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I've been getting excessive resource usage notification from ConfigServerFirewall about this. Is it safe to disable /usr/sbin/atd, or should I just let it be and ignore it?

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That depends, do you use it? at is a way of running commands at a specified time. I use it to run commands on servers and logout, leaving the command running in the background. Find out what processes (if any) are using the at daemon (atd). –  terdon Apr 4 '13 at 17:16
    
What terdon said; you could always try to attach lsof to the PID to see what it's doing. –  tink Apr 4 '13 at 19:00

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You should find out what jobs atd is running that are consuming so much time. As atd could be used to run all sorts of things, disabling it might disable all kinds of services you may need (like periodic backups or something).

Your problem may be that something is running more often than it should, or requeuing itself.

Run the command atq as superuser to see what kind of stuff is being queued.

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