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MongoDB 3.2.8 is in STARTUP2 mode building indexes at the moment. A replicaset with 3 nodes.

2016-08-15T08:11:19.385+0200 I -        [rsSync]   Index Build: 387200/2273552 17%
2016-08-15T08:11:19.425+0200 I COMMAND  [conn17] command admin.$cmd command: replSetHeartbeat { replSetHeartbeat: "etrer", configVersion: 8, from: "hostname", fromId: 0, term: 17 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:485 locks:{} protocol:op_command 1ms
2016-08-15T08:11:19.492+0200 I COMMAND  [conn146] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 1ms
2016-08-15T08:11:19.504+0200 I COMMAND  [conn145] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 8ms
2016-08-15T08:11:20.395+0200 I COMMAND  [conn158] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 3ms
2016-08-15T08:11:21.428+0200 I COMMAND  [conn17] command admin.$cmd command: replSetHeartbeat { replSetHeartbeat: "sfsfsf", configVersion: 8, from: "hostname", fromId: 0, term: 17 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:485 locks:{} protocol:op_command 2ms
2016-08-15T08:11:22.242+0200 I -        [rsSync]   Index Build: 387700/2273552 17%
2016-08-15T08:11:22.460+0200 I COMMAND  [conn1670] command admin.$cmd command: replSetHeartbeat { replSetHeartbeat: "srgewfef", configVersion: 8, from: "hostname", fromId: 2, term: 17 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:485 locks:{} protocol:op_command 1ms
2016-08-15T08:11:22.738+0200 I COMMAND  [conn1205] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 4ms
2016-08-15T08:11:23.053+0200 I COMMAND  [conn2969] command admin.$cmd command: serverStatus { serverStatus: 1, locks: false, recordStats: false } keyUpdates:0 writeConflicts:0 numYields:0 reslen:18641 locks:{} protocol:op_query 5ms
2016-08-15T08:11:23.750+0200 I COMMAND  [conn1098] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 2ms
2016-08-15T08:11:23.814+0200 I COMMAND  [conn1113] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 1ms
2016-08-15T08:11:23.836+0200 I COMMAND  [conn747] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 3ms
2016-08-15T08:11:23.940+0200 I COMMAND  [conn2197] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 1ms
2016-08-15T08:11:24.376+0200 I COMMAND  [conn2784] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 1ms
2016-08-15T08:11:24.518+0200 I COMMAND  [conn2648] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 5ms
2016-08-15T08:11:25.067+0200 I COMMAND  [conn1425] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 1ms
2016-08-15T08:11:25.316+0200 I COMMAND  [conn2848] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 2ms
2016-08-15T08:11:25.403+0200 I COMMAND  [conn2693] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 2ms
2016-08-15T08:11:25.472+0200 I COMMAND  [conn2908] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 1ms
2016-08-15T08:11:25.501+0200 I -        [rsSync]   Index Build: 388400/2273552 17%
2016-08-15T08:11:25.631+0200 I COMMAND  [conn2896] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 5ms

What does the this message (every second, 64680 times in less than one day) mean?

 COMMAND  [conn747] command admin.$cmd command: isMaster { isMaster: 1 } keyUpdates:0 writeConflicts:0 numYields:0 reslen:644 locks:{} protocol:op_query 2ms
1

MongoDB drivers and clients use the isMaster command to describe the current role of a mongod instance, monitor round trip time, and verify replica set configuration/status (if applicable).

Frequent isMaster commands are expected behaviour, although the occurrence will vary depending on how many clients/drivers you have connected as well as the driver versions.

For more information you might be interested in the Server Discovery and Monitoring (SDAM) specification which details the behaviour for officially supported MongoDB drivers.

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