How do I put an already-running process under nohup?

These are good answers above, I just wanted to add a clarification:

You can't disown a pid or process, you disown a job, and that is an important distinction.

A job is something that is a notion of a process that is attached to a shell, therefore you have to throw the job into the background (not suspend it) and then disown it.

Issue:

%  jobs
[1]  running java 
[2]  suspended vi
%  disown %1

See http://www.quantprinciple.com/invest/index.php/docs/tipsandtricks/unix/jobcontrol/ for a more detailed discussion of Unix Job Control.

Suppose for some reason Ctrl+Z is also not working, go to another terminal, find the process id (using ps) and run:

kill -SIGSTOP PID 
kill -SIGCONT PID

SIGSTOP will suspend the process and SIGCONT will resume the process, in background. So now, closing both your terminals won't stop your process.

The command to separate a running job from the shell ( = makes it nohup) is disown and a basic shell-command.

From bash-manpage (man bash):

disown [-ar] [-h] [jobspec ...]

Without options, each jobspec is removed from the table of active jobs. If the -h option is given, each jobspec is not removed from the table, but is marked so that SIGHUP is not sent to the job if the shell receives a SIGHUP. If no jobspec is present, and neither the -a nor the -r option is supplied, the current job is used. If no jobspec is supplied, the -a option means to remove or mark all jobs; the -r option without a jobspec argument restricts operation to running jobs. The return value is 0 unless a jobspec does not specify a valid job.

That means, that a simple

disown -a

will remove all jobs from the job-table and makes them nohup

Using the Job Control of bash to send the process into the background:

1. Ctrl+Z to stop (pause) the program and get back to the shell.
2. bg to run it in the background.
3. disown -h [job-spec] where [job-spec] is the job number (like %1 for the first running job; find about your number with the jobs command) so that the job isn't killed when the terminal closes.