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Shell Startup

What is interactive shell?

An interactive shell interacts with user inputs such as typing commands whereas non-interactive shell recieves input from another source such as script. An interactive shell will typically set the variable PS1 that is used to display the prompt in your shell. This variable is unset for non-interactive shell. You can test this by running following command in your shell

if [ -z "$PS1" ]; then
         echo This shell is not interactive
else
         echo This shell is interactive
fi

What is login shell?

A login shell is created upon login to a machine which is done via ssh. A non-login shell is typically started when you start another shell, run a program, or start graphical console. You can test if you are in login shell via following command:

elvis@cori> shopt -q login_shell && echo 'Login shell' || echo 'Not login shell'
Login shell

Note

shopt is builtin command for bash shell. This will not work if you are using csh/tcsh.

A script (including a jobscript submitted via sbatch) runs in a non-login shell, however one can configure script to run in login shell via bash --login <script> or csh -l <script>.

For more details on bash see following links:

Bash startup files

In table below you can see the bash startup files sourced depending on the shell mode. The numbers indicate the order of files being sourced.

Note

For Interactive Login, bash will read the files in the following order ~/.bash_profile, ~/.bash_login and ~/.profile and find first one that exists and is readable (r permission). For more details see bash startup files.

Note

BASH_ENV is an environment variable that generally points a file that is sourced when bash is in non-interactive mode such as running a script. Shown below is the expected values for Cori and Perlmutter.

elvis@cori> echo $BASH_ENV                                          
/etc/bash.bashrc.local

elvis@perlmutter> echo $BASH_ENV                                          
/usr/share/lmod/lmod/init/bash
File Interactive Login Interactive Non Login Non Interactive Non Login
/etc/profile 1
/etc/bash.bashrc 1
~/.bashrc 2
~/.bash_profile 2
~/.bash_login 3
~/.profile 4
~/.bash_logout 5 (logout)
Path included in BASH_ENV 1

A few important rules to remember when working with bash shell.

  • ~/.bash_logout is also run on both interactive and non-interactive login shells upon exit

  • bash --noprofile can be used to prevent loading startup files /etc/profile or any of the user startup files: ~/.bash_profile, ~/.bash_login, or ~/.profile when bash is invoked in login shell. This can be useful to help isolate issues with your startup configuration.

  • When you ssh into Cori (interactive login) the $HOME/.bashrc is sourced on Interactive Login shell. This was done to ensure consistency between startup configuration files (~/.bashrc vs ~/.bash_profile). The ~/.bashrc is typically used for defining alias and functions that needs to be accessible in subshells or as part of scripts whereas ~/.bash_profile is used for specifying configuration in your login shell that you expect to use in your terminal.

  • bash --rcfile option can be used to inform bash to execute commands from an alternate file instead of ~/.bashrc when running in interactive shell. You can avoid bash from reading any rc file by specifying bash --norc which will inform bash from not reading ~/.bashrc.

  • The ~/.profile is the original profile script for Bourne Shell (sh) whereas bash introduced ~/.bash_profile that is read by bash which is incompatible with standard Bourne Shell. If you want to define configuration compatible with sh and bash you should specify this in ~/.profile. For users changing shell from sh to bash please review the major difference in Bourne Shell.

  • Submitting a job such via sbatch will inherit the user environment, however you can use sbatch --export=NONE to prevent any environments to be set on compute node when running job. The default behavior of slurm is --export=ALL which will export all user environment into compute node. For more details on sbatch see man pages (man sbatch)

Bash Startup Files

CSH startup files

file Interactive Login Interactive Non Login
/etc/csh.cshrc 1 1
/etc/csh.login 2
~/.tcshrc 3 2
~/.cshrc 4 3
~/.history 5
~/.login 6
~/.cshdirs 7
~/.logout 8 (logout)
/etc/csh.logout 9 (logout)

Note

csh will read the following files (3-7) in table above in the order specified, if file is found csh will not read the remaining files.

For more details on csh see https://linux.die.net/man/1/csh