Only a single instance of the Directory Server can run at any time from the same installation root. If an instance is already running, then subsequent attempts to start the server will fail. Similarly, some other administrative operations can also prevent the server from being started. In such cases, the attempt to start the server should fail with a message like:
The PingDataSync Server could not acquire an exclusive lock on file 
/ds/the/locks/server.lock: The exclusive lock requested for file 
/ds/the/locks/ server.lock was not granted, which indicates 
that another process already holds a shared or exclusive lock on that 
file. This generally means that another instance of this server is already 
running

If the Directory Server is not running (and is not in the process of starting up or shutting down) and there are no other tools running that could prevent the server from being started, and the server still believes that it is running, then it is possible that a previously-held lock was not properly released. In that case, you can try removing all of the files in the locks directory before attempting to start the server.

If you wish to have multiple instances running at the same time on the same system, then you should create a completely separate installation in another location on the file system.