a first version

PracticalSession-1.md

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+# 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
+    ```
+    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` to `~/.config/htop/`  or execute the following lines
+  ```
+  mkdir -p ~/.config/htop/
+  cd ~/.config/htop/
+  cat > 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
+  ```
+

helpful/htoprc

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+# 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