Shell Environments

Linux systems support multiple shell environments that provide the command-line interface used for interacting with the system. Different shells offer different syntax, scripting capabilities, and user features.

Available Shells

The following shells are available on SAS HPC clusters.

DevanaPerun

The following shell environments are available:

• bash
• tcsh
• csh

The following shell environments are available:

• bash
• tcsh
• csh

Default shell

Bash is the default shell for all user accounts. If you need to change your default shell, contact the administration support.

---

Customizing the Shell Environment

After logging in, users may customize their shell environment by editing initialization files located in their home directory.

For Bash, the most commonly used configuration file is:

~/.bashrc

This file is executed when a new interactive Bash shell starts. It is commonly used to configure:

• environment variables
• command aliases
• shell functions
• module loading
• PATH modifications

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

Non-Interactive Sessions

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.

Module Environment

Applications on the clusters are managed using the Lmod module system. Modules allow users to dynamically configure their shell environment for specific software packages.

Modules automatically set:

• executable paths
• library paths
• required environment variables
• dependent software modules

Software on both clusters is built using EasyBuild. Available modules for the clusters can be browsed in the following documentation:

• Devana available modules
• Perun CPU nodes modules
• Perun GPU nodes modules

Available modules groups

Modules are organized into following logical categories:

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

Module Path Setup

When a module is loaded it automatically configures the required environment variables and library paths needed to run the application.

For more information about module usage see the Lmod documentation.

Created by: Andrej Sec