Arch linux on an eeepc 900

This is a summary of my attempt to install the Arch linux distro on my eeepc 900. I had some problems with the login manager and the desktop, but appart from that the base install was not that difficult if you follow the beginners guide. Arch is a hard core distro in that you have to set everything up yourself, but by doing that you get a better understanding of what is going on under the hood.

My little old eeepc 900 running on Arch

Download the Arch iso, I used an external CD-drive to install but alternatively a USB thumb drive could be used. To make it easier, initially I used gparted (http://gparted.sourceforge.net/) GUI to set the / to the 4gb SSD and /home to the 15gb SSD, I formatted both as ext4, which is not recommended because it will destroy your ssd, but apparently ext4 is SSD aware, I just need to work out how to turn journaling off.

Boot to the CD, chose “Boot Arch Linux”. This first section is almost word for word from the beginers guide, and that has a lot more detail, I have skipped the parts that are not relevant to the eeepc.

There was no wireless at startup, on the eeepc it is identified as “wlan0” and the interphase can be checked with, then bring it up and scan

#iwconfig
#ip link set wlan0 up
#iwlist wlan0 scan

Look for the ESSID:”yourwirelessnetworkname”

Backup the original file then modify and set it up for wpa encription.
# mv /etc/wpa_supplicant/wpa_supplicant.conf /etc/wpa_supplicant/wpa_supplicant.conf.original
# wpa_passphrase linksys "my_secret_passkey" > /etc/wpa_supplicant/wpa_supplicant.conf
#wpa_supplicant -B -Dwext -i wlan0 -c /etc/wpa_supplicant/wpa_supplicant.conf

Wait a few seconds for it to associate, now check and requiest an ip address, then ping google to check
#iwconfig wlan0
# dhcpcd wlan0
#ping -c 3 http://www.google.com

Now the hard drive
# fdisk -l

If you formatted your drives like I did (using gpartted) the output should indicate that you have sda1 which is your base and home is sdb1, since we used gparted I can skip all the ugly manual partitioning, so we just need to format them as ext4 (bad idea, see below).

# mkfs.ext4 /dev/sda1
# mkfs.ext4 /dev/sdb1

Remember that this is a bad idea, using ext2 would be safer, but I figure I can work out how to turn of journaling. Save your SSD, don’t make a swap partition!

Mount the base and the home and install the base and devel packages, then setup fstab
# mount /dev/sda1 /mnt
# mkdir /mnt/home && mount /dev/sdb1 /mnt/home
# pacstrap /mnt base base-devel
# genfstab -p /mnt >> /mnt/etc/fstab
#cat nano /mnt/etc/fstab

Modify the mount flags for drive to avoid unessary writes, more infomation at https://wiki.archlinux.org/index.php/Solid_State_Drives

Now install the graphics environment

pacman -S xorg-server xorg-xinit xorg-utils xorg-server-utils xterm

Now let’s enter the new system, start configuration by creating a hostname, or a name for your computer
#arch-chroot /mnt
#nano /etc/hostname

And add “daves-eeepc” or something like that, no quotes! Save [ctl][o] an exit [ctl][x], now modify the /etc/hosts and add the new name
#nano /etc/hosts
add the name as below
127.0.0.1   localhost.localdomain   localhost daves-eeepc
::1         localhost.localdomain   localhost daves-eeepc

Now configure the time, first find out the region and local time and settings
# ls /usr/share/zoneinfo/
America and then for the subdomain
# ls /usr/share/zoneinfo/America
I’m New_York
Now create a sim link to local time directory
# ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
Now set up local settings and uncomment the en_US.UTF-8 UTF-8
setting.
# nano /etc/locale.gen
Then generate the file
# locale-gen

Setup system wide preferences by adding “LANG=en_US.UTF-8” to (dont inc quotes) the file shown using nano.
#nano /etc/locale.conf
Then export the settings and set the clock to utc
# export LANG=en_US.UTF-8
# hwclock --systohc --utc

Now set the network, check the /etc/rc.conf file make sure “network” is between the brackets, also add “net-auto-wireless” for our wireless.
DAEMONS=(syslog-ng network net-auto-wireless netfs crond)

Since we are wireless, we need to do a little work!
#exit
# pacstrap /mnt wireless_tools netcfg
# pacstrap /mnt wpa_supplicant wpa_actiond
# pacstrap /mnt zd1211-firmware
# arch-chroot /mnt

Set the interface in /etc/conf.d/netcfg to
WIRELESS_INTERFACE="wlan0"

Finally create the ramdisk environment, and install the grub boot loader on the root drive, and get rid of any error messages
# mkinitcpio -p linux
# pacman -S grub-bios
# grub-install --target=i386-pc --recheck /dev/sda
# mkdir -p /boot/grub/locale
# cp /usr/share/locale/en\@quot/LC_MESSAGES/grub.mo /boot/grub/locale/en.mo

Now set up grub and create a root password
# pacman -S os-prober
# grub-mkconfig -o /boot/grub/grub.cfg
# passwd

Nearly done with the base install, finally lets reboot

# exit
# umount /mnt/{boot,home,}
# reboot

Once we are back refresh pacman and lets add you as a user and install sudo

# pacman -Syy
# pacman -Syu
# adduser

Add the following, blank is just hit return to accept defaults, add contact details when asked if you like. If you make a mistake just delete and try again (# userdel -r [username])

Login name for new user []: dave
User ID ('UID') [ defaults to next available ]:
Initial group [ users ]:
Additional groups (comma separated) []: audio,games,lp,optical,power,scanner,storage,video
Home directory [ /home/dave ]:
Shell [ /bin/bash ]:
Expiry date (YYYY-MM-DD) []:

Now install and setup sudo, we need to edit the sudoer file with a special editor that has vi underneath, only use this editor as it has failsafes.

#pacman -S sudo
#visudo

Scroll through the file, find the “root  ALL=(ALL) ALL” and on the next line add yourself (without quotes) “dave   ALL=(ALL) ALL”
Get tab complete working

#pacman -S bash-completion

Now install the X-server for graphics

#pacman -S xorg-server xorg-xinit xorg-utils xorg-server-utils xterm
#pacman -S xf86-video-intel xf86-input-synaptics

This is where I ran into trouble following the online guides, we are going to install the XDM login manager and the LXDE desktop both are light and work well on the eeepc.

Firstly, login as a user then

#sudo pacman -S xorg-xdm
#cp /etc/skel/.xsession /etc/skel/.xinitrc ~

These are the launch scripts, xsession calls xinitrc, change the permissions on them
#chmod 744 ~/.xinitrc ~/.xsession

Now we need to increase the run level, in /ect/inittab edit the top and bottom lines by
removing the quotes:
…..
#id:3:initdefault:
…..
id:5:initdefault
…. Unhash (may already be) the line that refers to xdm which we will be using as our desktom manager
x:5:respans:/usr/sbin/xdm -nodeamon

Now install dbus

#sudo pacman -S dbus
#sudo nano /etc/rc.conf

add dbus to the array
DAEMONS=(syslog-ng dbus network net-auto-wireless netfs crond)

Now install lxde and configure open box

#pacman -S lxde
#mkdir -p ~/.config/openbox
#cp /etc/xdg/openbox/menu.xml ~/.config/openbox
#cp /etc/xdg/openbox/rc.xml /etc/xdg/openbox/autostart ~/.config/openbox
# pacman -S gamin
# pacman -S leafpad obconf epdfview

finally add a exec command to the .xinitrc you created during the XDM, add at the bottom (no quotes) “exec startlxde”

That should be it! Reboot and hopefully you will have a simple graphics login page and a functioning (if not light) desktop,

Sources
http://8thstring.blogspot.com/2011/11/arch-linux-on-eee-pc-900-chronicle.html
https://wiki.archlinux.org/index.php/Beginners%27_Guide
https://wiki.archlinux.org/index.php/XDM
https://wiki.archlinux.org/index.php/LXDE

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Pandas, matplotlib and Ipython – all you need for great data anaylsis

I’ve been playing around a little with the stats-centric programming language R, mostly to get a better handle on the Bioconductor differential gene expression analysis packages edgeR and DEseq. The language is designed to allow for easy manipulation of tabular data as well as providing access to a rich library of statistical packages and graphing tools. One thing I learned was that often it was more efficient (at least for me) to spend a little time pre-formatting the data using python/perl before even getting started with R. The charting features of R are pretty cool, but once again I missed my familiar Python environment)-:

But, as always there is a Pythonic way, I came across a great book called Python for Data Analysis by Wes McKinney. The book introduced me to the pandas library, which contains R-like tools for tabular data manipulations and analyses. The book also introduced the Ipython development environment; basically a souped up feature rich but light weight “python IDLE”. The best features of Ipython for me are the logging capabilities, advanced history and de-bugging utilities – very cool! Ipython has been designed to work well with the matplotlib, thus allowing production and manipulation of nice looking graphs and charts within an interactive python environment. I’m still very much learning this (and I’m a hack programmer), but here is some fun data crunching based on a USDA food database wrangled into into Json format by Ashley Williams.

Ok, I think it would look better on one chart. Here is the top 50 protein containing foods with their fat content as part of one graph.

Note that I chopped the y-axis labels off, doh, no problem just modify them in real time using the slider editor!

Not too bad at all for a newbee. Hopefully by next post I will feel a little more comfortable to share some hard learned lessons on data manipulation using pandas.