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Shell Environment

Available Shells

In the Linux operating system, knowing the available shells on a Linux machine is vital for administrators and users who require different shell environments for their work. There are several different shells available, each with its own features and capabilities. Following shell environments are available at Devana: - bash - tcsh - csh

Default shell

BASH is the default shell and if the users wish to change that they should contanct our administration support.

Customizing Environment

After logging in, you may want to configure the environment. Write your preferred path definitions, aliases, functions, and module loads in the ~/.bashrc file.

Modifiable ~/.bashrc file 
# ~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples
# If not running interactively, don't do anything
case $- in
   *i*) ;;
      *) return;;
esac
# don't put duplicate lines or lines starting with space in the history.
# See bash(1) for more options
HISTCONTROL=ignoreboth

# append to the history file, don't overwrite it
shopt -s histappend

# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
HISTSIZE=1000
HISTFILESIZE=2000

# check the window size after each command and, if necessary,
# update the values of LINES and COLUMNS.
shopt -s checkwinsize

# If set, the pattern "**" used in a pathname expansion context will
# match all files and zero or more directories and subdirectories.
#shopt -s globstar

# make less more friendly for non-text input files, see lesspipe(1)
#[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"

# set variable identifying the chroot you work in (used in the prompt below)
if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
    debian_chroot=$(cat /etc/debian_chroot)
fi

# set a fancy prompt (non-color, unless we know we "want" color)
case "$TERM" in
    xterm-color|*-256color) color_prompt=yes;;
esac

# uncomment for a colored prompt, if the terminal has the capability; turned
# off by default to not distract the user: the focus in a terminal window
# should be on the output of commands, not on the prompt
#force_color_prompt=yes

if [ -n "$force_color_prompt" ]; then
    if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
    # We have color support; assume it's compliant with Ecma-48
    # (ISO/IEC-6429). (Lack of such support is extremely rare, and such
    # a case would tend to support setf rather than setaf.)
    color_prompt=yes
    else
    color_prompt=
    fi
fi

if [ "$color_prompt" = yes ]; then
    PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
else
    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
fi
unset color_prompt force_color_prompt

# If this is an xterm set the title to user@host:dir
case "$TERM" in
xterm*|rxvt*)
    PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
    ;;
*)
    ;;
esac

# enable color support of ls and also add handy aliases
if [ -x /usr/bin/dircolors ]; then
    test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
    alias ls='ls --color=auto'
    alias dir='dir --color=auto'
    alias vdir='vdir --color=auto'

    alias grep='grep --color=auto'
    alias fgrep='fgrep --color=auto'
    alias egrep='egrep --color=auto'
fi

# colored GCC warnings and errors
#export GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'

# some more ls aliases
#alias ll='ls -l'
#alias la='ls -A'
#alias l='ls -CF'

# Alias definitions.
# You may want to put all your additions into a separate file like
# ~/.bash_aliases, instead of adding them here directly.
# See /usr/share/doc/bash-doc/examples in the bash-doc package.

if [ -f ~/.bash_aliases ]; then
    . ~/.bash_aliases
fi

# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
   if [ -f /usr/share/bash-completion/bash_completion ]; then
      . /usr/share/bash-completion/bash_completion
   elif [ -f /etc/bash_completion ]; then
      . /etc/bash_completion
   fi
fi

# Aliases

# Paths
PATH=:$PATH
Warning

Do not run commands outputting to standard output (echo, module list, etc.) in .bashrc for non-interactive SSH sessions. It breaks the fundamental functionality (SCP) of your account. Take care for SSH session interactivity for such commands as stated in the previous example.

Available Modules

In order to configure your shell for running a particular application on clusters, we use a module package interface.

Application modules on clusters are built using EasyBuild. The modules are divided into the following groups:

Available modules groups

bio: Bioinformatics, biology and biomedicinal
cae: Computer Aided Engineering software
chem: Chemistry, computational chemistry and quantum chemistry software
compiler: Compilers
data: Data management and processing tools
devel: Development tools
geo: Earth sciences
lang: Languages and programming tools
lib: General purpose libraries
math: High-level mathematical software
mpi: MPI stacks
numlib: Numerical libraries
perf: Performance tools
phys: Physics simulation software
system: System utilities
toolchain: EasyBuild toolchains
tools: General purpose tools
vis: Visualization, plotting, documentation and typesetting software

PATHS

The modules set up the application paths, library paths and environment variables for running a particular application.

The modules may be loaded, unloaded, and switched according to momentary needs. For more details, see our list of Available modules and documentation regarding Lmod system.

Created by: Martin Blaško, marek.steklac