====== Installation CentOS 7 ======

===== Foreword =====
The CentOS will be installed at two disks: Solid state disk and Mechanical hard disk. The SSD should correspond to SATA interface I and the mechanical hard disk corresponds to SATA interface II. If not, then you should exchange the two disk cables that link to SATA interface. 

<code>
black IP: 101.6.121.172

white IP: 101.6.121.69
</code>
===== Prepare USB installation disk =====
  * Download the latest CentOS DVD iso [[https://mirrors.tuna.tsinghua.edu.cn/centos/7.9.2009/isos/x86_64/ | this link]]
  * Make bootable USB disk: 
    * Download [[https://rufus.ie/ | refu]], run it and load the .iso file into it.

===== BIOS setup =====
BIOS needs to setup to allow booting from USB disk
  * Press "Delete" in keyboard (depend on the PC) to go into BIOS
  * Change to "Boot" item and make "USB driver first"
  * Save and Exit

===== CentOS server installation =====
* Insert the USB driver and reboot the computer (Repeat the BIOS setup if the computer doesn't boot from USB).
<code>
Choose Install Centos 7
Choose English as language
Choose Shanghai as the time zone
Software Selection: GNOME Desktop (add-Ons: GNOME Applications; Compatibility Libraries; Development Tools; System Administration Tools)
Installation destination: select the two hard disks and then "I will configure a partitioning" 

^                             ^ Mount Point  ^ Capacity     ^ File System  ^
| Solid-state disk (sda1)     | /boot/efi    | 600M         | 默认         |
| Solid-state disk (sda2)     | swap         | 32G          | swap         |
| Solid-state disk (sda3)     | /            | other space  | ext4         |
| Mechanical hard disk (sdb1) | /home        | all space    | ext4         |

Connect the internet and rename the host name
Add root password and new user
</code>

===== Basic package installation =====
<code>
sudo yum update
sudo yum install gcc gcc-gfortran gcc-c++
sudo yum install vim-X11 mousepad imagemagick
sudo yum install tcsh cmake
sudo yum install xterm tcl tk
sudo yum install boost-devel

sudo yum install python2
sudo yum install python2-pip
sudo pip2 install --upgrade pip
sudo pip install numpy scipy
# when install matplotlib, error occurs for pyparsing
# need to manually delete pyparsing
sudo rm -r /usr/lib/python2.7/site-packages/pyparsing*
sudo pip install pyparsing
sudo yum install python-ipython
sudo yum install tkinter
sudo yum -y install tcl-devel tk-devel
sudo yum install python3
sudo pip3 install --upgrade pip
sudo pip3 install numpy matplotlib scipy ipython
#install python3 tkinter
sudo yum install python3-tk* -y
sudo yum install tk-devel -y
cd /bin
sudo ln -sf python3 python (this will mess up yum!)
sudo vi /usr/bin/ipython (to make the first line "#!/usr/bin/python")


sudo yum install ImageMagick gimp
</code>

 * if want to use higher version of gcc
  * https://ahelpme.com/linux/centos7/how-to-install-new-gcc-and-development-tools-under-centos-7/
  * https://stackoverflow.com/questions/36327805/how-to-install-gcc-5-3-with-yum-on-centos-7-2 
===== library and font installation for nmrPipe/Sparky/pymol/topspin =====
<code>
sudo yum install libstdc++.i686
sudo yum install libX11.i686
sudo yum install libXext.i686
sudo yum install xorg-x11-fonts-100dpi xorg-x11-fonts-75dpi
sudo yum install xorg-x11-fonts-ISO8859-1-100dpi xorg-x11-fonts-ISO8859-1-75dpi
sudo yum install mesa-libGLU
sudo yum install libXScrnSaver
# for topspin
sudo yum install libXft.i686
sudo yum install libXtst.i686
</code>

===== X2Go server & Xfce installation =====
<code>
sudo yum install epel-release
sudo yum -y install x2goserver-xsession
sudo yum -y groupinstall "Xfce"
</code>

===== Topspin installation =====
ATTENTION!!!

Topspin versions before 4.0 required 32-bite libraries, which are not installed automatically on RHEL-7/CentOS-7, first install these library: https://repo-bbio.bruker.com/CentOS/7/TopSpinInstallationRequirements.html

Topspin 3.6.2
  *step 1: //sudo bash topspin-3.6.2-linux.sh//
  *step 2: click next with the default
  *step 3: {{::topspin3.6.2installation.png?200|}}
  *step 4: request & input the licence key with educational email
  *step 5: set password(nmriscool!)
  *step 6: //mv /opt/topspin3.6.2/prog/mod/toolserver toolserver.bak// (if not, the toolserver can't work)

Topspin 4.1.0
  *step 1: //sudo bash topspin-4.1.0-linux.sh//
  *step 2: click next with the default
  *step 3: {{:soft:topspin4.1.0installation.jpg?200|}}
  *step 4: request & input the licence key with educational email
  *step 5: set password(nmriscool!)
  *step 6: the toolserver can work normally

===== Setup openssh server on spectrometer =====
  * Download OpenSSH-Win64.zip: https://github.com/PowerShell/Win32-OpenSSH/releases
  * Install it on spectrometer computer [[https://blog.csdn.net/youlinhuanyan/article/details/105925666 | ref]]
<code>
# first exact to C:\Program Files\OpenSSH
# then open "cmd" window, enter into this folder, and do the following
### Install sshd service
powershell.exe -ExecutionPolicy Bypass -File install-sshd.ps1
### enable port 22
netsh advfirewall firewall add rule name=sshd dir=in action=allow protocol=TCP localport=22
### configure startup of the service
sc config sshd start= auto
### start the service
net start sshd
</code>
  * add C:\Program Files\OpenSSH into Sys path in Windows 7
  * copy three rsync-relevant files from cygwin or mysys2 to C:\Program Files\OpenSSH [[https://github.com/PowerShell/Win32-OpenSSH/issues/1266 | ref]]

===== Mathematica installation =====
<code>
ssh -Y xuelab@localhost
密码：NMR1sC00L!
cd build/mathematica/12.1(software package）
sudo mkdir /mnt/iso (creat mount point)
sudo mount -o loop xxxx.iso /mnt/iso (mount the iso)
sh /mnt/iso/xxx.sh (run the installar)
> /home/usr/share/Wolfram/Mathematica/12.1 (Methematica install path)
> /home/usr/bin (scripts install path)
########################### CRACK ###############################
Crack folder: build/mathematica/12.1（copy from /mnt/iso/）
METHOD:
1 select active manually 
2 open https://ibugone.com/blog/2019/05/mathematica-keygen/ (from .url in crack, local PC may faster)
3 generate key for the code in first step
FINISH
##################################################################
cp build/mathematica/Poma2.m /home/usr/share/Wolfram/Mathematica/12.1/AddOns/ExtraPackages/(for pulse calculation)
last: umount -v /mnt/iso/ (unount the iso)
</code>

===== Nvidia driver installation =====
  * To install: https://www.server-world.info/en/note?os=CentOS_7&p=nvidia&f=1
  * To uninstall: https://computingforgeeks.com/how-to-uninstall-manually-installed-nvidia-drivers-in-linux/

===== Add & Del user =====
<code>
cd cmd
vim adduser.sh: change UserName:xuelab and uid:3500(uid according to /etc/passwd)
sudo ./adduser.sh
###remove user### 
sudo userdel -r username
</code>


====== Installation CentOS 8 ======

===== Foreword =====
The CentOS will be installed at two disks: Solid state disk and Mechanical hard disk. The SSD should correspond to SATA interface I and the mechanical hard disk corresponds to SATA interface II. If not, then you should exchange the two disk cables that link to SATA interface. 

===== Prepare USB installation disk =====
  * Download the latest CentOS <fc #ff0000>minimal</fc> iso [[http://isoredirect.centos.org/centos/8/isos/x86_64/ | this link]]
  * Make bootable USB disk: 
    * Download [[https://mbriza.fedorapeople.org/liveusb-creator.zip | <fc #ff0000>liveusb-creator</fc>]], run it and load the .iso file into it.

===== BIOS setup =====
BIOS needs to setup to allow booting from USB disk
  * Press "Delete" in keyboard (depend on the PC) to go into BIOS
  * Change to "Boot" item and make "USB driver first"
  * Save and Exit

===== CentOS server installation =====
* Insert the USB driver and reboot the computer (Repeat the BIOS setup if the computer doesn't boot from USB).
<code>
Choose Install Centos 8
Choose English as language
Choose Shanghai as the time zone
Choose to installl Sever version environment and select the additional software (1-3,6-12,15,18)
Installation destination: select the two hard disks and then "I will configure a partitioning" 

^                             ^ Mount Point  ^ Capacity     ^ File System  ^
| Solid-state disk (sda1)     | /boot/efi    | 600M         | 默认         |
| Solid-state disk (sda2)     | swap         | 32G          | swap         |
| Solid-state disk (sda3)     | /            | other space  | ext4         |
| Mechanical hard disk (sdb1) | /home        | all space    | ext4         |
Choose the network card the internet tube links to and switch on
Add the host name or you can alter it by command line (vim /etc/hostname and /etc/hosts)
</code>

===== Server with GUI installation =====
<code>
sudo yum group list
sudo yum  groupinstall "Server with GUI" -y
sudo systemctl set-default graphical
sudo reboot
</code>

===== Basic package installation =====
<code>
sudo yum update
sudo yum install gcc
sudo yum install python2
sudo yum install python38
sudo yum install gcc-gfortran
sudo yum install tcsh
</code>

===== x2go server installation =====
<code>
sudo dnf -y update
sudo dnf --enablerepo=PowerTools install perl-X2Go-Server-DB perl-File-BaseDir fuse-sshfs
sudo dnf install https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm
sudo dnf install -y x2goserver-xsession
</code>

===== Xfce installation =====
<code>
1 安装xfce: sudo dnf groupinstall -y "xfce"
2 安装好后进入桌面: sudo systemctl isolate graphical.target
3 设置默认启动为图形化界面: sudo systemctl set-default graphical.target
4 远程登录xfce后操作: Applications-->setting-->Screensaver-->Screensaver & LockScreen "OFF"
5 若登录xfce后屏幕失效：用putty或xshell登录：(1)top -u UserName, (2) k pid (of the xfce-Session), (3) operate step 4 
 </code>

===== Python package installation =====
<code>
sudo pip2 install --upgrade pip
sudo pip2 install numpy matplotlib scipy ipython tk
sudo yum install python3-tk
sudo yum -y install python-tkinter tcl-devel tkdevel
</code>


===== 32-bit library installation =====

  * Configure yum [[https://mirrors.tuna.tsinghua.edu.cn/help/centos/ | Ref]]
    编辑 /etc/yum.repos.d/CentOS-Base.repo 文件，在 mirrorlist= 开头行前面加 # 注释掉；并将 baseurl= 开头行取消注释（如果被注释的话），把该行内的域名（例如mirror.centos.org）替换为 mirrors.tuna.tsinghua.edu.cn。
<code>
sudo yum makecache
</code>

  * Make windows default in dual boot of CentOS/Win7
https://dareneiri.github.io/Configuring-Grub-2-on-CentOS-7/