As befits its name, the memory pool is kept in the process's memory. So if you quit and restart bitcoind, the memory pool will be cleared.
However, this may not fix your problem; unconfirmed transactions relating to your own wallet addresses are stored not only in the memory pool, but in wallet.dat, so a restart won't clear them. To accomplish that, you can start bitcoind with the recently added -zapwallettxes option. This will cause bitcoind to forget all transactions associated to your addresses, and rescan the block chain to reconstruct them. In particular, any unconfirmed transactions will be forgotten and not reconstructed.
Note that you will have to have waited long enough that other nodes on the network are no longer keeping your unconfirmed transaction in their own memory pools. If they are, then (1) they might send it back to you, defeating the purpose of this exercise, and (2) if you try to send a new transaction to replace the unconfirmed one, they may reject it as a double spend.
Running this command bitcoind just sits there... how long should it take? – Serj Sagan – 2016-06-15T08:14:44.990
@SerjSagan: Bitcoind is a daemon, it runs in the background. It's supposed to just sit there and respond to commands issued with
bitcoin-cli. If you want an interactive program, usebitcoin-qt. – Nate Eldredge – 2016-06-15T15:15:25.290That doesn't answer my question about how long the
-zapwallettxespart should take... I left it on for 24 hours and that seemed to do it. – Serj Sagan – 2016-06-16T02:41:44.993