++-multilib libxext-dev:i386 -y
-* 21 - Ruby Gems
-  sudo apt-get install rubygem
+* 21 - Install some fonts
-  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 libtiff4 t1-xfree86-nonfree ttf-xfree86-nonfree ttf-xfree86-nonfree-syriac xfonts-75dpi xfonts-100dpi
-  sudo apt-get install t1-xfree86-nonfree ttf-xfree86-nonfree ttf-xfree86-nonfree-syriac xfonts-75dpi xfonts-100dpi
+* 22 - Make sure that there is no file indexing (beagle)
-* 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)
+* 23 - Add/create to /etc/cron.daily/ntpdate for keep time adjusted (chmod 755 ntpdate)
-  echo -e "13 13   * * *   root    /usr/sbin/ntpdate ntp.ucsc.edu" | sudo tee -a /etc/crontab
+  #!/bin/sh
+ ntpdate-debian
-* 25 - Add a freenx server to your desktop
+* 24 - Add a freenx server to your desktop
+ sudo apt-get install python-software-properties
   sudo add-apt-repository ppa:freenx-team
   sudo apt-get update
   sudo apt-get install freenx-server
-* 26 - Add sendmail (no external forwarding)
+* 25 - Add sendmail (no external forwarding)
   sudo apt-get purge exim4
@@ Line 225: / Line 320: @@
-* 27- Install extra tools (should have been installed through dpkg --set-selection)
+* 26- Install extra tools (should have been installed through dpkg --set-selection)
-   sudo apt-get install -y git-core
+   sudo apt-get install -y git-core libjpeg62
-   sudo apt-get install -y libglib2.0-dev
+   sudo apt-get install -y libglib2.0-dev zlib1g-dev build-essential
    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 gridengine-client libtool mutrace
    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
+* 27 - 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
+   sudo ln -s /usr/lib/libtermcap.so.2.0.8 /usr/lib/libtermcap.so.2
+* 28 - Manually install glib for i386, and get some more 32 bit libs.
-==Upgrade from Ubuntu 11.04==
+  scp mascd9:/lib/i386-linux-gnu/libg.tar /tmp/
+  cd /lib/i386-linux-gnu
+  sudo tar zxvf /tmp/libg.tar
-* 1 - Upgrade the distribution:
+==Upgrade from Ubuntu 10.04==
+* 1- sudo apt-get dist-upgrade -y
+* 2- Upgrade to Ubuntu 1.10:
-   sudo apt-get dist-upgrade -y
+   https://help.ubuntu.com/community/MaverickUpgrades
-* 2 - install nvidia driver
+==Installing PBS Torque (server)==
- sudo apt-get --purge remove nvidia-*
- sudo apt-get update
- sudo apt-get install nvidia-current
- sudo shutdown -r now
-==Installing CUDA 3.2 ==
+* mada0 will be the headnode (pbsserver). Install the following packages on mada0:
-(Not validated yet!!!)
+ apt-get install torque-server torque-scheduler torque-client
-You will need sudo access to install CUDA 3.2. It can only be installed on machines with NVIDIA GPUS.
+* on other mada machines
-* Download the following
+ apt-get install torque-client torque-mom
-** Developer Drivers for Linux (260.24) http://developer.download.nvidia.com/compute/cuda/3_2/drivers/devdriver_3.2_linux_64_260.24.run
-** CUDA Toolkit for Ubuntu Linux 10.04 http://developer.download.nvidia.com/compute/cuda/3_2/toolkit/cudatoolkit_3.2.9_linux_64_ubuntu10.04.run
-Move these files to your home directory.
-* Make sure the following kernel modules are blacklisted
+* Torque will use TCP ports 15000-15004. Either open the ports or allow them for mada machines based on their IP address.
- 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
+ ufw allow proto tcp from EACH_MADA_IP to any port 15000:15004
+* Make sure server_name is properly set
+ vi /var/spool/torque/server_name
+ mada0
+* on mada0, add the other mada machines as compute node:
+ vi /var/spool/torque/server_priv/nodes
+* and add the following
+ mada8 np=16
+ mada1 np=48
+ mada2 np=4
+ mada3 np=4
+ mada4 np=4
+ mada5 np=4
+ mada6 np=4
+ mada7 np=4
+ mada0 np=10
+on the all mada machines, set the pbsserver
+ vi /var/spool/torque/mom_priv/config
+* add the following lines:
+ $pbsserver mada0
+ $logevent  255
+* Now create a queue and run the server on mada0
+ qmgr -c "set server scheduling=true"
+ qmgr -c "create queue batch queue_type=execution"
+ qmgr -c "set queue batch started=true"
+ qmgr -c "set queue batch enabled=true"
+ qmgr -c "set queue batch resources_default.walltime=240:00:00"
+ qmgr -c "set server default_queue=batch"
+ qmgr -c "set server operators = root@mada0"
+ qmgr -c "set server keep_completed = 0"
+ qmgr -c "set queue batch resources_default.neednodes = 1:ppn=1"
+* restart the pbs_server, pbs_client and pbs_sched on mada0, and pbs_mom and pbs_client on others
+* pbsnode -a should show the status of all nodes. If nodes are down, check the firewall log to make sure it does not block the requests.
+* check the queue
+ echo "sleep 10" | qsub -l nodes=1:ppn=1
+ qstat
+==Configuring mdadm RAID (servers)==
+* For mada0, we use mdadm raid 5.
+* To assemble the hard drives in a raid array:
+ mdadm --assemble /dev/md0 /dev/disk/by-id/ID-OF-DISK /dev/disk/by-id/ID-OF-DISK2 ...
+You can preserve the same alphabetic order in which the list of disk IDs appear.
+Note that this assembles the raid /dev/md0 from the devices already prepared for raid.
+You might need to stop the raid if it is already running to be able to reassemble it:
+ mdadm --stop /dev/md0
+* If the disk have not been prepared for raid before, then you need to create the raid partition tables first. We use the whole disk for raids.
+ mdadm --create --verbose /dev/md0 --level=5 --raid-devices=6 /dev/disk/by-id/ID-OF-DISK1 /dev/disk/by-id/ID-OF-DISK2 ...
+You can preserve the same alphabetic order in which the list of disk IDs appear.
+To see the preparation that will happen in the background:
+ watch cat /proc/mdstat
+To see the details of the array:
+ mdadm --detail /dev/md0
+* Then you need to format the disks:
+ mkfs.ext4 /dev/md0
+* update the /etc/fstab.
+Lets say we want to mount the raid at /mirror
+ mkdir /mirror
+ vi /etc/fstab
+and make sure you specify the mount point for the raind.
+ /dev/md0        /mirror            ext4        rw,intr,soft,noquota,relatime     0        0
+then mount the raid:
+ mount -a
+==Configuring zfs RAID (servers)==
+* Install the zfs kernel module (not fuse)
+ sudo add-apt-repository ppa:zfs-native/stable
+* Format the SDDs to have the following partitions:
+/boot : 4GB
+cache : 80GB
+log: 4GB
+root   : 32GB
+swap : 4GB
+* create the radz1 zpool
+  zpool create tank raidz1 sdc sdd sde sdf sdg sdh
+  zpool status tank
+  zpool iostat -v
+* add read and write caches. To make sure you add the right partition, use "lsblk" to ensure the right partition.
+  zppol add tank cache /dev/disk/by-id/ata-FOO_disk1_part2  /dev/disk/by-id/ata-FOO_disk2_part2 log mirror /dev/disk/by-id/ata-FOO_disk1_part3 /dev/disk/by-id/ata-FOO_disk2_part3
-*Get rid of any installed NVIDIA drivers:
+  zpool iostat -v
- sudo apt-get --purge remove nvidia-*
+* Now prepare the folders
-*Reboot the machine. X11 will not start. Switch to a terminal (CTRL + ALT + F1), and login.
+zfs create tank/users
+zfs create tank/software
+zfs create tank/servers
-* Stop X11
+==Setting up CUPS for Printing==
- sudo service gdm stop
+* 1. Make sure cups and cups-bsd are installed:
-* Install the downloaded device driver first.
+  sudo apt-get install cups
- 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
+* 2. Go to /etc/cups directory:
-* Install the CUDA toolkit (nvcc etc. )
+  cd /etc/cups
- 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.
+* 3. Add file called "client.conf" with this in it (you may need sudo access to create new file):
-* Reboot and login.
+  ServerName cups-01.cse.ucsc.edu
+  ServerName spooler4.cse.ucsc.edu
+  spooler4.cse.ucsc.edu
+* 4. Save the client.conf file and restart the cups server:
-* OPTIONAL: Download GPU Computing SDK code samples http://developer.download.nvidia.com/compute/cuda/3_2/sdk/gpucomputingsdk_3.2_linux.run. This will be installed in your home directory by default.
+  /etc/init.d/cups restart
+* You should now be able to print.  If you are not seeing a list of printer or are getting an error saying something like "client error: forbidden", then your machine does not have access to the VLAN printer network.  Contact the IT tech staff and this issue should be resolved (Eric Shell helped with this).
-==Installing grid-engine (server)==
+==Setting up Cadence Virtuoso on your Ubuntu 12.04 Desktop==
-* Firewall
+. '''cd /tmp'''
- ufw allow in 6444
+. '''sudo apt-get update'''
- ufw allow in 6445
-* packages
+. '''sudo apt-get install nscd csh ksh gawk libelf1 libelf-dev ia32-libs libelf1:i386'''
- apt-get purge gridengine-exec
+This installs the library dependencies.
- apt-get install gridengine-exec gridengine-client
-* Set SGE master
+. '''sudo apt-get update'''
- echo "mada0.cse.ucsc.edu" >/var/lib/gridengine/default/common/act_qmaster
+. '''sudo ln -s /usr/bin/awk /bin/awk'''
-* Start daemon (do not wait for the next reboot)
+This ensures the awk utility is also available at the locations typically found on Solaris, CentOS, SuSE flavors.
- /etc/init.d/gridengine-exec restart
+. For Hspice simulation, you may need to install libtiff4
+  '''apt-get install libtiff4'''
+If it won't work due to version difference, create a soft link using following command
+  '''sudo ln -s /usr/lib/x86_64-linux-gnu/libtiff.so.4 /usr/lib/libtiff.so.3'''