Speech Research

h1. Earthdevruis

@earth.dev.ru.is@ is a high-performance linux server owned by the RU Speech Research group under Jón Gúðnason <jg@ru.is>.  The machine lives in DevNet (the development network in the RU basement).

The main DevNet contact is Joe Foley <foley@ru.is>.  He also installed th machine machine.

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h2. Status

* Earth has been reinstalled with 12.04.2 64-bit [foley]

* Kerberos/AFS has been configured [foley]

* /home is being restored from the backup disk (mounted on /mnt/backup) [foley]

h2. Installation

h3. Turn on PXE for network boot/install

# Reboot

# While the machine is rebooting, hit F2 (or F1) so that it goes to BIOS setup

## Click on system options, then networking

## Set the network adapter to have PXE enabled

## Save options

# Make sure that the machine is connected to the DevNet switches

# Reboot

h3. Netboot and pick installer

# After PXE initializes, you should get an installer menu

# Choose Ubuntu 12.04.2 64-bit (Alternate)

# You'll have to pick region and keyboard.  You want to pick the Icelandic keyboard

h3. Partitioning the hard drive

It's a good idea to separate the operating system, home directory, and data storage.  In addition, you will need a swap file and an AFS cache partition.

The AFS cache partition should be ext2 or ext3.  To make this easier to manage, you should have all except for a boot partition in LVM (logical volume manager)

# Choose manual partitioning of hard drive

# Create a /boot primary paritition of around 300MB.  Make sure it is "bootable"

# Go into the LVM manager

## Create a new physical volume with the remaining space on the drive

## Create these logical volumes with these names and sizes.  You'll need to remember where they should be mounted also.

*** afscache 2GB (for @/var/cache/openafs@)

*** swap 8GB

*** slash 60GB  (for @/@)

*** home 50GB (for @/home@)

*** export [Remaining space] (for @/export@)

## Save changes and exit the manager

# In the partition manager, set these options for the partitions

** boot: labeled boot, format as ext2, mounted at /boot, set "bootable" flag

** afscache: 0% reserved, labeled afscache, format as ext2 or ext3, mounted at @/var/cache/openafs@

** swap: swapspace

** slash: labeled slash, format as ext4, mounted at @/@

** home: 0% reserved, labeled home, format as ext4, mounted at @/home@

** export: 0% reserved, labeled export, format as ext4, mounted at @/export@

# Save changes

# The installation should continue for a while

h3. Picking server options

You'll have to pick a user.  This is the default devnet user:

* user: devnet

* password: hakkavelin

Once everything is setup, you should delete the user (or change the password).  _Avoid logging in as root unless absolutely necessary!_

This may vary, but these are probably the settings you want:

* Basic Ubuntu Server

* SSH server

* Ubuntu Desktop

h3. Kerberos (single sign on) and AFS

Follow the directions at https://samvinna.ru.is/projects/projects/devnet-documentation/wiki/AFS_Client_Installation

Very brief synopsis without some details:

# Install the packages.  Remember that the Kerberos realm is DEV.RU.IS and theAFS cell is dev.ru.is.  Case matters!

<pre>

sudo apt-get install krb5-auth-dialog krb5-user krb5-clients libpam-ccreds libpam-krb5 build-essential dkms linux-headers-`uname -r` openafs-modules-dkms openafs-{client,krb5} libpam-afs-session

</pre>

# Get a kerberos administrator (currently foley) to generate a keytab for @/etc/krb5.keytab@

# Add the principals for administrators into @/root/.k5login@

<pre>

foley@DEV.RU.IS

jg@DEV.RU.IS

simonhk@DEV.RU.IS

</pre>

# Reboot

# Adjust the @/etc/ssh/sshd_config@ settings to allow GSSAPI options (set them all to yes)

# see if you can ssh in using your DevNet @DEV.RU.IS principal to the root account

To add users, you need to find out the user's AFS ID.  

# My AFS id is 7812 as below:

<pre> pts examine foley

libprot: unable to build security class (getting token)

libprot: Could not get afs tokens, running unauthenticated

Name: foley, id: 7812, owner: system:administrators, creator: foley.afsadm,

  membership: 25, flags: S----, group quota: 20.</pre>

# sudo adduser --uid 7812 foley

## Hit return when it asks for your password and do not retry

## Fill out the user's information

h3. Useful basic packages

# ssh in as root (or use ksu)

# install packages for various things

<pre>aptitude install zile language-pack-is-base texstudio</pre>

h2. Matlab (and licensing issues)

# ssh in as root

<pre>kinit; ssh root@earth.dev.ru.is</pre>

# Create a matlab user/group

<pre>adduser matlab</pre>

# Go add yourself to the matlab group

<pre>usermod -a -G matlab</pre>

# Create a place to store the matlab downloads more permanently for install

<pre>mkdir -p /export/downloads/matlab-2013a</pre>

chown matlab.matlab /export/downloads/matlab-2013a

# Give yourself the ability to login as the matlab user

<pre>vi /home/matlab/.k5login</pre>

** Add your kerberos principal e.g.: foley@DEV.RU.IS

# ssh in as the matlab user.  Make sure X11 is working

<pre> ssh matlab@earth.dev.ru.is</pre>

# Run firefox and go to @http://mathworks.se@

# Login and fill out the appropriate forms to download the latest version of matlab

#  Download it into your Downloads directory

# With the user account copy the downloaded matlab files into their new location

<pre>cp ~/Downloads/* /export/downloads/matlab-2013a</pre>

At the moment, I can only have one  "username" able to run matlab.  I have a workaround that I configured. The "matlab" user is the one who gets to use the license under my name.

If you have kerberized ssh and X11 setup properly, this means you can run matlab by logging in as the matlab user.  This is how I tested it for running programs out of my AFS directory:

<pre>kinit foley@DEV.RU.IS

ssh matlab@earth.dev.ru.is

aklog;  cd /afs/dev.ru.is/user/f/fo/foley

matlab &</pre>

h2. Matlab (and licensing issues) #2

# ssh in as your user

<pre>kinit; ssh <username>@earth.dev.ru.is</pre>

# execute activation script

<pre>/opt/MATLAB/2013a/bin/activate_matlab.sh</pre>

# follow the instructions 

* !matlab1.png!

* !matlab2.png!

* !matlab3.png!

* !matlab4.png!

* !matlab5.png!

# Now ssh to earth and run matlab

<pre>matlab &</pre>

h2. Environment Modules

h3. Installation

# ssh in as root

<pre>kinit; ssh root@earth.dev.ru.is</pre>

# get and prepare sources

<pre>mkdir -p /export/downloads/modules

cd /export/downloads/modules

wget "http://downloads.sourceforge.net/project/modules/Modules/modules-3.2.10/modules-3.2.10.tar.gz"

cd /export/install/

tar -xzvf /export/downloads/modules/modules-3.2.10.tar.gz

cd modules-3.2.10</pre>

# install tcl dependencies

<pre>aptitude install tcl tcl-dev</pre>

# configure and install 

<pre>./configure --prefix=/opt

make

make install

cd /opt/Modules

ln -s 3.2.10 default

</pre>

# an important file that will be sourced later seems to be not copied. It defines the default module version at login

<pre>cp /export/install/modules-3.2.10/etc/global/profile.modules /etc/</pre>

# update the skeleton files

<pre>env HOME=/etc/skel /opt/Modules/default/bin/add.modules

exit</pre>

h3. Activation

# every user should run the following to update their dot files to enable the module command

<pre>/opt/Modules/default/bin/add.modules</pre>

h3. Usage

# available modules can be displayed by

<pre>module avail</pre>

# modules are loaded by 

<pre>module load name_of_the_module[/desired_version]</pre>

# and unloaded by

<pre>module unload name_of_the_module</pre>

# currently loaded modules are displayd by

<pre>module list</pre>

h2. Installing HTK

# ssh in as root

<pre>kinit; ssh root@earth.dev.ru.is</pre>

# get and prepare sources

<pre>mkdir -p /export/install/htk

cd /export/install/htk

tar -xzvf /export/downloads/htk/HTK-3.4.1.tar.gz 

tar -xzvf /export/downloads/htk/HTK-samples-3.4.1.tar.gz 

cd htk</pre>

# install dependencies

<pre>aptitude install libc6-dev-i386 libx11-dev libx11-dev:i386</pre>

# configure and install

<pre>./configure --prefix=/opt/htk/3.4.1 --with-x

make all

mkdir -p /opt/htk/3.4.1/

make install</pre>

# install HTK samples

<pre>cd ..

cp -r samples /opt/htk/3.4.1/</pre>

# adding HTK module file

<pre>

cd /opt/Modules/default/modulefiles/

mkdir htk

cat > htk/3.4.1 <<EOF

#%Module1.0#####################################################################

proc ModulesHelp { } {

        global version binprefix

        puts stderr "\tHTK ${version}"

        puts stderr "\n\tThis adds ${binprefix} to the PATH "

        puts stderr "\tenvironment variable and defines the "

        puts stderr "\tenvironment variables HTK_ROOT and HTK_SAMPLEROOT."

        puts stderr "\n\tVersion $version\n"

}

module-whatis   "Loads HTK 3.4.1 and samples"

set     version         3.4.1

set     prefix       /opt/htk/${version}

set     binprefix    ${prefix}/bin

set     sampleprefix ${prefix}/samples

prepend-path PATH       ${prefix}/bin

setenv          HTK_ROOT $prefix

setenv          HTK_SAMPLEROOT $sampleprefix

EOF

</pre>

# now HTK can be loaded by

<pre>module load htk</pre>

# and unloaded by

<pre>module unload htk</pre>