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I am doing aprox 4000 service checks (most of them via snmp) and some of the checks are failing frome time to time. There is no obvious pattern on which services are failing.

But if I do the checks that are currently failing manually from the commandline on the Nagios-box everything is ok.

Any tips?

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Do you have historical graphs of the systems in question? Do the timeouts correspond to high load or other activity? Nagios will timeout checks after 10 seconds (default) if there is no response, and produce that message. –  cjc May 15 '12 at 12:03
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That is, 4000 checks overall (eg 200 hosts 20 checks each) on one nagios server? is snmp used directly or via a relay mechanism (nsca, nrpe, ssh) that will cause local snmp query on the target host itself (as is often done for security reasons)? Do you use_large_installation_tweaks? Can you catch a check fail with strace? Are you requesting sockets at a rate higher than the system can supply them (esp if some stuff leaves unused connections to time out)? –  rackandboneman May 15 '12 at 12:49
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