Mongodb – how to fix replica set error

I was able to get a solution for this problem on the mongoDB google group. Explicitly setting the oplogSize parameter in my config file solved the problem. By default, mongod tries to allocate 5% of the free space on the storage partition. I have my data on a very large shared disk and this seemed to be taking a long time. I manually set this value and the replica set came up quickly.

You really only have 2 choices when a primary is still processing deletes from previous migrations (which is why you are getting the failure to engage error):

1. Wait for the deletes to finish
2. Step down the primary of that shard (assuming it is a replica set)

The first action may take a long time if the shard in question is under heavy load, but it is the safest way forward. The second option will cause the primary to step down to secondary and terminate the background threads for the deletes - if you have only a single node then your only option is a restart, and downtime. Either way, this will allow the new primary (or restarted node) to accept migrations, but it will create orphans which you will need to manually clean up later.

If you are in any doubt, then the best thing to do is wait for the deletes to finish.