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Currently, there is a 3 way deadlock. Assume that we are transitioning from secondary to rollback.

Thread A (Read thread) acquires RSTL lock in IX and blocked by a prepared txn due to prepare conflict.
Rollback enqueues RSTL lock in X mode. And blocked behind A.
Prepared txn won’t be able commit until we transition out of rollback.

~~Alternatively, thread A might have got blocked on prepared transaction due to conflicting DB/ collection lock. For eg. dbhash cmd.~~

EDIT: Blocked due to conflicting mongoDB locks is not possible as secondary prepared txn yield mongoDB locks.

is documented by

DOCS-12710 Docs for SERVER-41035: Rollback should kill all user operations before taking RSTL lock in X.

is related to

SERVER-37574 Force reconfig should kill user operations

SERVER-40594 Range deleter in prepare conflict retry loop blocks step down

SERVER-40700 Deadlock between read prepare conflicts and state transitions

SERVER-40641 Ensure TTL delete in prepare conflict retry loop does not block step down

SERVER-41037 Stepup should kill all user operations(that encounters prepare conflict) before taking RSTL lock in X.

related to

SERVER-41216 Rename InterruptedDueToStepDown error code to InterruptedDueToReplStateChange

(1 is related to, 1 related to)