Using qsub within crontab?

Question

I'm trying to qsub a script within crontab. Within a crontab txt file, I tried:

    0 1 * * * qsub /script.sh

The error I get is "/bin/sh: qsub: command not found." I've tried a bunch of similar iterations and looked around online without success. I'd appreciate any help.

Answer 1

Programs executed under cron run with a limited set of environment variables. In particular, since it doesn't read your shell startup files (.bashrc, .profile, .cshrc, whatever), it won't have your $PATH settings; $PATH is likely to be something simple like /usr/bin:/bin.

You can set the PATH for a single command like this:

0 1 * * * PATH=/directory/containing/qsub:/usr/bin:/bin qsub /script.sh

You can also set environment variables globally; such settings will apply to all commands executed from your crontab:

PATH=/directory/containing/qsub:/usr/bin:/bin

0 1 * * * qsub /script.sh

man 5 crontab, or see here, for more information on writing crontabs.

If you want to see just what the environment for a cron job looks like, you can temporarily add this line to your crontab:

* * * * * printenv > cron-env

Wait until the top of the next minute, then cat ~/cron-env -- and then remove that line from your crontab so it doesn't keep executing.

(Is your script really in the root directory? Why isn't it under your home directory?)