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====== Quick Links ======
  * [[https://blog.udemy.com/debian-vs-ubuntu/ | Debian vs Ubuntu]] | [[https://www.debian.org/distrib/packages | Search package]]
  * [[debian/cookbook | Debian Cookbook]]

====== Installation ======
 
===== BIOS setup =====
BIOS needs to setup to allow booting from USB disk
<WRAP center round tip>
  * press F2         //# Go into BIOS Utility// 
  * press F5         //# Default setting//
  * press F7         //# Go into Advanced Mode//
</WRAP>

  * Go to Boot menu in BIOS interface and move to "CSM" item, and make sure you have the following setup

| Launch CSM                            | Enabled               |
| BOOT Device Control                   | UEFI only             |
| BOOT from Network Device              | UEFI driver first     |
| BOOT from Storage Devices             | UEFI driver first     |
| BOOT from PCI-E/PCI Expansion Devices | UEFI driver first     |

  * Move to "Secure Boot" item, and make sure you have the following setup

|OS Type               | other OS              |           

  * Exit/Save

===== Debian installation =====

  * Partition disks 
  
{{:partition_disks1.jpg?100|}} {{:partition_disks2.jpg?direct&100|}}
 Guided-use entire disk   
  * Software selection

|Debain desktop environment |
|Xfce                       |
|LXDE                       |
|SSH server                 |
|standard system utilities  |

===== Create user accounts =====
  * Log into root
  * Add group "xue"
<code>
groupadd -g 3500 xue
</code>
  * Add user by running cmd/adduser.sh
  * Setup sudo
<code>
apt-get install vim
visudo
</code>
Add the following block in the text file invoked by visudo command
<code>

</code>
===== Install common packages =====
  * Common tools
<code>
apt-get install tcsh mc python python-dev screen links
</code>
  * xfce
<code>
sudo apt-get install xfce4 xfce4-terminal
sudo dpkg --purge xscreensaver  # remove screensave to save CPU resources
sudo dpkg --purge xscreensaver-data
</code>
  * Common X11 applications
<code>
sudo apt-get install iceweasel
</code>
===== Installation of 32-bit library =====
  * Type the following commands
<code>
sudo apt-get update
sudo dpkg --add-architecture i386
sudo apt-get update
sudo apt-get install lib32z1
sudo apt-get install libx11-6:i386
sudo apt-get install libstdc++6:i386  # for sparky
sudo apt-get install libxext6:i386  # for nmrPipe
</code>

===== How to manually compile numpy =====
  * Install pip
<code>
sudo apt-get install python-pip
mkdir ~/build/numpy
cd ~/build/numpy
pip install -d . numpy  # download numpy source code
</code>
Now create a site.cfg file with the following content进行这一步
  * Ref: http://gromgull.net/blog/2013/07/multithreaded-scipynumpy-with-openblas-on-debian/
  * Install openblas
<code>
apt-cache search openblas # search for openblas
sudo apt-get install libopenblas-base libopenblas-dev
sudo apt-get install python2.7-dev
</code>
  * Compile numpy
<code>
sudo apt-get install python-pip
mkdir ~/build/numpy
cd ~/build/numpy
pip install -d . numpy
unzip numpy*.zip
cd numpy-*
cp site.cfg.example site.cfg

# Create site.cfg with the following content:
# [default]
# library_dirs= /usr/lib/openblas-base
# 
# [atlas]
# atlas_libs = openblas

python setup.py build
</code>
  * Check whether numpy is linked to openblas
<code>
ldd build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so
</code>

  You should see something like
  
<code>
linux-vdso.so.1 (0x00007ffe387f9000)
libopenblas.so.0 => /usr/lib/libopenblas.so.0 (0x00007f44e35ed000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f44e33cf000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f44e3024000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f44e2d23000)
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007f44e2a04000)
/lib64/ld-linux-x86-64.so.2 (0x000055a81f0ec000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f44e27c7000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f44e25b1000)
</code>

  * Install numpy
<code>
sudo python setup.py install
</code>

===== Install other scientific packages =====
<code>
sudo pip install scipy
sudo apt-get install matplotlib
sudo apt-get install ipython
</code>
===== remove numpy(if installed system NumPy) =====
  * remove numpy forcely
<code>
sudo dpkg --purge --force-all python-numpy
</code>

  * remove numpy only (after apt-get matplotlib, old version of numpy will be installed automatically)
<code>
sudo dpkg -r --ignore-depends=python-numpy python-numpy
</code>

===== Usage of dpkg =====
  * http://blog.csdn.net/sunjiajiang/article/details/7252593

http://www.tuicool.com/articles/iqumQz

===== change the boot option of debian =====
  * 'Debian GNU/Linux' -> press 'E' -> 'setparams' -> 'Linux ...' -> delete 'quiet', add 'text' 'nomodeset'
 
===== Install x2go server on debian =====
  * http://wiki.x2go.org/doku.php/doc:installation:x2goserver
  * Add our X2Go Debian Repository.
  * <code>
sudo -s
apt-key adv --recv-keys --keyserver keys.gnupg.net E1F958385BFE2B6E
editor /etc/apt/sources.list.d/x2go.list
apt-get update
apt-get install x2go-keyring && apt-get update
apt-cache search x2go
</code>
  * install
  * <code>
sudo apt-get install x2goserver x2goserver-xsession
</code>
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