I am writing continuously into a db file which has PRAGMA journal_mode=WAL,
PRAGMA journal_size_limit=0. My C++ program has two threads, one
reader(queries at 15 sec intervals) and one writer(inserts at 5 sec
intervals).

Every 3 min I am pausing insertion to run a sqlite3_wal_checkpoint_v2()
from the writer thread with the mode parameter as
SQLITE_CHECKPOINT_RESTART. To ensure that no active read operations are
going on at this point, I set a flag that checkpointing is about to take
place and wait for reader to complete (the connection is still open) before
running checkpoint. After checkpoint completion I again indicate to readers
it is okay to resume querying.

sqlite3_wal_checkpoint_v2() returns SQLITE_OK, and pnLog and Ckpt as
equal(around 4000), indicating complete wal file has been synced with main
db file. So next write should start from beginning according to
documentation. However, this does not seem to be happening as the
subsequent writes cause the WAL file to grow indefinitely, eventually up to
some GBs.

I did some searching and found that that readers can cause checkpoint
failure due to open transactions. However, the only reader I'm using is
ending its transaction before the checkpoint starts. What else could be
preventing the WAL file from not growing?
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