Linux configuration

Logging into a linux server

To logon to a linux server at the Faculty of Science you need a Science login as explained on the the C&CZ wiki

There are several ways to login

• Most PCs at the Faculty of Science are dual boot: simply select Ubuntu an logon
• From a linux computer or a terminal on a Mac use `ssh`:

 ssh lilo7.science.ru.nl

and use your username and password to logon

• From a Windows system follow these instructions: connecting to the cluster from a Windows computer

Learn linux command line basics

There are numerous introductions to the linux command line. Here is one example:Command line for beginners

Set permissions

By default other users cannot see your files, which makes it hard for others to help you. To make the files related to your project readable for members of the theoretical chemistry group follow these instructions:

First check whether you are a member of the thchem group, using the command

 groups

If thchem is not in the output, ask Gerrit or Herma.

For security, make your files only accessible to yourself and members of the theoretical chemistry group, but no one else:

 cd               # go to your home directory
 chmod 750 .      # the dot means "current directory"
 chgrp thchem .   # give members of the thchem group access to your files
 ls -ld .         # have a look at the settings for your home directory

Files that are not in the thchem group can still not be read by others.

Create a directory where you keep files for your theoretical chemistry project:

 mkdir projects

You can make this directory accessible to theoretical chemistry members using the chmod and chgrp commands, but there is a script that will do this for you:

 /vol/thchem/bin/for_theory.sh ~/projects    # the tilde (~) refers to your home directory

You may want to organize your files in subdirectories, e.g.:

 cd ~/projects
 mkdir molecule1
 mkdir scripts

If you want to save some typing when going to these directories from your home directory, you can set soft links, e.g.:

 cd          # go to your home directory
 ln -s projects/molecule1 .
 ln -s projects/scripts .

If you create new files in these directories, they will automatically be in the thchem, group, because the for_theory.sh script has set the sticky bit using the command

 chmod g+s ~/projects

However, if the permissions of the files are not correct, you can fix this for all files in ~/projects and its subdirectories by giving the above for_theory.sh command again.

Configure your .bashrc file

If you already added your own configurations to your .bashrc file you probably do not want to overwrite it with this example. Otherwise, follow these instructions:

 less /vol/thchem/bash/skel/Readme.txt

If you did not use the less command before: you can scroll through the file by pressing the space bar, and exit the file by pressing q