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We use MongoDB Ops Manager 1.6.2.251.

I searched Activity -> Alert Settings. Is there a way to monitor disk usage?

To get an alert if this changes to 90%:

# df -h /data/
Filesystem                Size  Used Avail Use% Mounted on
/dev/mapper/vdatavg-data   99G  295M   99G   1% /data
2

MongoDB Ops Manager 3.4.0 (released November, 2016) includes monitoring for hardware metrics (cpu, disk usage, and I/O utilization) via the Automation agent. For more information, see: System and Disk Alerts.

Prior versions of Ops Manager did not include hardware monitoring and required the use of an external tool (munin-node) for CPU & disk metrics. If you are still using an older version of Ops Manager and have installed Munin-node for monitoring CPU & I/O stats you could look into using the Munin df plugin to track free disk space. Munin supports sending alerts via email as well as through Nagios and external scripts.

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