Why aren’t SGE commands, or R, or matlab, or… available to my cron job?

cron jobs are not launched from a login shell, but the module commands and the JHPCE default environment is initialized automatically only when you log in. Consequently, in a cron job, you have to do the initialization yourself. Do this by wrapping your cron job in a bash script that initializes the module command and then loads the default sge modules. You bash shell script should start with the following lines:


# Source the global bashrc
if [ -f /etc/bashrc ]; then
. /etc/bashrc

This should allow your cron jobs to run within SGE.

Bookmark the permalink.