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

# 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.

NanoCourseReproducibleResearch/PracticalSession-1.md