Initialize zsh for Non-interactive Jobs

Each shell available to users has its own rules for run-time setup. This affects which files are read in different contexts; interactive, batch, and ssh commands use different files depending on the shell being used. For example, zsh (Z shell) does not initialize like bash, and when ssh launches a shell, the environment for bash users and zsh users is different. For bash users, this means that the modules command is available for remotely executed commands, and for zsh users it is not available.

Users of zsh may find that bash scripts executed as part of batch scheduled jobs do not have the same environment as the login node they are submitted from because they are invoked on non-local MOM nodes. As a result, some commands that work interactively outside of the job script may fail when the batch scheduler tries to invoke the job script. In the context of ssh commands under zsh, only one type of file from two possible locations is read: the zshenv file. To enable the job script to operate, users with accounts on the remote machine can make changes to ~/.zshenv on the remote machine. If the system administrator believes that all users should automatically have a change made, the contents of /etc/zshenv can be modified by a site-local Ansible play.

There are two methods of affecting the environment for the bash scripts that comprise the batch scheduler jobs. If zsh makes environment changes before the bash script is invoked, they can be inherited by the script. Alternatively, zsh can nominate a file that provides the environment that bash processes, including scripts, should use in the environment variable BASH_ENV. Remember that the contents of zshenv are executed by every zsh process, so if ssh is heavily used for purposes other than batch scheduler jobs, it might be more efficient to use zshenv to nominate BASH_ENV and only 'pay' the cost for batch scheduler jobs.

method 1

Export an environment variable that will enable bash scripts (like the job script) to include the module command when the script starts. To enable bash scripts to execute with modules for zsh users as they would for bash users, append the following line to the zshenv file:

export BASH_ENV=/etc/bash.bashrc.local

method 2

Modify zsh initialization to always execute interactive startup code every time zsh is launched. To force every zsh shell to perform the startup that an interactive zsh shell does, append the following line to the zshenv file:

source /etc/zshrc

These two methods can be used by individual zsh users or by system administrators who wish to make system-wide changes.