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Here is a comparison of Checkmk and Zabbix:

Monitoring Approach:

Checkmk takes a more agent-based approach where agents run on the monitored systems and report back to the Checkmk server. Zabbix can use agents but also supports agentless monitoring via protocols like SNMP, IPMI, etc.

Checkmk can monitor a large number of systems but may have scalability limitations compared to Zabbix for very large infrastructures with tens of thousands of systems. Zabbix is designed to scale out more easily.
Monitoring Capabilities:

Both can monitor systems, services, applications, etc. Checkmk has more robust OS and hardware monitoring capabilities out of the box. Zabbix requires more customization for deeper OS and hardware metrics.
Dashboards and Visualization:

Checkmk has more robust dashboard and visualization capabilities with its web-based UI. Zabbix dashboards require more customization.

Both support alerts via email, SMS etc. Checkmk has more flexible alerting capabilities with its ACK system and escalation paths.
Configuration and Customization:

Checkmk configurations are template-based so easier to deploy and maintain for similar systems. Zabbix requires more manual configuration for each system or service. But Zabbix is more customizable overall.
Pricing and Licensing:

Checkmk has both open source and commercial versions. Zabbix is open source only.
In summary, Checkmk is generally better for monitoring large homogeneous environments due to its agent-based approach and templates. Zabbix is more customizable and scalable for very large heterogeneous infrastructures due to its ability to use various protocols and scale out well. Both are very capable monitoring solutions.