user56031: I tried stopping bitcoind using bitcoin-cli stop and got the following error.
bitcoin-cli stop
error: Could not locate RPC credentials. No authentication cookie could be found, and RPC password is not set.  See -rpcpassword and -stdinrpcpass.  Configuration file: (/home/user/.bitcoin/bitcoin.conf)

I confirmed that bitcoind is running (using ps -A). 
ps -A | grep bitcoind
643 pts/0    00:17:23 bitcoind

bitcoind was started in a datadir on the usb storage. I can kill the process but i want to shut it down in a correct way.

user60443: As @Raghav Sood mentioned, you can stop bitcoin for a different datadir (the location of .bitcoin folder) using:
$ bitcoin-cli -datadir=<dir> stop

56031: <p>I tried stopping bitcoind using bitcoin-cli stop and got the following error.</p>

<pre><code>bitcoin-cli stop
error: Could not locate RPC credentials. No authentication cookie could be found, and RPC password is not set.  See -rpcpassword and -stdinrpcpass.  Configuration file: (/home/user/.bitcoin/bitcoin.conf)
</code></pre>

<p>I confirmed that bitcoind is running (using ps -A). </p>

<pre><code>ps -A | grep bitcoind
643 pts/0    00:17:23 bitcoind
</code></pre>

<p>bitcoind was started in a datadir on the usb storage. I can kill the process but i want to shut it down in a correct way.</p>
 60443: <p>As @Raghav Sood mentioned, you can stop bitcoin for a different datadir (the location of <code>.bitcoin</code> folder) using:</p>

<p><code>$ bitcoin-cli -datadir=&lt;dir&gt; stop</code></p>
