PracticalSession-1.md

# Practical Session 1

AIM: Learn how to efficiently and securely connect to the institute computers.


## Connecting to MPIMG computers via `ssh`

- try to connect using the command `ssh USER@geniux.molgen.mpg.de` in your powershell(windows) or terminal (mac/linux) where USER is your username. Once you have given your password you should see:


  ```
  #     #                  ###         #     #  geniux
  ##   ##    ##    #####    #   #    #  #   #   system Dell PowerEdge R420
  # # # #   #  #   #    #   #   #    #   # #    cpu    16x E5-2470 @ 2.30GHz
  #  #  #  #    #  #    #   #   #    #    # 64  ram    64.2 GB
  #     #  ######  #####    #   #    #   # #    arch   x86_64 / 64-bit
  #     #  #    #  #   #    #   #    #  #   #   glibc  2.33
  #     #  #    #  #    #  ###   ####  #     #  kernel 5.10.70.mx64.403 #1

    / to bee or not to bee /   tags: amd mx64 server 
  ** internet gateway / multiple purpose **
  ** not a compute server **
  ```

  If you only have `putty` on windows - the setup is a bit more cumbersome.




## Two Factor Authentication

There is a lot of very precious data in our computer system. We there **strongly** recommend to use Two Factor Authentication (2FA). Besides your password you then also need a temporary passcode, e.g. generated by your smart phone, to login. 


- To use 2FA run `google-authenticator` after login to `geniux` (see above). Answer the questions with `yes` and scan the QR code with an appropriate app on your phone. I made positive experiences with
  - Duo Mobile
  - Authy
  - Authenticator

- Logout and try to login again. This time you also need to type a "Verification code" (a 6 digit number) which you get from your smart phone.

If you lost your phone or or do not want to use this security feature  remove the file `~/.google_authenticator` or ask `helpdesk@molgen.mpg.de` to do this for you.


## SSH connection with RSA keys and config 
To login into our system is now quite cumbersome. Using a public/private RSA key pair you can make this process much simpler. To do this:


- generate a RSA key pair on your local computer using `ssh-keygen`. You will be asked to provide a file and "passphrase". Answer all request with `[return]`:
  ```
  # ssh-keygen 
  Generating public/private rsa key pair.
  Enter file in which to save the key (/home/USER/.ssh/id_rsa):
  Enter passphrase (empty for no passphrase): 
  Enter same passphrase again: 
  Your identification has been saved in /home/USER/.ssh/id_rsa
  Your public key has been saved in /home/USER/.ssh/id_rsa.pub
  The key fingerprint is:
  SHA256:B7QqVl8BbV3wUKLjNGz7KiYXkSN412C7ts5htZ8 USER@geniux.molgen.mpg.de
  The key's randomart image is:
  +---[RSA 3072]----+
  |        o  ...+++|
  |       . +o..oo+.|
  |       .=..=O.  .|
  |      .+o.**.+   |
  |    + o.Soo++    |
  |   + o   .+. o   |
  |  .      .oo. .  |
  |        .o=. o . |
  |         =o.. E  |
  +----[SHA256]-----+
  ```


- on your local computer generate a file `.ssh/config` - this can easily be done using "VS Code" - 
  with the following contents:
  ```
  Host elcattivo
        Hostname elcattivo
        User USER
        ProxyJump geniux
        LocalForward PORT elcattivo:PORT

   Host geniux 
        Hostname geniux.molgen.mpg.de
        User USER
  ```
  where `USER` is your username and `PORT` is a random number between 20000 and 65535. 



- Next the **public** key needs to deposited on the remote computer, i.e. `geniux`.  `Assuming your public key is stored in `.ssh/id_rsa.pub`. Open this file using "VS Code" - it should look something like this:
  ```
  ssh-rsa AAAAB3Nza...qHBJE= xyz@blo.org
  ```

  This line needs to be **appended** to the file `.ssh/authorized_keys` on geniux. 
  - With some luck you can achieve this by (please copy paste to avoid typos)
    ```
    cat ~/.ssh/id_rsa.pub | ssh USER@geniux.molgen.mpg.de 'cat >> .ssh/authorized_keys && echo "Key copied"'
    ```
    A _last_ time you need to provide your password and a verification code.
  - Otherwise use VS Code to edit the remote copy `.ssh/authorized_keys` - see below.



- Logout and connect again `ssh USER@geniux.molgen.mpg.de` to check that you did not need to type your password etc.


- now try reconnect - it should work without asking for a password and verification code.

## Edit files (local and remote):
The editor `VS Code` is quite powerful to edit text files and notebooks. One can also it to edit files an **remote** computers - to do so:
   - install the package VS Code `Remote - SSH`
   - open the `Command Palette`
   - choose `Remote SSH: Connect to host ...`
   - choose `geniux`, give password and verification code
   - click open
   - navigate to the file
  


## Customizing your mariux shell
It is time to customize your `shell` on geniux. 
- Edit the file `~/.bashrc` on geniux and add the following lines
  ```bash
  # history
  export HISTCONTROL=ignoredups:erasedups  # no duplicate entries
  export HISTSIZE=100000                   # big history
  export HISTFILESIZE=100000               # big history
  shopt -s histappend                      # append to history, don't overwrite it

  # make history searchable with prefixes and arrow keys 
  bind '"\e[A"':history-search-backward
  bind '"\e[B"':history-search-forward

  # saver versions
  alias cp='cp -i'
  alias rm='rm -i'
  alias mv='mv -i'

  # process control
  alias pu='ps -u ${USER} -o pid,user,pcpu,size,start_time,args --sort start_time'
  alias top='htop'
  alias topu='htop -u $USER'

  # helpful
  complete -d cd

  # tmux helper
  alias tm='tmux attach || tmux new'
  ```

- To monitor a remote computer it is recommended to use `htop`. You can adjust the shown information - copy the file `helpful/htoprc` in this repository to `~/.config/htop/htoprc`  or execute the following lines
  ```
  mkdir -p ~/.config/htop/
  cat > ~/.config/htop/htoprc << EOF
  # Beware! This file is rewritten by htop when settings are changed in the interface.
  # The parser is also very primitive, and not human-friendly.
  fields=0 48 17 20 18 38 39 40 2 46 47 49 1
  sort_key=46
  sort_direction=1
  hide_threads=1
  hide_kernel_threads=0
  hide_userland_threads=1
  shadow_other_users=0
  show_thread_names=0
  show_program_path=0
  highlight_base_name=0
  highlight_megabytes=1
  highlight_threads=0
  tree_view=0
  header_margin=1
  detailed_cpu_time=0
  cpu_count_from_zero=0
  show_cpu_usage=1
  show_cpu_frequency=0
  update_process_names=0
  account_guest_in_cpu_meter=0
  color_scheme=6
  enable_mouse=1
  delay=15
  left_meters=CPU Memory Swap
  left_meter_modes=1 1 1
  right_meters=LoadAverage Uptime Hostname
  right_meter_modes=2 2 2
  vim_mode=0
  EOF
  ```

## Assignment 
Please make a screenshot of a terminal session in which you monitor the CPU usage on `elcattivo.molgen.mpg.de`.