Software Guide of Ubuntu 16.04 for my Research

Hello everybody, today I am sharing my first guide which is about building my new research computer. This is a small guide for setting up Ubuntu 16.04 and necessary software for my research.

Specs of my computer

Operating System and System type / version: Ubuntu 16.04.2 LTS

Processor type and speed: Ryzen 7 1700x, 16 Threat, 3.4 to 3.8 GHz

RAM amount: 32GB

GPU: Nvidia 1080 gtx, 8GB

Hard drive size: 256 GB M.2 SSD, 1 TB SSD, 2TB SATA

Steps to Software Installation/Configuration

  • Install Nvidia drivers

    Ubuntu 16.04 Nvidia ppa now has 375 and it seems stable so we will go with that now.

    • sudo add-apt-repository ppa:graphics-drivers/ppa
    • sudo apt update
    • sudo apt-get install nvidia-375
    • sudo reboot # Restarts your system

  • Install some required packages:

    • sudo apt-get install openjdk-8-jdk git build-essential libcurl3-dev
    • sudo apt-get install software-properties-common
  • Installing CUDA

    We will first install the toolkit Go to Nvidia CUDA Website. Choose Linux > x86_64 > Ubuntu > 16.04 > deb(local)

    • sudo dpkg -i cuda-repo-ubuntu1604-8-0-local-ga2_8.0.61-1_amd64.deb
    • sudo apt-get update
    • sudo apt-get install cuda

    Then we add the path updates to the .bashrc with the following oneliners.

    • export PATH=/usr/local/cuda-8.0/bin${PATH:+:${PATH}}
    • export LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64\${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}

    To test the CUDA if it’s working:

    • cd /usr/local/cuda-8.0/samples/5_Simulations/nbody
    • sudo make
    • ./nbody
  • Install cuDNN

    Go to Nvidia cuDNN website download the latest for CUDA 8.0 and linux Carefull because we will be using cuDNN v5.1 for our setup.

      $ sudo tar -xzvf cudnn-8.0-linux-x64-v5.1.tgz
  $ sudo cp cuda/include/cudnn.h /usr/local/cuda/include
  $ sudo cp cuda/lib64/libcudnn* /usr/local/cuda/lib64
  $ sudo chmod a+r /usr/local/cuda/include/cudnn.h /usr/local/cuda/lib64/libcudnn*
  • Install Anaconda Python Distribution

    Anaconda distribution is really easy Python distributor that I can manage my libraries.

    • Download Anaconda Python 3.6 from here
    • bash Downloads/Anaconda3-4.3.1-Linux-x86_64.sh
  • Install Jupyter Themes

    Installing the most updated version of jupyterthemes

    • pip install --upgrade jupyterthemes
    • jt -t solarizedl -T -N

  • Install Tensorflow

    • For dependencies: sudo apt-get install libcupti-dev
    • Then we install Tensorflow with pip: pip install tensorflow-gpu

  • Install Chrome

    wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
sudo dpkg -i --force-depends google-chrome-stable_current_amd64.deb
sudo apt-get install -f
rm google-chrome-stable_current_amd64.deb

    If chrome lags when you highlight or something just go and unchecked Use ‘Hardware acceleration if available’ in advance settings of chrome settings

  • Configure workspaces in Ubuntu

    • system settings > Appearance > Behavior > Check ‘Enable Workspaces’
    • If you want to configure new shortcuts:
      • System Settings > Keyboard > Shortcuts > Navigation > You can assign new shortcuts
  • Install gdebi package manager

    Gdebi is a better way to install deb files for me.

    • sudo apt-get install gdebi
  • Install vim
    • sudo apt-get install vim
  • Install git
    • sudo apt-get install git
    • git config --global user.name "name"
    • git config --global user.email "email"
  • Install htop

    It is really nice command line tool to see and control system

    • sudo apt-get install htop

  • Install Atom text editor

    • sudo add-apt-repository ppa:webupd8team/atom
    • sudo apt-get update
    • sudo apt-get install atom
  • Install Restricted Extras for Ubuntu

    package of several codecs that are not included by default in Ubuntu system, media codecs and Flash Support.

    • sudo apt-get install ubuntu-restricted-extras
  • Install a good Theme for Ubuntu

    It is really nice to have a new look…

    • sudo apt install unity-tweak-tool
    • sudo apt-add-repository ppa:numix/ppa
    • sudo apt-get update
    • sudo apt-get install numix-gtk-theme
    • sudo apt-get install numix-icon-theme numix-folders
    • sudo apt-get install numix-icon-theme-circle
    • sudo apt-get install numix-icon-theme-square
    • Open unity tweak tool
    • Select Appearance > Theme and Icons
  • Install R and RStudio

    I love R since it’s amazing tool for statistics and learning mathematical background of most algorithms. Also Rstudio is really high quality interpreter for R.

    • sudo echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list
    • gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
    • gpg -a --export E084DAB9 | sudo apt-key add -
    • sudo apt-get update
    • sudo apt-get install r-base r-base-dev
    • sudo apt-get install gdebi-core
    • wget https://download1.rstudio.org/rstudio-xenial-1.0.153-amd64.deb
    • sudo gdebi -n rstudio-xenial-1.0.153-amd64.deb
    • rm rstudio-xenial-1.0.153-amd64.deb
  • Install Mendeley Desktop

    Mendeley is a beautiful way to keep track of papers.

    • wget https://www.mendeley.com/repositories/ubuntu/stable/amd64/mendeleydesktop-latest
    • sudo dpkg -i mendeleydesktop
    • sudo apt-get update
    • sudo rm mendeleydesktop
  • Install Redshift (Night Shift software)

    Since I usually work at night and the light from the screen is too much, so I use redshift and configure it.

    • sudo apt-get install redshift gtk-redshift geoclue
    • vim ~/.config/redshift.conf
    • Copy and Paste the following in the vim:
    ; Global settings for redshift
[redshift]
; Set the day and night screen temperatures
temp-day=4500
temp-night=3500

; Enable/Disable a smooth transition between day and night
; 0 will cause a direct change from day to night screen temperature.
; 1 will gradually increase or decrease the screen temperature
transition=1

; Set the screen brightness. Default is 1.0
;brightness=0.8
; It is also possible to use different settings for day and night since version
; 1.8.
brightness-day=0.9
brightness-night=0.7
; Set the screen gamma (for all colors, or each color channel individually)
gamma=0.8
;gamma=0.8:0.7:0.8

; Set the location-provider. Type 'redshift -l list' to see possible values.
; The location provider settings are in a different section.
location-provider=geoclue2

; Set the adjustment-method: 'randr', 'vidmode'
; type 'redshift -m list' to see all possible values
; 'randr' is the preferred method, 'vidmode' is an older API
; but works in some cases when 'randr' does not.
; The adjustment method settings are in a different section.
adjustment-method=randr

; Configuration of the location-provider:
; type 'redshift -l PROVIDER:help' to see the settings
; ex: 'redshift -l manual:help'
[manual]
; set these values if you've set the location-provider to manual instead of
; geoclue
;lat=51.522698
;lon=-0.085358

; Configuration of the adjustment-method
; type 'redshift -m METHOD:help' to see the settings
; ex: 'redshift -m randr:help'

[randr]
screen=0
  • Install GIMP for image editing

    This is a similar software like Photoshop for linux

    • sudo add-apt-repository ppa:otto-kesselgulasch/gimp-edge
    • sudo apt update && sudo apt install gimp gimp-gmic
  • Install VLC for Video
    • sudo apt install vlc
  • Install GooglePlayMusic Desktop Player
  • Install BleachBit

    To keep things neat and clean

  • Install PomoDoneApp

    This is the time tracking app that I’ve integrated with Trello

    Hey do you know there is a comment section below that you can share your ideas with me?

    Until next time, be safe…