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Read the "about JNDI" pages on Sun.
Anyway, JNDI is just the extension API for Java-based programming access to local and remote network information servers (NIS). The "service" is actually a server that provides protocol access to multiple hosted services.
LDAP, ActiveDirectory, etc. are all NIS servers. However, without having to know the exacts of each of these servers, a client using JNDI can "query" the machine for information. In fact, a file system is an information service itself.
I could query an MS server for "guest" and be returned an LDAP entry for the user, or a MSX e-mail address, or some the file or folder on the hard drive with that name, etc.
I don't need access or knowledge of each server - LDAP, Microsoft Exchange, the local file system (i.e. NTFS, FAT, etc), I just query the service and it comes back.
NIS servers are basically just a shell that allows for one protocol to access the information contained by many other services that use many different protocols.
So yes, Question 1: Any organization, business, person that sells a POP3 e-mail server, an LDAP directory server, various 'directory' servers, etc. all provide NIS Servers that can be queried by an NIS service.
Q2: When the JVM starts, JNDI service is setup, and if properly configured, can connect to LDAP, ActiveDirectory, etc. When the JVM shutsdown, the NDI service shutsdown.